Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008490.1 Hibiscus syriacus cultivar Beakdansim tig00111332_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: 604809
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 3
Found at i:239193 original size:52 final size:52
Alignment explanation
Indices: 239112--239211 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
239102 AATACTTCGC
* ** * *
239112 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTTAAAAAAAAAAAAGAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAGAACGT
* *
239164 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAGAAAAAAGA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAGA
239212 GAAAAAAGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.15
Consensus pattern (52 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAGAACGT
Found at i:240118 original size:105 final size:106
Alignment explanation
Indices: 239936--240192 Score: 444
Period size: 105 Copynumber: 2.4 Consensus size: 106
239926 AGGTTTTACC
239936 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
240001 ACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAACTTCCCAACTT
240041 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
240106 ACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAACTT
66 ACGAAGGGACCGCTGGTTGTCAACAAATAACTTCCCAACTT
* *
240147 CAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
240193 GTATAATTTC
Statistics
Matches: 144, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
105 91 0.63
106 53 0.37
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAATAACTTCCCAACTT
Found at i:240221 original size:43 final size:43
Alignment explanation
Indices: 240154--240261 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 43
240144 CTTCAGAGCC
* **
240154 AATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAGTAT
1 AATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACAT
* * * *
240197 AATTTCAACTTCACAATGAAGGATATTGGATTCCAGACAACGT
1 AATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACAT
* *
240240 AAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGG
240262 GACCGCTGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (43 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACAT
Found at i:240224 original size:149 final size:148
Alignment explanation
Indices: 240048--240366 Score: 494
Period size: 149 Copynumber: 2.1 Consensus size: 148
240038 TTTCAGAGCC
240048 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
240113 GACCGCTGGTTGTCAATAAATAACTTCCCAACTTCAGAGCCAATTTCAACTTCACAACGAGGGAT
66 GACCGCTGGTTGTCAACAAA-AACTTCCCAACTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
**
240178 ATTGGACTCAAGACAGTAT
130 ATTGGACTCAAGACAACAT
* * *
240197 AATTTCAACTTCACAATGAAGGATATTGGATTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * * *
240262 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 GACCGCTGGTTGTCAACAAAAACTTCCCAACTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
* *
240327 TTGGACTCCAGACAACGT
131 TTGGACTCAAGACAACAT
* *
240345 AAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGG
240367 GACCGCTGGT
Statistics
Matches: 154, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
148 73 0.47
149 81 0.53
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (148 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAAAACTTCCCAACTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
TTGGACTCAAGACAACAT
Found at i:240762 original size:105 final size:105
Alignment explanation
Indices: 240197--240754 Score: 1008
Period size: 105 Copynumber: 5.3 Consensus size: 105
240187 AAGACAGTAT
* *
240197 AATTTCAACTTCACAATGAAGGATATTGGATTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
240262 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
240302 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
*
240367 GACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
* *
240407 AATTTCAACTTCACAATGAAGGATATTGGATTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
240472 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
*
240512 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
* *
240577 GACCGCTGGTTGTCAACGAATATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
** * *
240617 AATTTCTGCTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
240682 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
240722 AATTTCAACTTCACAACGAAGGATATTGGACTC
1 AATTTCAACTTCACAACGAAGGATATTGGACTC
240755 GAAACAACAC
Statistics
Matches: 435, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 435 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (105 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
Found at i:241073 original size:11 final size:11
Alignment explanation
Indices: 241047--241085 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
241037 CGTCCTTATG
*
241047 TTATATATATAT
1 TTATAT-TATAA
241059 TTATATTATAA
1 TTATATTATAA
241070 TTATATTATATA
1 TTATATTATA-A
241082 TTAT
1 TTAT
241086 TTACATGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATATTATAA
Found at i:242093 original size:2 final size:2
Alignment explanation
Indices: 242086--242114 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
242076 TTTAGACACC
242086 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
242115 ATTATTACGT
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:242427 original size:16 final size:18
Alignment explanation
Indices: 242398--242442 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
242388 CCATTATTAA
242398 TAAATATATATTATTTTT
1 TAAATATATATTATTTTT
242416 TAAATAT-T-TTATTTTT
1 TAAATATATATTATTTTT
*
242432 TATATATATAT
1 TAAATATATAT
242443 ATATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 14 0.58
17 2 0.08
18 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAAATATATATTATTTTT
Found at i:242845 original size:4 final size:4
Alignment explanation
Indices: 242836--242932 Score: 51
Period size: 4 Copynumber: 25.0 Consensus size: 4
242826 TTTCCTCATC
* * * *
242836 TTAT TTAT TTAG TTAT CTAT TTAT TTA- TT-T TTCT TTA- TT-T TTCT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * **
242880 TTAT CT-T TGAT TTAT TTACT CATAT TTGT TTAT TTAT TTAT CCAT TTAT
1 TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
242929 TTAT
1 TTAT
242933 GTATGTTGTC
Statistics
Matches: 68, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
3 9 0.13
4 55 0.81
5 2 0.03
6 2 0.03
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:242874 original size:10 final size:10
Alignment explanation
Indices: 242859--242883 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
242849 TATCTATTTA
242859 TTTATTTTTC
1 TTTATTTTTC
242869 TTTATTTTTC
1 TTTATTTTTC
242879 TTTAT
1 TTTAT
242884 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:250405 original size:23 final size:23
Alignment explanation
Indices: 250361--250422 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
250351 CAGCTAGTAT
*
250361 AAATGCACCGAAGTACCA-CGTAG
1 AAATGCACCGAAGT-GCAGCGTAG
* *
250384 AATTGCACCGTAGTGCAGCGTAG
1 AAATGCACCGAAGTGCAGCGTAG
250407 AAATGCACCGAAGTGC
1 AAATGCACCGAAGTGC
250423 TATATAAGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCAGCGTAG
Found at i:251921 original size:20 final size:21
Alignment explanation
Indices: 251893--251932 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
251883 CTTGATATGT
251893 ATATAATTATAC-ATTGATAC
1 ATATAATTATACAATTGATAC
* *
251913 ATATTATTATCCAATTGATA
1 ATATAATTATACAATTGATA
251933 TACTCCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (21 bp):
ATATAATTATACAATTGATAC
Found at i:252187 original size:21 final size:21
Alignment explanation
Indices: 252161--252215 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
252151 TTACCCTTGA
*
252161 TGCATCGGTGCACCTTGAATG
1 TGCATCGATGCACCTTGAATG
252182 TGCATCGATGCACCTTGAATG
1 TGCATCGATGCACCTTGAATG
252203 TGCATCGATGCAC
1 TGCATCGATGCAC
252216 ATAGCCCAGA
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:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCACCTTGAATG
Found at i:257570 original size:24 final size:24
Alignment explanation
Indices: 257543--257602 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
257533 TGATAGATCG
257543 AAATCGAATTAAATATCAAATCTA
1 AAATCGAATTAAATATCAAATCTA
257567 AAATCGAATTAAATATCAAATCTA
1 AAATCGAATTAAATATCAAATCTA
257591 AAATCGAATTAA
1 AAATCGAATTAA
257603 TTATATTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (24 bp):
AAATCGAATTAAATATCAAATCTA
Found at i:258032 original size:2 final size:2
Alignment explanation
Indices: 258025--258072 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
258015 TATAATATGA
258025 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
258067 AT AT AT
1 AT AT AT
258073 CGATGTGATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:268315 original size:3 final size:3
Alignment explanation
Indices: 268309--268376 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
268299 TAATTATTTG
* *
268309 ATA ATA AT- ATA AT- ATA TATA AT- ATA ATA ATA ATA TTT ATA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
268352 ATA ATA ATA ATT TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
268377 ATTTAAGTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
2 6 0.11
3 44 0.83
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:268368 original size:15 final size:15
Alignment explanation
Indices: 268350--268382 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
268340 ATATTTATAA
*
268350 TAATAATAATAATTT
1 TAATAATAATAAATT
268365 TAATAATAATAAATT
1 TAATAATAATAAATT
268380 TAA
1 TAA
268383 GTAACATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATAATAATAAATT
Found at i:269999 original size:13 final size:13
Alignment explanation
Indices: 269981--270006 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
269971 CTGCCAGTCA
269981 TCTCGATCTATCC
1 TCTCGATCTATCC
269994 TCTCGATCTATCC
1 TCTCGATCTATCC
270007 CTGTTTGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (13 bp):
TCTCGATCTATCC
Found at i:277125 original size:8 final size:8
Alignment explanation
Indices: 277105--277190 Score: 81
Period size: 8 Copynumber: 10.9 Consensus size: 8
277095 CAAACCCTCC
277105 TTTTTTC-
1 TTTTTTCA
*
277112 TCTTTTCA
1 TTTTTTCA
277120 TTTTTTCA
1 TTTTTTCA
277128 TTTCTTT--
1 TTT-TTTCA
*
277135 TTTTCATCA
1 TTTT-TTCA
277144 TTTTTTCA
1 TTTTTTCA
277152 -TTTTTCA
1 TTTTTTCA
277159 TTTTTTCA
1 TTTTTTCA
*
277167 TTTTTTTA
1 TTTTTTCA
*
277175 TTTGTTTCT
1 TTT-TTTCA
277184 TTTTTTC
1 TTTTTTC
277191 TTCAAGCATA
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
6 1 0.02
7 17 0.26
8 34 0.52
9 13 0.20
ACGTcount: A:0.09, C:0.14, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTTTCA
Found at i:277147 original size:24 final size:24
Alignment explanation
Indices: 277117--277190 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 24
277107 TTTTCTCTTT
277117 TCATTTTTTCATTTCTTTTTTTCA
1 TCATTTTTTCATTTCTTTTTTTCA
*
277141 TCATTTTTTCATTTTTCATTTTTTCA
1 TCATTTTTTCA--TTTCTTTTTTTCA
** **
277167 TTTTTTTATTTGTTTCTTTTTTTC
1 TCATTTT-TTCATTTCTTTTTTTC
277191 TTCAAGCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
24 11 0.27
25 11 0.27
26 17 0.41
27 2 0.05
ACGTcount: A:0.11, C:0.14, G:0.01, T:0.74
Consensus pattern (24 bp):
TCATTTTTTCATTTCTTTTTTTCA
Found at i:291355 original size:13 final size:13
Alignment explanation
Indices: 291337--291361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291327 CATAAAAAAT
291337 AAATTAAAATTTC
1 AAATTAAAATTTC
291350 AAATTAAAATTT
1 AAATTAAAATTT
291362 ATATTGTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAAAATTTC
Found at i:297206 original size:18 final size:19
Alignment explanation
Indices: 297162--297207 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
297152 ACTTTAGATA
297162 AAATATCAATTTAACATAT
1 AAATATCAATTTAACATAT
*
297181 -AATATCAATTTAACATCT
1 AAATATCAATTTAACATAT
297199 AAAT-TCAAT
1 AAATATCAAT
297208 CGAAATCCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATCAATTTAACATAT
Found at i:299962 original size:3 final size:3
Alignment explanation
Indices: 299956--300015 Score: 79
Period size: 3 Copynumber: 19.7 Consensus size: 3
299946 TTCATTTGAA
299956 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAAT TAT TA- TAT ATAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT -TAT
300002 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
300016 AAATAATTAC
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.06
3 42 0.81
4 7 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:307138 original size:1 final size:1
Alignment explanation
Indices: 307127--307168 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
307117 AAAGAAGAAG
* **
307127 AAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
307169 GAAGGAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:307145 original size:15 final size:15
Alignment explanation
Indices: 307113--307168 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
307103 CTCATCCAGC
* * *
307113 AAAGAAAGAAGAAGA
1 AAAGAAAAAAAAAAA
307128 AAAGAAAAAAAAAAA
1 AAAGAAAAAAAAAAA
307143 AAA-AAAAAAAAAAA
1 AAAGAAAAAAAAAAA
*
307157 AAGGAAAAAAAA
1 AAAGAAAAAAAA
307169 GAAGGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
14 13 0.36
15 23 0.64
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAAA
Found at i:307173 original size:13 final size:13
Alignment explanation
Indices: 307135--307177 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
307125 AGAAAAGAAA
**
307135 AAAAAAAAAAAAA
1 AAAAAAAAAAAGG
307148 AAAAAAAAAAAGG
1 AAAAAAAAAAAGG
*
307161 AAAAAAAAGAAGG
1 AAAAAAAAAAAGG
307174 AAAA
1 AAAA
307178 TTGAATCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:309640 original size:113 final size:112
Alignment explanation
Indices: 309441--309764 Score: 481
Period size: 113 Copynumber: 2.9 Consensus size: 112
309431 TAGTAGAAAT
309441 AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACC
1 AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACC
* *
309506 CCAAAAACCAATCATTGGATTTGAAAA-ATGAATTTGCTCATGTTATGA
66 CCAAAAACCAATCATTAGATTT-AAAAGATGAATTTGCTCATGGTA-GA
*
309554 AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGCTATCTGATCTGGTTTGGTATGAACC
1 AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACC
*
309619 CCAAAAACTAATCATTAGATTTAAAAGATGAATTTGCTCATGGTAGA
66 CCAAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCATGGTAGA
* ** *
309666 AATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCAGTAGGA
1 AAGAA-GA--CCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGA
* * * *
309731 ACCAC-AGAACCAATCATTGGAATTAAAAGATGAA
63 ACCCCAAAAACCAATCATTAGATTTAAAAGATGAA
309765 CTGCATGATC
Statistics
Matches: 193, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
112 10 0.05
113 103 0.53
114 25 0.13
115 55 0.28
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (112 bp):
AAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACC
CCAAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCATGGTAGA
Found at i:310988 original size:76 final size:76
Alignment explanation
Indices: 310908--311102 Score: 356
Period size: 76 Copynumber: 2.6 Consensus size: 76
310898 ACAAGAAGCG
*
310908 AATGTT-GTGGCATGCTGAAAACCCCTTTCAATCAGAATCAGTAATATTAAAGTATTCTGAATAT
1 AATGTTAG-GGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATAT
310972 TTATATCAGCAA
65 TTATATCAGCAA
310984 AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
1 AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
311049 TATATCAGCAA
66 TATATCAGCAA
*
311060 AATGTTAGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGA
1 AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGA
311103 CTGTTGATGC
Statistics
Matches: 116, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
76 115 0.99
77 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (76 bp):
AATGTTAGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
TATATCAGCAA
Found at i:311002 original size:34 final size:34
Alignment explanation
Indices: 310964--311078 Score: 79
Period size: 34 Copynumber: 3.1 Consensus size: 34
310954 TTAAAGTATT
310964 CTGAATATTTATATCAGCAAAATGTTAGGGCATG
1 CTGAATATTTATATCAGCAAAATGTTAGGGCATG
* * * ** * *
310998 CTGAAAACCCCTTTCA-ATCAGAATCAGGAATATTAAAGTATT
1 CTGAATA----TTT-ATATCAG---CA-AAATGTTAGGGCATG
311040 CTGAATATTTATATCAGCAAAATGTTAGGGCATG
1 CTGAATATTTATATCAGCAAAATGTTAGGGCATG
311074 CTGAA
1 CTGAA
311079 AGCCCCTTTC
Statistics
Matches: 57, Mismatches: 14, Indels: 20
0.63 0.15 0.22
Matches are distributed among these distances:
34 20 0.35
35 2 0.04
37 1 0.02
38 16 0.28
39 1 0.02
41 2 0.04
42 15 0.26
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (34 bp):
CTGAATATTTATATCAGCAAAATGTTAGGGCATG
Found at i:312530 original size:22 final size:22
Alignment explanation
Indices: 312499--312553 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
312489 ATCTACACTC
*
312499 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
312521 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
312543 TTCAAAGATGA
1 TTCAAAGATGA
312554 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:313377 original size:225 final size:228
Alignment explanation
Indices: 312950--313456 Score: 747
Period size: 225 Copynumber: 2.2 Consensus size: 228
312940 GCAAAGATTC
* * *
312950 AAATCCATTACTTGATGGATCAA-ATTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCACTTGATGGATCAACA-TTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAA
*
313014 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTTTAATTCATCACCCCGA
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTTGAATTCATCACCCCGA
* * * *
313079 TGGATTAGCATTGCCAGAGAAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGT
130 TGGATCAACATTACCAGAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
313144 TCATAATGAGAAGAACTTGTTCAACCTTTTGTTT
195 TCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * * **
313178 GAATTCATCATTTGATGGATCAGCATTTCCAGGTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCACTTGATGGATCAACATTTCCA-GAAGAAGTTCATAATGAGAAGAACTCATCTGAA
**
313242 GAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTCGCTTGAATTCATCA-TTCG
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTT-GCTTGAATTCATCACCCCG
*** *
313304 ATGGATCAACATTACCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAG
129 ATGGATCAACATTACCAGAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
*
313368 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
194 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
*
313403 AAATTCATCACTTGATGGATCAACTTTTCCAGAAGAAGTTCATAATGAGAAGAA
1 AAATTCATCACTTGATGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAA
313457 TTTGTTCAAC
Statistics
Matches: 248, Mismatches: 27, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
224 2 0.01
225 119 0.48
226 21 0.08
227 49 0.20
228 55 0.22
229 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (228 bp):
AAATTCATCACTTGATGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTTGAATTCATCACCCCGAT
GGATCAACATTACCAGAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAACCTTTTGCTT
Found at i:313423 original size:113 final size:113
Alignment explanation
Indices: 312959--313456 Score: 700
Period size: 113 Copynumber: 4.4 Consensus size: 113
312949 CAAATCCATT
* *
312959 ACTTGATGGATCAA-ATTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 ACTTGATGGATCAACA-TTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* *
313023 AGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTTTAATTCATC
65 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC
** * * * * *
313072 ACCCCGATGGATTAGCATTGCCAGAGAAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAG
1 A-CTTGATGGATCAACATTTCCAG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
*
313137 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATC
64 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC
* * **
313187 ATTTGATGGATCAGCATTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAA
1 ACTTGATGGATCAACATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
313251 GAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATC
66 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTTGAATTCATC
* ** *
313299 A-TTCGATGGATCAACATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATA
1 ACTT-GATGGATCAACATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* *
313363 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATC
65 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC
*
313412 ACTTGATGGATCAACTTTTCCA-GAAGAAGTTCATAATGAGAAGAA
1 ACTTGATGGATCAACATTTCCAGGAAG-AGTTCATAATGAGAAGAA
313457 TTTGTTCAAC
Statistics
Matches: 347, Mismatches: 29, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
111 7 0.02
112 102 0.29
113 112 0.32
114 39 0.11
115 87 0.25
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
ACTTGATGGATCAACATTTCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC
Found at i:313454 original size:186 final size:182
Alignment explanation
Indices: 313247--313640 Score: 648
Period size: 186 Copynumber: 2.1 Consensus size: 182
313237 CTGAAGAAGA
313247 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
** *
313312 ACATTACCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAAT
66 ACATTACCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAA-G---AAGAAGTTCACAAT
313376 GAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCC
126 GAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCC
*
313433 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
* * **
313498 TCTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAA
66 ACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAA
313563 GAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCC
131 GAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCC
313615 AG-AGAAAGTTCATAATGAGAAGAACT
1 AGAAG-AAGTTCATAATGAGAAGAACT
313641 CATCTGAAGA
Statistics
Matches: 197, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
181 2 0.01
182 92 0.47
185 1 0.01
186 101 0.51
187 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (182 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCA
ACATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAA
GAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCC
Found at i:313481 original size:73 final size:73
Alignment explanation
Indices: 313362--313529 Score: 261
Period size: 73 Copynumber: 2.3 Consensus size: 73
313352 AAGAAGGAAT
313362 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTT-GATGGATCAA
1 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCA-TTCGATGGATCAA
313426 CTTTTCCAG
65 CTTTTCCAG
* *
313435 AAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAT
1 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTTAAATTCATCATTCGATGGATCAA
*
313499 CTTTTTCAG
65 CTTTTCCAG
313508 -AGAAAGTTCATAATGAGAAGAA
1 AAG-AAGTTCATAATGAGAAGAA
313530 CTCATCTGAA
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
72 9 0.10
73 80 0.90
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (73 bp):
AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTCGATGGATCAAC
TTTTCCAG
Found at i:313669 original size:295 final size:296
Alignment explanation
Indices: 313135--313753 Score: 910
Period size: 295 Copynumber: 2.1 Consensus size: 296
313125 TGAAGAAGGA
* *
313135 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
** *
313200 GCATTTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGA
66 GCATTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCT--AGAAGAAGAAGAAGTTCACAATGA
* **
313265 GAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTACCAGGTCGAGTT
129 GAAGAACTTGTTCAACTTTTCGCTTAAATTCATCATTCGATGGATCAACATTACCAGGTAAAGTT
* * *
313330 CATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
194 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAATTGTTCAACC
*
313395 TTTTGCTTAAATTCATCACTTGATGGATCAACTTTTCC
259 TTTTGCTTAAATTCATCACTCGATGGATCAACTTTTCC
*
313433 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCGCTTGAATTCATCATTCGATGGATC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTTGAATTCATCATTCGATGGATC
* * *
313497 ATCTTTTTCAGAG-AAAGTTCATAATGAGAAGAACTCATCT-GAAGAAGAAGAAGTTCACAATGA
65 AGCATTTCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTAGAAGAAGAAGAAGTTCACAATGA
* * *
313560 GAAGAATTTGTTCAACCTTTT-GCTTAAATTCATCACTT-GATGGATCAACTTTTCCAGAG-AAA
129 GAAGAACTTGTTCAA-CTTTTCGCTTAAATTCATCA-TTCGATGGATCAACATTACCAG-GTAAA
313622 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAATTGTTCA
191 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAATTGTTCA
* *
313687 ACCTTTTGCTTGAATTCATCACTCGATGTATCAACTTTTCC
256 ACCTTTTGCTTAAATTCATCACTCGATGGATCAACTTTTCC
* *
313728 AG-AGAAAGTTCATGATAAGAAGAACT
1 AGAAG-AAGTTCATAATGAGAAGAACT
313754 CATCTGAAGA
Statistics
Matches: 291, Mismatches: 24, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
294 2 0.01
295 187 0.64
296 8 0.03
297 5 0.02
298 88 0.30
299 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (296 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
GCATTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCTAGAAGAAGAAGAAGTTCACAATGAGA
AGAACTTGTTCAACTTTTCGCTTAAATTCATCATTCGATGGATCAACATTACCAGGTAAAGTTCA
TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTT
TTGCTTAAATTCATCACTCGATGGATCAACTTTTCC
Found at i:313720 original size:113 final size:113
Alignment explanation
Indices: 313433--313821 Score: 592
Period size: 113 Copynumber: 3.5 Consensus size: 113
313423 CAACTTTTCC
*
313433 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCGCTTGAATTCATCATTCGATGGATC
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTTGAATTCATCACTCGATGGATC
* *
313497 ATCTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAA-GA
65 AACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
313542 AGAAGAAGTTCACAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCA
313607 ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
313655 AGAAGAAATTCATAATGAGAAGAAATTGTTCAACCTTTTGCTTGAATTCATCACTCGATGTATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCA
* *
313720 ACTTTTCCAGAGAAAGTTCATGATAAGAAGAACTCATCTGAAGAAGGA
66 ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
313768 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCATG-ATTCTATCAC
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTC-ATCAC
313822 AGAAGGAGAT
Statistics
Matches: 256, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
109 92 0.36
110 5 0.02
112 7 0.03
113 152 0.59
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (113 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCA
ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:314077 original size:9 final size:10
Alignment explanation
Indices: 314065--314134 Score: 62
Period size: 9 Copynumber: 7.4 Consensus size: 10
314055 TCATTTGAAG
314065 ATTATTTA-T
1 ATTATTTATT
314074 ATTA-TTATT
1 ATTATTTATT
314083 ATTA-TTATT
1 ATTATTTATT
* *
314092 ATTA-TAAAT
1 ATTATTTATT
314101 ATTA-TTATT
1 ATTATTTATT
314110 ATTATTATATAT
1 ATTATT-TAT-T
314122 ATTA-TTATT
1 ATTATTTATT
314131 ATTA
1 ATTA
314135 AAAAAAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
8 3 0.06
9 37 0.70
10 4 0.08
11 4 0.08
12 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTATTTATT
Found at i:314081 original size:3 final size:3
Alignment explanation
Indices: 314073--314134 Score: 90
Period size: 3 Copynumber: 20.7 Consensus size: 3
314063 AGATTATTTA
* *
314073 TAT TAT TAT TAT TAT TAT TAT TAT AAA TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
314120 ATAT TAT TAT TAT TA
1 -TAT TAT TAT TAT TA
314135 AAAAAAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:314082 original size:12 final size:11
Alignment explanation
Indices: 314065--314132 Score: 82
Period size: 12 Copynumber: 5.7 Consensus size: 11
314055 TCATTTGAAG
314065 ATTATTTATATT
1 ATTA-TTATATT
314077 ATTATTATTATT
1 ATTATTA-TATT
*
314089 ATTATTATAAAT
1 ATTATTAT-ATT
314101 ATTATTATTATT
1 ATTATTA-TATT
314113 ATTATATATATT
1 ATTAT-TATATT
314125 ATTATTAT
1 ATTATTAT
314133 TAAAAAAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
11 7 0.14
12 40 0.80
13 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTATTATATT
Found at i:314091 original size:21 final size:21
Alignment explanation
Indices: 314065--314134 Score: 88
Period size: 21 Copynumber: 3.2 Consensus size: 21
314055 TCATTTGAAG
314065 ATTATTTATATTATTATTATT
1 ATTATTTATATTATTATTATT
*
314086 ATTATTATTATAAATATTATTATT
1 ATTA-T-TTAT-ATTATTATTATT
314110 ATTA-TTATATATATTATTATT
1 ATTATTTATAT-TATTATTATT
314131 ATTA
1 ATTA
314135 AAAAAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.02
21 22 0.51
22 1 0.02
23 4 0.09
24 15 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTATTTATATTATTATTATT
Found at i:315434 original size:9 final size:9
Alignment explanation
Indices: 315420--315444 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
315410 GTTTACTTTT
315420 TATTATTAC
1 TATTATTAC
315429 TATTATTAC
1 TATTATTAC
315438 TATTATT
1 TATTATT
315445 TAACTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTATTAC
Found at i:316194 original size:30 final size:30
Alignment explanation
Indices: 316152--316259 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
316142 ACTATAGTAT
*
316152 ATGTTTTGATAAAAAAAATACTTTAAATAC
1 ATGTTTTGATAAAAAAAATAATTTAAATAC
*
316182 ATGTTTAT-ATAAAAATAATAATTTAAATAC
1 ATGTTT-TGATAAAAAAAATAATTTAAATAC
* * * * *
316212 ATATTTTAACAAAAAAAGATAACTTCAAATAT
1 ATGTTTTGATAAAAAAA-ATAA-TTTAAATAC
* *
316244 TTATTTTGATAAAAAA
1 ATGTTTTGATAAAAAA
316260 TATTTTAGAT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.02
30 38 0.59
31 5 0.08
32 20 0.31
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.37
Consensus pattern (30 bp):
ATGTTTTGATAAAAAAAATAATTTAAATAC
Found at i:316265 original size:15 final size:16
Alignment explanation
Indices: 316245--316275 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
316235 TTCAAATATT
316245 TATTTT-GATAAAAAA
1 TATTTTAGATAAAAAA
316260 TATTTTAGATAAAAAA
1 TATTTTAGATAAAAAA
316276 AAGACGTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
TATTTTAGATAAAAAA
Found at i:321874 original size:14 final size:15
Alignment explanation
Indices: 321855--321883 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
321845 AAAATAAATT
321855 ATATTTTTT-GAAAA
1 ATATTTTTTGGAAAA
321869 ATATTTTTTGGAAAA
1 ATATTTTTTGGAAAA
321884 CGTTTTACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
ATATTTTTTGGAAAA
Found at i:322174 original size:23 final size:24
Alignment explanation
Indices: 322139--322187 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
322129 TATTATAATA
322139 TTAAAAATATTAATAAAT-ATATT
1 TTAAAAATATTAATAAATAATATT
* * *
322162 TTAAATATTTTAATAATTAATATT
1 TTAAAAATATTAATAAATAATATT
322186 TT
1 TT
322188 GATTAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAAAAATATTAATAAATAATATT
Found at i:324076 original size:22 final size:21
Alignment explanation
Indices: 324051--324091 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
324041 TATAAAAAAA
324051 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
324073 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
324092 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:326108 original size:35 final size:35
Alignment explanation
Indices: 326062--326200 Score: 215
Period size: 35 Copynumber: 4.0 Consensus size: 35
326052 CCTTCAAAGT
326062 AGTCTTGATGAGTTTGAGAGTTTCTCCAAGATCAG
1 AGTCTTGATGAGTTTGAGAGTTTCTCCAAGATCAG
326097 AGTCTTGATGAGTTTGAGAGTTTCTCCAAGATCAG
1 AGTCTTGATGAGTTTGAGAGTTTCTCCAAGATCAG
* ** *
326132 AGTCTTGATGCGTTTGAGAGTTTCTTTAAGATCAT
1 AGTCTTGATGAGTTTGAGAGTTTCTCCAAGATCAG
* * *
326167 AGTCTTGATGAGTTTGAGAGCTTCTTCAAAATCA
1 AGTCTTGATGAGTTTGAGAGTTTCTCCAAGATCA
326201 TCACACAACT
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 96 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (35 bp):
AGTCTTGATGAGTTTGAGAGTTTCTCCAAGATCAG
Found at i:332718 original size:20 final size:20
Alignment explanation
Indices: 332678--332732 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
332668 AAATCATAAT
332678 TCTTAAACCTTAAAACTTAAA
1 TCTTAAACC-TAAAACTTAAA
*
332699 -CTTAAACCTAAAATTATAAA
1 TCTTAAACCTAAAACT-TAAA
*
332719 TTCTAAAACCTAAA
1 -TCTTAAACCTAAA
332733 TATGATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 6 0.21
20 12 0.41
22 11 0.38
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (20 bp):
TCTTAAACCTAAAACTTAAA
Found at i:334210 original size:73 final size:73
Alignment explanation
Indices: 334081--334223 Score: 198
Period size: 73 Copynumber: 2.0 Consensus size: 73
334071 AGTTTCAAAA
* * * *
334081 GTTGGGTGACCAAAATACAAGCACCCTAAAAGTTCGTAGACTATTTATATACTTTACCCTAAAAT
1 GTTGGGTGACCAAAATACAAGCACCCTAAAAATTCGGAGACTAATTATAGACTTTACCCTAAAAT
334146 TAAATAAT
66 TAAATAAT
* * * *
334154 GTTGTGTGACCAAAATGCAAGCGCCCTAAAAATTCGGATACTAATTATACGA-TTTACCCTAAAA
1 GTTGGGTGACCAAAATACAAGCACCCTAAAAATTCGGAGACTAATTATA-GACTTTACCCTAAAA
334218 TTAAAT
65 TTAAAT
334224 CATGACAAGG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 60 0.98
74 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (73 bp):
GTTGGGTGACCAAAATACAAGCACCCTAAAAATTCGGAGACTAATTATAGACTTTACCCTAAAAT
TAAATAAT
Found at i:335471 original size:4 final size:4
Alignment explanation
Indices: 335448--335482 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
335438 CAGAACCCAT
* *
335448 ATAC ATGC ATAC ATAT ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
335483 AAGAAAAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:339807 original size:31 final size:30
Alignment explanation
Indices: 339769--339954 Score: 117
Period size: 31 Copynumber: 6.1 Consensus size: 30
339759 TTTAAAATTT
339769 ATAAGAATAAAATAAAAATATTTAAATTAAG
1 ATAAGAATAAAAT-AAAATATTTAAATTAAG
* * *
339800 ATAAGAATAAAATATATTATTTTAAGTTAAG
1 ATAAGAATAAAATAAAATA-TTTAAATTAAG
* * *
339831 ATAATAACAAAATATAAAT-TTTAAATTTAAT
1 ATAAGAATAAAATA-AAATATTTAAA-TTAAG
* * * *
339862 AAAAGAATAAACT-ATATTTTTAAAATTAAG
1 ATAAGAATAAAATAAAATATTT-AAATTAAG
* * ** * * *
339892 ATAAGAGTAAGAT-GTATTTTTAAGTTAAA
1 ATAAGAATAAAATAAAATATTTAAATTAAG
* * *
339921 ATAAAAATAAAATATATTATTTAAACTTAAG
1 ATAAGAATAAAATAAAATATTTAAA-TTAAG
339952 ATA
1 ATA
339955 TGGATTTAAG
Statistics
Matches: 117, Mismatches: 31, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
29 19 0.16
30 38 0.32
31 58 0.50
32 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (30 bp):
ATAAGAATAAAATAAAATATTTAAATTAAG
Found at i:339824 original size:26 final size:26
Alignment explanation
Indices: 339765--339831 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 26
339755 TACTTTTAAA
339765 ATTTATAAGAATAA-AATAAAAATATTT
1 ATTT-TAAG-ATAAGAATAAAAATATTT
**
339792 AAATTAAGATAAGAAT-AAAATATATT
1 ATTTTAAGATAAGAATAAAAATAT-TT
*
339818 ATTTTAAGTTAAGA
1 ATTTTAAGATAAGA
339832 TAATAACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
25 11 0.33
26 20 0.61
27 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (26 bp):
ATTTTAAGATAAGAATAAAAATATTT
Found at i:339843 original size:62 final size:61
Alignment explanation
Indices: 339777--339895 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 61
339767 TTATAAGAAT
* * *
339777 AAAATAAAAATATTTAAA-TTAAGATAAGAATAAAATATATTATTTTAAGTTAAGATAATAAC
1 AAAATAAAAAT-TTTAAATTTAAGAAAAGAATAAAATATATT-TTTAAAATTAAGATAATAAC
* * *
339839 AAAATATAAATTTTAAATTTAATAAAAGAATAAACTATATTTTTAAAATTAAGATAA
1 AAAATAAAAATTTTAAATTTAAGAAAAGAATAAAATATATTTTTAAAATTAAGATAA
339896 GAGTAAGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 20 0.40
62 30 0.60
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (61 bp):
AAAATAAAAATTTTAAATTTAAGAAAAGAATAAAATATATTTTTAAAATTAAGATAATAAC
Found at i:341774 original size:20 final size:20
Alignment explanation
Indices: 341751--341837 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
341741 AATTTGTAAA
341751 TCGCAACACAGA-AGTCAAAT
1 TCGCAACAC-GATAGTCAAAT
*
341771 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGATAGTCAAAT
* * *
341791 TTGTAACGCGATAGTCAAAT
1 TCGCAACACGATAGTCAAAT
* *
341811 TCGCAACACAAAAGTCAAAT
1 TCGCAACACGATAGTCAAAT
341831 TCGCAAC
1 TCGCAAC
341838 GTGAAAGTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 2 0.03
20 56 0.97
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (20 bp):
TCGCAACACGATAGTCAAAT
Found at i:341844 original size:20 final size:20
Alignment explanation
Indices: 341762--341850 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
341752 CGCAACACAG
341762 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
* * *
341782 TAGTCAAATTTGTAACGCGA
1 AAGTCAAATTCGCAACGCGA
* * *
341802 TAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACGCGA
*
341822 AAGTCAAATTCGCAACGTGA
1 AAGTCAAATTCGCAACGCGA
341842 AAGTCAAAT
1 AAGTCAAAT
341851 GTTTTTACGC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:342372 original size:19 final size:20
Alignment explanation
Indices: 342348--342405 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
342338 AATTGCAACA
342348 CGATTTT-AGTTCCGCGTTG
1 CGATTTTCAGTTCCGCGTTG
* *
342367 CGATTTTCATTTTCGCGTTG
1 CGATTTTCAGTTCCGCGTTG
* *
342387 CGATTTTCATTTTCGCGTT
1 CGATTTTCAGTTCCGCGTT
342406 ACGAATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 7 0.19
20 29 0.81
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.48
Consensus pattern (20 bp):
CGATTTTCAGTTCCGCGTTG
Found at i:342385 original size:20 final size:20
Alignment explanation
Indices: 342360--342405 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
342350 ATTTTAGTTC
342360 CGCGTTGCGATTTTCATTTT
1 CGCGTTGCGATTTTCATTTT
342380 CGCGTTGCGATTTTCATTTT
1 CGCGTTGCGATTTTCATTTT
342400 CGCGTT
1 CGCGTT
342406 ACGAATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.48
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATTTT
Found at i:344393 original size:12 final size:12
Alignment explanation
Indices: 344378--344419 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
344368 TTTTTCGGCA
*
344378 TTATTTATTTAT
1 TTATTTATTAAT
*
344390 TTATTTACTAAT
1 TTATTTATTAAT
*
344402 TTATGTATTAAT
1 TTATTTATTAAT
344414 TTATTT
1 TTATTT
344420 TCAGCAGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:344589 original size:21 final size:21
Alignment explanation
Indices: 344565--344616 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
344555 TGCACCTATC
* *
344565 ATCGTTCAAGAGGTGTCTCAT
1 ATCGTTCAAGAGATGCCTCAT
*
344586 ATCGTTCAAGAGATGCCTCCT
1 ATCGTTCAAGAGATGCCTCAT
344607 ATCGTTCAAG
1 ATCGTTCAAG
344617 TGGCCCCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (21 bp):
ATCGTTCAAGAGATGCCTCAT
Found at i:344766 original size:12 final size:12
Alignment explanation
Indices: 344751--344776 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
344741 ACCCCCTCCC
344751 ATACCCGATATG
1 ATACCCGATATG
344763 ATACCCGATATG
1 ATACCCGATATG
344775 AT
1 AT
344777 GGATGCGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (12 bp):
ATACCCGATATG
Found at i:346168 original size:61 final size:62
Alignment explanation
Indices: 346068--346207 Score: 194
Period size: 66 Copynumber: 2.2 Consensus size: 62
346058 TTTTACATTG
*
346068 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTATTGATTAATTGATTTGTA
* * *
346128 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTACTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA--TTTTTA-TTGATTAATTGATTTGT
346193 A
62 A
346194 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
346208 GTTTCTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 17 0.24
61 18 0.26
64 4 0.06
66 31 0.44
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTATTGATTAATTGATTTGTA
Found at i:346292 original size:20 final size:20
Alignment explanation
Indices: 346266--346323 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
346256 ATTGAAGGTA
346266 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
346286 TAAATTCGCAACGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
346306 CAAATTCGCAACACGAAA
1 CAAATTCGCAACGCGAAA
346324 TAAGCGTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:346426 original size:20 final size:20
Alignment explanation
Indices: 346364--346426 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
346354 AATTTTCGGT
346364 TTGCGAATTTGACTTTCAGC-
1 TTGCGAATTTGACTTTC-GCG
* *
346384 TTGCGAATTTGACTTTTGAG
1 TTGCGAATTTGACTTTCGCG
346404 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
346424 TTG
1 TTG
346427 ATCGCAACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:346656 original size:39 final size:39
Alignment explanation
Indices: 346602--346685 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 39
346592 CCAAGTTGTA
* *
346602 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTAATTTCCTTTTGCTTGGAACCATATGAGATTTG
* *
346641 GATTTTAATTTCCTTTTTCTTGGAACCATATGAGCTTTG
1 GATTTTAATTTCCTTTTGCTTGGAACCATATGAGATTTG
346680 GATTTT
1 GATTTT
346686 GATGAGCATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (39 bp):
GATTTTAATTTCCTTTTGCTTGGAACCATATGAGATTTG
Found at i:347429 original size:20 final size:20
Alignment explanation
Indices: 347384--347422 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
347374 CAAATAATGT
* *
347384 ACAACATGAAAGTTAAATTC
1 ACAACGTGAAAGTCAAATTC
347404 ACAACGTGAAAGTCAAATT
1 ACAACGTGAAAGTCAAATT
347423 TGCAACGCGA
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:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (20 bp):
ACAACGTGAAAGTCAAATTC
Found at i:347434 original size:20 final size:20
Alignment explanation
Indices: 347391--347434 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
347381 TGTACAACAT
* *
347391 GAAAGTTAAATTCACAACGT
1 GAAAGTCAAATTCACAACGC
**
347411 GAAAGTCAAATTTGCAACGC
1 GAAAGTCAAATTCACAACGC
347431 GAAA
1 GAAA
347435 TAAGCGTTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (20 bp):
GAAAGTCAAATTCACAACGC
Found at i:347466 original size:20 final size:20
Alignment explanation
Indices: 347443--347487 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
347433 AATAAGCGTT
*
347443 GCGATAGTCAAATTCGCAAC
1 GCGATAGCCAAATTCGCAAC
*
347463 GCGAAAGCCAAATTCGCAAC
1 GCGATAGCCAAATTCGCAAC
347483 GCGAT
1 GCGAT
347488 TTTCGGTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.16
Consensus pattern (20 bp):
GCGATAGCCAAATTCGCAAC
Found at i:349900 original size:12 final size:12
Alignment explanation
Indices: 349885--349909 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
349875 TTTTCGGGGA
349885 CTTTTTCTTCTT
1 CTTTTTCTTCTT
349897 CTTTTTCTTCTT
1 CTTTTTCTTCTT
349909 C
1 C
349910 AGGGTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:350121 original size:24 final size:24
Alignment explanation
Indices: 350094--350143 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
350084 ATCAAAATCC
350094 GAGTATTGACCAAGATCAAAGTTT
1 GAGTATTGACCAAGATCAAAGTTT
*
350118 GAGTATTGACCAAGATCAAATTTT
1 GAGTATTGACCAAGATCAAAGTTT
350142 GA
1 GA
350144 ATACTGACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (24 bp):
GAGTATTGACCAAGATCAAAGTTT
Found at i:350151 original size:24 final size:24
Alignment explanation
Indices: 350100--350151 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
350090 ATCCGAGTAT
* *
350100 TGACCAAGATCAAAGTTTGAGTAT
1 TGACCAAGATCAAAGTTTGAATAC
*
350124 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAAGTTTGAATAC
350148 TGAC
1 TGAC
350152 TAGTACTCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTTGAATAC
Found at i:351288 original size:2 final size:2
Alignment explanation
Indices: 351281--351325 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
351271 CAAACTTAGA
351281 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
351323 AT A
1 AT A
351326 ACGTAATGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:353241 original size:106 final size:106
Alignment explanation
Indices: 353049--353271 Score: 340
Period size: 106 Copynumber: 2.1 Consensus size: 106
353039 CCAATGCAAG
*
353049 TTGTGTTGTTTCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGT
1 TTGTGTTGTCTCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGT
*
353114 GTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGCGGCCCATTCGTTGTGAAGTTGAAC
* * * * *
353155 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACA-TTGGGAAGT
1 TTGTGTTGTCTCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAG-
* *
353219 TGTTTGTTGACAGCCAGTGGCCCATTCGTTGTGAAGTTGAAC
65 TGTTTGTTGACAACCAGCGGCCCATTCGTTGTGAAGTTGAAC
*
353261 TTGTGCTGTCT
1 TTGTGTTGTCT
353272 TAAACTGGGA
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
105 7 0.07
106 99 0.93
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (106 bp):
TTGTGTTGTCTCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGT
GTTTGTTGACAACCAGCGGCCCATTCGTTGTGAAGTTGAAC
Found at i:353311 original size:64 final size:64
Alignment explanation
Indices: 353178--353720 Score: 795
Period size: 64 Copynumber: 8.5 Consensus size: 64
353168 AGTCCAATAT
* * * * * * *
353178 CCTTCGTTGTGAAGTTGAAATTG-G--CTCTGACATTGGGAAGTTGTTTGTTGACAGCCAGTGGC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAA-AT-TTTGTTGACAACCAGCGGC
353240 C
64 C
* * * *
353241 CATTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAATTTTGTTGACAACCAACGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
* *
353305 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTCGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAA-TTTTGTTGACAACCAGCGGCC
*
353370 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGAAAATTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
* * *
353434 CCTTCGTCGTGAAGTTGAACATGTGTTGTCTGACACTGGGAAATTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
* * * *
353498 CATTCGTTGTGAAGTTGAACTTGTGTTGTCTAAAACTAGAAAATTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
* *
353562 CCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGACACTGGGAAATTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
* * *
353626 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTAAAACTAGAAAATTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
*
353690 CCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
353721 TGAGTTGAAC
Statistics
Matches: 434, Mismatches: 42, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
63 21 0.05
64 341 0.79
65 61 0.14
66 11 0.03
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (64 bp):
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
Found at i:364964 original size:2 final size:2
Alignment explanation
Indices: 364957--364999 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
364947 CAGACTTAGA
364957 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
364999 A
1 A
365000 ACGTAATGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:366812 original size:14 final size:16
Alignment explanation
Indices: 366777--366813 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
366767 GAAATCATTG
366777 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
366793 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
366807 AAAATTA
1 AAAATTA
366814 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:366994 original size:19 final size:19
Alignment explanation
Indices: 366970--367040 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
366960 ACTAAAACCT
366970 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
366989 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
* **
367008 GTTGCGAATTT-AACTTTGT
1 GTTGCGAATTTGAA-ATTCA
367027 GTTGCGAATTTGAA
1 GTTGCGAATTTGAA
367041 TATCGCGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 2 0.04
19 43 0.91
20 2 0.04
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:367087 original size:40 final size:39
Alignment explanation
Indices: 367008--367134 Score: 125
Period size: 40 Copynumber: 3.2 Consensus size: 39
366998 TTGAAATTCA
* *
367008 GTTGCGAATTTAACTTTGTGTTGCGAATTT--GAATATCGC
1 GTTGCGAATTTGACTTTGTGTTGCG-ATTTACAAAT-TCGC
*
367047 GTTTCGAATTTGACTTATGTGTTGCGATTTACAAATTCGC
1 GTTGCGAATTTGACTT-TGTGTTGCGATTTACAAATTCGC
* * * *
367087 GTTGCGATTTATAGA-TTCGCGTTGCGATTTACAGATTCGC
1 GTTGCGAATT-T-GACTTTGTGTTGCGATTTACAAATTCGC
367127 GTTGCGAA
1 GTTGCGAA
367135 ATTGGAAACT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
39 18 0.24
40 48 0.65
41 6 0.08
42 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (39 bp):
GTTGCGAATTTGACTTTGTGTTGCGATTTACAAATTCGC
Found at i:367092 original size:20 final size:20
Alignment explanation
Indices: 367067--367133 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
367057 TGACTTATGT
*
367067 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAGATTCGC
*
367087 GTTGCGATTTATAGATTCGC
1 GTTGCGATTTACAGATTCGC
367107 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
367127 GTTGCGA
1 GTTGCGA
367134 AATTGGAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:367151 original size:40 final size:40
Alignment explanation
Indices: 367067--367153 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 40
367057 TGACTTATGT
* * * *
367067 GTTGCGATTTACAAATTCGCGTTGCGATTTATAGATTCGC
1 GTTGCGATTTACAAATTCGCGTTGCGAATTAGAAACTCGC
* * *
367107 GTTGCGATTTACAGATTCGCGTTGCGAAATTGGAAACT-GG
1 GTTGCGATTTACAAATTCGCGTTGCG-AATTAGAAACTCGC
367147 GTTGCGA
1 GTTGCGA
367154 GATTTGAGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 33 0.85
41 6 0.15
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (40 bp):
GTTGCGATTTACAAATTCGCGTTGCGAATTAGAAACTCGC
Found at i:367179 original size:19 final size:19
Alignment explanation
Indices: 367148--367197 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
367138 GGAAACTGGG
*
367148 TTGCGAGATTTGAGTTCGCA
1 TTGCGA-ATTTGAGATCGCA
*
367168 TTGCGAATTTGAGATCGCG
1 TTGCGAATTTGAGATCGCA
367187 TTGCGAATTTG
1 TTGCGAATTTG
367198 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (19 bp):
TTGCGAATTTGAGATCGCA
Found at i:369134 original size:32 final size:33
Alignment explanation
Indices: 369098--369173 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 33
369088 ATTTAAAGTG
369098 ATGATATAACATATATTACATCAC-CTAAAAT-A
1 ATGATATAACATATATTACATCACTC-AAAATAA
** * *
369130 ATGATATATTATGTATTACGTCACTCAAAATAA
1 ATGATATAACATATATTACATCACTCAAAATAA
369163 AT-ATATAACAT
1 ATGATATAACAT
369174 GTGACGTGTC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.34
Consensus pattern (33 bp):
ATGATATAACATATATTACATCACTCAAAATAA
Found at i:369223 original size:2 final size:2
Alignment explanation
Indices: 369216--369250 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
369206 TATTATATCA
369216 AT AT AT 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 AT AT AT A
369251 ATCATTAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:382740 original size:67 final size:67
Alignment explanation
Indices: 382664--382790 Score: 227
Period size: 67 Copynumber: 1.9 Consensus size: 67
382654 GGTCCACTGC
*
382664 GGTGCACTCTTTTGATAGCCATTTCACACAAGATAGAGATAATACAGTGTCTTATAAGGTCCGCT
1 GGTGCACTCTTTTGATAGCCATTTCACAAAAGATAGAGATAATACAGTGTCTTATAAGGTCCGCT
382729 AT
66 AT
* *
382731 GGTGCACTCTTTTGATAGTCATTTCGCAAAAGATAGAGATAATACAGTGTCTTATAAGGT
1 GGTGCACTCTTTTGATAGCCATTTCACAAAAGATAGAGATAATACAGTGTCTTATAAGGT
382791 ATGTATAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (67 bp):
GGTGCACTCTTTTGATAGCCATTTCACAAAAGATAGAGATAATACAGTGTCTTATAAGGTCCGCT
AT
Found at i:390380 original size:23 final size:19
Alignment explanation
Indices: 390331--390392 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
390321 ATTCAAATAA
390331 TATACTTAAAAGTATATTT
1 TATACTTAAAAGTATATTT
*
390350 TAT-TTTAAAGTAGTAGTATATT
1 TATACTTAAA--AGTA-TAT-TT
*
390372 TATACTTAAAA-AATATTT
1 TATACTTAAAAGTATATTT
390390 TAT
1 TAT
390393 TCTTTTATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
18 10 0.29
19 6 0.17
20 5 0.14
21 4 0.11
22 5 0.14
23 5 0.14
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (19 bp):
TATACTTAAAAGTATATTT
Found at i:390475 original size:21 final size:22
Alignment explanation
Indices: 390451--390505 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
390441 TTAATAAAAG
*
390451 AATAATAA-AAATTTT-ATTTAA
1 AATAA-AATAAATTTTAAGTTAA
*
390472 AATAAAATATATTTTAAGTTAA
1 AATAAAATAAATTTTAAGTTAA
390494 AATAAAAATAAA
1 AAT-AAAATAAA
390506 ATATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.07
21 11 0.39
22 8 0.29
23 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAAAATAAATTTTAAGTTAA
Found at i:390504 original size:28 final size:30
Alignment explanation
Indices: 390470--390542 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
390460 AATTTTATTT
390470 AAAATAAAATATATTT-TAAGTT-AA-AATA
1 AAAATAAAATATATTTATAAGTTCAATAA-A
*
390498 AAAATAAAATATATTTAATAATTTCAATAAA
1 AAAATAAAATATATTT-ATAAGTTCAATAAA
390529 AAAATAAAATATAT
1 AAAATAAAATATAT
390543 ATTTTATTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 16 0.40
30 5 0.12
31 17 0.43
32 2 0.05
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (30 bp):
AAAATAAAATATATTTATAAGTTCAATAAA
Found at i:390574 original size:36 final size:32
Alignment explanation
Indices: 390533--390731 Score: 126
Period size: 30 Copynumber: 6.6 Consensus size: 32
390523 AATAAAAAAA
390533 TAAAATATATATTTTATTCTTTTATGTTCCAACTT
1 TAAAATATATATTTTATTCTTTTAT-TT-CAAC-T
*
390568 TAAAAATATATATTTTA-T-TTTTATTTTAACT
1 T-AAAATATATATTTTATTCTTTTATTTCAACT
390599 TAAAATATAT-TTTTATTCTTTTA-TT-AA-T
1 TAAAATATATATTTTATTCTTTTATTTCAACT
* * * * *
390627 TAGAA-ATATATTTTCTT-ATTAATAT-AACT
1 TAAAATATATATTTTATTCTTTTATTTCAACT
* * *
390656 TATTAA-ATATATTTTA-T-ATTTATTTTAACT
1 TA-AAATATATATTTTATTCTTTTATTTCAACT
*
390686 T-AAA-ATATA-TTTATTCTTTTA-TT-AATT
1 TAAAATATATATTTTATTCTTTTATTTCAACT
*
390713 TAAAATATATTTTGTTATT
1 TAAAATATATATT-TTATT
390732 AATATATATT
Statistics
Matches: 136, Mismatches: 14, Indels: 32
0.75 0.08 0.18
Matches are distributed among these distances:
27 15 0.11
28 27 0.20
29 25 0.18
30 29 0.21
31 12 0.09
32 3 0.02
33 2 0.01
34 6 0.04
35 2 0.01
36 15 0.11
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (32 bp):
TAAAATATATATTTTATTCTTTTATTTCAACT
Found at i:390605 original size:30 final size:30
Alignment explanation
Indices: 390533--390695 Score: 138
Period size: 30 Copynumber: 5.3 Consensus size: 30
390523 AATAAAAAAA
*
390533 TAAAATATATATTTTATTCTTTTATGTTCCAACTT
1 TAAAATATATATTTTA-T-TTTTAT-TT-TAAC-T
390568 TAAAAATATATATTTTATTTTTATTTTAACT
1 T-AAAATATATATTTTATTTTTATTTTAACT
*
390599 TAAAATATAT-TTTTATTCTTT-TATTAA-T
1 TAAAATATATATTTTATT-TTTATTTTAACT
* * * * *
390627 TAGAA-ATATATTTTCTTATTAATATAACT
1 TAAAATATATATTTTATTTTTATTTTAACT
* *
390656 TATTAA-ATATATTTTATATTTATTTTAACT
1 TA-AAATATATATTTTATTTTTATTTTAACT
390686 TAAAATATAT
1 TAAAATATAT
390696 TTATTCTTTT
Statistics
Matches: 106, Mismatches: 15, Indels: 19
0.76 0.11 0.14
Matches are distributed among these distances:
27 6 0.06
28 14 0.13
29 17 0.16
30 39 0.37
31 2 0.02
32 3 0.03
33 2 0.02
34 6 0.06
35 2 0.02
36 15 0.14
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.55
Consensus pattern (30 bp):
TAAAATATATATTTTATTTTTATTTTAACT
Found at i:390640 original size:57 final size:56
Alignment explanation
Indices: 390575--390725 Score: 157
Period size: 57 Copynumber: 2.7 Consensus size: 56
390565 CTTTAAAAAT
*
390575 ATATATTTTATTTTTATTTTAACTTAAAATATATTTT-TATTCTTTTATTAA-TTAGAA
1 ATATATTTTATTTTTATTTTAACTTAAAATATATTTTATATT-TATT-TTAACTTA-AA
* * * *
390632 ATATATTTTCTTATTAATATAACTTATTAAATATATTTTATATTTATTTTAACTTAAA
1 ATATATTTTATTTTTATTTTAACTTA--AAATATATTTTATATTTATTTTAACTTAAA
* *
390690 ATATA-TTTATTCTTT-TATTAATTTAAAATATATTTT
1 ATATATTTTATT-TTTATTTTAACTTAAAATATATTTT
390726 GTTATTAATA
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
55 11 0.14
57 33 0.42
58 13 0.17
59 17 0.22
60 4 0.05
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (56 bp):
ATATATTTTATTTTTATTTTAACTTAAAATATATTTTATATTTATTTTAACTTAAA
Found at i:390739 original size:87 final size:86
Alignment explanation
Indices: 390575--390737 Score: 276
Period size: 85 Copynumber: 1.9 Consensus size: 86
390565 CTTTAAAAAT
*
390575 ATATATTTTATTTTTATTTTAACTTAAAATATATTTTTATTCTTTTATTAATTAGAAATATATTT
1 ATATATTTTATATTTATTTTAACTTAAAATATA-TTTTATTCTTTTATTAATTAGAAATATATTT
390640 TCTTATTAATATAACTTATTAA
65 TCTTATTAATATAACTTATTAA
390662 ATATATTTTATATTTATTTTAACTTAAAATATA-TTTATTCTTTTATTAATTTA-AAATATATTT
1 ATATATTTTATATTTATTTTAACTTAAAATATATTTTATTCTTTTATTAA-TTAGAAATATATTT
*
390725 TGTTATTAATATA
65 TCTTATTAATATA
390738 TATTCAAATT
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
85 38 0.52
86 3 0.04
87 32 0.44
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (86 bp):
ATATATTTTATATTTATTTTAACTTAAAATATATTTTATTCTTTTATTAATTAGAAATATATTTT
CTTATTAATATAACTTATTAA
Found at i:391371 original size:23 final size:23
Alignment explanation
Indices: 391328--391371 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
391318 TTTATGAATT
*
391328 TAATATTAATAAATATTTTAAAA
1 TAATATTAATAAATATATTAAAA
*
391351 TAATTTTAATCAAA-ATATTAA
1 TAATATTAAT-AAATATATTAA
391372 TTATTAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATATTAATAAATATATTAAAA
Found at i:391417 original size:22 final size:22
Alignment explanation
Indices: 391397--391442 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
391387 AAAATATATT
391397 TATTAATATTTCTAATCATATAA
1 TATT-ATATTTCTAATCATATAA
*
391420 TATTATATTTTTAAT-ATTATAA
1 TATTATATTTCTAATCA-TATAA
391442 T
1 T
391443 CAAATACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 16 0.76
23 4 0.19
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATATTTCTAATCATATAA
Found at i:394140 original size:12 final size:12
Alignment explanation
Indices: 394125--394172 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
394115 TAGAAATCAA
*
394125 AACAGAATTTAG
1 AACAGAATTCAG
*
394137 AACAGAATCCAG
1 AACAGAATTCAG
* *
394149 ATCAGAAATCAG
1 AACAGAATTCAG
394161 AACAGAATTCAG
1 AACAGAATTCAG
394173 GTCATGTATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:394207 original size:24 final size:25
Alignment explanation
Indices: 394153--394211 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 25
394143 ATCCAGATCA
* * *
394153 GAAATCAGAACAGAATTCAGGTCAT
1 GAAATCAGAATAGAATTCAAGTCAG
*
394178 G-TATCAGAATAGAATTCAAGTC-G
1 GAAATCAGAATAGAATTCAAGTCAG
394201 GAAATCA-AATA
1 GAAATCAGAATA
394212 AAAATAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 5 0.18
24 22 0.79
25 1 0.04
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.22
Consensus pattern (25 bp):
GAAATCAGAATAGAATTCAAGTCAG
Found at i:397434 original size:2 final size:2
Alignment explanation
Indices: 397423--397477 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
397413 AAACATTTTC
397423 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* *
397465 TG CA TA TA TA TA T
1 TA TA TA TA TA TA T
397478 CATGCATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 44 0.94
3 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:400280 original size:23 final size:24
Alignment explanation
Indices: 400236--400288 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
400226 CAGTGTCTTC
400236 GAGCACTCGTGAATTAGTGCAATT
1 GAGCACTCGTGAATTAGTGCAATT
* *
400260 GAGCACTCTTGTA-TAGTGCAATT
1 GAGCACTCGTGAATTAGTGCAATT
*
400283 GTGCAC
1 GAGCAC
400289 CCATGTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (24 bp):
GAGCACTCGTGAATTAGTGCAATT
Found at i:400295 original size:23 final size:23
Alignment explanation
Indices: 400250--400296 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
400240 ACTCGTGAAT
* *
400250 TAGTGCAATTGAGCACTCTTGTA
1 TAGTGCAATTGAGCACCCATGTA
*
400273 TAGTGCAATTGTGCACCCATGTA
1 TAGTGCAATTGAGCACCCATGTA
400296 T
1 T
400297 TATTGCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (23 bp):
TAGTGCAATTGAGCACCCATGTA
Found at i:401099 original size:41 final size:41
Alignment explanation
Indices: 401054--401134 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
401044 AAAACATAAC
401054 TATTTACAAGAGAATAAAAATAAATAGTGAAAAGCTCTTCA
1 TATTTACAAGAGAATAAAAATAAATAGTGAAAAGCTCTTCA
401095 TATTTACAAGAGAATAAAAATAAATAGTGAAAAGCTCTTC
1 TATTTACAAGAGAATAAAAATAAATAGTGAAAAGCTCTTC
401135 TCTTATGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (41 bp):
TATTTACAAGAGAATAAAAATAAATAGTGAAAAGCTCTTCA
Found at i:404758 original size:18 final size:19
Alignment explanation
Indices: 404735--404777 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
404725 CAGTAATCCT
404735 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
404753 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
404773 ATTCC
1 ATTCC
404778 GTGAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:404765 original size:20 final size:20
Alignment explanation
Indices: 404740--404777 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
404730 ATCCTATTCC
404740 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
404760 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
404778 GTGAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:405718 original size:48 final size:48
Alignment explanation
Indices: 405646--405741 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
405636 CCACAAAAAC
* *
405646 TATTATCCAAATAAACCCAGCAGAAATGATTTGAATACCTCTGATTCT
1 TATTATCCAAATAAACCCAACAGAAATGATTAGAATACCTCTGATTCT
*
405694 TATTATCCAGATAAACCCAACAGAAATGATTAGAATACCTCTGATTCT
1 TATTATCCAAATAAACCCAACAGAAATGATTAGAATACCTCTGATTCT
405742 AACATAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (48 bp):
TATTATCCAAATAAACCCAACAGAAATGATTAGAATACCTCTGATTCT
Found at i:406944 original size:21 final size:23
Alignment explanation
Indices: 406920--406980 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 23
406910 ATTTAAAATT
406920 TAAATAAATTAAATT-AATTTA-
1 TAAATAAATTAAATTAAATTTAC
406941 TAAAT--ATTAAATATTAAATTTAC
1 TAAATAAATT-AA-ATTAAATTTAC
406964 TAAATTAAGATTAAATT
1 TAAA-TAA-ATTAAATT
406981 GCTAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 8 0.25
22 6 0.19
23 4 0.12
24 1 0.03
25 3 0.09
26 2 0.06
27 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATAAATTAAATTAAATTTAC
Found at i:408322 original size:118 final size:118
Alignment explanation
Indices: 408114--408339 Score: 321
Period size: 118 Copynumber: 1.9 Consensus size: 118
408104 AAACCACTTG
* * *
408114 AGCGCTGGGAATTTGATCTGGAAACTCTGTTTCTTGCTTGTTTCTTTTTGAACATGGCTTTGCTT
1 AGCGCTGGGAATTTGATATGGAAACTCTGTTTCTTGCTTGGTTCTTTTTGAACATGGCTTGGCTT
*
408179 CAGTTTTTCTTAATGATAAAGCTAGAAGAAGATGACACCAGCCTTGTTGCTTC
66 CAGTTTTTCTTAACGATAAAGCTAGAAGAAGATGACACCAGCCTTGTTGCTTC
* *
408232 AGCGCTGGGAATTTG-TATGGACAACTCTGTTTCTTGTTTGGTTCTTTTTTACACATGGCTTGGC
1 AGCGCTGGGAATTTGATATGGA-AACTCTGTTTCTTGCTTGGTTCTTTTTGA-ACATGGCTTGGC
* * ** *
408296 TTCTGTTTTT-TTAACGCTAGGGCTAGAAGAAGTTGACACCAGCC
64 TTCAGTTTTTCTTAACGATAAAGCTAGAAGAAGATGACACCAGCC
408340 AGCCATGTTA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
117 5 0.05
118 70 0.74
119 20 0.21
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (118 bp):
AGCGCTGGGAATTTGATATGGAAACTCTGTTTCTTGCTTGGTTCTTTTTGAACATGGCTTGGCTT
CAGTTTTTCTTAACGATAAAGCTAGAAGAAGATGACACCAGCCTTGTTGCTTC
Found at i:410242 original size:31 final size:32
Alignment explanation
Indices: 410173--410253 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
410163 AAGTTAGATC
*
410173 AATTTAATAATTATTTTATAACAATTCAATAA
1 AATTTAATGATTATTTTATAACAATTCAATAA
* *
410205 AATTTAATGATTATTTTGTAATAGA-TCAAT-A
1 AATTTAATGATTATTTTATAACA-ATTCAATAA
* *
410236 AATTTAATGGTCATTTTA
1 AATTTAATGATTATTTTA
410254 CGAGTTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 16 0.38
32 25 0.60
33 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (32 bp):
AATTTAATGATTATTTTATAACAATTCAATAA
Found at i:422122 original size:3 final size:3
Alignment explanation
Indices: 422116--422147 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
422106 TGATGACGCC
422116 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
422148 GGCCATTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:427221 original size:23 final size:23
Alignment explanation
Indices: 427195--427258 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
427185 CATCTCATAT
427195 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
427218 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
427241 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
427259 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:427477 original size:101 final size:101
Alignment explanation
Indices: 427274--427488 Score: 378
Period size: 101 Copynumber: 2.1 Consensus size: 101
427264 TAATGTCCAT
* *
427274 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATA-ATATACCAAGGATCAAGTATGTGTCTCACCA
427339 GACTTACACATGTTCCAAAGAATACATATATGTCCCG
65 GACTTACACATGTTCCAAAGAATACATATATGTCCCG
*
427376 AAGGACCACATATCATTCCTTAAGAATCATAT-ATATGCCAAGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAATCATATAATATACCAAGGATCAAGTATGTGTCTCACCAG
427440 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 ACTT-ACACATGTTCCAAAGAATACATATATGTCCCG
427477 AAGGACCACATA
1 AAGGACCACATA
427489 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
100 33 0.30
101 44 0.40
102 32 0.29
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (101 bp):
AAGGACCACATATCATTCCTTAAGAATCATATAATATACCAAGGATCAAGTATGTGTCTCACCAG
ACTTACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:428339 original size:64 final size:64
Alignment explanation
Indices: 428231--428451 Score: 254
Period size: 64 Copynumber: 3.5 Consensus size: 64
428221 TAATGAAGGT
* * * * *
428231 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
428294 G
64 G
*
428295 ATGCATCGATGCA-TGACTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* * **
428359 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
428422 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
428452 ACACCTTCAA
Statistics
Matches: 138, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
63 4 0.03
64 128 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:433061 original size:23 final size:23
Alignment explanation
Indices: 433035--433098 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
433025 CAGCTCATAT
433035 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
433058 AATTTCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
433081 AATTGCACCGTAA-TGCCA
1 AATTGCACCG-AAGTGCCA
433099 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 33 0.97
24 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:433285 original size:103 final size:103
Alignment explanation
Indices: 433114--433331 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
433104 TAATGTCCAT
* *
433114 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
433179 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
433217 AATGATCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
433282 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
433320 AAGGACCACATA
1 AAGGACCACATA
433332 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:434187 original size:63 final size:64
Alignment explanation
Indices: 434080--434235 Score: 185
Period size: 63 Copynumber: 2.5 Consensus size: 64
434070 TAATGAAGGT
* * *
434080 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACT-GG
1 ATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTT-TCATTATTAATGGG
* * *
434143 ATGCATCGATGCA-TGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCCTTATTAATGG
1 ATGCATCGATGCACT-ACTGATGCATCGATGCA-TAAAATGCATTCGATGTTTCATTATTAATGG
434206 G
64 G
**
434207 ATGCATCGATGCACTACCAATGCATCGAT
1 ATGCATCGATGCACTACTGATGCATCGAT
434236 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
62 2 0.03
63 49 0.61
64 28 0.35
65 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTTCATTATTAATGGG
Found at i:435691 original size:22 final size:22
Alignment explanation
Indices: 435666--435707 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
435656 CATATAAATA
435666 TAAAT-ATATATATATATTTAAT
1 TAAATAATA-ATATATATTTAAT
*
435688 TAAATAATAATATTTATTTA
1 TAAATAATAATATATATTTA
435708 TTTTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAATAATAATATATATTTAAT
Found at i:436530 original size:73 final size:73
Alignment explanation
Indices: 436411--436607 Score: 313
Period size: 73 Copynumber: 2.7 Consensus size: 73
436401 CTCCGCTGGG
* * *
436411 GAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTATTTTTCTTGAAACAAACTGTTTC
1 GAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAAAAACTGTTTC
436476 TCGCTTGA
66 TCGCTTGA
* * *
436484 GAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTTTTAAAAAAAATTGTTTT
1 GAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAAAAACTGTTTC
436549 TCGCTTGA
66 TCGCTTGA
* * *
436557 GAAAATTTCACTCGAAATAGCAATTTATCTCACTTTAGATTGTTTTTCTTA
1 GAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
436608 TTACGAACTC
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 114 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (73 bp):
GAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAAAAACTGTTTC
TCGCTTGA
Found at i:436722 original size:36 final size:36
Alignment explanation
Indices: 436682--436796 Score: 117
Period size: 36 Copynumber: 3.2 Consensus size: 36
436672 AGTGAAATTT
436682 TCTCAAGCGAGAAACAATTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGAAACAATTTGTTTTAAGAAAAACAA
* * ** **
436718 TCTCAAGTGAGATA-AA-TTGTTATTTCAAGTGAAACTT
1 TCTCAAGCGAGAAACAATTTG-T-TTT-AAGAAAAACAA
* *
436755 TCTCAAGCGATAAACAGTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGAAACAATTTGTTTTAAGAAAAACAA
436791 TCTCAA
1 TCTCAA
436797 TTGAGATAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
34 3 0.05
35 3 0.05
36 28 0.47
37 21 0.35
38 2 0.03
39 3 0.05
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (36 bp):
TCTCAAGCGAGAAACAATTTGTTTTAAGAAAAACAA
Found at i:436760 original size:37 final size:37
Alignment explanation
Indices: 436647--436831 Score: 121
Period size: 37 Copynumber: 5.1 Consensus size: 37
436637 AAAAACAATT
* *
436647 TCAAGTGAGATAAATT-TCTATTTCGAGTGAAATTTTC
1 TCAAGTGAGATAAATTGT-TATTTCAAGTGAAACTTTC
* * ** **
436684 TCAAGCGAGAAACAATT-TGT-TTT-AAGAAAAACAATC
1 TCAAGTGAGATA-AATTGT-TATTTCAAGTGAAACTTTC
436720 TCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTC
1 TCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTC
* ** * * ** **
436757 TCAA--GCGATAAACAGTTTGTTTTAAGAAAAACAATC
1 TCAAGTGAGATAAATTG-TTATTTCAAGTGAAACTTTC
* *
436793 TCAATTGAGATAAATTGCTATTTCAAGTGAAACTTTC
1 TCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTC
436830 TC
1 TC
436832 CAGCGAGAAA
Statistics
Matches: 107, Mismatches: 34, Indels: 14
0.69 0.22 0.09
Matches are distributed among these distances:
35 13 0.12
36 39 0.36
37 41 0.38
38 14 0.13
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (37 bp):
TCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTC
Found at i:436858 original size:146 final size:148
Alignment explanation
Indices: 436628--436913 Score: 373
Period size: 146 Copynumber: 1.9 Consensus size: 148
436618 TTTCAGGAAA
* * * *
436628 TGTTTTAAGAAAAACAATTTCAAGTGAGATAAATTTCTATTTCGAGTGAAATTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
*
436693 AAACAATTTGTTTTAAGAAAAACAA-TCTCAAGTGAGATAAATTG-TTATTTCAAGTGAAACTT-
66 AAACAATTTGCTTTAAGAAAAACAACT-TCAAGTGAGATAAATTGTTTATTTCAAGTGAAACTTG
*
436755 TCTCAAGCGATAAACAGTT
130 TATCAAGCGATAAACAGTT
* *
436774 TGTTTTAAGAAAAACAATCTCAATTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
* * ** * * * *
436839 AAA-ATCTTTGCTTTGAGAAAAATTACTTCGAGTGAGATAATTTGTTTTGTTTCGAGTGAAACTT
66 AAACA-ATTTGCTTTAAGAAAAACAACTTCAAGTGAGATAAATTG-TTTATTTCAAGTGAAACTT
436903 GTATCAAGCGA
129 GTATCAAGCGA
436914 GACAAATCTT
Statistics
Matches: 119, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
145 1 0.01
146 92 0.77
147 1 0.01
148 16 0.13
149 9 0.08
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (148 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
AAACAATTTGCTTTAAGAAAAACAACTTCAAGTGAGATAAATTGTTTATTTCAAGTGAAACTTGT
ATCAAGCGATAAACAGTT
Found at i:436860 original size:73 final size:73
Alignment explanation
Indices: 436628--436841 Score: 347
Period size: 73 Copynumber: 2.9 Consensus size: 73
436618 TTTCAGGAAA
* * * *
436628 TGTTTTAAGAAAAACAATTTCAAGTGAGATAAATTTCTATTTCGAGTGAAATTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
436693 AAACAATT
66 AAACAATT
* *
436701 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTCTCAAGCGAT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
*
436766 AAACAGTT
66 AAACAATT
* *
436774 TGTTTTAAGAAAAACAATCTCAATTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
436839 AAA
66 AAA
436842 ATCTTTGCTT
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 130 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCAAGCGAG
AAACAATT
Found at i:438040 original size:122 final size:123
Alignment explanation
Indices: 437704--438047 Score: 505
Period size: 123 Copynumber: 2.8 Consensus size: 123
437694 ACAAAAACTT
*
437704 GAACTCATCTAAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTTGACT
1 GAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTTGACT
* *
437769 CTATCGCAGAAGAAGATATAGT-AGCATCAACATTTCCAAAAGGAGTTCATAATAAGAA
66 CTATCGCAGAAGGAGATATA-TAAACATCAACATTTCCAAAAGGAGTTCATAATAAGAA
437827 GAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTTGACT
1 GAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTTGACT
** * * * * *
437892 CTATCATAAAATGAGATA-AAACAACATCAACATTTCCAGAAGGAGTTCGTAAT-AGAA
66 CTATCGCAGAAGGAGATATATA-AACATCAACATTTCCAAAAGGAGTTCATAATAAGAA
* * * * *
437949 TAACTCATCTGAAGAGGAAGAAGAAGTTCATAATATGAAGAACTTGTTCAACATTTTCCTTGACT
1 GAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTTGACT
*
438014 CTATCGCAGAAGGAGACATATAAACATCAACATT
66 CTATCGCAGAAGGAGATATATAAACATCAACATT
438048 GTCATTCTTA
Statistics
Matches: 197, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
122 90 0.46
123 107 0.54
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (123 bp):
GAACTCATCTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTTGACT
CTATCGCAGAAGGAGATATATAAACATCAACATTTCCAAAAGGAGTTCATAATAAGAA
Found at i:441829 original size:32 final size:31
Alignment explanation
Indices: 441793--441869 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
441783 CGGGGCCGTG
*
441793 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
441825 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
441856 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
441870 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:441852 original size:63 final size:63
Alignment explanation
Indices: 441746--441869 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
441736 CCCTAAGGGA
* * ** *
441746 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
441809 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
441870 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Done.