Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007773.1 Hibiscus syriacus cultivar Beakdansim tig00110054_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: 557494
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:189533 original size:21 final size:21
Alignment explanation
Indices: 189509--189552 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
189499 GAGCTGGAGG
* *
189509 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
189530 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
189551 AG
1 AG
189553 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:190593 original size:13 final size:13
Alignment explanation
Indices: 190565--190603 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
190555 TGGGCAATGT
*
190565 TTTGAAAA-ACTA
1 TTTGAAAATAATA
190577 TTTGAAAATAATA
1 TTTGAAAATAATA
*
190590 TTTGTAAATAATA
1 TTTGAAAATAATA
190603 T
1 T
190604 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:191162 original size:24 final size:24
Alignment explanation
Indices: 191142--191204 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
191132 GCATCAACAT
*
191142 GATGAATCGATGCACATTCAAAGG
1 GATGCATCGATGCACATTCAAAGG
191166 GATGCATCGATGCACATTCAAAGG
1 GATGCATCGATGCACATTCAAAGG
191190 GATGCATCGATGCAC
1 GATGCATCGATGCAC
191205 TGTTATGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (24 bp):
GATGCATCGATGCACATTCAAAGG
Found at i:197130 original size:65 final size:65
Alignment explanation
Indices: 197006--197156 Score: 200
Period size: 65 Copynumber: 2.3 Consensus size: 65
196996 GCACTAAGAG
* * *
197006 TGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTGCATCGA
1 TGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTAGTGCATCGA
* * *
197070 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TAAGTGCATC
1 TGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-AGTGCATC
197133 GA
64 GA
*
197135 TGCATGAAATGCATTCGATGTT
1 TGCATCAAATGCATTCGATGTT
197157 CAATTTAATT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
64 20 0.26
65 54 0.70
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
TGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTAGTGCATCGA
Found at i:197204 original size:65 final size:63
Alignment explanation
Indices: 197006--197206 Score: 194
Period size: 65 Copynumber: 3.1 Consensus size: 63
196996 GCACTAAGAG
* * *
197006 TGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCTGGTGCATCG
1 TGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTTGGTGCATCG
197069 A
63 A
* **
197070 TGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAAGTGCATCGA
1 TGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTTGGTGCATCGA
* ** *
197135 TGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGGTGTATC
1 TGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGTGCATC
*
197198 GG
62 GA
197200 TGCATCA
1 TGCATCA
197207 CTCTGAAAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 39 0.34
65 64 0.56
66 4 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
TGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGCATCGA
Found at i:199615 original size:23 final size:24
Alignment explanation
Indices: 199562--199617 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
199552 ATAAGGAACG
199562 TGTCACAAGAGCAAAGAAAAAGCA
1 TGTCACAAGAGCAAAGAAAAAGCA
* * * *
199586 TGCCACAAGAGTAGAGAAAAA-CT
1 TGTCACAAGAGCAAAGAAAAAGCA
199609 TGTCACAAG
1 TGTCACAAG
199618 GATAAAGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.12
Consensus pattern (24 bp):
TGTCACAAGAGCAAAGAAAAAGCA
Found at i:205849 original size:320 final size:320
Alignment explanation
Indices: 205255--205903 Score: 1262
Period size: 320 Copynumber: 2.0 Consensus size: 320
205245 TGATTCACCA
*
205255 GGAAGCTTTAGCAATAAAAATCAAGGGAAAGATATTACGAGATATAGAAAAGCTTAAGATGTTAC
1 GGAAGTTTTAGCAATAAAAATCAAGGGAAAGATATTACGAGATATAGAAAAGCTTAAGATGTTAC
205320 TCAAGAAATAGAAAAACTTCAAAATGTGTGAATAAACTCCCCAGAAAGAGGCACGTGTAAGAAAA
66 TCAAGAAATAGAAAAACTTCAAAATGTGTGAATAAACTCCCCAGAAAGAGGCACGTGTAAGAAAA
205385 CCCAATAAGAAATCAGCAAAATCTTACAAAACCCAACTCGAGTCGAGAAGGTTCAATGCCTTGAA
131 CCCAATAAGAAATCAGCAAAATCTTACAAAACCCAACTCGAGTCGAGAAGGTTCAATGCCTTGAA
205450 TATTCAGAGTAATAATCGTAAGTTATGGCTTAAACTACGCCACTATAACCACTATAACCAGCAAC
196 TATTCAGAGTAATAATCGTAAGTTATGGCTTAAACTACGCCACTATAACCACTATAACCAGCAAC
205515 CCTTAGGGGTTTCTTAGGTCATTACTGTAACATCCCAAAATCAGGGCTAGTGACTAAAAT
261 CCTTAGGGGTTTCTTAGGTCATTACTGTAACATCCCAAAATCAGGGCTAGTGACTAAAAT
*
205575 GGAAGTTTTAGTAATAAAAATCAAGGGAAAGATATTACGAGATATAGAAAAGCTTAAGATGTTAC
1 GGAAGTTTTAGCAATAAAAATCAAGGGAAAGATATTACGAGATATAGAAAAGCTTAAGATGTTAC
*
205640 TCTAGAAATAGAAAAACTTCAAAATGTGTGAATAAACTCCCCAGAAAGAGGCACGTGTAAGAAAA
66 TCAAGAAATAGAAAAACTTCAAAATGTGTGAATAAACTCCCCAGAAAGAGGCACGTGTAAGAAAA
205705 CCCAATAAGAAATCAGCAAAATCTTACAAAACCCAACTCGAGTCGAGAAGGTTCAATGCCTTGAA
131 CCCAATAAGAAATCAGCAAAATCTTACAAAACCCAACTCGAGTCGAGAAGGTTCAATGCCTTGAA
205770 TATTCAGAGTAATAATCGTAAGTTATGGCTTAAACTACGCCACTATAACCACTATAACCAGCAAC
196 TATTCAGAGTAATAATCGTAAGTTATGGCTTAAACTACGCCACTATAACCACTATAACCAGCAAC
205835 CCTTAGGGGTTTCTTAGGTCATTACTGTAACATCCCAAAATCAGGGCTAGTGACTAAAAT
261 CCTTAGGGGTTTCTTAGGTCATTACTGTAACATCCCAAAATCAGGGCTAGTGACTAAAAT
*
205895 GGATGTTTT
1 GGAAGTTTT
205904 GAAACTTTGA
Statistics
Matches: 325, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
320 325 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (320 bp):
GGAAGTTTTAGCAATAAAAATCAAGGGAAAGATATTACGAGATATAGAAAAGCTTAAGATGTTAC
TCAAGAAATAGAAAAACTTCAAAATGTGTGAATAAACTCCCCAGAAAGAGGCACGTGTAAGAAAA
CCCAATAAGAAATCAGCAAAATCTTACAAAACCCAACTCGAGTCGAGAAGGTTCAATGCCTTGAA
TATTCAGAGTAATAATCGTAAGTTATGGCTTAAACTACGCCACTATAACCACTATAACCAGCAAC
CCTTAGGGGTTTCTTAGGTCATTACTGTAACATCCCAAAATCAGGGCTAGTGACTAAAAT
Found at i:214420 original size:25 final size:25
Alignment explanation
Indices: 214386--214441 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
214376 TTAATGGTTG
214386 ACTTTACCCTCTTATATTATATTTT
1 ACTTTACCCTCTTATATTATATTTT
214411 ACTTTACCCTCTTATATTATATTTT
1 ACTTTACCCTCTTATATTATATTTT
214436 ACTTTA
1 ACTTTA
214442 TTAGATAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (25 bp):
ACTTTACCCTCTTATATTATATTTT
Found at i:215593 original size:2 final size:2
Alignment explanation
Indices: 215586--215614 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
215576 AAATTCGGAA
215586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
215615 GGACTAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:216853 original size:13 final size:13
Alignment explanation
Indices: 216813--216883 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 13
216803 TTGGACCTGA
216813 AAAAAC-AA-AAT
1 AAAAACAAATAAT
*
216824 AAATA-AAATAA-
1 AAAAACAAATAAT
*
216835 ATAAAACGAATAAT
1 A-AAAACAAATAAT
*
216849 AAAAATAAA-AA-
1 AAAAACAAATAAT
216860 AAAAACAAATAAT
1 AAAAACAAATAAT
216873 AAAAACAAATA
1 AAAAACAAATA
216884 TATATTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
11 15 0.32
12 9 0.19
13 22 0.47
14 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.01, T:0.14
Consensus pattern (13 bp):
AAAAACAAATAAT
Found at i:216870 original size:24 final size:23
Alignment explanation
Indices: 216812--216877 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
216802 GTTGGACCTG
216812 AAAAAACAA-AATAAATAAAATAA
1 AAAAAACAATAATAAA-AAAATAA
*
216835 ATAAAACGAATAATAAAAATAA-AA
1 AAAAAAC-AATAATAAAAA-AATAA
216859 AAAAAACAAATAATAAAAA
1 AAAAAAC-AATAATAAAAA
216878 CAAATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.16
24 23 0.62
25 8 0.22
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (23 bp):
AAAAAACAATAATAAAAAAATAA
Found at i:217017 original size:34 final size:33
Alignment explanation
Indices: 216979--217090 Score: 109
Period size: 34 Copynumber: 3.2 Consensus size: 33
216969 TAAAAAATTA
*
216979 TATATTTTCAAAAATACTTTTAAAAATTATATAT
1 TATATTTTCAAAAAT-GTTTTAAAAATTATATAT
217013 TATATGTTTTC-AAAATGTTTTAAAAACTATATAATAT
1 TATA--TTTTCAAAAATGTTTTAAAAA-T-TAT-ATAT
* *
217050 ATAAATATTTTCAAACATGTTTTCAAAATTATATAT
1 -T--ATATTTTCAAAAATGTTTTAAAAATTATATAT
217086 TATAT
1 TATAT
217091 ATATATTTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 19
0.75 0.03 0.22
Matches are distributed among these distances:
33 4 0.06
34 13 0.20
35 7 0.11
36 12 0.18
37 7 0.11
38 7 0.11
39 13 0.20
40 3 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (33 bp):
TATATTTTCAAAAATGTTTTAAAAATTATATAT
Found at i:217070 original size:39 final size:39
Alignment explanation
Indices: 216977--217142 Score: 170
Period size: 38 Copynumber: 4.4 Consensus size: 39
216967 TTTAAAAAAT
*
216977 TATATATTTTCAAAAATACTTTTAAAAA-T-TAT-ATAT-
1 TATATATTTTCAAAAAT-GTTTTAAAAACTATATAATATA
*
217013 TATATGTTTTC-AAAATGTTTTAAAAACTATATAATATA
1 TATATATTTTCAAAAATGTTTTAAAAACTATATAATATA
* * * * *
217051 TAAATATTTTCAAACATGTTTTCAAAATTATATATTATA
1 TATATATTTTCAAAAATGTTTTAAAAACTATATAATATA
*
217090 TATATA-TTT-AAAAATGATTTCAAAAACTATATAATATA
1 TATATATTTTCAAAAATG-TTTTAAAAACTATATAATATA
*
217128 T-T-TATTTTCGAAAAT
1 TATATATTTTCAAAAAT
217143 TGATTTCTGA
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
34 9 0.08
35 6 0.06
36 15 0.14
37 14 0.13
38 35 0.33
39 28 0.26
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (39 bp):
TATATATTTTCAAAAATGTTTTAAAAACTATATAATATA
Found at i:217199 original size:2 final size:2
Alignment explanation
Indices: 217188--217235 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
217178 ACCTTTTCAA
217188 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
217229 AT AT AT A
1 AT AT AT A
217236 AATAAATAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228388 original size:20 final size:20
Alignment explanation
Indices: 228352--228390 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
228342 AAGCTTGAAT
*
228352 AATGATTAAAATCAATTGGA
1 AATGATTAAAATAAATTGGA
228372 AATG-TTAAAGATAAATTGG
1 AATGATTAAA-ATAAATTGG
228391 GTTAAGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.31
Consensus pattern (20 bp):
AATGATTAAAATAAATTGGA
Found at i:230972 original size:23 final size:23
Alignment explanation
Indices: 230910--230973 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
230900 CTCCTGAACC
230910 AGTGCAATTGAACACTCCTATATT
1 AGTGCAATTG-ACACTCCTATATT
*
230934 AGTGCGAATATG-CACTCCTTTA-T
1 AGTGC-AAT-TGACACTCCTATATT
230957 AGTGCAATTGTACACTC
1 AGTGCAATTG-ACACTC
230974 TAGCATTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
21 2 0.06
22 3 0.09
23 11 0.31
24 14 0.40
25 3 0.09
26 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (23 bp):
AGTGCAATTGACACTCCTATATT
Found at i:233251 original size:13 final size:13
Alignment explanation
Indices: 233233--233259 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
233223 TACAGATGCT
233233 TATATGAAGTCTA
1 TATATGAAGTCTA
233246 TATATGAAGTCTA
1 TATATGAAGTCTA
233259 T
1 T
233260 TCAACTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TATATGAAGTCTA
Found at i:233539 original size:42 final size:42
Alignment explanation
Indices: 233476--233569 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
233466 TTCCCCGAAA
*
233476 TCCCGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAACGTTT
1 TCCCGTGTTTATTTCATGTAATTCGTTTTCCGGAAAACGTTT
* * *
233518 TCCCTTGTTTATTTCATGTAATTCGTTTTTCGGAAAATGTTT
1 TCCCGTGTTTATTTCATGTAATTCGTTTTCCGGAAAACGTTT
233560 TCCCGTGTTT
1 TCCCGTGTTT
233570 GTGTAACAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.16, C:0.18, G:0.17, T:0.49
Consensus pattern (42 bp):
TCCCGTGTTTATTTCATGTAATTCGTTTTCCGGAAAACGTTT
Found at i:234322 original size:17 final size:18
Alignment explanation
Indices: 234293--234337 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
234283 TTGACCGGTC
*
234293 TGACCCAACCCGACCCGT
1 TGACCCGACCCGACCCGT
*
234311 TGA-CCGACCCGACCTGT
1 TGACCCGACCCGACCCGT
234328 TGACCCGACC
1 TGACCCGACC
234338 AAGTGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (18 bp):
TGACCCGACCCGACCCGT
Found at i:234390 original size:29 final size:29
Alignment explanation
Indices: 234340--234553 Score: 152
Period size: 29 Copynumber: 7.3 Consensus size: 29
234330 ACCCGACCAA
234340 GTGACATTTT-GG-ATTATTTTTTGAAAAAG
1 GTGACATTTTGGGAATTA--TTTTGAAAAAG
* * * *
234369 GTAATATTTTAGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAG
234398 GTGACATTTTGGGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
234427 GTGACATTTTGGGAATT-TGTTT-AAAATA-
1 GTGACATTTTGGGAATTAT-TTTGAAAA-AG
* ** * * *
234455 GTGAAATTCCGGTAATTATTTTTAAAACG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* * * *
234484 ATGACATTTTAGAAATTA-TTTGTAAAACG
1 GTGACATTTTGGGAATTATTTTG-AAAAAG
* * * *
234513 ATGATATTTGTGGTAATTATTTTAAATAAAG
1 GTGACATTT-TGGGAATTATTTTGAA-AAAG
*
234544 GTGATATTTT
1 GTGACATTTT
234554 TGAATTTTCG
Statistics
Matches: 149, Mismatches: 25, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
28 24 0.16
29 95 0.64
30 12 0.08
31 18 0.12
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.43
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAG
Found at i:234436 original size:58 final size:57
Alignment explanation
Indices: 234340--234553 Score: 168
Period size: 58 Copynumber: 3.7 Consensus size: 57
234330 ACCCGACCAA
* *
234340 GTGACATTTT-GG-ATTATTTTTTGAAAAAGGTAATATTTTAGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTA--TTTTGAAAAAGGTGACATTTTAGGAATTATTTTG-AAAAT
*
234398 GTGACATTTTGGGAATTATTTTGAAAAAGGTGACATTTTGGGAATT-TGTTT-AAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAGGTGACATTTTAGGAATTAT-TTTGAAAAT
* ** * * * * * *
234454 AGTGAAATTCCGGTAATTATTTTTAAAACGATGACATTTTAGAAATTA-TTTGTAAAAC
1 -GTGACATTTTGGGAATTATTTTGAAAAAGGTGACATTTTAGGAATTATTTTG-AAAAT
* * * *
234512 GATGATATTTGTGGTAATTATTTTAAATAAAGGTGATATTTT
1 G-TGACATTT-TGGGAATTATTTTGAA-AAAGGTGACATTTT
234554 TGAATTTTCG
Statistics
Matches: 126, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
56 8 0.06
57 39 0.31
58 48 0.38
59 16 0.13
60 15 0.12
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.43
Consensus pattern (57 bp):
GTGACATTTTGGGAATTATTTTGAAAAAGGTGACATTTTAGGAATTATTTTGAAAAT
Found at i:241965 original size:28 final size:28
Alignment explanation
Indices: 241923--242075 Score: 132
Period size: 28 Copynumber: 5.4 Consensus size: 28
241913 ACCCGACCTA
*
241923 GTGACATTTTGGGAATT-TTTTGAAAAAG
1 GTGACATTTTAGGAATTATTTT-AAAAAG
*
241951 GTGACATTTTAGGAATTATTTTAAAAAT
1 GTGACATTTTAGGAATTATTTTAAAAAG
* *
241979 GTGACATTTTAGGAA-AATTTTAAAAATA
1 GTGACATTTTAGGAATTATTTTAAAAA-G
* * * *
242007 ATGACATTCT-GGTAATTATTTTTAGAACG
1 GTGACATTTTAGG-AATTA-TTTTAAAAAG
* *
242036 GTGATATTTTAGTAATTATTTTTAATAAAG
1 GTGACATTTTAGGAATTA-TTTTAA-AAAG
*
242066 GTGATATTTT
1 GTGACATTTT
242076 TGTAATTTTT
Statistics
Matches: 102, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
27 12 0.12
28 46 0.45
29 23 0.23
30 21 0.21
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (28 bp):
GTGACATTTTAGGAATTATTTTAAAAAG
Found at i:242050 original size:29 final size:30
Alignment explanation
Indices: 242018--242082 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
242008 TGACATTCTG
*
242018 GTAATTATTTTT-AGAACGGTGATATTTTA
1 GTAATTATTTTTAAGAAAGGTGATATTTTA
* *
242047 GTAATTATTTTTAATAAAGGTGATATTTTT
1 GTAATTATTTTTAAGAAAGGTGATATTTTA
242077 GTAATT
1 GTAATT
242083 TTTGAATGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (30 bp):
GTAATTATTTTTAAGAAAGGTGATATTTTA
Found at i:244010 original size:26 final size:24
Alignment explanation
Indices: 243948--244010 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
243938 CATTTTCATC
243948 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
243972 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
243995 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
244011 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:244012 original size:22 final size:23
Alignment explanation
Indices: 243965--244028 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
243955 TAATTATTAA
* *
243965 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
243986 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
244009 -ATATTTTTAATATTATAATA
1 AATATTTATAATAATATAATA
244029 AAACAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:244042 original size:32 final size:32
Alignment explanation
Indices: 243976--244055 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
243966 ATATTTAAAA
* *
243976 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAACAATAT
244008 TATATTT-TTAATA-TTATAATAAAACAATCAAT
1 TATATTTATTAATATTTATAATAAAACAAT--AT
*
244040 TATATTATAATAATAT
1 TATATT-TATTAATAT
244056 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAACAATAT
Found at i:244168 original size:19 final size:18
Alignment explanation
Indices: 244100--244170 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
244090 TACATTTTTT
*
244100 ATATATTTAATAATGAATA
1 ATAT-TTTAATAATTAATA
*
244119 ATATTATTTATATATTTAATA
1 ATA-T-TTTA-ATAATTAATA
* * *
244140 TTAATATAATAATCTAATA
1 ATATTTTAATAAT-TAATA
244159 ATATTTTAATAA
1 ATATTTTAATAA
244171 AGATATTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 4 0.10
19 20 0.50
20 6 0.15
21 10 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATATTTTAATAATTAATA
Found at i:246997 original size:55 final size:55
Alignment explanation
Indices: 246938--247190 Score: 278
Period size: 55 Copynumber: 4.6 Consensus size: 55
246928 TGATAGGTTC
* * * *
246938 GCTCCCTATTCCTTCAGGGAGTACAGAACTTGAACAATATTCAGCAAACGTGTCT
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCT
* * * *
246993 GCTCCCTATTCGTTCAGGGAGTATA-AGACTCGGATAATCTTCAGCAAACAG-GT-T
1 GCTCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAAC-GTGTCT
* * * * *
247047 CGCTCCCTATTCATTCAGGAAGTATAGAACTCGAGCAATCTTCAATAAACATGTCT
1 -GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCT
* * *
247103 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAACAAACGGGTCT
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCT
* * * *
247158 TCTCTCTATTCCATCAGAGAGTATAGAACTCGA
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGA
247191 TCTTCATAAA
Statistics
Matches: 167, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
54 2 0.01
55 162 0.97
56 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCT
Found at i:247316 original size:37 final size:37
Alignment explanation
Indices: 247202--247316 Score: 169
Period size: 37 Copynumber: 3.1 Consensus size: 37
247192 CTTCATAAAA
247202 TGAATTTGCTTCACTACTCTTCCGTGAAGGCTTATAGA-
1 TGAA-TTGCTTCACTACTCTTCCGTGAAGGCTTA-AGAT
* *
247240 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAATAT
1 TGAATTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
* *
247277 TGAATTGCTTGACTACTCTTTCGTGAAGGCTTAAGAT
1 TGAATTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
247314 TGA
1 TGA
247317 CTTGTTTCGA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
36 2 0.03
37 65 0.93
38 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (37 bp):
TGAATTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
Found at i:248487 original size:9 final size:9
Alignment explanation
Indices: 248475--248587 Score: 54
Period size: 9 Copynumber: 13.6 Consensus size: 9
248465 TTTTTCTCTA
248475 TTTTTTCA-
1 TTTTTTCAT
248483 -TTTTTCAT
1 TTTTTTCAT
*
248491 TTTTCTC--
1 TTTTTTCAT
*
248498 TTTATTC-T
1 TTTTTTCAT
248506 TTTTTT-A-
1 TTTTTTCAT
248513 TTTTTTCA-
1 TTTTTTCAT
248521 TTTTTT-AT
1 TTTTTTCAT
***
248529 TTTCACCA-
1 TTTTTTCAT
248537 -TTTTTCAT
1 TTTTTTCAT
248545 TTTTTTC-T
1 TTTTTTCAT
248553 CATTTTTT-ATT
1 --TTTTTTCA-T
248564 TTTTCTTCAT
1 TTTT-TTCAT
248574 TTTTTTCAT
1 TTTTTTCAT
248583 TTTTT
1 TTTTT
248588 ATTTATTCTT
Statistics
Matches: 80, Mismatches: 10, Indels: 29
0.67 0.08 0.24
Matches are distributed among these distances:
7 23 0.29
8 16 0.20
9 26 0.32
10 13 0.16
11 2 0.03
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:248488 original size:7 final size:7
Alignment explanation
Indices: 248476--248548 Score: 56
Period size: 7 Copynumber: 9.7 Consensus size: 7
248466 TTTTCTCTAT
248476 TTTTTCA
1 TTTTTCA
248483 TTTTTCA
1 TTTTTCA
*
248490 TTTTTCTC
1 TTTTTC-A
*
248498 TTTATTCT
1 TTT-TTCA
*
248506 TTTTTTA
1 TTTTTCA
248513 TTTTTTCA
1 -TTTTTCA
*
248521 TTTTTTA
1 TTTTTCA
*
248528 TTTTCACCA
1 TTTT--TCA
248537 TTTTTCA
1 TTTTTCA
248544 TTTTT
1 TTTTT
248549 TTCTCATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
7 32 0.62
8 12 0.23
9 8 0.15
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:248557 original size:11 final size:10
Alignment explanation
Indices: 248537--248587 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
248527 ATTTTCACCA
248537 TTTTTCATTT
1 TTTTTCATTT
248547 TTTTCTCA--T
1 TTTT-TCATTT
248556 TTTTT-ATTT
1 TTTTTCATTT
248565 TTTCTTCA-TT
1 TTT-TTCATTT
248575 TTTTTCATTT
1 TTTTTCATTT
248585 TTT
1 TTT
248588 ATTTATTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 13 0.37
10 16 0.46
11 4 0.11
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:248567 original size:27 final size:27
Alignment explanation
Indices: 248540--248599 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 27
248530 TTCACCATTT
248540 TTCATTTTTTTCTCATTTTTTATTTTTTC
1 TTCA-TTTTTT-TCATTTTTTATTTTTTC
*
248569 TTCATTTTTTTCATTTTTTATTTATTC
1 TTCATTTTTTTCATTTTTTATTTTTTC
248596 TTCA
1 TTCA
248600 AGTGAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 20 0.67
28 6 0.20
29 4 0.13
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (27 bp):
TTCATTTTTTTCATTTTTTATTTTTTC
Found at i:248579 original size:38 final size:37
Alignment explanation
Indices: 248475--248587 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 37
248465 TTTTTCTCTA
* *
248475 TTTTTTCATTTTTCATTTTTCTCTTTATTCTTTTT--TT
1 TTTTTTCATTTTTTATTTTT-TCTTCATT-TTTTTCATT
**
248512 ATTTTTTCATTTTTTA--TTTTCACCA--TTTTTCATT
1 -TTTTTTCATTTTTTATTTTTTCTTCATTTTTTTCATT
248546 TTTTTCTCATTTTTTATTTTTTCTTCATTTTTTTCATT
1 TTTTT-TCATTTTTTATTTTTTCTTCATTTTTTTCATT
248584 TTTT
1 TTTT
248588 ATTTATTCTT
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
32 5 0.08
33 5 0.08
34 12 0.19
35 3 0.05
36 10 0.16
38 27 0.44
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (37 bp):
TTTTTTCATTTTTTATTTTTTCTTCATTTTTTTCATT
Found at i:253010 original size:22 final size:22
Alignment explanation
Indices: 252979--253021 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
252969 CGGAATTGCA
*
252979 CCAACCTGATAGAA-CCAAGGCT
1 CCAACATGAT-GAATCCAAGGCT
253001 CCAACATGATGAATCCAAGGC
1 CCAACATGATGAATCCAAGGC
253022 CTTCCCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.14
Consensus pattern (22 bp):
CCAACATGATGAATCCAAGGCT
Found at i:261680 original size:20 final size:20
Alignment explanation
Indices: 261643--261681 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
261633 TCAGAAAACG
**
261643 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
261663 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
261682 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:261688 original size:29 final size:30
Alignment explanation
Indices: 261655--261728 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
261645 TTCCAGAAAT
261655 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* *
261684 GTAATTCATTTTCCAGTTATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
261714 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
261729 AAACACCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:261691 original size:15 final size:15
Alignment explanation
Indices: 261655--261721 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
261645 TTCCAGAAAT
**
261655 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
261670 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
261684 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
* *
261699 GTTATTCAAATTTCA
1 GTAATTCAAATTCCA
261714 GTAATTCA
1 GTAATTCA
261722 TTTTCCAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 12 0.29
15 30 0.71
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:262640 original size:29 final size:29
Alignment explanation
Indices: 262608--262664 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
262598 TTGGGATGAT
262608 TTCAAATGAGAATGCCTAGACCTATTTAA
1 TTCAAATGAGAATGCCTAGACCTATTTAA
262637 TTCAAATGAGAATGCCTAGACCTATTTA
1 TTCAAATGAGAATGCCTAGACCTATTTA
262665 TAGTGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (29 bp):
TTCAAATGAGAATGCCTAGACCTATTTAA
Found at i:270053 original size:20 final size:20
Alignment explanation
Indices: 270030--270078 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
270020 ACAGGAAAAA
*
270030 GAAAATGAAGTAAAAGAAAT
1 GAAAATGAAGGAAAAGAAAT
* *
270050 GAAAATTAAGGAAATGAAAT
1 GAAAATGAAGGAAAAGAAAT
*
270070 GAATATGAA
1 GAAAATGAA
270079 TATGTTGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.18
Consensus pattern (20 bp):
GAAAATGAAGGAAAAGAAAT
Found at i:271404 original size:15 final size:16
Alignment explanation
Indices: 271373--271405 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
271363 AAATACTTAA
271373 TAAATTTATATTATTT
1 TAAATTTATATTATTT
271389 TAAATTTATA-TATTT
1 TAAATTTATATTATTT
271404 TA
1 TA
271406 TTCCTCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAAATTTATATTATTT
Found at i:272125 original size:51 final size:51
Alignment explanation
Indices: 272043--272157 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 51
272033 GTAACTACTA
* * * *
272043 AATAAAATAATAATAAACTAAAGATACTATTTTGATTCTATCCTAATTCTT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
* * *
272094 AATAAAATAATAATGAACTAAAGGTAATATTTTAACTCTATCTTAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
272145 AATAAAATAATAA
1 AATAAAATAATAA
272158 ATTTAATCCT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
Found at i:276118 original size:22 final size:21
Alignment explanation
Indices: 276080--276121 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
276070 TCATTAAAAA
* *
276080 TAAATAAATTTATTATTATTT
1 TAAATAAAATTAATATTATTT
276101 TAAATAATAATTAATATTATT
1 TAAATAA-AATTAATATTATT
276122 ATAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATAAAATTAATATTATTT
Found at i:278309 original size:2 final size:2
Alignment explanation
Indices: 278302--278359 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
278292 ATAGAGATGG
278302 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
278344 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
278360 TATTCTCTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:278531 original size:65 final size:65
Alignment explanation
Indices: 278422--278549 Score: 202
Period size: 65 Copynumber: 2.0 Consensus size: 65
278412 AGATAATTAA
* * * *
278422 AAATCAGATCTTTCTGTAAGAACAAAGACGAGTCCGAAAGGTTTTGTTTTTAGATTTAAGCTTAC
1 AAATCAGATCTATATGTAAGAACAAAGACGAGTCCGAAAGGTTTTCTTTTTAGACTTAAGCTTAC
* *
278487 AAATTAGATCTATATGTAAGAACAAGGACGAGTCCGAAAGGTTTTCTTTTTAGACTTAAGCTT
1 AAATCAGATCTATATGTAAGAACAAAGACGAGTCCGAAAGGTTTTCTTTTTAGACTTAAGCTT
278550 GAGCTTGCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (65 bp):
AAATCAGATCTATATGTAAGAACAAAGACGAGTCCGAAAGGTTTTCTTTTTAGACTTAAGCTTAC
Found at i:281280 original size:3 final size:3
Alignment explanation
Indices: 281265--281304 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
281255 GGTTAAAAAA
*
281265 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
281305 AGTGTGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:285019 original size:18 final size:18
Alignment explanation
Indices: 284996--285044 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
284986 TATTTCTGAG
284996 GGAATTGGAATCTGTAAA
1 GGAATTGGAATCTGTAAA
* *
285014 GGAATTGGAATATGTGAA
1 GGAATTGGAATCTGTAAA
*
285032 GGAATTAGAATCT
1 GGAATTGGAATCT
285045 AAATCTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.39, C:0.04, G:0.29, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTAAA
Found at i:287213 original size:5 final size:5
Alignment explanation
Indices: 287203--287237 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
287193 TAGTAATGTA
287203 TATAT TATAT TATAT TATATT ATATAT TATAT TAT
1 TATAT TATAT TATAT TATA-T -TATAT TATAT TAT
287238 GATCCGACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 22 0.79
6 2 0.07
7 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:287228 original size:12 final size:12
Alignment explanation
Indices: 287201--287237 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
287191 AATAGTAATG
287201 TATATATTATA-
1 TATATATTATAT
287212 T-TATATTATAT
1 TATATATTATAT
287223 TATATATTATAT
1 TATATATTATAT
287235 TAT
1 TAT
287238 GATCCGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.38
11 2 0.08
12 13 0.54
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATATTATAT
Found at i:292101 original size:32 final size:32
Alignment explanation
Indices: 292037--292101 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
292027 TGAGCACGAT
* ****
292037 ATCCTTCATCGTGAAGTTGAAATCGTGGTCGA
1 ATCCTTCATCGTGAAGTTAAAATCAAACTCGA
*
292069 ATCCTTCATCTTGAAGTTAAAATCAAACTCGA
1 ATCCTTCATCGTGAAGTTAAAATCAAACTCGA
292101 A
1 A
292102 ATCTGAACTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (32 bp):
ATCCTTCATCGTGAAGTTAAAATCAAACTCGA
Found at i:296290 original size:5 final size:5
Alignment explanation
Indices: 296120--296288 Score: 212
Period size: 5 Copynumber: 33.8 Consensus size: 5
296110 ATATAAATAT
* * * * * * * * * *
296120 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT
1 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
* *
296170 TTAGC ATAGT ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
1 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
296220 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
1 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
* *
296270 ATAGC ATAGT ATAGT ATAG
1 ATAGC ATAGC ATAGC ATAG
296289 TAGACGGGCT
Statistics
Matches: 158, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 158 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (5 bp):
ATAGC
Found at i:296397 original size:2 final size:2
Alignment explanation
Indices: 296390--296473 Score: 67
Period size: 2 Copynumber: 45.0 Consensus size: 2
296380 TATTAATAAT
* *
296390 TA TA TA TA -A TA TA AA TA TA TA TA -A TA TA -A TA CTA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
296430 TA TA T- TA TA TA CTA TA AA TA TA TA -A TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
296469 -A TA TA
1 TA TA TA
296474 ATACAGTACA
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
1 8 0.12
2 54 0.82
3 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:296403 original size:5 final size:5
Alignment explanation
Indices: 296393--296476 Score: 90
Period size: 5 Copynumber: 17.6 Consensus size: 5
296383 TAATAATTAT
*
296393 ATATA ATATA A-ATA TATATA ATATA ATACT- ATATA A-AT- ATATT ATATA
1 ATATA ATATA ATATA -ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA
*
296441 CTATA A-AT- ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
296477 CAGTACAGTA
Statistics
Matches: 68, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
3 2 0.03
4 12 0.18
5 50 0.74
6 4 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:296405 original size:25 final size:24
Alignment explanation
Indices: 296372--296471 Score: 82
Period size: 25 Copynumber: 4.0 Consensus size: 24
296362 TAAAACAAAA
*
296372 AATAAAAATATTA-ATAATTATATAT
1 AATATAAATATTATATAA-TATA-AT
296397 AATATAAATA-TATATAATATAAT
1 AATATAAATATTATATAATATAAT
*
296420 ACTATATAAATATATTATATACTAT-A-
1 A--ATAT-AA-ATATTATATAATATAAT
*
296446 AATATATAATATAATATAATATAAT
1 AATATA-AATATTATATAATATAAT
296471 A
1 A
296472 TAATACAGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
23 16 0.26
24 12 0.19
25 18 0.29
26 3 0.05
27 4 0.06
28 9 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATAAATATTATATAATATAAT
Found at i:296445 original size:18 final size:18
Alignment explanation
Indices: 296373--296476 Score: 78
Period size: 18 Copynumber: 6.1 Consensus size: 18
296363 AAAACAAAAA
*
296373 ATAAAAATATTA-ATAAT
1 ATAAATATATTATATAAT
* *
296390 -TATATATAATATA-AAT
1 ATAAATATATTATATAAT
* *
296406 ATATATAATATAATACT-AT
1 ATAAAT-ATATTATA-TAAT
*
296425 ATAAATATATTATATACT
1 ATAAATATATTATATAAT
*
296443 ATAAATATATAATATAAT
1 ATAAATATATTATATAAT
296461 AT-AATATA--ATATAAT
1 ATAAATATATTATATAAT
296476 A
1 A
296477 CAGTACAGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
15 8 0.11
16 11 0.15
17 13 0.18
18 32 0.45
19 7 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATATATTATATAAT
Found at i:296475 original size:15 final size:14
Alignment explanation
Indices: 296385--296476 Score: 109
Period size: 15 Copynumber: 6.4 Consensus size: 14
296375 AAAAATATTA
296385 ATAATTATATATAAT
1 ATAA-TATATATAAT
296400 ATAAATATATATAAT
1 AT-AATATATATAAT
296415 ATAATACTATATAA-
1 ATAATA-TATATAAT
*
296429 AT-ATATTATATACT
1 ATAATA-TATATAAT
296443 ATAA-ATATATAAT
1 ATAATATATATAAT
296456 ATAATATAATATAAT
1 ATAATAT-ATATAAT
296471 ATAATA
1 ATAATA
296477 CAGTACAGTA
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
13 20 0.29
14 11 0.16
15 35 0.51
16 2 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATATATATAAT
Found at i:296483 original size:5 final size:5
Alignment explanation
Indices: 296453--296656 Score: 309
Period size: 5 Copynumber: 40.8 Consensus size: 5
296443 ATAAATATAT
* * * * * * * * *
296453 AATAT AATAT AATAT AATAT AATAC AGTAC AGTAC AGTAC AGTAC AGTAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* *
296503 AGTAC AGTAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
296553 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
296603 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
296653 AATA
1 AATA
296657 TATGACAACT
Statistics
Matches: 196, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 196 1.00
ACGTcount: A:0.57, C:0.18, G:0.03, T:0.22
Consensus pattern (5 bp):
AATAC
Found at i:301261 original size:24 final size:24
Alignment explanation
Indices: 301217--301262 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
301207 CTTTCAACTT
*
301217 CTTTTTCTTTGTATTTTTTCTTTC
1 CTTTTTCTTTGTATTTCTTCTTTC
301241 CTTTTTCTTTTGT-TTTCTTCTT
1 CTTTTTC-TTTGTATTTCTTCTT
301263 GAGTGCTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (24 bp):
CTTTTTCTTTGTATTTCTTCTTTC
Found at i:302736 original size:43 final size:42
Alignment explanation
Indices: 302528--302738 Score: 203
Period size: 42 Copynumber: 5.0 Consensus size: 42
302518 ATAAAATTGT
* * *
302528 GGCGTTTGTGATGAAACATGCCACTATATA-CAT-ACTCAATATC
1 GGCGTTTGAG-TGAAA-ATGCCACTATATATCATGACT-ATTAGC
* * * *
302571 GACGTTTGGGTGAAAATGCCACTAAATACCATGACTATTAGC
1 GGCGTTTGAGTGAAAATGCCACTATATATCATGACTATTAGC
* *
302613 GGCGTTTGAGTGAAAAATGTCATTATA-ATCATGACTATTAGC
1 GGCGTTTGAGTG-AAAATGCCACTATATATCATGACTATTAGC
* * * *
302655 GACGTTTGAGTGAAAATACTACTATATATCAAGACTATTAGC
1 GGCGTTTGAGTGAAAATGCCACTATATATCATGACTATTAGC
* * * *
302697 GGCGTTTGTGTAGGAAACGCCACTATATATCATGGCTATTAG
1 GGCGTTTGAGT-GAAAATGCCACTATATATCATGACTATTAG
302739 TGGTGTTTTC
Statistics
Matches: 138, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
41 22 0.16
42 70 0.51
43 46 0.33
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (42 bp):
GGCGTTTGAGTGAAAATGCCACTATATATCATGACTATTAGC
Found at i:304957 original size:20 final size:20
Alignment explanation
Indices: 304928--304965 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
304918 TTTCAAAGTG
304928 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
304948 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
304966 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:310931 original size:24 final size:24
Alignment explanation
Indices: 310904--310984 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
310894 ACACTTAACA
310904 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
310928 GTGCATCGATTCAT-CATATTGAA-
1 GTGCATCGATGCATCCCT-TTGAAT
*
310951 --GCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
310972 GTGCATCGATGCA
1 GTGCATCGATGCA
310985 CAGGGTCGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 5 0.11
21 9 0.20
22 1 0.02
23 12 0.27
24 18 0.40
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:313701 original size:19 final size:20
Alignment explanation
Indices: 313677--313729 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
313667 AATGCATTTT
* *
313677 ATGCATCGATGCAC-ATATC
1 ATGCATCGATGCACAAGACC
313696 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
*
313716 ATGCATCAATGCAC
1 ATGCATCGATGCAC
313730 TCAGGCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (20 bp):
ATGCATCGATGCACAAGACC
Found at i:313789 original size:19 final size:19
Alignment explanation
Indices: 313762--313813 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
313752 ATGCATTTTA
*
313762 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
313781 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
313800 TGCACCGATGCACT
1 TGCACCGATGCACT
313814 GAGAGTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:315229 original size:7 final size:7
Alignment explanation
Indices: 315217--315247 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
315207 AGAATTTCCT
315217 TATTATA
1 TATTATA
315224 TATTATA
1 TATTATA
315231 TATTATA
1 TATTATA
315238 TATTA-A
1 TATTATA
315244 TATT
1 TATT
315248 TGAGTCTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATTATA
Found at i:319298 original size:31 final size:31
Alignment explanation
Indices: 319253--319388 Score: 209
Period size: 31 Copynumber: 4.4 Consensus size: 31
319243 TCTGTGACAT
*
319253 AAACTTTTCAGTGATATATCACTTCATTCAG
1 AAACTTTTCAGTGATAAATCACTTCATTCAG
* *
319284 AAACTTGTCCGTGATAAATCACTTCATTCAG
1 AAACTTTTCAGTGATAAATCACTTCATTCAG
319315 AAACTTTTCAGTGATAAATCACTTCATTCAG
1 AAACTTTTCAGTGATAAATCACTTCATTCAG
** *
319346 AAACTTTTCAGTGATGTATAACTTCATTCAG
1 AAACTTTTCAGTGATAAATCACTTCATTCAG
*
319377 AAAATTTTCAGT
1 AAACTTTTCAGT
319389 CATATACCAA
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 96 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (31 bp):
AAACTTTTCAGTGATAAATCACTTCATTCAG
Found at i:327012 original size:60 final size:59
Alignment explanation
Indices: 326899--327083 Score: 192
Period size: 60 Copynumber: 3.1 Consensus size: 59
326889 ATATAATTTG
* * * *
326899 GGATGAAATTGAAATTTTCAAAAAGTTTAAGGGCCAATTTAGAATGAAGGTCATAGTTTAA
1 GGATGAAAATGAAATATTC-AAAAGTTTAAGGACTAATTTAGAATGAA-GTCATAGTTTAA
* * *
326960 GGATGAAAATGAAATGTTCAAAAGTTTGAGGACTAATATAGAATGATAGTCATAGTTTAA
1 GGATGAAAATGAAATATTCAAAAGTTTAAGGACTAATTTAGAATGA-AGTCATAGTTTAA
* * * * * * *
327020 GGAT-AAAATTAAAATATTTAAAAGTTTAATGACTAATTTAAAATAAGAGTCATAATTTAG
1 GGATGAAAA-TGAAATATTCAAAAGTTTAAGGACTAATTTAGAATGA-AGTCATAGTTTAA
327080 GGAT
1 GGAT
327084 TTGTGAGATG
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
59 4 0.04
60 83 0.79
61 18 0.17
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (59 bp):
GGATGAAAATGAAATATTCAAAAGTTTAAGGACTAATTTAGAATGAAGTCATAGTTTAA
Found at i:341822 original size:31 final size:31
Alignment explanation
Indices: 341777--341857 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
341767 TTCGATAATA
* *
341777 TAATAATTATTTTTATAGT-ATTTAGATAAATT
1 TAATAAGTA-TTTTATAATCATTTA-ATAAATT
* *
341809 TATTAA-TAATTTTATAATCTTTTAATAAATT
1 TAATAAGT-ATTTTATAATCATTTAATAAATT
341840 TAATAAGTATTTTATAAT
1 TAATAAGTATTTTATAAT
341858 TTTTTAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 31 0.74
32 11 0.26
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (31 bp):
TAATAAGTATTTTATAATCATTTAATAAATT
Found at i:341835 original size:19 final size:20
Alignment explanation
Indices: 341811--341860 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
341801 GATAAATTTA
*
341811 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
341830 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
341851 TT-ATAATTTT
1 TTAATAATTTT
341861 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:341863 original size:31 final size:31
Alignment explanation
Indices: 341797--341864 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
341787 TTTTATAGTA
*
341797 TTTAGATAAATTTATTAATAATTTTATAATCT
1 TTTA-ATAAATTTAATAATAATTTTATAATCT
*
341829 TTTAATAAATTTAATAAGT-ATTTTATAATTT
1 TTTAATAAATTTAATAA-TAATTTTATAATCT
341860 TTTAA
1 TTTAA
341865 ACTTTATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAATAAATTTAATAATAATTTTATAATCT
Found at i:342635 original size:31 final size:30
Alignment explanation
Indices: 342589--342671 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
342579 TCAATAAAGT
*
342589 TTAAAAATTATAAAA-TACTTATTAAATTTA
1 TTAAAAATTATAAAATTA-TTAATAAATTTA
*
342619 TTAAAAGATTGTAAAATTATTAATAAATTTA
1 TTAAAA-ATTATAAAATTATTAATAAATTTA
* * *
342650 TCTAAATACTATAAAATAATTA
1 T-TAAAAATTATAAAATTATTA
342672 TTATATTATC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 6 0.14
31 32 0.73
32 6 0.14
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (30 bp):
TTAAAAATTATAAAATTATTAATAAATTTA
Found at i:344865 original size:228 final size:228
Alignment explanation
Indices: 344416--345362 Score: 1715
Period size: 228 Copynumber: 4.1 Consensus size: 228
344406 GTTATATTGC
* * *
344416 AAAGTATTTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
344480 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAA-AATCAA
*
344545 ATAATTTTGTGTGTAAATGAAATTATTAAATTAATATTTGTAGGTGGAAAACATGAAACACTATT
130 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATA-TTGTAGGTGGAAAACATGAAACACTATT
344610 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
194 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
344645 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
344710 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAAAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
*
344774 TAATTTTTAGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-A
344839 AAAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAAATTGAAACATAAATTACATAACTTTAAAA
* *
344873 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGAGGAAAGCATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
344938 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
*
345003 TAATTTTTTTTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-A
345068 AAAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAAATTGAAACATAAATTACATAACTTTAAAA
345102 AAAG--TATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
345165 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAAATATC-AAAAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTAT-AAAATATCAAAAAATCAA
*
345229 ATAATTTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATT
130 ATAA-TTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT
*
345294 AAAAAAATTGAAAAATAAATTACATAACTTTAAAA
194 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
345329 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
345363 GTATAAAAGT
Statistics
Matches: 697, Mismatches: 14, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
227 182 0.26
228 258 0.37
229 186 0.27
230 71 0.10
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (228 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:345434 original size:20 final size:19
Alignment explanation
Indices: 345411--345457 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
345401 CGATATACCA
345411 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
345431 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
345451 GGTAAAA
1 GGTAAAA
345458 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:345609 original size:20 final size:19
Alignment explanation
Indices: 345581--345636 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
345571 GATCCACAAC
*
345581 GATATAACAGGTAAAAATAT
1 GATAAAACAGGTAAAAA-AT
*
345601 GATAAAACAGGTATCAAAAT
1 GATAAAACAGGTA-AAAAAT
*
345621 GATAAAACCGGTAAAA
1 GATAAAACAGGTAAAA
345637 TGATACCGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 26 0.84
21 3 0.10
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.20
Consensus pattern (19 bp):
GATAAAACAGGTAAAAAAT
Found at i:347888 original size:21 final size:21
Alignment explanation
Indices: 347864--347907 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
347854 AAGACAATCA
347864 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
347885 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
347906 AG
1 AG
347908 GCATAAGGGG
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:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:347982 original size:33 final size:33
Alignment explanation
Indices: 347940--348005 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
347930 AAATAGATGG
*
347940 AGTGGTGAAAGAAGTAGAGGTGTTGAGAGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
* * *
347973 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
348006 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
Found at i:349824 original size:19 final size:19
Alignment explanation
Indices: 349800--349848 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
349790 AATGTAGGGT
349800 TAATTTTGTATAAGAGTTA
1 TAATTTTGTATAAGAGTTA
* *
349819 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGAGTTA
*
349838 TATTTTTGTAT
1 TAATTTTGTAT
349849 GTGAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGAGTTA
Found at i:350515 original size:199 final size:199
Alignment explanation
Indices: 349967--351131 Score: 2146
Period size: 199 Copynumber: 5.9 Consensus size: 199
349957 CAATATGGCC
* * * *
349967 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAATCATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
350032 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
350097 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATA-TTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
350161 TGGAA
195 TGGAA
*
350166 AACAGGGTGCACCCATAAAGTGTCGATCCGTATAT-AAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
350230 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
350295 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
350360 GGAA
196 GGAA
*
350364 AACAGGGTGCACCCATAAAGTGTCGATCCGTATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
350429 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* *
350494 AATATGTCTAAATAATGTGTCGATACTATTTTAGTTTGTGTCGATATTTTTGTTCCATAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
350559 GGAA
196 GGAA
* *
350563 AACAGGGTGCAACCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAAATATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
350627 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
350692 AATATGTCTAAATAATGTGTCAACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
350757 GGAA
196 GGAA
*
350761 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
350826 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
350891 AATATGTCTAAATAATGTGTCG--ACTA-TTTAGTTTGTGTCGATA-TTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
350952 GGAA
196 GGAA
*
350956 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCAAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
351021 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
351086 AATATATCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATA
351132 CTAATTTAAA
Statistics
Matches: 940, Mismatches: 20, Indels: 13
0.97 0.02 0.01
Matches are distributed among these distances:
195 171 0.18
196 17 0.02
197 122 0.13
198 289 0.31
199 341 0.36
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
GGAA
Found at i:350700 original size:397 final size:395
Alignment explanation
Indices: 349967--351131 Score: 2154
Period size: 397 Copynumber: 2.9 Consensus size: 395
349957 CAATATGGCC
* * * *
349967 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAATCATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
350032 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
350097 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTGTTCCAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGA-ACTATTTTAGTTTGTGTCGATATTTTGTTCCAGAATGAAT
*
350162 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCGTATATAAAAGTGTCGATCCCAAAAACATCGA
194 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAAACATCGA
350227 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
259 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
350292 GAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATG
324 GAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATG
350357 AATGGAA
389 AATGGAA
*
350364 AACAGGGTGCACCCATAAAGTGTCGATCCGTATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
350429 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
350494 AATATGTCTAAATAATGTGTCGATACTATTTTAGTTTGTGTCGATATTTTTGTTCCATAATGAAT
131 AATATGTCTAAATAATGTGTCGA-ACTATTTTAGTTTGTGTCGATA-TTTTGTTCCAGAATGAAT
* *
350559 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAAATATCGA
194 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAAACATCGA
350624 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
259 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGA
*
350689 GAGAATATGTCTAAATAATGTGTCAACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATG
324 GAGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATG
350754 AATGGAA
389 AATGGAA
*
350761 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
350826 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
350891 AATATGTCTAAATAATGTGTCG-ACTA-TTTAGTTTGTGTCGATATTTTGTTCCAGAATGAATGG
131 AATATGTCTAAATAATGTGTCGAACTATTTTAGTTTGTGTCGATATTTTGTTCCAGAATGAATGG
*
350954 AAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCAAA
196 AAAACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAAACATCGAA
351019 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
260 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
*
351084 AGAATATATCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATA
325 AGAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATA
351132 CTAATTTAAA
Statistics
Matches: 747, Mismatches: 19, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
393 55 0.07
394 153 0.20
395 4 0.01
396 113 0.15
397 422 0.56
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (395 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGAACTATTTTAGTTTGTGTCGATATTTTGTTCCAGAATGAATGG
AAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAAACATCGAAC
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
TGGAA
Found at i:352628 original size:6 final size:6
Alignment explanation
Indices: 352604--352695 Score: 76
Period size: 6 Copynumber: 15.3 Consensus size: 6
352594 AGCGGTCGCA
* * * * * *
352604 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * * *
352652 GACGAT GAAGAT GATGAA GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
352696 TGATCCAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:352646 original size:9 final size:9
Alignment explanation
Indices: 352619--352699 Score: 81
Period size: 9 Copynumber: 9.0 Consensus size: 9
352609 TGAAGCTGAC
*
352619 GATGAAGAT
1 GATGATGAT
*
352628 GACGATGAT
1 GATGATGAT
*
352637 GATGACGAT
1 GATGATGAT
* * *
352646 GAAGCTGAC
1 GATGATGAT
*
352655 GATGAAGAT
1 GATGATGAT
*
352664 GATGAAGAT
1 GATGATGAT
352673 GATGATGAT
1 GATGATGAT
*
352682 GATGATGAA
1 GATGATGAT
352691 GATGATGAT
1 GATGATGAT
352700 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 57 1.00
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.23
Consensus pattern (9 bp):
GATGATGAT
Found at i:352654 original size:36 final size:36
Alignment explanation
Indices: 352607--352683 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
352597 GGTCGCAGAA
*
352607 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGAAGATGATGAC
* *
352643 GATGAAGCTGACGATGAAGATGATGAAGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGAAGATGATGAC
352679 GATGA
1 GATGA
352684 TGATGAAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGAAGATGATGAC
Found at i:352699 original size:12 final size:12
Alignment explanation
Indices: 352607--352695 Score: 97
Period size: 12 Copynumber: 7.4 Consensus size: 12
352597 GGTCGCAGAA
*
352607 GATGAAGCTGAC
1 GATGAAGATGAC
352619 GATGAAGATGAC
1 GATGAAGATGAC
*
352631 GATGATGATGAC
1 GATGAAGATGAC
*
352643 GATGAAGCTGAC
1 GATGAAGATGAC
*
352655 GATGAAGATGAT
1 GATGAAGATGAC
* * *
352667 GAAGATGATGAT
1 GATGAAGATGAC
* *
352679 GATGATGATGAA
1 GATGAAGATGAC
352691 GATGA
1 GATGA
352696 TGATCCAAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 67 1.00
ACGTcount: A:0.38, C:0.07, G:0.34, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:353911 original size:16 final size:16
Alignment explanation
Indices: 353879--353912 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
353869 TATCCACAAC
* *
353879 AAAGTGTCGATTTAAA
1 AAAGTGTCGACTGAAA
353895 AAAGTGTCGACTGAAA
1 AAAGTGTCGACTGAAA
353911 AA
1 AA
353913 TGTAATAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (16 bp):
AAAGTGTCGACTGAAA
Found at i:354326 original size:23 final size:23
Alignment explanation
Indices: 354270--354341 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
354260 ATAGGTAAAA
*
354270 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
354293 ATA-AATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
354315 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
354338 ATAT
1 ATAT
354342 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 19 0.45
23 23 0.55
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:357506 original size:25 final size:25
Alignment explanation
Indices: 357472--357536 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
357462 TTATCATTAA
357472 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
357497 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
357522 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
357537 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:357891 original size:20 final size:21
Alignment explanation
Indices: 357866--357937 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 21
357856 ACTTTCAATA
357866 TAATAGGTAA-AC-ATATGATG
1 TAATAGGTAACACTATAT-ATG
*
357886 TAATAGGTAACGCTATATATG
1 TAATAGGTAACACTATATATG
* *
357907 TAATAGGTATCATTTATATATG
1 TAATAGGTAACA-CTATATATG
357929 TAATAGGTA
1 TAATAGGTA
357938 GTGGTTATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.22
21 14 0.31
22 21 0.47
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (21 bp):
TAATAGGTAACACTATATATG
Found at i:358390 original size:21 final size:22
Alignment explanation
Indices: 358363--358426 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
358353 AACATATGAT
358363 GTAATAGGTAGCGCTTATATAA
1 GTAATAGGTAGCGCTTATATAA
* *
358385 -TAATAGGTATCGTTTATATAA
1 GTAATAGGTAGCGCTTATATAA
* *
358406 TGTAATAGGTAGTGGTTATAT
1 -GTAATAGGTAGCGCTTATAT
358427 TGTAAAGTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 19 0.54
23 16 0.46
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (22 bp):
GTAATAGGTAGCGCTTATATAA
Found at i:358411 original size:23 final size:23
Alignment explanation
Indices: 358356--358426 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
358346 ATAGGTAAAC
*
358356 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
358379 ATATAA--TAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
358400 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
358423 ATAT
1 ATAT
358427 TGTAAAGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 19 0.47
23 21 0.52
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:358578 original size:478 final size:479
Alignment explanation
Indices: 357536--359063 Score: 2725
Period size: 479 Copynumber: 3.2 Consensus size: 479
357526 AGGTATATAC
357536 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGA-TTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
*
357600 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATA-TTACATATTTTTATTATCTT
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATTTACATATTATTATTATCTT
*
357664 TGGTTAATGTTGTTAAATTTAAATTATAAATAATTTTTATAAAATATCAAAACAATCAAATAATT
131 TGGTTAATGTTGTTAAATTTAAATTCTAAAT-A-TTTTAT-AAATATCAAAACAATCAAATAATT
357729 TTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAA
193 TTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAA
357794 TTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACT
258 TTGAAACATAAATTACATAACTTTT-AAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACT
* * *
357859 TTCAATATAATAGGTAAACATATGATGTAATAGGTAACGC-TATATATGTAATAGGTATCATTTA
322 TTCAATATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATA-ATAATAGGTATCGTTTA
357923 TAT-ATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTATAAAAGTGTCCATACTTT
386 TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTATAAAAGTGTCCATACTTT
357987 TTTCACTGTGGAAAACATTAATTTAAGGTT
451 TTTCACTGTGGAAAACA-TAATTTAAGGTT
358017 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
358082 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATTTACATATTATTATTATCTT
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATTTACATATTATTATTATCTT
358147 TGGTTAATGTTGTTAAATTTAAATTCTAAATATTTT-TAAATATCAAAACAATCAAATAATTTTT
131 TGGTTAATGTTGTTAAATTTAAATTCTAAATATTTTATAAATATCAAAACAATCAAATAATTTTT
358211 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTG
196 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTG
358276 AAACATAAATTACATAACTTTTAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCA
261 AAACATAAATTACATAACTTTTAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCA
358341 ATATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATAATAATAGGTATCGTTTATATAA
326 ATATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATAATAATAGGTATCGTTTATATAA
358406 TGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATAC-TTTTTC
391 TGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCC-TTTTATAAAAGTGTCCATACTTTTTTC
358470 ACTGTGGAAAACATAATTTAAGGTT
455 ACTGTGGAAAACATAATTTAAGGTT
358495 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
358560 GTTACGGTATATATTATTATTAAATT-AAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATAT-TTACATA-TTATTATTATC
358624 TTTGGTTAA---TGTTAAATTTAAATTCTAAATAATATTTTATAAATTATCAAAACAATCAAATA
129 TTTGGTTAATGTTGTTAAATTTAAATTCT--A-AATATTTTATAAA-TATCAAAACAATCAAATA
358686 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAA
190 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAA
358751 AAATTGAAACAT-AATTACATAACTTTTAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACA
255 AAATTGAAACATAAATTACATAACTTTTAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACA
358815 CTTTCAATAT-ATAGGTAAACATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCG-
320 CTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATAA--TAATAGGTATCGT
*
358878 TT-TATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCATTTTATAAAAGTGTCCATAC
383 TTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTATAAAAGTGTCCATAC
358942 TTTTTTCACTGTGGAAAAC--AATTTAAGGTT
448 TTTTTTCACTGTGGAAAACATAATTTAAGGTT
*
358972 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTAT
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
359036 GTTAC-G-ATATATTATTATTAAATTAAAA
66 GTTACGGTATATATTATTATTAAATTAAAA
359064 TTCTAAATAT
Statistics
Matches: 1024, Mismatches: 7, Indels: 38
0.96 0.01 0.04
Matches are distributed among these distances:
474 18 0.02
475 4 0.00
476 28 0.03
477 86 0.08
478 227 0.22
479 303 0.30
480 89 0.09
481 164 0.16
482 56 0.05
483 49 0.05
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (479 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATTTACATATTATTATTATCTT
TGGTTAATGTTGTTAAATTTAAATTCTAAATATTTTATAAATATCAAAACAATCAAATAATTTTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTG
AAACATAAATTACATAACTTTTAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCA
ATATAATAGGTAAACATATGATGTAATAGGTAGCGCTTATATAATAATAGGTATCGTTTATATAA
TGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTATAAAAGTGTCCATACTTTTTTCA
CTGTGGAAAACATAATTTAAGGTT
Found at i:358885 original size:21 final size:23
Alignment explanation
Indices: 358835--358905 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
358825 ATAGGTAAAC
*
358835 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
358858 ATATAATGTAATAGGTATCG-TT
1 ATATAATGTAATAGGTAGCGCTT
* *
358880 -TATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
358902 ATAT
1 ATAT
358906 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.40
22 4 0.10
23 21 0.50
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:358909 original size:21 final size:21
Alignment explanation
Indices: 358841--358910 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
358831 AAACATATGA
*
358841 TGTAATAGGTAGCGCTTATAT
1 TGTAATAGGTAGTGCTTATAT
* *
358862 AATGTAATAGGTA-TCGTTTATAA
1 --TGTAATAGGTAGT-GCTTATAT
*
358885 TGTAATAGGTAGTGGTTATAT
1 TGTAATAGGTAGTGCTTATAT
358906 TGTAA
1 TGTAA
358911 AGTGTCTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 22 0.55
22 1 0.03
23 17 0.43
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (21 bp):
TGTAATAGGTAGTGCTTATAT
Found at i:359206 original size:25 final size:25
Alignment explanation
Indices: 359172--359222 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
359162 ACAACAAATC
*
359172 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
359197 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
359222 A
1 A
359223 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:359589 original size:18 final size:18
Alignment explanation
Indices: 359568--359604 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
359558 GTAATTGGAG
359568 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
359586 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
359604 T
1 T
359605 ATATATTTCG
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:359612 original size:24 final size:24
Alignment explanation
Indices: 359560--359606 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
359550 TTTCATATGT
* *
359560 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
359584 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
359607 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:359906 original size:39 final size:39
Alignment explanation
Indices: 359863--359949 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
359853 TCCGATGCTC
*
359863 ATCAAAATCCAAAGCTCATATGGTGCAAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCAAAGCAAAAGGAA
* *
359902 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCAAAGCAAAAGGAA
359941 ATCAAAATC
1 ATCAAAATC
359950 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCAAAGCAAAAGGAA
Found at i:360376 original size:23 final size:23
Alignment explanation
Indices: 360345--360417 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
360335 ATAGGTAAAC
*
360345 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
360368 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
360391 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
360414 ATAT
1 ATAT
360418 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:364172 original size:25 final size:26
Alignment explanation
Indices: 364142--364191 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
364132 TTATATTAAG
364142 GATGAATTTAT-AAAATTTTAAAAAC
1 GATGAATTTATAAAAATTTTAAAAAC
364167 GATGAATTTATAAAAATTTTAAAAA
1 GATGAATTTATAAAAATTTTAAAAA
364192 ATAAAAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (26 bp):
GATGAATTTATAAAAATTTTAAAAAC
Found at i:364452 original size:30 final size:28
Alignment explanation
Indices: 364400--364456 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
364390 AATTACAGTT
* *
364400 TAAAAAAAATAAAGTTTAGATATTAAAA
1 TAAAAAAAATAAAATATAGATATTAAAA
364428 TAAAAAATAATAATAATATAGATATTAAA
1 TAAAAAA-AATAA-AATATAGATATTAAA
364457 CATGTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 5 0.20
30 13 0.52
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (28 bp):
TAAAAAAAATAAAATATAGATATTAAAA
Found at i:365705 original size:204 final size:200
Alignment explanation
Indices: 365310--366041 Score: 760
Period size: 204 Copynumber: 3.6 Consensus size: 200
365300 CTTCATTGCT
* * * * * * * * *
365310 ACTCTCTTTGGTTTCAGCAACTGGAGAATCAGCTTTCGAAAGAG-GCACTGATGTATTCTCTTGG
1 ACTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCG-ACCGGTGTATTCTCTTGA
* * * *
365374 GAGATACTATCCATGTCTCCGGTGTCGAGGACCGAATTATCATCGATCGAATTCGAAGAAGAAGG
65 GAGAGACTATCCATATCTCCGGTGTCGAGGACCGAATTATCA-C-A--GCA---GAAGGAGAAGG
* * * **
365439 AGAAGTTAGGCTATTGTTGTCACCTTTGGTTTCAACAGTTTGAGGAATAGAGGTGTTTTCTTGTT
123 AGAAG-TA-GCTATTGTTATCACCTTTGGTTTCAACAG-TAGAGGAACAGAGGTGTTTTCTTGGA
*
365504 CAATAACTCCAATGCC
185 CAGTAACTCCAATGCC
* * * * * *
365520 ACTCCCTTTGGTTTCGGCGGATGGAGGATCGGCATTCAATCGAGGGACCGGTGTATTCTCTTGAG
1 ACTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCGACCGGTGTATTCTCTTGAG
* *
365585 AGAGACTATCCATATCTCTGGTGTTGAGGACCGAATTATCGACAGCAGAAGGAGAAGGAGAAGTA
66 AGAGACTATCCATATCTCCGGTGTCGAGGACCGAATTATC-ACAGCAGAAGGAGAAGGAGAAGT-
*
365650 AAGCTATTGTTATCACCTTTGGTTTCAACAGTAGCAGGAAGAGAGGTGTTTTCTTGGACAGTAAC
129 -AGCTATTGTTATCACCTTTGGTTTCAACAGTAG-AGGAACAGAGGTGTTTTCTTGGACAGTAAC
365715 TCCAATGCC
192 TCCAATGCC
* * * *
365724 ATTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCAACCGGCGTATTCTCTCGAG
1 ACTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCGACCGGTGTATTCTCTTGAG
* * ** * * *
365789 AGAGACTATCCGTATCTCCAGCATTGAGGTCTGAATTATCA-A-CA-ACAGGAGAAGGAGAAG--
66 AGAGACTATCCATATCTCCGGTGTCGAGGACCGAATTATCACAGCAGA-AGGAGAAGGAGAAGTA
* * * * *
365849 GCTATTGTTATTACCTTTGGATTCAACAGTAGGAGGAACAGAGGTGTTTACTTGGGCAGTAACAC
130 GCTATTGTTATCACCTTTGGTTTCAACAGTA-GAGGAACAGAGGTGTTTTCTTGGACAGTAACTC
365914 CAATGCC
194 CAATGCC
* * * **
365921 GCTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTTGATAGAGCGACTGAAGTATTCTCTCTCG
1 ACTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCGACCGGTGTATTCTCT-T-G
* * *
365986 AGA-A-ACTATCCGTATCTCTGGTGTCGAGGACCGAATTATCAACAACAGAAGGAGAA
64 AGAGAGACTATCCATATCTCCGGTGTCGAGGACCGAATTATC-ACAGCAGAAGGAGAA
366042 ATCGGGATAT
Statistics
Matches: 445, Mismatches: 64, Indels: 36
0.82 0.12 0.07
Matches are distributed among these distances:
197 147 0.33
198 3 0.01
199 5 0.01
200 10 0.02
201 17 0.04
202 1 0.00
203 4 0.01
204 166 0.37
205 1 0.00
207 2 0.00
209 1 0.00
210 86 0.19
211 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (200 bp):
ACTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCGACCGGTGTATTCTCTTGAG
AGAGACTATCCATATCTCCGGTGTCGAGGACCGAATTATCACAGCAGAAGGAGAAGGAGAAGTAG
CTATTGTTATCACCTTTGGTTTCAACAGTAGAGGAACAGAGGTGTTTTCTTGGACAGTAACTCCA
ATGCC
Found at i:365929 original size:197 final size:200
Alignment explanation
Indices: 365446--366041 Score: 705
Period size: 197 Copynumber: 3.0 Consensus size: 200
365436 AGGAGAAGTT
* ** * ** *
365446 AGGCTATTGTTGTCACCTTTGGTTTCAACAGTTTGAGGAATAGAGGTGTTTTCTTGTTCAATAAC
1 AGGCTATTGTTATCACCTTTGGTTTCAACAGTAGGAGGAACAGAGGTGTTTTCTTGGACAGTAAC
* * * * * * *
365511 TCCAATGCCACTCCCTTTGGTTTCGGCGGATGGAGGATCGGCATTCAATCGAGGGACCGGTGTAT
66 TCCAATGCCACTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCGACCGGAGTAT
* * ** **
365576 TCTCTTGAGAGAGACTATCCATATCTCTGGTGTTGAGGACCGAATTATCGACAGCAGAAGGAGAA
131 TCTCTCGAGAGAGACTATCCGTATCTCCAGCATTGAGGACCGAATTATCGACAGCAGAAGGAGAA
365641 GGAGA
196 GGAGA
* *
365646 AGTAAAGCTATTGTTATCACCTTTGGTTTCAACAGTAGCAGGAAGAGAGGTGTTTTCTTGGACAG
1 AG----GCTATTGTTATCACCTTTGGTTTCAACAGTAGGAGGAACAGAGGTGTTTTCTTGGACAG
* * *
365711 TAACTCCAATGCCATTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCAACCGGC
62 TAACTCCAATGCCACTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCGACCGGA
* *
365776 GTATTCTCTCGAGAGAGACTATCCGTATCTCCAGCATTGAGGTCTGAATTATC-A-A-CA-ACAG
127 GTATTCTCTCGAGAGAGACTATCCGTATCTCCAGCATTGAGGACCGAATTATCGACAGCAGA-AG
365837 GAGAAGGAGA
191 GAGAAGGAGA
* * * *
365847 AGGCTATTGTTATTACCTTTGGATTCAACAGTAGGAGGAACAGAGGTGTTTACTTGGGCAGTAAC
1 AGGCTATTGTTATCACCTTTGGTTTCAACAGTAGGAGGAACAGAGGTGTTTTCTTGGACAGTAAC
* * * * *
365912 ACCAATGCCGCTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTTGATAGAGCGACTGAAGTAT
66 TCCAATGCCACTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCGACCGGAGTAT
** * ** ** * * *
365977 TCTCTCTCGAGAAACTATCCGTATCTCTGGTGTCGAGGACCGAATTATCAACAACAGAAGGAGAA
131 TCTCTCGAGAGAGACTATCCGTATCTCCAGCATTGAGGACCGAATTATCGACAGCAGAAGGAGAA
366042 ATCGGGATAT
Statistics
Matches: 338, Mismatches: 49, Indels: 18
0.83 0.12 0.04
Matches are distributed among these distances:
197 153 0.45
198 1 0.00
199 1 0.00
200 12 0.04
201 17 0.05
202 1 0.00
203 1 0.00
204 152 0.45
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (200 bp):
AGGCTATTGTTATCACCTTTGGTTTCAACAGTAGGAGGAACAGAGGTGTTTTCTTGGACAGTAAC
TCCAATGCCACTCCCTTTGGTTTCAGCAGCTGGAGGATCGGCATTCGATAGAGCGACCGGAGTAT
TCTCTCGAGAGAGACTATCCGTATCTCCAGCATTGAGGACCGAATTATCGACAGCAGAAGGAGAA
GGAGA
Found at i:374628 original size:42 final size:42
Alignment explanation
Indices: 374569--374651 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
374559 ATCAACGAAC
*
374569 AGATGAGTAAACTTACATTAGTTGTGAGTCGTTTGGAATCTT
1 AGATGAGTAAACTTACATTAGTTGTGAGTCGATTGGAATCTT
* *
374611 AGATGAGTCAACTTACATTAGTTGTGATTCGATTGGAATCT
1 AGATGAGTAAACTTACATTAGTTGTGAGTCGATTGGAATCT
374652 CAGGGAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (42 bp):
AGATGAGTAAACTTACATTAGTTGTGAGTCGATTGGAATCTT
Found at i:376732 original size:15 final size:15
Alignment explanation
Indices: 376712--376747 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
376702 TTTTTTCATT
*
376712 AAAAAAATG-TTCCA
1 AAAAAAATGCTCCCA
376726 AAAAAAATGCTCCCA
1 AAAAAAATGCTCCCA
376741 AAAAAAA
1 AAAAAAA
376748 AAGAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.64, C:0.17, G:0.06, T:0.14
Consensus pattern (15 bp):
AAAAAAATGCTCCCA
Found at i:376781 original size:25 final size:23
Alignment explanation
Indices: 376725--376782 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
376715 AAAATGTTCC
376725 AAAAAAAATGCTCCCAAAAAAAA
1 AAAAAAAATGCTCCCAAAAAAAA
* *
376748 AAGAGAAAAATGTTCGCAAAGAAAAGA
1 AA-A-AAAAATGCTCCCAAA-AAAA-A
376775 AAAAAAAA
1 AAAAAAAA
376783 GAGAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 2 0.07
24 1 0.03
25 18 0.62
26 5 0.17
27 3 0.10
ACGTcount: A:0.69, C:0.10, G:0.12, T:0.09
Consensus pattern (23 bp):
AAAAAAAATGCTCCCAAAAAAAA
Found at i:391922 original size:21 final size:21
Alignment explanation
Indices: 391896--391950 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
391886 GATTCTGACT
391896 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
391917 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
*
391938 ATCGCAATGCGAT
1 ATCGCAACGCGAT
391951 TTTCAAAGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:392120 original size:22 final size:22
Alignment explanation
Indices: 392095--392145 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
392085 CTACAGCGAC
392095 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
392117 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
392139 ATCCGTC
1 ATCCGTC
392146 TATCTCGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:392571 original size:20 final size:20
Alignment explanation
Indices: 392546--392598 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
392536 CGATTTTAGT
392546 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
392566 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
392586 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
392599 TTTCATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:392604 original size:20 final size:20
Alignment explanation
Indices: 392535--392621 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 20
392525 AAACCGCAAC
*
392535 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** **
392554 GCGATAGTCAAATTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** *
392574 GCGATAGTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
*
392594 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
*
392614 ACGATTTT
1 GCGATTTT
392622 AAGTTTCAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 6 0.11
20 51 0.89
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:392628 original size:20 final size:20
Alignment explanation
Indices: 392585--392628 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
392575 CGATAGTCAT
* * *
392585 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTACGATTTTAAG
392605 TTTCGTGTTACGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
392625 TTTC
1 TTTC
392629 AGAAACTATT
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:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:394187 original size:21 final size:21
Alignment explanation
Indices: 394144--394199 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
394134 CGGTGCATGG
* * *
394144 CGTGATGAGGTATCTACTTTA
1 CGTGATGAGGTAGCCACTCTA
*
394165 CGTGATGAGGTAGCCGCTCTA
1 CGTGATGAGGTAGCCACTCTA
394186 CGTGA-GATGGTAGC
1 CGTGATGA-GGTAGC
394200 ATCGTTACAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (21 bp):
CGTGATGAGGTAGCCACTCTA
Found at i:394492 original size:20 final size:20
Alignment explanation
Indices: 394469--394517 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
394459 GAAACTTAAA
394469 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
394489 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
394509 ATCGCAACG
1 ATCGCAACG
394518 GGATAATCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:394562 original size:20 final size:20
Alignment explanation
Indices: 394534--394574 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
394524 TCGTAATGCG
*
394534 AAATAAAAATCACAATGCAA
1 AAATAAAAATCACAACGCAA
* *
394554 AAATGAAAATCGCAACGCAA
1 AAATAAAAATCACAACGCAA
394574 A
1 A
394575 TTTAGTTTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.17, G:0.10, T:0.12
Consensus pattern (20 bp):
AAATAAAAATCACAACGCAA
Found at i:394602 original size:19 final size:20
Alignment explanation
Indices: 394575--394613 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
394565 GCAACGCAAA
*
394575 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
394595 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
394614 ATCCCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:394647 original size:20 final size:20
Alignment explanation
Indices: 394618--394686 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
394608 GCGATTATCC
394618 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
394638 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
394658 GGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
394678 CGTTGCGAT
1 CGTTGCGAT
394687 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:394696 original size:20 final size:20
Alignment explanation
Indices: 394673--394716 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
394663 CGATAGTCAT
394673 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
394693 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
394713 TTTC
1 TTTC
394717 AGAAACCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:395269 original size:21 final size:21
Alignment explanation
Indices: 395245--395314 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
395235 CTATCATCCC
*
395245 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCAT
* ** *
395266 TCAAGAGGCCCCTGTCATCAT
1 TCAAGAGTCCCCTCCCACCAT
*
395287 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCAT
395308 TCAAGAG
1 TCAAGAG
395315 CCCAATTCAC
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCAT
Found at i:395269 original size:42 final size:41
Alignment explanation
Indices: 395221--395317 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 41
395211 CCTATTCTAT
*
395221 CATTCAAGATGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CATTCAAGA-GCCCCTATCATCACTCAAGAGGT-CCCTCCCAC
* * * *
395263 CGTTCAAGAGGCCCCTGTCATCATTGAAGAGGTCCCTCCCAC
1 CATTCAAGA-GCCCCTATCATCACTCAAGAGGTCCCTCCCAC
395305 CATTCAAGAGCCC
1 CATTCAAGAGCCC
395318 AATTCACACA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 4 0.09
42 41 0.87
43 2 0.04
ACGTcount: A:0.24, C:0.40, G:0.15, T:0.21
Consensus pattern (41 bp):
CATTCAAGAGCCCCTATCATCACTCAAGAGGTCCCTCCCAC
Found at i:396914 original size:20 final size:20
Alignment explanation
Indices: 396891--396938 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
396881 GCAACCTGAA
396891 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
396911 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
396931 ATTCAAAT
1 AGTCAAAT
396939 GAATGTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTCAAATTCGCGTTGCGAT
Found at i:399396 original size:24 final size:24
Alignment explanation
Indices: 399362--399415 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
399352 CTGAAACATC
*
399362 ATCAAAATCCGATTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
399386 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
399410 ATCAAA
1 ATCAAA
399416 TTTTGAATAT
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:399426 original size:24 final size:24
Alignment explanation
Indices: 399362--399429 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
399352 CTGAAACATC
* *
399362 ATCAAAATCCGATTATTGACCAAG
1 ATCAAAGTCCGAATATTGACCAAG
**
399386 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATATTGACCAAG
* **
399410 ATCAAATTTTGAATATTGAC
1 ATCAAAGTCCGAATATTGAC
399430 TAGTACTTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (24 bp):
ATCAAAGTCCGAATATTGACCAAG
Found at i:400091 original size:17 final size:17
Alignment explanation
Indices: 400069--400104 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
400059 CGGATGGGGA
400069 AGGATGTCATTGGATAT
1 AGGATGTCATTGGATAT
*
400086 AGGATGTCGTTGGATAT
1 AGGATGTCATTGGATAT
400103 AG
1 AG
400105 AAACGAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.33, T:0.33
Consensus pattern (17 bp):
AGGATGTCATTGGATAT
Done.