Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008268.1 Hibiscus syriacus cultivar Beakdansim tig00110925_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: 492505
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:190428 original size:52 final size:47
Alignment explanation
Indices: 190261--190428 Score: 174
Period size: 54 Copynumber: 3.3 Consensus size: 47
190251 AAGCAATCCA
* *
190261 TATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAAT--A--AAT
*
190312 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 ---TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAAT
* * *
190362 TATTTTAAAATAAATCAATCTATATTTTATAATAATTTATTTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATA----ATAATAAATTA-TTTAAAATAAAT
190414 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
190429 TATTTTAAAA
Statistics
Matches: 104, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
47 23 0.22
50 3 0.03
51 9 0.09
52 27 0.26
54 42 0.40
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (47 bp):
TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAAT
Found at i:190687 original size:20 final size:20
Alignment explanation
Indices: 190662--190703 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
190652 AAAACAAACA
190662 CAAGCTAAGATATCGTGATT
1 CAAGCTAAGATATCGTGATT
190682 CAAGCTAAGATATCGTGATT
1 CAAGCTAAGATATCGTGATT
190702 CA
1 CA
190704 TGTTAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (20 bp):
CAAGCTAAGATATCGTGATT
Found at i:194233 original size:2 final size:2
Alignment explanation
Indices: 194226--194259 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
194216 GAATAAATAA
194226 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
194260 GACTTAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194287 original size:14 final size:15
Alignment explanation
Indices: 194268--194301 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
194258 ATGACTTAAG
194268 ATAATAAT-AAAAAA
1 ATAATAATGAAAAAA
*
194282 ATAATAATGAAAATA
1 ATAATAATGAAAAAA
194297 ATAAT
1 ATAAT
194302 TTAAACTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
ATAATAATGAAAAAA
Found at i:194296 original size:12 final size:12
Alignment explanation
Indices: 194270--194358 Score: 58
Period size: 12 Copynumber: 7.4 Consensus size: 12
194260 GACTTAAGAT
194270 AATAATAA-AAA
1 AATAATAATAAA
*
194281 AATAATAATGAA
1 AATAATAATAAA
*
194293 AATAATAATTTAA
1 AATAATAA-TAAA
* *
194306 ACTCAT-ATAAAA
1 AATAATAAT-AAA
194318 AATAATAATAAA
1 AATAATAATAAA
* * *
194330 ACAAAACAA-AAT
1 A-ATAATAATAAA
*
194342 AATAATAATCAA
1 AATAATAATAAA
194354 AATAA
1 AATAA
194359 AAGAAATTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
11 14 0.24
12 30 0.52
13 14 0.24
ACGTcount: A:0.70, C:0.06, G:0.01, T:0.24
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:194365 original size:24 final size:24
Alignment explanation
Indices: 194314--194360 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
194304 AAACTCATAT
194314 AAAA-AATAATAATAAAACAAAAC
1 AAAATAATAATAATAAAACAAAAC
*
194337 AAAATAATAATAATCAAAATAAAA
1 AAAATAATAATAAT-AAAACAAAA
194361 GAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 9 0.43
25 8 0.38
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (24 bp):
AAAATAATAATAATAAAACAAAAC
Found at i:194404 original size:16 final size:17
Alignment explanation
Indices: 194377--194411 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
194367 AAAAGCAATA
194377 ATATTAAAATGAAAAAT
1 ATATTAAAATGAAAAAT
194394 ATATT-AAATGAAAAAT
1 ATATTAAAATGAAAAAT
194410 AT
1 AT
194412 CAAACTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
ATATTAAAATGAAAAAT
Found at i:195577 original size:3 final size:3
Alignment explanation
Indices: 195569--195617 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
195559 CTCTTTTATT
195569 TAA TAA TAA TATA TATA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
195615 TAA
1 TAA
195618 CATGAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.80
4 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:195807 original size:45 final size:45
Alignment explanation
Indices: 195743--196023 Score: 456
Period size: 45 Copynumber: 6.3 Consensus size: 45
195733 GATGGAAGTG
*
195743 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
195788 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* * *
195833 TTGAAAACATCATGCACTTAAGGGCTTACAGATGACTCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
195878 TTGAAAACATTATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* * *
195923 TTGAAAATATCATGCACTGAAGGGCTTACATATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* * *
195968 TTGAAAACATCATGCACTGAAGGACTTACAGATGACTCAAAGGCT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
196013 TT-AAAACATCA
1 TTGAAAACATCA
196024 AAAAGCTCCC
Statistics
Matches: 218, Mismatches: 18, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
44 9 0.04
45 209 0.96
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
Found at i:196104 original size:45 final size:45
Alignment explanation
Indices: 196031--196138 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
196021 TCAAAAAGCT
* * * ***
196031 CCCGAAGGCTTTTTGAAAATATCCTGCACTGCAGGTCTTATGGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGTCTTACAAATGA
*
196078 CCCGAAGGTTTTGAAAGCATCATGCACTGAAGGTCTTACAAATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAAATGA
*
196123 CCCGAAGGCTTTGAAA
1 CCCGAAGGTTTTGAAA
196139 CATTAAAAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 45 0.85
47 8 0.15
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAAATGA
Found at i:196224 original size:44 final size:44
Alignment explanation
Indices: 196167--196262 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
196157 GGCTTTTTAA
* * * * *
196167 AAACATCTTGCACTGCATGTCTTATAGATGACCCGAA-GTTTTG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
196210 AAAGCATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTG
1 AAA-CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
196255 AAACATCA
1 AAACATCA
196263 AAAAGCTCCC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 3 0.07
44 34 0.76
45 8 0.18
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (44 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
Found at i:196260 original size:119 final size:120
Alignment explanation
Indices: 195954--196359 Score: 634
Period size: 120 Copynumber: 3.4 Consensus size: 120
195944 GGGCTTACAT
* * * *
195954 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACTCAAAGGCTTTAAAA
1 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAA
* *
196019 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAATATCCTGCACTGCAGGTCTTATGG
66 CATCAAAAAGCTCCCGAAGGCTTTTTAAAAACATCCTGCACTGCAGGTCTTATGG
* *
196074 ATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGTCTTACAAATGACCCGAAGGCTTTGAAA
1 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAA
* * * * *
196139 CATTAAAAAGCTTCCGAAGGCTTTTTAAAAACATCTTGCACTGCATGTCTTATAG
66 CATCAAAAAGCTCCCGAAGGCTTTTTAAAAACATCCTGCACTGCAGGTCTTATGG
* *
196194 ATGACCCGAA-GTTTTGAAAGCATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAA
1 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAA
* *
196258 CATCAAAAAGCTCCCAAAGGCTTTTTAAAAACATCCTACACTGCAGGTCTTATGG
66 CATCAAAAAGCTCCCGAAGGCTTTTTAAAAACATCCTGCACTGCAGGTCTTATGG
* *
196313 ATGACCCGAAGATTTTGAAAATATCATGCACTGAAGGTCTTACAGAT
1 ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGAT
196360 ATGGGAAATA
Statistics
Matches: 259, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
119 110 0.42
120 149 0.58
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (120 bp):
ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAA
CATCAAAAAGCTCCCGAAGGCTTTTTAAAAACATCCTGCACTGCAGGTCTTATGG
Found at i:197054 original size:22 final size:22
Alignment explanation
Indices: 197024--197065 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
197014 ATCTCTAAAG
*
197024 AAATCTATCATCTTTGAAGAGA
1 AAATATATCATCTTTGAAGAGA
197046 AAATATATCATCTTTGAAGA
1 AAATATATCATCTTTGAAGA
197066 ATGTAGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (22 bp):
AAATATATCATCTTTGAAGAGA
Found at i:197530 original size:54 final size:54
Alignment explanation
Indices: 197430--197540 Score: 132
Period size: 54 Copynumber: 2.1 Consensus size: 54
197420 ATAATAACTG
* *** *
197430 GTTCATAAAACATTTGACAACAAATTCATCATCTCATGTGGTTTCTGCCCAGAT
1 GTTCATAAAACATTTAACAACAAATTCATCATCTCATGTAACTTCTGCACAGAT
* * * * *
197484 GTTCGTAAAGCATTTAACAACACATTCATCATTTCCTGTAACTTCTGCACAGAT
1 GTTCATAAAACATTTAACAACAAATTCATCATCTCATGTAACTTCTGCACAGAT
197538 GTT
1 GTT
197541 TTGGTCAGGG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (54 bp):
GTTCATAAAACATTTAACAACAAATTCATCATCTCATGTAACTTCTGCACAGAT
Found at i:202284 original size:2 final size:2
Alignment explanation
Indices: 202277--202306 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
202267 ACGACAAGGG
*
202277 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
202307 TTAAAAGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:206917 original size:2 final size:2
Alignment explanation
Indices: 206912--206955 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
206902 TTAAAAAATA
206912 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
206954 AT
1 AT
206956 TATGAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:207869 original size:3 final size:3
Alignment explanation
Indices: 207861--207931 Score: 55
Period size: 3 Copynumber: 24.7 Consensus size: 3
207851 ATGAATTAAG
* *
207861 ATA ATA ATA A-A ATA ATA ATA AT- TTA A-A CATA TATCA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A ATA ATA ATA
207906 ATA A-A ATA A-A ATA A-A ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
207932 CAAAATAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
2 10 0.18
3 40 0.73
4 4 0.07
5 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:207877 original size:11 final size:11
Alignment explanation
Indices: 207861--207930 Score: 63
Period size: 11 Copynumber: 5.9 Consensus size: 11
207851 ATGAATTAAG
207861 ATAATAATAAA
1 ATAATAATAAA
207872 ATAATAATAATTTA
1 ATAATAATAA---A
207886 A-ACATATATCAAAA
1 ATA-ATA-AT--AAA
207900 ATAATAATAAA
1 ATAATAATAAA
207911 ATAA-AATAAA
1 ATAATAATAAA
207921 ATAATAATAA
1 ATAATAATAA
207931 TCAAAATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
10 10 0.20
11 22 0.44
13 3 0.06
14 10 0.20
15 3 0.06
17 2 0.04
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:207915 original size:5 final size:5
Alignment explanation
Indices: 207897--207951 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
207887 ACATATATCA
*
207897 AAAAT AATAAT AAAAT AAAAT AAAAT --AAT AATAAT CAAAAT AAATT
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AA-AAT -AAAAT AAAAT
*
207943 AAATT AAAA
1 AAAAT AAAA
207952 GCAATAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
3 3 0.07
5 27 0.63
6 11 0.26
7 2 0.05
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:207945 original size:25 final size:23
Alignment explanation
Indices: 207866--207946 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 23
207856 TTAAGATAAT
207866 AATAAAATAATAATAATTTAAACATA
1 AATAAAATAATAATAA--TAAA-ATA
* *
207892 TATCAAA-AATAATAATAAAATAA
1 AATAAAATAATAATAATAAAAT-A
207915 AATAAAATAATAATAATCAAAATA
1 AATAAAATAATAATAAT-AAAATA
*
207939 AATTAAAT
1 AATAAAAT
207947 TAAAAGCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
22 2 0.04
23 10 0.21
24 17 0.36
25 13 0.28
26 5 0.11
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (23 bp):
AATAAAATAATAATAATAAAATA
Found at i:207980 original size:17 final size:17
Alignment explanation
Indices: 207945--207992 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
207935 AATAAATTAA
*
207945 ATTAAAA-GCAATA-AT
1 ATTAAAATGCAAAATAT
207960 ATTAAAATGCAAAATAT
1 ATTAAAATGCAAAATAT
*
207977 ATT-AAATGAAAAATAT
1 ATTAAAATGCAAAATAT
207993 CAAACTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 17 0.59
17 5 0.17
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.29
Consensus pattern (17 bp):
ATTAAAATGCAAAATAT
Found at i:209331 original size:13 final size:15
Alignment explanation
Indices: 209296--209330 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
209286 CTTTTTTATT
209296 TAAT-ATATATAATA
1 TAATAATATATAATA
209310 TAATAATATATAATAA
1 TAATAATATATAAT-A
209326 TAATA
1 TAATA
209331 TGAAATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 9 0.47
16 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAATATATAATA
Found at i:215270 original size:23 final size:23
Alignment explanation
Indices: 215226--215300 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
215216 AAAATGTTAA
* * * *
215226 CATGAAAAGACTTGACTTTTTTG
1 CATGAAAATAATTAACTATTTTG
* *
215249 GATG-AAATGAATTAACTATTTTT
1 CATGAAAAT-AATTAACTATTTTG
* *
215272 CATGAAAATACTTAACTATTTTT
1 CATGAAAATAATTAACTATTTTG
215295 CATGAA
1 CATGAA
215301 TAGAGATGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.07
23 35 0.83
24 4 0.10
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (23 bp):
CATGAAAATAATTAACTATTTTG
Found at i:215280 original size:24 final size:23
Alignment explanation
Indices: 215253--215300 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
215243 TTTTTGGATG
215253 AAATGAATTAACTATTTTTCATGA
1 AAAT-AATTAACTATTTTTCATGA
*
215277 AAATACTTAACTATTTTTCATGA
1 AAATAATTAACTATTTTTCATGA
215300 A
1 A
215301 TAGAGATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATAATTAACTATTTTTCATGA
Found at i:216380 original size:19 final size:20
Alignment explanation
Indices: 216351--216388 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
216341 AGAAATTTGT
216351 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
216371 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
216389 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:216431 original size:63 final size:62
Alignment explanation
Indices: 216356--216514 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 62
216346 TTTGTTGAAG
* * * *
216356 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATATCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATACCCTCA
** ** *
216419 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATACCCTCA
216482 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
216515 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 79 0.94
64 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATACCCTCA
Found at i:217866 original size:17 final size:18
Alignment explanation
Indices: 217832--217866 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
217822 AGGAATGATA
217832 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
217850 TGTGGTCCTTC-GGACAT
1 TGTGGTCCTTCGGGACAT
217867 ATGTATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.11, C:0.23, G:0.31, T:0.34
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:217973 original size:18 final size:18
Alignment explanation
Indices: 217950--217985 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
217940 AGGAATGATA
217950 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
217968 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
217986 ATATGTATTC
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:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:218047 original size:121 final size:121
Alignment explanation
Indices: 217729--218089 Score: 620
Period size: 118 Copynumber: 3.0 Consensus size: 121
217719 CGAGGGTCTA
*
217729 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
217794 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
217850 TGTGGTCC-TTCGGAC--ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
217912 GATCCCTAACATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* **
217968 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGATGAGATGCATACTT
1 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* **
218033 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
218089 T
1 T
218090 ATTATATGGC
Statistics
Matches: 226, Mismatches: 11, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
118 110 0.49
119 6 0.03
120 5 0.02
121 105 0.46
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:218164 original size:23 final size:23
Alignment explanation
Indices: 218096--218156 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
218086 CATTATTATA
*
218096 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
218119 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
218142 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
218157 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:222050 original size:63 final size:62
Alignment explanation
Indices: 221980--222135 Score: 188
Period size: 63 Copynumber: 2.5 Consensus size: 62
221970 TTTGAAGGTA
* * * *
221980 CATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCAGTG
1 CATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCAGTG
** **
222043 CATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCAGTG
1 CATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCAGTG
*
222106 CATCGATGCATCAGGAGTGCATTGATGCAT
1 CATCGATGCAT-AGGAGTGCATCGATGCAT
222136 GCCTCCATTA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 76 0.94
64 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (62 bp):
CATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCAGTG
Found at i:223521 original size:103 final size:103
Alignment explanation
Indices: 223342--223567 Score: 434
Period size: 103 Copynumber: 2.2 Consensus size: 103
223332 GTCGAGGGTC
*
223342 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
223407 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
223445 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
223510 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
223548 TATGTGGTCCTTCGGGACAT
1 TATGTGGTCCTTCGGGACAT
223568 TGTGGTCCTT
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 121 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
Found at i:223583 original size:18 final size:18
Alignment explanation
Indices: 223550--223585 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
223540 AGGAATGATA
*
223550 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCAGGACAT
*
223568 TGTGGTCCTTTAGGACAT
1 TGTGGTCCTTCAGGACAT
223586 ATATGTATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCAGGACAT
Found at i:223661 original size:121 final size:121
Alignment explanation
Indices: 223447--223689 Score: 414
Period size: 121 Copynumber: 2.0 Consensus size: 121
223437 AAGAATGATA
*
223447 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* *
223512 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGCGGTCCTTAGGGACAT
* * *
223568 TGTGGTCCTTTAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATGCTT
1 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* *
223633 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGCGGTCCTTATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGCGGTCCTTAGGGACAT
223689 T
1 T
223690 ATTATATGGC
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 114 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGCGGTCCTTAGGGACAT
Found at i:223764 original size:23 final size:23
Alignment explanation
Indices: 223696--223756 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
223686 CATTATTATA
*
223696 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
223719 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
223742 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
223757 TTTATATGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:228536 original size:18 final size:18
Alignment explanation
Indices: 228503--228537 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
228493 ACAGGGCAAC
*
228503 TCTTCTTACGTCAACTCT
1 TCTTCTTAAGTCAACTCT
*
228521 TCTTCTTAAGTTAACTC
1 TCTTCTTAAGTCAACTC
228538 CTCCTCCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.46
Consensus pattern (18 bp):
TCTTCTTAAGTCAACTCT
Found at i:237483 original size:18 final size:18
Alignment explanation
Indices: 237462--237506 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
237452 CTACCTTGGT
*
237462 TATCGATACTCCCTTGAG
1 TATCAATACTCCCTTGAG
237480 TATCAATACTCCCTTGAG
1 TATCAATACTCCCTTGAG
237498 TATCAATAC
1 TATCAATAC
237507 CAAAATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (18 bp):
TATCAATACTCCCTTGAG
Found at i:239967 original size:2 final size:2
Alignment explanation
Indices: 239960--239996 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
239950 TAGTTTACCC
239960 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
239997 TAAGTAATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:245359 original size:47 final size:44
Alignment explanation
Indices: 245308--245474 Score: 130
Period size: 43 Copynumber: 3.7 Consensus size: 44
245298 AAAACAAATA
245308 AATAAAATAATAATAATAAAGTAAAAATGATATATATATATATATAT
1 AATAAAATAATAA-AATAAA-TAAAAAT-ATATATATATATATATAT
* * *
245355 AAT-AAATAAATAAAAT-AA-AAAAATAGTAAATATATATATGTGT
1 AATAAAAT-AATAAAATAAATAAAAATA-TATATATATATATATAT
* *
245398 -ATAAATTAATAAAACTGATATAAAAAAATATATATATATATATATAT
1 AATAAAATAATAAAA-T-A-A-ATAAAAATATATATATATATATATAT
* * *
245445 ATATATAAT-CTAAAA-AAATAAAGATATATA
1 A-ATAAAATAATAAAATAAATAAAAATATATA
245475 CTAAAGTAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
42 10 0.10
43 35 0.36
44 1 0.01
45 3 0.03
46 8 0.08
47 23 0.24
48 12 0.12
49 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (44 bp):
AATAAAATAATAAAATAAATAAAAATATATATATATATATATAT
Found at i:245430 original size:2 final size:2
Alignment explanation
Indices: 245425--245451 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
245415 ATATAAAAAA
245425 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 A
245452 ATCTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:246546 original size:84 final size:84
Alignment explanation
Indices: 246431--246645 Score: 259
Period size: 84 Copynumber: 2.6 Consensus size: 84
246421 ATAATTTTAT
* * * * * *
246431 TGACATATAGCCCTTCTTGTCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGTTGAGCGTAGTC
1 TGACAGATAGCCCTTCTAGACTTGAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCATAGTC
*
246496 AAACTCGAAGGTCTTTAGT
66 AAACTCGAAGGTCTTTAGG
* * * * * *
246515 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTCCCTTAGAGCTGAGCATAGTC
1 TGACAGATAGCCCTTCTAGACTTGAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCATAGTC
* *
246580 GAACTCGAAGGTCTTTTGG
66 AAACTCGAAGGTCTTTAGG
* * * *
246599 TGATAGATAACCCTTCTAGCCTTGAGTTACGCTGTAAATGATGTGCC
1 TGACAGATAGCCCTTCTAGACTTGAGTTATGCTGTAAATGATGTGCC
246646 CTTGAAGCTG
Statistics
Matches: 107, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
84 107 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (84 bp):
TGACAGATAGCCCTTCTAGACTTGAGTTATGCTGTAAATGATGTGCCTTAGAGCTGAGCATAGTC
AAACTCGAAGGTCTTTAGG
Found at i:246796 original size:36 final size:36
Alignment explanation
Indices: 246747--246815 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
246737 AAAGGTTGAA
*
246747 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
246783 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
246816 ACTTCCAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:246831 original size:34 final size:34
Alignment explanation
Indices: 246757--246845 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 34
246747 GTTTCAAGGG
* *
246757 AAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAG
1 AAACTGTCTCAAGAGAGACAAAAC-T-TTCCAAGAA
246793 AAACTGTCTCAAGAGAGACAAAAAC-TTCC-AGAAA
1 AAACTGTCTCAAGAGAGAC-AAAACTTTCCAAG-AA
* *
246827 AAACTATCTCAAGGGAGAC
1 AAACTGTCTCAAGAGAGAC
246846 GAAATTTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 2 0.04
34 21 0.45
36 19 0.40
37 5 0.11
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (34 bp):
AAACTGTCTCAAGAGAGACAAAACTTTCCAAGAA
Found at i:246969 original size:37 final size:36
Alignment explanation
Indices: 246914--246997 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
246904 AAGTTTATGC
* * **
246914 TTCAAGAGAAACTGTCTCAATG-GAGACAAAATTTTGT
1 TTCAAGGGAAACTATCTCAA-GAGAGACAAAA-TTCAT
*
246951 TTCAAGGGAACCTATCTCAAGAGAGACAAAATTCAT
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
246987 TTCAAGGGAAA
1 TTCAAGGGAAA
246998 TGTTTTCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 14 0.35
37 26 0.65
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (36 bp):
TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
Found at i:247087 original size:100 final size:100
Alignment explanation
Indices: 246896--247144 Score: 408
Period size: 100 Copynumber: 2.5 Consensus size: 100
246886 CAAATAAAAT
* * *
246896 TGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAATGGAGACAAAATTTTGTTTCAAGGGAA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC--AATTTTGTTTCAAGGGAA
246961 CCTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
64 CCTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
246998 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAATTTTGTTTCAAGGGAACC
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAATTTTGTTTCAAGGGAACC
* *
247063 TATCTCAAGAGATACAAAATTCATTTCATGGGAAA
66 TATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
* * *
247098 TGTTTTTAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAA
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
247145 AACTTAGTTC
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
100 97 0.70
102 42 0.30
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (100 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAATTTTGTTTCAAGGGAACC
TATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
Found at i:247183 original size:100 final size:101
Alignment explanation
Indices: 246896--247258 Score: 389
Period size: 100 Copynumber: 3.6 Consensus size: 101
246886 CAAATAAAAT
* *
246896 TGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAATG-GAGACAAAATTTTGTTTCAAGGGA
1 TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAA-GAGAGACAAAATTTTGTTTCAA-GGA
246960 ACCTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
64 ACCTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
* * *
246998 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC--AATTTTGTTTCAAGGGAA
1 TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCAA-GGAA
* *
247061 CCTATCTCAAGAGATACAAAATTCATTTCATGGGAAA
65 CCTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
* * * * * * *
247098 TGTTTTTAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAA-AAAA
1 TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCAAGGAAC
* * * * ** *
247162 ATGTCTCAAGGGAGACGAAATTTGTTTCAAAGGAAA
66 CTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
* * * * **
247198 CAG-ATTCAAAGATTT-TCTTTTAAGAGAAACTATCTCAAGAGAGAC-AAATTTCATTTCAAGG
1 -TGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCAAGG
247259 GAAATTTTTT
Statistics
Matches: 223, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
99 10 0.04
100 157 0.70
101 5 0.02
102 51 0.23
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (101 bp):
TGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCAAGGAAC
CTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
Found at i:247337 original size:37 final size:36
Alignment explanation
Indices: 247287--247691 Score: 143
Period size: 36 Copynumber: 11.6 Consensus size: 36
247277 ATGTTTCAAG
* *
247287 AGAAACTGTCTCAAGGGAGACAAAATTTAGTTCTAAA
1 AGAAAATGTCTCAAGAGAGACAAAATTTAGTT-TAAA
* * *
247324 AGAAAATGTCTCAAGGGAGACGAAA-TTAGTTTCAA
1 AGAAAATGTCTCAAGAGAGACAAAATTTAGTTTAAA
** * *
247359 AGAAAA-----C---AGATTCAAAGATTTTGTTTCAAG
1 AGAAAATGTCTCAAGAGAGACAAA-ATTTAGTTT-AAA
* * * *
247389 GGAAACTGTCTCAAGAAAGACAAAATTT-GTTTCAA
1 AGAAAATGTCTCAAGAGAGACAAAATTTAGTTTAAA
* * *
247424 GGAAAACTGTCTCAAGAGAGACAAAATTT-GTTTCTAG
1 AGAAAA-TGTCTCAAGAGAGACAAAATTTAGTTT-AAA
* * * *
247461 AGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAA
1 AGAAAATGTCTCAAGAGAGACAAAATTTAGTT-TAAA
* * ** *
247498 AGAAATTGTCTCAAGGGAGACGGAA-TTAGTTTCAA
1 AGAAAATGTCTCAAGAGAGACAAAATTTAGTTTAAA
* ** * * *
247533 GGAAAA-----C---AGATTCAATTATTTTGTTTCAAG
1 AGAAAATGTCTCAAGAGAGACAA-AATTTAGTTT-AAA
* * *
247563 GGAAACTGTCTCAAGAGAGACAAAATTT-GTTTCAAG
1 AGAAAATGTCTCAAGAGAGACAAAATTTAGTTT-AAA
* * * * * *
247599 GGAAACTGTATCAAGGGAGAAAAAATTT-GTTTCAAG
1 AGAAAATGTCTCAAGAGAGACAAAATTTAGTTT-AAA
* * *
247635 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
1 AGAAAATGTCTCAAGAGAGACAAAATTTAGTT-TAAA
* * *
247672 AGAAATTGTCTAAAGGGAGA
1 AGAAAATGTCTCAAGAGAGA
247692 TGGAATTAGT
Statistics
Matches: 277, Mismatches: 63, Indels: 56
0.70 0.16 0.14
Matches are distributed among these distances:
27 8 0.03
28 2 0.01
29 12 0.04
30 13 0.05
35 23 0.08
36 125 0.45
37 82 0.30
38 12 0.04
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (36 bp):
AGAAAATGTCTCAAGAGAGACAAAATTTAGTTTAAA
Found at i:247418 original size:36 final size:36
Alignment explanation
Indices: 247378--247973 Score: 432
Period size: 36 Copynumber: 17.0 Consensus size: 36
247368 ATTCAAAGAT
*
247378 TTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
247414 TTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
247450 TTTGTTTCTAGAGAAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * **
247486 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGGAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * ** *
247523 TTAGTTTCAAGGAAAACAGAT-TC-----A-A-TTAT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
247552 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
247588 TTTGTTTCAAGGGAAACTGTATCAAGGGAGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
247624 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * * ***
247660 CTTAGTTCCAAAAGAAATTGTCTAAAGGGAGATGGAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * **
247697 TTAGTTTCAAGGAAAACATAT-TC-------A-ATTA
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
* *
247725 TTTTTTTCCAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
247761 TTTGATTCAAGGGAAACTGTCTCAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
247797 TTTGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * *
247833 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
247870 TTTGTTTCAAGTGAAACAGAT-TC-----A-A-ATAT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
*
247899 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
247935 TTTGTTGTTTCAATGGAAACTGTCTCAAGAGAGACAAAA
1 --T-TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
247974 CTTGGAAAAT
Statistics
Matches: 435, Mismatches: 91, Indels: 65
0.74 0.15 0.11
Matches are distributed among these distances:
27 2 0.00
28 18 0.04
29 39 0.09
30 2 0.00
31 2 0.00
34 2 0.00
35 3 0.01
36 245 0.56
37 88 0.20
38 1 0.00
39 33 0.08
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:247527 original size:174 final size:174
Alignment explanation
Indices: 247278--247973 Score: 1072
Period size: 174 Copynumber: 4.0 Consensus size: 174
247268 TCAATGTTTA
* * * *
247278 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCTAAAAGAAAATGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAG
* *
247343 ACGAAATTAGTTTCAAAGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAAAG
66 ACGAAATTAGTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
*
247408 ACAAAATTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATT
131 ACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
247452 TGTTTCTAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAG
* * *
247517 ACGGAATTAGTTTCAAGGAAAACAGATTCAATTATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
66 ACGAAATTAGTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
* * *
247582 ACAAAATTTGTTTCAAGGGAAACTGTATCAAGGGAGAAAAAATT
131 ACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
247626 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTAAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAG
* * * * * *
247691 ATGGAATTAGTTTCAAGGAAAACATATTCAATTATTTT-TTTCCAGGGAAACTGTCTCAAGAGAG
66 ACGAAATTAGTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
* *
247755 ACAAAATTTGATTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
131 ACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
247799 TGCTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAG
* * *
247864 ACGAAATTTGTTTC-AAGTGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGA
66 ACGAAATTAGTTTCAAAG-AAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGA
*
247928 GACAAAATTTGTTGTTTCAATGGAAACTGTCTCAAGAGAGACAAAA
130 GACAAAA--T-TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
247974 CTTGGAAAAT
Statistics
Matches: 478, Mismatches: 39, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
172 2 0.00
173 156 0.33
174 287 0.60
176 1 0.00
177 32 0.07
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (174 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAG
ACGAAATTAGTTTCAAAGAAAACAGATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
ACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:247530 original size:73 final size:72
Alignment explanation
Indices: 247381--247886 Score: 242
Period size: 73 Copynumber: 7.2 Consensus size: 72
247371 CAAAGATTTT
* * * * *
247381 GTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGGAAAACTGTCTCAAGAGAGAC
1 GTTTCAAGAGAAACTGTCTCAAGAAAGAAAAAATTAGTTCCAAAGAAAACTGTCTCAAGAGAGAC
*
247446 AAAATTT
66 AAAATTA
* * * *
247453 GTTTCTAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAA-AGAAATTGTCTCAAGGGAG
1 GTTTCAAGAGAAACTGTCTCAAGAAAGAAAAAA-TTAGTTCCAAAGA-AAACTGTCTCAAGAGAG
**
247517 ACGGAATTA
64 ACAAAATTA
* *** ** * * * * *
247526 GTTTCAAG-GAAA-----AC-AGATTCAATTATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 GTTTCAAGAGAAACTGTCTCAAGAAAGAAAAAATTAGTTCCAAAGAAAACTGTCTCAAGAGAGAC
*
247584 AAAATTT
66 AAAATTA
* * ** * *
247591 GTTTCAAGGGAAACTGTATCAAGGGAGAAAAAATTTGTTTC-AAGAGAAACTGTCTCAAGAGAGA
1 GTTTCAAGAGAAACTGTCTCAAGAAAGAAAAAATTAGTTCCAAAGA-AAACTGTCTCAAGAGAGA
247655 CAAAACTTA
65 CAAAA-TTA
* * * * ** *** * * *
247664 GTTCCAAAAGAAATTGTCTAAAGGGAGATGGAATTAGTTTCAAGGAAAACATAT-TC-------A
1 GTTTCAAGAGAAACTGTCTCAAGAAAGAAAAAATTAGTTCCAAAGAAAAC-TGTCTCAAGAGAGA
** *
247721 -ATTATTT
65 CAAAATTA
* * * * * * * * *
247728 TTTTCCAGGGAAACTGTCTCAAGAGAGACAAAATTTGATT-CAAGGGAAACTGTCTCAAGGGAGA
1 GTTTCAAGAGAAACTGTCTCAAGAAAGAAAAAATTAG-TTCCAAAGAAAACTGTCTCAAGAGAGA
*
247792 CAAAATTT
65 CAAAATTA
* * * *
247800 GCTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA-AGAAACTGTCTCAAGGGAG
1 GTTTCAAGAGAAACTGTCTCAAGAAAGA-AAAAATTAGTTCCAAAGA-AAACTGTCTCAAGAGAG
* *
247864 ACGAAATTT
64 ACAAAATTA
*
247873 GTTTCAAGTGAAAC
1 GTTTCAAGAGAAAC
247887 AGATTCAAAT
Statistics
Matches: 324, Mismatches: 83, Indels: 53
0.70 0.18 0.12
Matches are distributed among these distances:
63 2 0.01
64 38 0.12
65 41 0.13
66 11 0.03
67 1 0.00
71 4 0.01
72 101 0.31
73 121 0.37
74 5 0.02
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (72 bp):
GTTTCAAGAGAAACTGTCTCAAGAAAGAAAAAATTAGTTCCAAAGAAAACTGTCTCAAGAGAGAC
AAAATTA
Found at i:247665 original size:138 final size:138
Alignment explanation
Indices: 247414--247666 Score: 382
Period size: 138 Copynumber: 1.8 Consensus size: 138
247404 AAAGACAAAA
* *
247414 TTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCTAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTATCAAGAGA
* * **
247479 GAAAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGGAATTAGTTTCAAGGAAAACAGAT
66 GAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGGAAAACAGAT
247544 TCAATTAT
131 TCAATTAT
* * *
247552 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTATCAAGGGA
1 TTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTATCAAGAGA
* * *
247617 GAAAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
66 GAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTAGTT
247667 CCAAAAGAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
137 29 0.28
138 73 0.72
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.27
Consensus pattern (138 bp):
TTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTATCAAGAGA
GAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTAGTTTCAAGGAAAACAGAT
TCAATTAT
Found at i:247817 original size:347 final size:350
Alignment explanation
Indices: 247116--247973 Score: 1183
Period size: 347 Copynumber: 2.5 Consensus size: 350
247106 ATGTTTATGT
* *
247116 TTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAA-AAA-TGTCTCAAGGGAGACG
1 TTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACG
* * * * *
247179 AAATTTGTTTCAAAG-GAAACAGATTCAAAGATTTTCTTTTAAGAGAAACTATCTCAAGAGAGAC
66 AAATTAGTTTC-AAGTGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
** * * * * *
247243 -AAATT-TCATTTCAAGGGAAATTTTTTC-A-A-TG-----TTTATGTTTCAAGAGAAACTGTCT
130 AAAATTGTTGTTTCAAGGGAAACTGTATCAAGAGAGAAAAAATT-TGTTTCAAGAGAAACTGTCT
* * * *
247298 CAAGGGAGACAAAATTTAGTTCTAAAAGAAAATGTCTCAAGGGAGACGAAATTAGTTTCAAAGAA
194 CAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTAAAGGGAGACGAAATTAGTTTCAAAGAA
*
247363 AACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGGAA
259 AACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATTTGATTCAAGGAA
*
247428 AACTGTCTCAAGAGAGACAAAATTTGT
324 AACTGTCTCAAGAGAGACAAAATTTGC
* *
247455 TTCTAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACG
1 TTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACG
* * *
247520 GAATTAGTTTCAAG-GAAAACAGATTCAATTATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
66 AAATTAGTTTCAAGTG-AAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
*
247584 AAAA-T-TTGTTTCAAGGGAAACTGTATCAAGGGAGAAAAAATTTGTTTCAAGAGAAACTGTCTC
130 AAAATTGTTGTTTCAAGGGAAACTGTATCAAGAGAGAAAAAATTTGTTTCAAGAGAAACTGTCTC
* * * *
247647 AAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTAAAGGGAGATGGAATTAGTTTCAAGGAAA
195 AAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTAAAGGGAGACGAAATTAGTTTCAAAGAAA
* ** * * *
247712 ACATATTCAATTATTTT-TTTCCAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGGGAA
260 ACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATTTGATTCAAGGAAA
*
247776 ACTGTCTCAAGGGAGACAAAATTTGC
325 ACTGTCTCAAGAGAGACAAAATTTGC
*
247802 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACG
1 TTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACG
*
247867 AAATTTGTTTCAAGTGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
66 AAATTAGTTTCAAGTGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
* * *
247932 AAATTTGTTGTTTCAATGGAAACTGTCTCAAGAGAGACAAAA
131 AAA-TTGTTGTTTCAAGGGAAACTGTATCAAGAGAGAAAAAA
247974 CTTGGAAAAT
Statistics
Matches: 456, Mismatches: 47, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
339 41 0.09
340 7 0.02
341 85 0.19
342 4 0.01
344 1 0.00
347 191 0.42
348 93 0.20
349 3 0.01
350 31 0.07
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (350 bp):
TTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACG
AAATTAGTTTCAAGTGAAACAGATTCAAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
AAATTGTTGTTTCAAGGGAAACTGTATCAAGAGAGAAAAAATTTGTTTCAAGAGAAACTGTCTCA
AGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTAAAGGGAGACGAAATTAGTTTCAAAGAAAA
CAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAAAGACAAAATTTGATTCAAGGAAAA
CTGTCTCAAGAGAGACAAAATTTGC
Found at i:249192 original size:31 final size:32
Alignment explanation
Indices: 249109--249220 Score: 138
Period size: 32 Copynumber: 3.5 Consensus size: 32
249099 TTTGCATCAG
* * * *
249109 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCT-CAAAAAATGCCCCAACATTT
249141 GATGTTGAATCTCAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
* *
249173 GATGTTAAATCT-AAAAAATGCCCAAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTT
249204 GATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
249221 GATGCCCTCG
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
31 28 0.40
32 38 0.54
33 4 0.06
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAACATTT
Found at i:250260 original size:69 final size:69
Alignment explanation
Indices: 250149--250286 Score: 195
Period size: 69 Copynumber: 2.0 Consensus size: 69
250139 TGTCTCTCTC
* * * *
250149 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCAAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGATTCATCAATC
250214 TCAT
66 TCAT
* * * * *
250218 TTGATGCTCTATGATTTTCAAGTGAAGTGGTTCGGTGATTCAGAAATGATTGTGATTCATCAATC
1 TTGATGCTCCATGATCTTCAAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGATTCATCAATC
250283 TCAT
66 TCAT
250287 GGTTTGAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCAAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGATTCATCAATC
TCAT
Found at i:250377 original size:29 final size:28
Alignment explanation
Indices: 250345--250412 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
250335 CATCTTGTCT
250345 TCTTTTTTCTTCAAT-TTTCCTTTGTTTTC
1 TCTTTTTTCTTC--TCTTTCCTTTGTTTTC
* * *
250374 TCTTTTTATTTTCTCTTTGCTTTTTTTTC
1 TCTTTTT-TCTTCTCTTTCCTTTGTTTTC
250403 TCTTTTTTCT
1 TCTTTTTTCT
250413 CTTTTTGTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 3 0.09
29 26 0.79
30 4 0.12
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (28 bp):
TCTTTTTTCTTCTCTTTCCTTTGTTTTC
Found at i:253504 original size:45 final size:45
Alignment explanation
Indices: 253419--253532 Score: 106
Period size: 45 Copynumber: 2.5 Consensus size: 45
253409 TGAAAAAAAC
* * * * * *
253419 AAATTAAATAAAAGATAAGATAAAGAAAGCAAAGATAAAATA-GT
1 AAATAAAATAAAAAATAAAATAAAGAAAGAAAAGAAAAAATATAT
*
253463 AAGTAAAATAAATAAATAAAATAAAGAAA-AAGAAGAAAAAATATAT
1 AAATAAAATAAA-AAATAAAATAAAGAAAGAA-AAGAAAAAATATAT
* *
253509 AAATAAAACAAACAAACAAAATAA
1 AAATAAAATAAA-AAATAAAATAA
253533 TAATAATAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
44 11 0.20
45 24 0.43
46 21 0.38
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.16
Consensus pattern (45 bp):
AAATAAAATAAAAAATAAAATAAAGAAAGAAAAGAAAAAATATAT
Found at i:255595 original size:22 final size:22
Alignment explanation
Indices: 255570--255612 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
255560 TATTTCAAAT
*
255570 AAATTAGTGGTTTATTTATTTC
1 AAATTAGTGATTTATTTATTTC
* *
255592 AAATTATTTATTTATTTATTT
1 AAATTAGTGATTTATTTATTT
255613 AAAAGGGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
AAATTAGTGATTTATTTATTTC
Found at i:255609 original size:26 final size:26
Alignment explanation
Indices: 255552--255613 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
255542 TTTCTTTTTG
*
255552 TATTCATTTATTTCAAATAAATTAGT
1 TATTTATTTATTTCAAATAAATTAGT
** * * *
255578 GGTTTATTTATTTCAAATTATTTATT
1 TATTTATTTATTTCAAATAAATTAGT
255604 TATTTATTTA
1 TATTTATTTA
255614 AAAGGGTATG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (26 bp):
TATTTATTTATTTCAAATAAATTAGT
Found at i:257292 original size:18 final size:18
Alignment explanation
Indices: 257266--257308 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
257256 CCCTTACTTT
257266 AACACTTCTCCCATTTAA
1 AACACTTCTCCCATTTAA
* *
257284 AACATTTCTCTCATTTAA
1 AACACTTCTCCCATTTAA
257302 AACACTT
1 AACACTT
257309 AACACTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.37
Consensus pattern (18 bp):
AACACTTCTCCCATTTAA
Found at i:257585 original size:15 final size:15
Alignment explanation
Indices: 257559--257606 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
257549 TTCAAACATC
*
257559 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
257575 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
257592 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
257607 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:258392 original size:15 final size:16
Alignment explanation
Indices: 258359--258392 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
258349 CGAAACCACC
*
258359 AAGAAATCGTTAGATG
1 AAGAAAACGTTAGATG
258375 AAGAAAACGTTA-ATG
1 AAGAAAACGTTAGATG
258390 AAG
1 AAG
258393 GTCTAAGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.21
Consensus pattern (16 bp):
AAGAAAACGTTAGATG
Found at i:259588 original size:21 final size:21
Alignment explanation
Indices: 259562--259601 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
259552 CAGAACCCTA
*
259562 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
259583 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
259602 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:259636 original size:20 final size:21
Alignment explanation
Indices: 259584--259644 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
259574 TTCCCCTGTG
259584 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
259607 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
259627 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
259645 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:263488 original size:20 final size:20
Alignment explanation
Indices: 263446--263488 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
263436 TTATTTTCAT
* *
263446 TTTTTAATTTTGAAACACCA
1 TTTTTAATTTTGAAAAACAA
263466 TTTTTATATTTT-AAAAACAA
1 TTTTTA-ATTTTGAAAAACAA
263486 TTT
1 TTT
263489 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAACAA
Found at i:270120 original size:13 final size:12
Alignment explanation
Indices: 270101--270135 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
270091 AAATTAGACG
270101 TACTTAATTAAA
1 TACTTAATTAAA
*
270113 TCACTTAAATAAA
1 T-ACTTAATTAAA
270126 TACTTAATTA
1 TACTTAATTA
270136 CATATGCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (12 bp):
TACTTAATTAAA
Found at i:270328 original size:20 final size:20
Alignment explanation
Indices: 270300--270338 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
270290 GGGTCAGACC
* *
270300 GTTCGGGTTGACACTGTTCG
1 GTTCAGGTTGACACAGTTCG
270320 GTTCAGGTTGACACAGTTC
1 GTTCAGGTTGACACAGTTC
270339 AGTCAAACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33
Consensus pattern (20 bp):
GTTCAGGTTGACACAGTTCG
Found at i:276367 original size:118 final size:120
Alignment explanation
Indices: 276138--276378 Score: 380
Period size: 118 Copynumber: 2.0 Consensus size: 120
276128 ATACTCAAAT
*
276138 ATGATAATATAAAATTTAAAAGTAATATTAACATAAAACAAATAGAAAAACAGATTAGAATTTAT
1 ATGATAATAT-AAATTTAAAAGTAATATTAACATAAAACAAATACAAAAACAGATTAGAATTTAT
* *
276203 ATAATATGGATAGTTAACAATAAAATATGTCTCTGTTGTTATAATATATTTAATTA
65 ATAATATGAATAGTTAACAATAAAATATGTCTCTATTGTTATAATATATTTAATTA
* * *
276259 ATGATAATAT-AGTTTAAAAGTAATATTAACGTAAAAC-AATACAAAAACATATTAGAATTTATA
1 ATGATAATATAAATTTAAAAGTAATATTAACATAAAACAAATACAAAAACAGATTAGAATTTATA
*
276322 TAATATGAATAGTTAACAATAAAAATATGTCTGTATTGTTA-AATATATTTAATTA
66 TAATATGAATAGTTAACAAT-AAAATATGTCTCTATTGTTATAATATATTTAATTA
276377 AT
1 AT
276379 TTGATGTCAT
Statistics
Matches: 112, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
118 59 0.53
119 43 0.38
121 10 0.09
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (120 bp):
ATGATAATATAAATTTAAAAGTAATATTAACATAAAACAAATACAAAAACAGATTAGAATTTATA
TAATATGAATAGTTAACAATAAAATATGTCTCTATTGTTATAATATATTTAATTA
Found at i:282190 original size:19 final size:19
Alignment explanation
Indices: 282173--282210 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
282163 TTAATTTAAT
282173 TATATTTTAATAAATTAAAA
1 TATA-TTTAATAAATTAAAA
*
282193 TATATTTAATAATTTAAA
1 TATATTTAATAAATTAAA
282211 GTAATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATTTAATAAATTAAAA
Found at i:282301 original size:30 final size:30
Alignment explanation
Indices: 282261--282373 Score: 149
Period size: 30 Copynumber: 3.8 Consensus size: 30
282251 AAGTTAAAGC
*
282261 AATAATAATAAAATATATTTTTAAACTTTA
1 AATAAGAATAAAATATATTTTTAAACTTTA
282291 AATAAGAATAAAATATATTTTTAAACTTTA
1 AATAAGAATAAAATATATTTTTAAACTTTA
* **
282321 AATAAGAATAAAATATACCTTTTAAA-TAAA
1 AATAAGAATAAAATATA-TTTTTAAACTTTA
* *
282351 AATAAAAATAAAATA-CTTTTTAA
1 AATAAGAATAAAATATATTTTTAA
282374 TTAATTTAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 6 0.08
30 62 0.83
31 7 0.09
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (30 bp):
AATAAGAATAAAATATATTTTTAAACTTTA
Found at i:283230 original size:114 final size:115
Alignment explanation
Indices: 283015--283239 Score: 283
Period size: 114 Copynumber: 2.0 Consensus size: 115
283005 GGACTTTTAA
* *
283015 TTTTTATATTTATAATTAAGATCCTTAATTTTTATAATTTCATAAAATTTTTAATTTTAACTCTA
1 TTTTTATATTTATAATTAAGATCCCTAATTTTTATAATTTCATAAAATATTTAATTTTAACTCTA
* * *
283080 TTTTACTATTTGTGTTATTAATTCATCCGATATTGAATCAAATTTACCAT
66 TTTTACTATTTCTCTTATTAATTCATCCAATATTGAATCAAATTTACCAT
* * * *
283130 TTTTTATATTTATAATTACGA-CCCTAATTTTTATAATTTCATAAAATATTTACTTTTTGACTTT
1 TTTTTATATTTATAATTAAGATCCCTAATTTTTATAATTTCATAAAATATTTA-ATTTTAACTCT
* * * ** * *
283194 CTTTTTC-ATTTCTCTTATTTATTCATTTAATTTTGAATTAAATTTA
65 ATTTTACTATTTCTCTTATTAATTCATCCAATATTGAATCAAATTTA
283240 ATCATGTTTT
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
114 60 0.65
115 33 0.35
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.55
Consensus pattern (115 bp):
TTTTTATATTTATAATTAAGATCCCTAATTTTTATAATTTCATAAAATATTTAATTTTAACTCTA
TTTTACTATTTCTCTTATTAATTCATCCAATATTGAATCAAATTTACCAT
Found at i:284977 original size:43 final size:43
Alignment explanation
Indices: 284900--285087 Score: 184
Period size: 43 Copynumber: 4.4 Consensus size: 43
284890 GCCTTTTAAT
* ** * *
284900 TTTTTTCAATATCAACTTTTTACATTTACAATTGATGACCCTAA
1 TTTTTTCAATCTC-ACTTTTTATTTTTATAATTGAGGACCCTAA
* * ** * *
284944 GTTTTTCAATCCCACTTTGCATCTTTATAATTGA--ACTTCTAA
1 TTTTTTCAATCTCACTTTTTATTTTTATAATTGAGGAC-CCTAA
* * *
284986 TTTTTTTAATCTCATTTTTTTATTTTTATAATTGAGGCCCCTAA
1 TTTTTTCAATCTCA-CTTTTTATTTTTATAATTGAGGACCCTAA
* *
285030 TTTTTTCAATCTCATTTTTTATTTTTATAATTGAGGCCCCTAA
1 TTTTTTCAATCTCACTTTTTATTTTTATAATTGAGGACCCTAA
285073 TTTTTT-AATCTCACT
1 TTTTTTCAATCTCACT
285088 GTTACAATAT
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.02
42 23 0.19
43 67 0.56
44 27 0.22
45 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.51
Consensus pattern (43 bp):
TTTTTTCAATCTCACTTTTTATTTTTATAATTGAGGACCCTAA
Found at i:285028 original size:86 final size:87
Alignment explanation
Indices: 284896--285085 Score: 204
Period size: 86 Copynumber: 2.2 Consensus size: 87
284886 TTGAGCCTTT
* *
284896 TAATTTTTTTCAATATCAACTTTTTACATTTACAATTGATGACCCTAAGTTTTTCAATCCCACTT
1 TAATTTTTTT-AATCTCAACTTTTTACATTTACAATTGAGGACCCTAAGTTTTTCAATCCCACTT
**
284961 TGCATCTTTATAATTGA-ACTTC
65 TGCATCTTTATAATTGAGACCCC
** ** * * * * *
284983 TAATTTTTTTAATCTCATTTTTTTATTTTTATAATTGAGGCCCCTAATTTTTTCAATCTCATTTT
1 TAATTTTTTTAATCTCAACTTTTTACATTTACAATTGAGGACCCTAAGTTTTTCAATCCCACTTT
** * *
285048 TTATTTTTATAATTGAGGCCCC
66 GCATCTTTATAATTGAGACCCC
285070 TAA-TTTTTTAATCTCA
1 TAATTTTTTTAATCTCA
285086 CTGTTACAAT
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
86 70 0.82
87 15 0.18
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (87 bp):
TAATTTTTTTAATCTCAACTTTTTACATTTACAATTGAGGACCCTAAGTTTTTCAATCCCACTTT
GCATCTTTATAATTGAGACCCC
Found at i:285493 original size:43 final size:43
Alignment explanation
Indices: 285437--285598 Score: 172
Period size: 42 Copynumber: 3.8 Consensus size: 43
285427 AATTCTAACA
285437 CTCAC-TTTTACTTTTATAATTGAGGTCCCTAATTTTTTCAAT
1 CTCACTTTTTACTTTTATAATTGAGGTCCCTAATTTTTTCAAT
* * **
285479 CTCACTTTTTACTTTCA-AAATGAGGTATCTAATCTTTTT-AAT
1 CTCACTTTTTACTTTTATAATTGAGGTCCCTAAT-TTTTTCAAT
* * *
285521 CTCACTTTTTACCTTTATAATTGAGGTTCCTAATGTTTTCAAT
1 CTCACTTTTTACTTTTATAATTGAGGTCCCTAATTTTTTCAAT
* * * *
285564 -TATACTTTTTAC-TTTATAATTTATGCCCCTAATTT
1 CT-CACTTTTTACTTTTATAATTGAGGTCCCTAATTT
285599 AATCATCTTA
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 59 0.60
43 40 0.40
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (43 bp):
CTCACTTTTTACTTTTATAATTGAGGTCCCTAATTTTTTCAAT
Found at i:286687 original size:29 final size:29
Alignment explanation
Indices: 286652--286733 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
286642 AAACTAAATT
*
286652 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
286681 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
286710 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
286734 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:287098 original size:10 final size:10
Alignment explanation
Indices: 287083--287112 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
287073 CTGAGTTCTG
287083 ACGCACCGCC
1 ACGCACCGCC
287093 ACGCACCGCC
1 ACGCACCGCC
287103 ACGCACCGCC
1 ACGCACCGCC
287113 GGAAGACTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (10 bp):
ACGCACCGCC
Found at i:291459 original size:29 final size:29
Alignment explanation
Indices: 291424--291505 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
291414 AAACTAAATT
*
291424 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
291453 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
291482 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
291506 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:296462 original size:2 final size:2
Alignment explanation
Indices: 296444--296477 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
296434 TTGATTTGTT
* *
296444 TA TA GA TA TA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
296478 AAGATAATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:302963 original size:32 final size:34
Alignment explanation
Indices: 302902--302980 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 34
302892 AATTCTAAAT
*
302902 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATAATTACATAAATATTA-TTTAATAAAAA
* *
302937 AAATAATATTTACATAAATA-TA-TTAATATAAA
1 AAATAATAATTACATAAATATTATTTAATAAAAA
*
302969 ATATAATAATTA
1 AAATAATAATTA
302981 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 19 0.49
34 2 0.05
35 18 0.46
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (34 bp):
AAATAATAATTACATAAATATTATTTAATAAAAA
Found at i:303002 original size:34 final size:34
Alignment explanation
Indices: 302930--303003 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
302920 TATTATTTTA
* * *
302930 ATAAAAAAAATAATATTTACATAAATATATTAAT
1 ATAAAAAAAATAATATTTACATAAAAATACTAAC
*
302964 ATAAAATATAATAATTATTTA-A-AAAAATACTAAC
1 ATAAAA-AAAATAA-TATTTACATAAAAATACTAAC
302998 ATAAAA
1 ATAAAA
303004 CTAAATTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
34 21 0.62
35 7 0.21
36 6 0.18
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (34 bp):
ATAAAAAAAATAATATTTACATAAAAATACTAAC
Found at i:305675 original size:42 final size:42
Alignment explanation
Indices: 305624--305722 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
305614 TCGAATTTTT
* ** *
305624 GTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATTTTTCC
1 GTGTTTGTTTCACGTAATTCATTTTTCAAAAAATATTTTCCC
* *
305666 GTGTTTGTTTCATGTAATTCATTTTTCAAAAAATGTTTTCCC
1 GTGTTTGTTTCACGTAATTCATTTTTCAAAAAATATTTTCCC
*
305708 ATGTTTGTTTCACGT
1 GTGTTTGTTTCACGT
305723 TTGATTTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.51
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCATTTTTCAAAAAATATTTTCCC
Found at i:305977 original size:29 final size:29
Alignment explanation
Indices: 305938--306041 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
305928 TATTTATTAA
*
305938 TATTTATAATAATATATGATATTATATTTT
1 TATTT-TAATAATATATAATATTATATTTT
** *
305968 TATTTTAATAATATATAATAAAAAATTTT
1 TATTTTAATAATATATAATATTATATTTT
*
305997 ATATATTTAATAATGA-ATAATATTAT-TTATA
1 -TAT-TTTAATAAT-ATATAATATTATATT-TT
*
306028 TATTTAAATAATAT
1 TATTTTAATAATAT
306042 TTTAATAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
28 1 0.02
29 28 0.47
30 13 0.22
31 17 0.28
32 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
TATTTTAATAATATATAATATTATATTTT
Found at i:306019 original size:19 final size:19
Alignment explanation
Indices: 305997--306049 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
305987 AAAAAATTTT
*
305997 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
306016 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
306038 ATAT-TTTAATAA
1 ATATATTTAATAA
306050 ATATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:306052 original size:12 final size:11
Alignment explanation
Indices: 306012--306079 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
306002 TTTAATAATG
306012 AATAATATTATT
1 AATAATATT-TT
* *
306024 TAT-ATATTTA
1 AATAATATTTT
306034 AATAATATTTT
1 AATAATATTTT
306045 AATAAATATATTT
1 AAT-AATAT-TTT
**
306058 AA-AATATACT
1 AATAATATTTT
306068 AATTAATATTTT
1 AA-TAATATTTT
306080 TAAAATATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
10 6 0.14
11 19 0.44
12 13 0.30
13 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (11 bp):
AATAATATTTT
Found at i:306063 original size:15 final size:14
Alignment explanation
Indices: 306025--306060 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
306015 AATATTATTT
306025 ATATATTTAAAT-A
1 ATATATTTAAATAA
306038 ATAT-TTT-AATAA
1 ATATATTTAAATAA
306050 ATATATTTAAA
1 ATATATTTAAA
306061 ATATACTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.15
12 8 0.40
13 7 0.35
14 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATTTAAATAA
Found at i:306063 original size:23 final size:23
Alignment explanation
Indices: 306025--306088 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
306015 AATATTATTT
**
306025 ATATATTTAAATAATATTTTAATAA
1 ATATATTT-AA-AATATACTAATAA
*
306050 ATATATTTAAAATATACTAATTA
1 ATATATTTAAAATATACTAATAA
*
306073 ATATTTTTAAAATATA
1 ATATATTTAAAATATA
306089 ATATAACACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 25 0.71
24 2 0.06
25 8 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATTTAAAATATACTAATAA
Found at i:306217 original size:48 final size:47
Alignment explanation
Indices: 306161--306270 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 47
306151 ATACAAAAAT
*
306161 TATTATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TATTATTTTTATT-ATAAAATAATAAAAATAA-ATTTAATAATAAATAA
* * * * *
306210 -ATTATTTTAATATTTTAAAATAATAATATTAAATTTTATGATAAATAA
1 TATTATTTT--TATTATAAAATAATAAAAATAAATTTAATAATAAATAA
306258 TATTATTTATTAT
1 TATTATTT-TTAT
306271 ATTTAATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
48 25 0.49
49 21 0.41
50 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (47 bp):
TATTATTTTTATTATAAAATAATAAAAATAAATTTAATAATAAATAA
Found at i:306494 original size:21 final size:21
Alignment explanation
Indices: 306444--306495 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
306434 ATTCATTTTC
*
306444 CAAAATTCAAATTCCAGTAATT
1 CAAATTTC-AATTCCAGTAATT
**
306466 CATTTTTCAATTCCAGTAATT
1 CAAATTTCAATTCCAGTAATT
306487 CAAATTTCA
1 CAAATTTCA
306496 GTAATTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (21 bp):
CAAATTTCAATTCCAGTAATT
Found at i:306798 original size:29 final size:30
Alignment explanation
Indices: 306756--306831 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
306746 TATAGATTTT
* *
306756 TTTTAGTTTAGTGTTTAATGTTT-ATTTCG
1 TTTTAATTTGGTGTTTAATGTTTCATTTCG
306785 TTTTAATTTGGTGTTTAATGTTTCATTTCG
1 TTTTAATTTGGTGTTTAATGTTTCATTTCG
*
306815 TTATTTATTTAGGTGTT
1 TT-TTAATTT-GGTGTT
306832 CGGACCGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
29 21 0.51
30 8 0.20
31 6 0.15
32 6 0.15
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.62
Consensus pattern (30 bp):
TTTTAATTTGGTGTTTAATGTTTCATTTCG
Found at i:307998 original size:2 final size:2
Alignment explanation
Indices: 307991--308022 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
307981 ACATGACCCG
307991 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
308023 TATTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:308465 original size:16 final size:17
Alignment explanation
Indices: 308443--308480 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
308433 CCGATTTCAA
* *
308443 ATATTCGATTATTAAAT
1 ATATTCGAATATCAAAT
308460 -TATTCGAATATCAAAT
1 ATATTCGAATATCAAAT
308476 ATATT
1 ATATT
308481 ACTCCAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (17 bp):
ATATTCGAATATCAAAT
Found at i:314873 original size:21 final size:23
Alignment explanation
Indices: 314849--314908 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
314839 ATCCTCACTA
314849 TGTATCGATACACT-A-TGAAAG
1 TGTATCGATACACTCATTGAAAG
* * *
314870 TGTACCGATACATTCATTGAATG
1 TGTATCGATACACTCATTGAAAG
314893 TGTATCGATACACTCA
1 TGTATCGATACACTCA
314909 ATAGTGTACC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 12 0.38
22 1 0.03
23 19 0.59
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (23 bp):
TGTATCGATACACTCATTGAAAG
Found at i:315414 original size:13 final size:13
Alignment explanation
Indices: 315396--315430 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
315386 ATATTATGAT
315396 TTTTCAAACAAT-G
1 TTTTCAAA-AATAG
315409 TTTTCAAAAATAG
1 TTTTCAAAAATAG
315422 TTTTCAAAA
1 TTTTCAAAA
315431 TTACCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATAG
Found at i:317608 original size:21 final size:21
Alignment explanation
Indices: 317584--317643 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
317574 TGAATTTTAC
317584 AGAGTGTACCGATACACCTAG
1 AGAGTGTACCGATACACCTAG
*
317605 AGAGTGTACTGATACACCTAG
1 AGAGTGTACCGATACACCTAG
317626 AGAGTGTACCGATACACC
1 AGAGTGTACCGATACACC
317644 CACGCTCCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
AGAGTGTACCGATACACCTAG
Found at i:321351 original size:17 final size:17
Alignment explanation
Indices: 321326--321361 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
321316 AAAAATAAAG
321326 ATAAAGTATGTGTGTAT
1 ATAAAGTATGTGTGTAT
*
321343 ATAATGTATGTGTGTAT
1 ATAAAGTATGTGTGTAT
321360 AT
1 AT
321362 TTCTGTAAGT
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (17 bp):
ATAAAGTATGTGTGTAT
Found at i:322314 original size:22 final size:23
Alignment explanation
Indices: 322289--322351 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
322279 TAAATTATAT
322289 TAATAAT-TTATTAAAATAAGAA
1 TAATAATATTATTAAAATAAGAA
*
322311 TAAT-ATATTATTAAAATAATAA
1 TAATAATATTATTAAAATAAGAA
* *
322333 TAATAATAATAGTAAAATA
1 TAATAATATTATTAAAATA
322352 TTAAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.06
22 22 0.61
23 12 0.33
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (23 bp):
TAATAATATTATTAAAATAAGAA
Found at i:322382 original size:22 final size:22
Alignment explanation
Indices: 322297--322385 Score: 97
Period size: 23 Copynumber: 4.0 Consensus size: 22
322287 ATTAATAATT
* * *
322297 TATTAAAATAAGAATAATATAT
1 TATTAAAATAAAAATATTATAA
* *
322319 TATTAAAATAATAATAATAATAA
1 TATTAAAATAAAAAT-ATTATAA
* *
322342 TAGTAAAATATTAAATATTATAA
1 TATTAAAATA-AAAATATTATAA
322365 TATTAAAATAAAAATATTATA
1 TATTAAAATAAAAATATTATA
322386 CTATATTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
22 24 0.44
23 28 0.51
24 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TATTAAAATAAAAATATTATAA
Found at i:331149 original size:3 final size:3
Alignment explanation
Indices: 331141--331171 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
331131 GAAATCAGAT
331141 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
331172 GGACAGATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:332772 original size:11 final size:12
Alignment explanation
Indices: 332747--332774 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
332737 AAAGTTAAGC
332747 TTTTAAAGTATT
1 TTTTAAAGTATT
332759 TTTTAAAGTATT
1 TTTTAAAGTATT
332771 TTTT
1 TTTT
332775 CTTTCTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (12 bp):
TTTTAAAGTATT
Found at i:337651 original size:20 final size:21
Alignment explanation
Indices: 337628--337667 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
337618 TGTTTGGCTC
*
337628 TGAATG-GAACTGTTCAGCGT
1 TGAATGTGAACCGTTCAGCGT
337648 TGAATGTTGAACCGTTCAGC
1 TGAATG-TGAACCGTTCAGC
337668 ATTAAGCGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TGAATGTGAACCGTTCAGCGT
Found at i:346527 original size:21 final size:21
Alignment explanation
Indices: 346498--346550 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
346488 ATTATGACTA
346498 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
346519 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
346540 TCGCAATGCGA
1 TCGCATTGCGA
346551 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:346565 original size:20 final size:20
Alignment explanation
Indices: 346540--346646 Score: 117
Period size: 20 Copynumber: 5.3 Consensus size: 20
346530 TTTTCCTAAT
346540 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** ** *
346560 TCGCAACACGAATTTTGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
346581 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
346601 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
346621 TCGCAATGCAAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
346641 TCGCAA
1 TCGCAA
346647 CGAGATTCTG
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
19 1 0.01
20 55 0.79
21 14 0.20
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:346590 original size:41 final size:40
Alignment explanation
Indices: 346540--346647 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 40
346530 TTTTCCTAAT
**
346540 TCGCAATGCGAATACGTAAATCGCAACACGAATTTTGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACACGAA-TACGAAAA
* * ** *
346581 TCGCAATGCGATTACGTAAATCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACACGAATACGAAAA
*
346621 TCGCAATGCAAAT-CTGTAAATCGCAAC
1 TCGCAATGCGAATAC-GTAAATCGCAAC
346648 GAGATTCTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
39 1 0.02
40 26 0.47
41 28 0.51
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACACGAATACGAAAA
Found at i:347535 original size:24 final size:24
Alignment explanation
Indices: 347508--347561 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
347498 GTATTCGAAA
347508 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
347532 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
347556 TTTGAT
1 TTTGAT
347562 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:350021 original size:20 final size:20
Alignment explanation
Indices: 349996--350084 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
349986 CAACGCGGAA
*
349996 ATCGCAACG-TGAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
350016 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* * *
350036 ATTGCAACGCGGAATTGACA
1 ATCGCAACGCGGAAATGACT
*
350056 ATCGCAACGCGGAAATAACT
1 ATCGCAACGCGGAAATGACT
350076 ATCGCAACG
1 ATCGCAACG
350085 AGAGAATCGC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 55 0.95
21 3 0.05
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:350060 original size:40 final size:41
Alignment explanation
Indices: 349996--350084 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 41
349986 CAACGCGGAA
* * *
349996 ATCGCAACG-TGAATATGACTATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAATATGACAATCGCAACACGGAAATAACT
* *
350036 ATTGCAACGCGGAAT-TGACAATCGCAACGCGGAAATAACT
1 ATCGCAACGCGGAATATGACAATCGCAACACGGAAATAACT
350076 ATCGCAACG
1 ATCGCAACG
350085 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGGAATATGACAATCGCAACACGGAAATAACT
Found at i:350175 original size:33 final size:34
Alignment explanation
Indices: 350118--350181 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
350108 AATCGCTTCA
*
350118 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTACGATTTTCATTTTCGCATTGCGATTCACT
350152 CGTTACGATTTTCA-TTTCGCATTGCGATTC
1 CGTTACGATTTTCATTTTCGCATTGCGATTC
350182 TCTCATTGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 16 0.55
34 13 0.45
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (34 bp):
CGTTACGATTTTCATTTTCGCATTGCGATTCACT
Found at i:350200 original size:33 final size:33
Alignment explanation
Indices: 350133--350202 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
350123 CGATTTTCAT
* **
350133 TTTCGCATTGCGATTCACTCGTTACGATTTTCA
1 TTTCGCATTGCGATTCACTCATTACGATAGTCA
* *
350166 TTTCGCATTGCGATTCTCTCATTGCGATAGTCA
1 TTTCGCATTGCGATTCACTCATTACGATAGTCA
350199 TTTC
1 TTTC
350203 CGCGTTACGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (33 bp):
TTTCGCATTGCGATTCACTCATTACGATAGTCA
Found at i:350334 original size:14 final size:14
Alignment explanation
Indices: 350315--350351 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
350305 CATCAATTAA
350315 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
350329 ACAAATCATCTTTT
1 ACAAATCAACATTT
350343 ACAAATCAA
1 ACAAATCAA
350352 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:351774 original size:42 final size:42
Alignment explanation
Indices: 351709--351791 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
351699 TCTAGAATAT
* *
351709 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGGAACTCTTCAACGATGACAGGGGCCTCTTGAACGG
* ** *
351751 TGGGAGGGAACTCTTGAGGGATGATAGGGGCCTCTTGAACG
1 TGGGAGGGAACTCTTCAACGATGACAGGGGCCTCTTGAACG
351792 ATGACAGGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (42 bp):
TGGGAGGGAACTCTTCAACGATGACAGGGGCCTCTTGAACGG
Found at i:351794 original size:21 final size:21
Alignment explanation
Indices: 351713--351799 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
351703 GAATATTGGG
*
351713 AGGGACCTCTTCAACGATGAC
1 AGGGACCTCTTGAACGATGAC
* **
351734 AGTGG-CCTCTTGAACGGTGGG
1 AG-GGACCTCTTGAACGATGAC
* ** *
351755 AGGGAACTCTTGAGGGATGAT
1 AGGGACCTCTTGAACGATGAC
*
351776 AGGGGCCTCTTGAACGATGAC
1 AGGGACCTCTTGAACGATGAC
351797 AGG
1 AGG
351800 TGAGTCGTGC
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 2 0.04
21 45 0.92
22 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
AGGGACCTCTTGAACGATGAC
Found at i:352298 original size:20 final size:20
Alignment explanation
Indices: 352275--352428 Score: 111
Period size: 20 Copynumber: 8.3 Consensus size: 20
352265 GAAACTTAAA
352275 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
352295 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
352315 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
* * **
352329 ATCGCAATGCG-AAATAAAA
1 ATCGCAACGCGAAAATGACT
352348 ATCGCAA--C-AACAA--A--
1 ATCGCAACGCGAA-AATGACT
352362 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
352382 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
** **
352402 ATCGCAATACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
352422 ATCGCAA
1 ATCGCAA
352429 AGAGAGAATC
Statistics
Matches: 113, Mismatches: 7, Indels: 28
0.76 0.05 0.19
Matches are distributed among these distances:
14 14 0.12
16 10 0.09
17 7 0.06
18 5 0.04
19 7 0.06
20 70 0.62
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:352498 original size:20 final size:20
Alignment explanation
Indices: 352473--352584 Score: 156
Period size: 20 Copynumber: 5.6 Consensus size: 20
352463 GCGATTCTTT
*
352473 CATTGCGATAGTCAAATTTG
1 CATTGCGATAGTCAATTTTG
352493 CATTGCGATAGTC-ATTTTCG
1 CATTGCGATAGTCAATTTT-G
*
352513 CATTGCGATAGTCATTTTTG
1 CATTGCGATAGTCAATTTTG
*
352533 CATTGCGATAGTCATTTTTG
1 CATTGCGATAGTCAATTTTG
*
352553 CGTTGCGATAGTC-ATTTTCG
1 CATTGCGATAGTCAATTTT-G
352573 CATTGCGATAGT
1 CATTGCGATAGT
352585 AAACTATTCT
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
19 8 0.10
20 72 0.86
21 4 0.05
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (20 bp):
CATTGCGATAGTCAATTTTG
Found at i:352533 original size:40 final size:40
Alignment explanation
Indices: 352473--352584 Score: 179
Period size: 40 Copynumber: 2.8 Consensus size: 40
352463 GCGATTCTTT
**
352473 CATTGCGATAGTCAAATTTGCATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTTGCATTGCGATAGTCATTTTCG
*
352513 CATTGCGATAGTCATTTTTGCATTGCGATAGTCATTTTTG
1 CATTGCGATAGTCATTTTTGCATTGCGATAGTCATTTTCG
* *
352553 CGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 CATTGCGATAGTCATTTTTGCATTGCGATAGT
352585 AAACTATTCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (40 bp):
CATTGCGATAGTCATTTTTGCATTGCGATAGTCATTTTCG
Found at i:354975 original size:22 final size:21
Alignment explanation
Indices: 354914--354975 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 21
354904 TGACCGTGAA
* *
354914 TGATTTCGCCGAAGATGGAGAC
1 TGATTTCGTCG-AGATGGGGAC
*
354936 TGATATCGTC--G-TGGGGAC
1 TGATTTCGTCGAGATGGGGAC
354954 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTC-GAGATGGGGAC
354976 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
21 1 0.03
22 15 0.47
ACGTcount: A:0.21, C:0.16, G:0.37, T:0.26
Consensus pattern (21 bp):
TGATTTCGTCGAGATGGGGAC
Found at i:355180 original size:20 final size:20
Alignment explanation
Indices: 355155--355246 Score: 112
Period size: 20 Copynumber: 4.5 Consensus size: 20
355145 GCTATGTAAA
355155 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
355175 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
* * **
355195 TCGCATTGCAATTTTCCAAAT
1 TCGCATTGCGA-TTTACGTAT
*
355216 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
355236 TCGTATTGCGA
1 TCGCATTGCGA
355247 ATTAGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:355269 original size:21 final size:21
Alignment explanation
Indices: 355243--355288 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
355233 TATTCGTATT
355243 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
355264 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
355285 GCGA
1 GCGA
355289 TAGTTAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:356596 original size:369 final size:369
Alignment explanation
Indices: 355626--357101 Score: 2927
Period size: 369 Copynumber: 4.0 Consensus size: 369
355616 TTCCTGACGT
*
355626 CTTATTGGACTTCACCAACAACATTCATTTTAATGTCTTTATTTTTTTCATATGAATTGGTCATT
1 CTTATTGGACTTCACCAACAACATTTATTTTAATGTCTTTATTTTTTTCATATGAATTGGTCATT
355691 CTTTAACTTAGCTAGCGGCCCAACATGTATATGTACCAATATTCTACCTTAGCACATGGAATTAA
66 CTTTAACTTAGCTAGCGGCCCAACATGTATATGTACCAATATTCTACCTTAGCACATGGAATTAA
355756 ATAGAAAAAAATATAGAGTGAATACATATGGTATAAGAGTTCATCATCTATAGTCTATACATTCA
131 ATAGAAAAAAATATAGAGTGAATACATATGGTATAAGAGTTCATCATCTATAGTCTATACATTCA
*
355821 GAAACTCAAGTGTGTATAAATCATAATTACCCATAACTAATACACAACCAAAAACCAATAAGCTG
196 GAAACTCAAGTGTGTATAAATCATAATTACCCATAACTAACACACAACCAAAAACCAATAAGCTG
355886 CAATAACAAATGTGGGTCATCTAAGACATCCTAAGCACATGGTGTAATATACTAATAAGACTGAC
261 CAATAACAAATGTGGGTCATCTAAGACATCCTAAGCACATGGTGTAATATACTAATAAGACTGAC
355951 CAACAACAACAAAAATTGTTACAAGCGCTGTCCCATGGCAGTGG
326 CAACAACAACAAAAATTGTTACAAGCGCTGTCCCATGGCAGTGG
355995 CTTATTGGACTTCACCAACAACATTTATTTTAATGTCTTTA-TTTTTTCATATGAATTGGTCATT
1 CTTATTGGACTTCACCAACAACATTTATTTTAATGTCTTTATTTTTTTCATATGAATTGGTCATT
356059 CTTTAACTTAGCTAGCGGCCCAACATGTATATGTACCAATATTCTACCTTAGCACATGGAATTAA
66 CTTTAACTTAGCTAGCGGCCCAACATGTATATGTACCAATATTCTACCTTAGCACATGGAATTAA
356124 ATAGAAAAAAATATAGAGTGAATACATATGGTATAAGAGTTCATCATCTATAGTCTATACATTCA
131 ATAGAAAAAAATATAGAGTGAATACATATGGTATAAGAGTTCATCATCTATAGTCTATACATTCA
356189 GAAACTCAAGTGTGTATAAATCATAATTACCCATAACTAACACACAACCAAAAACCAATAAGCTG
196 GAAACTCAAGTGTGTATAAATCATAATTACCCATAACTAACACACAACCAAAAACCAATAAGCTG
356254 CAATAACAAATGTGGGTCATCTAAGACATCCTAAGCACATGGTGTAATATACTAATAAGACTGAC
261 CAATAACAAATGTGGGTCATCTAAGACATCCTAAGCACATGGTGTAATATACTAATAAGACTGAC
356319 CAACAACAACAAAAATTGTTACAAGCGCTGTCCCATGGCAGTGG
326 CAACAACAACAAAAATTGTTACAAGCGCTGTCCCATGGCAGTGG
356363 CTTATTGGACTTCACCAACAACATTTATTTTAATGTCTTTATTTTTTTCATATGAATTGGTCATT
1 CTTATTGGACTTCACCAACAACATTTATTTTAATGTCTTTATTTTTTTCATATGAATTGGTCATT
356428 CTTTAACTTAGCTAGCGGCCCAACATGTATATGTACCAATATTCTACCTTAGCACATGGAATTAA
66 CTTTAACTTAGCTAGCGGCCCAACATGTATATGTACCAATATTCTACCTTAGCACATGGAATTAA
356493 ATAGAAAAAAATATAGAGTGAATACATATGGTATAAGAGTTCATCATCTATAGTCTATACATTCA
131 ATAGAAAAAAATATAGAGTGAATACATATGGTATAAGAGTTCATCATCTATAGTCTATACATTCA
356558 GAAACTCAAGTGTGTATAAATCATAATTACCCATAACTAACACACAACCAAAAACCAATAAGCTG
196 GAAACTCAAGTGTGTATAAATCATAATTACCCATAACTAACACACAACCAAAAACCAATAAGCTG
356623 CAATAACAAATGTGGGTCATCTAAGACATCCTAAGCACATGGTGTAATATACTAATAAGACTGAC
261 CAATAACAAATGTGGGTCATCTAAGACATCCTAAGCACATGGTGTAATATACTAATAAGACTGAC
356688 CAACAACAACAAAAATTGTTACAAGCGCTGTCCCATGGCAGTGG
326 CAACAACAACAAAAATTGTTACAAGCGCTGTCCCATGGCAGTGG
356732 CTTATTGGACTTCACCAACAACATTTATTTTAATGTCTTTATTTTTTTCATATGAATTGGTCATT
1 CTTATTGGACTTCACCAACAACATTTATTTTAATGTCTTTATTTTTTTCATATGAATTGGTCATT
356797 CTTTAACTTAGCTAGCGGCCCAACATGTATATGTACCAATATTCTACCTTAGCACATGGAATTAA
66 CTTTAACTTAGCTAGCGGCCCAACATGTATATGTACCAATATTCTACCTTAGCACATGGAATTAA
356862 ATAGAAAAAAATATAGAGTGAATACATATGGTATAAGAGTTCATCATCTATAGTCTATACATTCA
131 ATAGAAAAAAATATAGAGTGAATACATATGGTATAAGAGTTCATCATCTATAGTCTATACATTCA
356927 GAAACTCAAGTGTGTATAAATCATAATTACCCATAACTAACACACAACCAAAAACCAATAAGCTG
196 GAAACTCAAGTGTGTATAAATCATAATTACCCATAACTAACACACAACCAAAAACCAATAAGCTG
356992 CAATAACAAATGTGGGTCATCTAAGACATCCTAAGCACATGGTGTAATATACTAATAAGACTGAC
261 CAATAACAAATGTGGGTCATCTAAGACATCCTAAGCACATGGTGTAATATACTAATAAGACTGAC
357057 CAACAACAACAAAAATTGTTACAAGCGCTGTCCCATGGCAGTGG
326 CAACAACAACAAAAATTGTTACAAGCGCTGTCCCATGGCAGTGG
357101 C
1 C
357102 ACCATATCCA
Statistics
Matches: 1104, Mismatches: 2, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
368 367 0.33
369 737 0.67
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (369 bp):
CTTATTGGACTTCACCAACAACATTTATTTTAATGTCTTTATTTTTTTCATATGAATTGGTCATT
CTTTAACTTAGCTAGCGGCCCAACATGTATATGTACCAATATTCTACCTTAGCACATGGAATTAA
ATAGAAAAAAATATAGAGTGAATACATATGGTATAAGAGTTCATCATCTATAGTCTATACATTCA
GAAACTCAAGTGTGTATAAATCATAATTACCCATAACTAACACACAACCAAAAACCAATAAGCTG
CAATAACAAATGTGGGTCATCTAAGACATCCTAAGCACATGGTGTAATATACTAATAAGACTGAC
CAACAACAACAAAAATTGTTACAAGCGCTGTCCCATGGCAGTGG
Found at i:362221 original size:10 final size:10
Alignment explanation
Indices: 362208--362242 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
362198 AAACGACAAC
362208 AAATGGATC-G
1 AAATGGA-CGG
362218 AAATGGACGG
1 AAATGGACGG
362228 AAATGGACGG
1 AAATGGACGG
362238 AAATG
1 AAATG
362243 CTATGGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 1 0.04
10 23 0.96
ACGTcount: A:0.43, C:0.09, G:0.34, T:0.14
Consensus pattern (10 bp):
AAATGGACGG
Found at i:376780 original size:54 final size:54
Alignment explanation
Indices: 376717--376828 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
376707 GGGAACTGAA
376717 GCTGTTTCATGGTCATCCAAGAAGCAATCCATTGTTACTTTACCAACAACAGAT
1 GCTGTTTCATGGTCATCCAAGAAGCAATCCATTGTTACTTTACCAACAACAGAT
*
376771 GCTGTTTCATGGTCATCCAAGAAGCAATCCATTGTTACTTTATCAACAACAGAT
1 GCTGTTTCATGGTCATCCAAGAAGCAATCCATTGTTACTTTACCAACAACAGAT
376825 GCTG
1 GCTG
376829 AATTTGTTGC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (54 bp):
GCTGTTTCATGGTCATCCAAGAAGCAATCCATTGTTACTTTACCAACAACAGAT
Found at i:387845 original size:29 final size:30
Alignment explanation
Indices: 387807--387875 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
387797 TAAGACTTTG
387807 ATTTTCTAAAATTATCAAATAAGAGTTTAAC
1 ATTTT-TAAAATTATCAAATAAGAGTTTAAC
*
387838 -TTTTTAAAATTGTCAAATAAGAGTTTAAC
1 ATTTTTAAAATTATCAAATAAGAGTTTAAC
387867 ATTTTTAAA
1 ATTTTTAAA
387876 TCTATTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (30 bp):
ATTTTTAAAATTATCAAATAAGAGTTTAAC
Done.