Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009571.1 Hibiscus syriacus cultivar Beakdansim tig00116934_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: 592744
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:205666 original size:13 final size:13
Alignment explanation
Indices: 205666--205709 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
205656 CCGTTGACCC
205666 GACCCGACCCGTT
1 GACCCGACCCGTT
*
205679 TACCCGACCCGTT
1 GACCCGACCCGTT
*
205692 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
205707 GAC
1 GAC
205710 TGTTGACCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.16, C:0.41, G:0.23, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:205667 original size:18 final size:18
Alignment explanation
Indices: 205644--205689 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
205634 GACCGTCACA
205644 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
205662 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
205680 ACCCGACCCG
1 ACCCGACCCG
205690 TTGACCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:205704 original size:15 final size:15
Alignment explanation
Indices: 205684--205717 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
205674 CCGTTTACCC
205684 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
205699 GACCCGTTGACTGTT
1 GACCCGTTGACCGTT
205714 GACC
1 GACC
205718 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.32, G:0.26, T:0.26
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:207039 original size:18 final size:18
Alignment explanation
Indices: 207013--207048 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
207003 TCGAAAGGAC
*
207013 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
207031 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
207049 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:208248 original size:24 final size:24
Alignment explanation
Indices: 208178--208267 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
208168 TCCGACTTGA
* *
208178 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
208201 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
208224 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
208248 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
208268 TGAATTATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 32 0.56
24 25 0.44
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:210463 original size:13 final size:13
Alignment explanation
Indices: 210463--210506 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
210453 CCGTTGACCC
210463 GACCCGACCCGTT
1 GACCCGACCCGTT
*
210476 TACCCGACCCGTT
1 GACCCGACCCGTT
*
210489 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
210504 GAC
1 GAC
210507 TGTTGACCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.16, C:0.41, G:0.23, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:210464 original size:18 final size:18
Alignment explanation
Indices: 210441--210486 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
210431 ACCGGTCACA
210441 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
210459 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
210477 ACCCGACCCG
1 ACCCGACCCG
210487 TTGACCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:210501 original size:15 final size:15
Alignment explanation
Indices: 210481--210514 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
210471 CCGTTTACCC
210481 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
210496 GACCCGTTGACTGTT
1 GACCCGTTGACCGTT
210511 GACC
1 GACC
210515 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.32, G:0.26, T:0.26
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:211835 original size:18 final size:18
Alignment explanation
Indices: 211809--211844 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
211799 TCGAAAGGAC
*
211809 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
211827 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
211845 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:213048 original size:24 final size:24
Alignment explanation
Indices: 212978--213067 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
212968 TCCGACTTGA
* *
212978 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
213001 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
213024 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
213048 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
213068 TTGAATTATG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 32 0.56
24 25 0.44
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:215259 original size:13 final size:13
Alignment explanation
Indices: 215259--215302 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
215249 CCGTTGACCC
215259 GACCCGACCCGTT
1 GACCCGACCCGTT
*
215272 TACCCGACCCGTT
1 GACCCGACCCGTT
*
215285 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
215300 GAC
1 GAC
215303 TGTTGACCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.16, C:0.41, G:0.23, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:215260 original size:18 final size:18
Alignment explanation
Indices: 215237--215282 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
215227 ACCGGTCACA
215237 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
215255 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
215273 ACCCGACCCG
1 ACCCGACCCG
215283 TTGACCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:215297 original size:15 final size:15
Alignment explanation
Indices: 215277--215310 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
215267 CCGTTTACCC
215277 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
215292 GACCCGTTGACTGTT
1 GACCCGTTGACCGTT
215307 GACC
1 GACC
215311 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.32, G:0.26, T:0.26
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:216628 original size:18 final size:18
Alignment explanation
Indices: 216602--216637 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
216592 TCGAAAGGAC
*
216602 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
216620 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
216638 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:217838 original size:24 final size:24
Alignment explanation
Indices: 217768--217857 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
217758 TCCGACTTGA
* *
217768 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
217791 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
217814 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
217838 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
217858 TTGAATTATG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 32 0.56
24 25 0.44
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:220040 original size:18 final size:17
Alignment explanation
Indices: 220002--220061 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 17
219992 ACCGGTCACA
220002 ACCCGACCCGACCGTTG
1 ACCCGACCCGACCGTTG
*
220019 ACCCGACCCGACCCGTTT
1 ACCCGACCCGA-CCGTTG
220037 ACCCGACCCGTTGACCGTTG
1 ACCCGACCC---GACCGTTG
220057 ACCCG
1 ACCCG
220062 TTGACTGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 11 0.30
18 14 0.38
20 10 0.27
21 2 0.05
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.15
Consensus pattern (17 bp):
ACCCGACCCGACCGTTG
Found at i:220042 original size:13 final size:13
Alignment explanation
Indices: 220024--220048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220014 CGTTGACCCG
220024 ACCCGACCCGTTT
1 ACCCGACCCGTTT
220037 ACCCGACCCGTT
1 ACCCGACCCGTT
220049 GACCGTTGAC
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:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:220061 original size:15 final size:15
Alignment explanation
Indices: 220041--220074 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
220031 CCGTTTACCC
220041 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
220056 GACCCGTTGACTGTT
1 GACCCGTTGACCGTT
220071 GACC
1 GACC
220075 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.32, G:0.26, T:0.26
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:221379 original size:18 final size:18
Alignment explanation
Indices: 221353--221388 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
221343 TCGAAAGGAC
*
221353 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
221371 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
221389 CGGATGGAAG
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:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:222581 original size:24 final size:24
Alignment explanation
Indices: 222511--222600 Score: 121
Period size: 23 Copynumber: 3.8 Consensus size: 24
222501 TCCGACTTGA
* *
222511 ATTCTGTTATGAT-CCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
222534 ATTCTGATATGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
222557 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
222581 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
222601 TTGAATTATG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 32 0.56
24 25 0.44
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:230313 original size:19 final size:19
Alignment explanation
Indices: 230277--230352 Score: 91
Period size: 19 Copynumber: 4.1 Consensus size: 19
230267 TCTGAATTAG
*
230277 AACTTATTTCCAG-TTCAT
1 AACTTATTTTCAGATTCAT
*
230295 AACTTATTTTCAGACTCAT
1 AACTTATTTTCAGATTCAT
* *
230314 AACTTACTGTCAGATTCAT
1 AACTTATTTTCAGATTCAT
* *
230333 ATCTTATTTTCAAATTCAT
1 AACTTATTTTCAGATTCAT
230352 A
1 A
230353 GCCTAATGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
18 12 0.25
19 36 0.75
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (19 bp):
AACTTATTTTCAGATTCAT
Found at i:244883 original size:15 final size:16
Alignment explanation
Indices: 244863--244894 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
244853 GGGTCATTAA
244863 AAATTATTTTA-GTTT
1 AAATTATTTTAGGTTT
244878 AAATTATTTTAGGTTT
1 AAATTATTTTAGGTTT
244894 A
1 A
244895 TTTTCCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
AAATTATTTTAGGTTT
Found at i:247998 original size:2 final size:2
Alignment explanation
Indices: 247991--248035 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
247981 ATCAGAAATT
247991 TA TA 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 TA TA TA
248032 TA TA
1 TA TA
248036 AAGTTTACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:248298 original size:2 final size:2
Alignment explanation
Indices: 248287--248315 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
248277 AATATTAAAA
248287 AT AT -T 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
248316 TTAAAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:258911 original size:34 final size:34
Alignment explanation
Indices: 258873--258942 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
258863 AGTCAATATA
258873 CATCCAAGTTATTAAATTATTAAACATGAATTAG
1 CATCCAAGTTATTAAATTATTAAACATGAATTAG
*
258907 CATCCAAGTTATTAAATTATTAAACATGCATTAG
1 CATCCAAGTTATTAAATTATTAAACATGAATTAG
258941 CA
1 CA
258943 GCGACTATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (34 bp):
CATCCAAGTTATTAAATTATTAAACATGAATTAG
Found at i:268995 original size:32 final size:32
Alignment explanation
Indices: 268936--268997 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
268926 AATTTCCTTT
** *
268936 ACGCTAAATCATAATAATTTTTTTTTAATAAA
1 ACGCTAAATCATAATAAACTTTGTTTAATAAA
268968 ACGCTAAATCATAATAAACTTTGTTTAATA
1 ACGCTAAATCATAATAAACTTTGTTTAATA
268998 TATATTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (32 bp):
ACGCTAAATCATAATAAACTTTGTTTAATAAA
Found at i:270253 original size:15 final size:15
Alignment explanation
Indices: 270227--270264 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
270217 TAATTTTACG
270227 TTAAATTTTT-TAAAA
1 TTAAATTTTTAT-AAA
270242 TTTAAATTTTTATAAA
1 -TTAAATTTTTATAAA
270258 TTAAATT
1 TTAAATT
270265 AATATGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 13 0.62
17 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAATTTTTATAAA
Found at i:270258 original size:16 final size:15
Alignment explanation
Indices: 270227--270264 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
270217 TAATTTTACG
270227 TTAAATTTTTTAAAA
1 TTAAATTTTTTAAAA
270242 TTTAAA-TTTTTATAAA
1 -TTAAATTTTTTA-AAA
270258 TTAAATT
1 TTAAATT
270265 AATATGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAATTTTTTAAAA
Found at i:270681 original size:16 final size:17
Alignment explanation
Indices: 270646--270687 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
270636 TATTTTATGT
270646 ATTAAAATTGATAAACA
1 ATTAAAATTGATAAACA
*
270663 ATTAAAATT-ATATACA
1 ATTAAAATTGATAAACA
270679 ATTCAAAAT
1 ATT-AAAAT
270688 CAACTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (17 bp):
ATTAAAATTGATAAACA
Found at i:273055 original size:21 final size:20
Alignment explanation
Indices: 273008--273062 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
272998 ACTGATTCAA
*
273008 GAGGTATCGATACCGAAAGG
1 GAGGTATCGATACCAAAAGG
273028 G-GGTATCGATACCAAAAGG
1 GAGGTATCGATACCAAAAGG
273047 GAAGGTATCGATACCA
1 G-AGGTATCGATACCA
273063 TTGATAACAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 18 0.56
20 1 0.03
21 13 0.41
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.16
Consensus pattern (20 bp):
GAGGTATCGATACCAAAAGG
Found at i:273494 original size:63 final size:62
Alignment explanation
Indices: 273401--273607 Score: 204
Period size: 63 Copynumber: 3.3 Consensus size: 62
273391 TTTTCAAAGG
*
273401 CATGCATCGATGCATCAATCCATGCATCGATGCAC-T-GATGAATA-AATTTAACATCGAATGCA
1 CATGCACCGATGCAT--ATCCATGCATCGATGCACTTGGAT-AATAGAA---AACATCGAATGCA
273463 TTT
60 TTT
**
273466 CATGCACCGATGCATATCCATGCATCGATGCACTTGGATTTTAGGAAAACATCGAATGCATTT
1 CATGCACCGATGCATATCCATGCATCGATGCACTTGGATAATA-GAAAACATCGAATGCATTT
* ** * * ***
273529 GATGCACCGATGCATATCCATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCATATCCATGCATCGATGCACTTGGATA-ATAGAAAACATCGAATGCATTT
* *
273592 TATGCATCGATGCATA
1 CATGCACCGATGCATA
273608 CTTAGTGCAC
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
63 100 0.81
64 5 0.04
65 17 0.14
66 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (62 bp):
CATGCACCGATGCATATCCATGCATCGATGCACTTGGATAATAGAAAACATCGAATGCATTT
Found at i:279267 original size:24 final size:22
Alignment explanation
Indices: 279239--279319 Score: 85
Period size: 24 Copynumber: 3.6 Consensus size: 22
279229 CATTTAACAA
279239 TGCATCGATGCATCCCTTTGAAT
1 TGCATCGATGCATCCC-TTGAAT
*
279262 GTGCATCGATGCATCCACATG-A-
1 -TGCATCGATGCATCC-CTTGAAT
* *
279284 TGCACCGATGCATGCCTTGAAT
1 TGCATCGATGCATCCCTTGAAT
279306 ATGCATCGATGCAT
1 -TGCATCGATGCAT
279320 AAGACCATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.06
21 14 0.29
23 13 0.27
24 17 0.35
25 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCCTTGAAT
Found at i:279274 original size:44 final size:42
Alignment explanation
Indices: 279218--279341 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 42
279208 TTTGTGCTTA
* * *
279218 ATGCACCGATGCATTTAACAATGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATGCA-TAAACAATGCACCGATGCATCCC-TTGAAT
* ** *
279262 GTGCATCGATGCATCCACATGATGCACCGATGCATGCCTTGAAT
1 ATGCATCGATGCATAAACA--ATGCACCGATGCATCCCTTGAAT
*
279306 ATGCATCGATGCATAAGACCATGCACCGATGCATCC
1 ATGCATCGATGCATAA-ACAATGCACCGATGCATCC
279342 GTCGGGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
43 19 0.29
44 30 0.45
45 17 0.26
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCATCGATGCATAAACAATGCACCGATGCATCCCTTGAAT
Found at i:281959 original size:63 final size:61
Alignment explanation
Indices: 281864--282070 Score: 202
Period size: 63 Copynumber: 3.3 Consensus size: 61
281854 TTTTCAAAGG
*
281864 CATGCACCGATGCATCAATCCATGCACCGATGCACTGATGAATAAATT-G-AACATCGAATGCAT
1 CATGCACCGATGCAT--ATCCATGCATCGATGCACT--TGAAT--ATTAGAAACATCGAATGCAT
281927 TT
60 TT
* *
281929 CATGCACCGATGCATATCCATGCATCGATGCACTTGGATTTTAGGAAAACATCGAATGCATTT
1 CATGCACCGATGCATATCCATGCATCGATGCACTTGAATATTA-G-AAACATCGAATGCATTT
* ** * * **
281992 GATGCACCGATGCATATCCATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCATATCCATGCATCGATGCA-CTTG-AATATTAGAAACATCGAATGCATTT
* *
282055 TATGCATCGATGCATA
1 CATGCACCGATGCATA
282071 CTTAGTGCAC
Statistics
Matches: 125, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
59 2 0.02
61 5 0.04
63 96 0.77
64 2 0.02
65 20 0.16
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (61 bp):
CATGCACCGATGCATATCCATGCATCGATGCACTTGAATATTAGAAACATCGAATGCATTT
Found at i:291731 original size:52 final size:50
Alignment explanation
Indices: 291656--291758 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 50
291646 TGCAGTAAAA
291656 GATAAAGGAGGAGAAAATATGAGCAGACCTCTGATGCATATCCCGGAGTT
1 GATAAAGGAGGAGAAAATATGAGCAGACCTCTGATGCATATCCCGGAGTT
291706 GATAAAGGAGGAGAGAAAATATGAGCAGACCTCTGATGCATATCCCGGAGTT
1 GATAAAGGA-G-GAGAAAATATGAGCAGACCTCTGATGCATATCCCGGAGTT
291758 G
1 G
291759 TACCAGCAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 9 0.18
51 1 0.02
52 41 0.80
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (50 bp):
GATAAAGGAGGAGAAAATATGAGCAGACCTCTGATGCATATCCCGGAGTT
Found at i:304629 original size:60 final size:60
Alignment explanation
Indices: 304536--304702 Score: 171
Period size: 60 Copynumber: 2.8 Consensus size: 60
304526 ACATACACAT
* *
304536 AATTT-AGGAT-AAAATTGAAATATTCAAAAAGTTTAGGGACTAGTTTAGAATGAATA-TCAC
1 AATTTAAGGATGAAAA-TGAAATGTTC-AAAAGTTTAGGGACTAATTTAGAAT-AATAGTCAC
* * *
304596 AATTTGTA-GATGAAAATGAAATGTTCAAAAGTTTAAGGACTAATTTAGAATAATAGTCAT
1 AATTT-AAGGATGAAAATGAAATGTTCAAAAGTTTAGGGACTAATTTAGAATAATAGTCAC
** * * * *
304656 TGTTTAAGGATGAAATTAAAATGTTTAAAAGTTTAGGGACCAATTTA
1 AATTTAAGGATGAAAATGAAATGTTCAAAAGTTTAGGGACTAATTTA
304703 AAATGAGAGT
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
59 5 0.06
60 68 0.76
61 12 0.13
62 5 0.06
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (60 bp):
AATTTAAGGATGAAAATGAAATGTTCAAAAGTTTAGGGACTAATTTAGAATAATAGTCAC
Found at i:304726 original size:60 final size:60
Alignment explanation
Indices: 304604--304727 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 60
304594 ACAATTTGTA
* * * * * *
304604 GATGAAAATGAAATGTTCAAAAGTTTAAGGACTAATTTAGAATAATAGTCATTGTTTAAG
1 GATGAAAATAAAATGTTCAAAAGTTTAAGGACCAATTTAAAATAAGAGTCATAGATTAAG
* * * * *
304664 GATGAAATTAAAATGTTTAAAAGTTTAGGGACCAATTTAAAATGAGAGTCATAGATTGAG
1 GATGAAAATAAAATGTTCAAAAGTTTAAGGACCAATTTAAAATAAGAGTCATAGATTAAG
304724 GATG
1 GATG
304728 TATGATGTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (60 bp):
GATGAAAATAAAATGTTCAAAAGTTTAAGGACCAATTTAAAATAAGAGTCATAGATTAAG
Found at i:305106 original size:20 final size:20
Alignment explanation
Indices: 305068--305106 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
305058 TTATCATACC
* * *
305068 AATTTTTCTCAATTTCTCTA
1 AATTTCTCTCAAATACTCTA
305088 AATTTCTCTCAAATACTCT
1 AATTTCTCTCAAATACTCT
305107 CTTTTTAAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTCTCTCAAATACTCTA
Found at i:307453 original size:26 final size:24
Alignment explanation
Indices: 307381--307453 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
307371 TTATATTTGT
307381 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
307406 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
307429 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
307454 GTTGACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:330243 original size:16 final size:16
Alignment explanation
Indices: 330219--330251 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
330209 TATCGCCGAC
*
330219 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
330235 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
330251 C
1 C
330252 ATGAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:334881 original size:83 final size:84
Alignment explanation
Indices: 334772--335093 Score: 414
Period size: 83 Copynumber: 3.9 Consensus size: 84
334762 AAAATATATG
* *
334772 TTTAATATT-TAAATTTAAACA-CTATTATTATCTATTTAAATTTAGATATTAAAAGAGTTTT-G
1 TTTAATATTATAAATTTAAA-AGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTAG
334834 ATTGAAGTAAAACTCCT-AGA
65 -TTGAAGTAAAACTCCTCAGA
* * * * *
334854 TTTAATATCATAAATTTAAAAGATATTATAATTTGTTTAAATTTATATATTAAAAGAGTTTTCGT
1 TTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTAGT
*
334919 TGGAGTAAAACT-CTCAGA
66 TGAAGTAAAACTCCTCAGA
*
334937 TTTATTATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTAGT
1 TTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTAGT
*
335002 T-AGAGAAAAAC-CCTCAGA
66 TGA-AGTAAAACTCCTCAGA
* * *
335020 TTTAATATTGTAAATTTAAAAGATATTATTATCTA-TT---TTTATATATTAAAAGAGTTTTAGT
1 TTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTAGT
*
335081 TGGAGTAAAACTC
66 TGAAGTAAAACTC
335094 TCTCGAAATT
Statistics
Matches: 211, Mismatches: 21, Indels: 18
0.84 0.08 0.07
Matches are distributed among these distances:
79 31 0.15
80 1 0.00
82 13 0.06
83 165 0.78
84 1 0.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.43
Consensus pattern (84 bp):
TTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTAGT
TGAAGTAAAACTCCTCAGA
Found at i:341630 original size:2 final size:2
Alignment explanation
Indices: 341623--341648 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
341613 CACCTCCCTC
341623 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
341649 CTGAATGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:343440 original size:2 final size:2
Alignment explanation
Indices: 343435--343463 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
343425 TTTGTGTGTT
343435 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 T
343464 CAAATAAGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:347870 original size:29 final size:29
Alignment explanation
Indices: 347825--347881 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
347815 ATTTTGAATG
* *
347825 TGGTAGTAAAATGAAACAAAAACTAAACA
1 TGGTACTAAAATAAAACAAAAACTAAACA
*
347854 TGGTACTAAAATAAAACAAAAGCTAAAC
1 TGGTACTAAAATAAAACAAAAACTAAAC
347882 TTTAGGTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (29 bp):
TGGTACTAAAATAAAACAAAAACTAAACA
Found at i:348930 original size:23 final size:23
Alignment explanation
Indices: 348903--348949 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
348893 GTGATTGAGC
348903 AAGAAAGCTCTTGAGATTGCACA
1 AAGAAAGCTCTTGAGATTGCACA
348926 AAGAAAGCTCTTGAGATTGCACA
1 AAGAAAGCTCTTGAGATTGCACA
348949 A
1 A
348950 CTCCTTACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (23 bp):
AAGAAAGCTCTTGAGATTGCACA
Found at i:354117 original size:61 final size:60
Alignment explanation
Indices: 354040--354181 Score: 196
Period size: 61 Copynumber: 2.4 Consensus size: 60
354030 CTTTATTAAG
* ** *
354040 TCTCTCGACTATTAAAAGTTACATAATGTTCCTCTGCCTATAGAAGGTTGTTTTGTTGAAAA
1 TCTCTCGACTATTAAAAGTTACAAAATGAGCCTCTGACTATAGAAGGTTGTTTTGTTG--AA
* * *
354102 T-TCTCGACTATTAAAAGTTAGAAAATGAGCCTCTGACTATAGAATGTTGTTTTGTTGAG
1 TCTCTCGACTATTAAAAGTTACAAAATGAGCCTCTGACTATAGAAGGTTGTTTTGTTGAA
354161 TCTCTCGACTATTAAAAGTTA
1 TCTCTCGACTATTAAAAGTTA
354182 TAGAATTGTC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
59 2 0.03
60 19 0.26
61 50 0.69
62 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (60 bp):
TCTCTCGACTATTAAAAGTTACAAAATGAGCCTCTGACTATAGAAGGTTGTTTTGTTGAA
Found at i:354531 original size:60 final size:59
Alignment explanation
Indices: 354409--354540 Score: 131
Period size: 60 Copynumber: 2.2 Consensus size: 59
354399 CGTGTAACCA
* * * ** *
354409 ATTTGTAACTTTTAATAGTCGAAAGACTTAACAAAACAATATTTTATAATCGAATGATT
1 ATTTATAACTTTTAATAGTCAAAAAACTTAACAAAACAATACCTTATAATCGAATGACT
* ** * *
354468 ATTTTATAACTTTTAATAGTTAAAAAACTTATTAAAATAATACCTTATAATCG-GTGAACT
1 A-TTTATAACTTTTAATAGTCAAAAAACTTAACAAAACAATACCTTATAATCGAATG-ACT
354528 ATTTATATACTTT
1 ATTTATA-ACTTT
354541 ATCCTAGAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
59 9 0.15
60 50 0.85
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.41
Consensus pattern (59 bp):
ATTTATAACTTTTAATAGTCAAAAAACTTAACAAAACAATACCTTATAATCGAATGACT
Found at i:360643 original size:19 final size:18
Alignment explanation
Indices: 360619--360696 Score: 54
Period size: 19 Copynumber: 4.3 Consensus size: 18
360609 AAATATGGAC
360619 TTAAATAATTTTCAACAAT
1 TTAAATAA-TTTCAACAAT
* *
360638 TTAAAT-ATTTAAATAATT
1 TTAAATAATTTCAACAA-T
* *
360656 TTCAACAATTT-AA-ATAT
1 TTAAATAATTTCAACA-AT
*
360673 TTAAATAATTTTCAACGAT
1 TTAAATAA-TTTCAACAAT
360692 TTAAA
1 TTAAA
360697 CAGTGTATGA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
17 15 0.33
18 12 0.26
19 19 0.41
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (18 bp):
TTAAATAATTTCAACAAT
Found at i:360651 original size:27 final size:27
Alignment explanation
Indices: 360619--360696 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
360609 AAATATGGAC
360619 TTAAATAATTTTCAACAATTTAAATAT
1 TTAAATAATTTTCAACAATTTAAATAT
360646 TTAAATAATTTTCAACAATTTAAATAT
1 TTAAATAATTTTCAACAATTTAAATAT
*
360673 TTAAATAATTTTCAACGATTTAAA
1 TTAAATAATTTTCAACAATTTAAA
360697 CAGTGTATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (27 bp):
TTAAATAATTTTCAACAATTTAAATAT
Found at i:360974 original size:30 final size:30
Alignment explanation
Indices: 360918--360976 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
360908 GTTTGTTTTG
* * *
360918 AAAGTTTAGGGGCTAAAGTATAAATTTGTA
1 AAAGTTTAGGGCCAAAAATATAAATTTGTA
*
360948 AAAGTTTAGGGACCAAAAATATAATTTTG
1 AAAGTTTAGGG-CCAAAAATATAAATTTG
360977 AAAGGTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.32
Consensus pattern (30 bp):
AAAGTTTAGGGCCAAAAATATAAATTTGTA
Found at i:363468 original size:236 final size:234
Alignment explanation
Indices: 362998--363468 Score: 807
Period size: 236 Copynumber: 2.0 Consensus size: 234
362988 TATTCATTTG
362998 GTAAGCTTATAGAATTATGGAATGAGTTAAGGATGCTAATAAAGAAAGTTGTCCAGAAATTTTGA
1 GTAAGCTTATAGAATTATGGAATGAGTTAAGGATGCTAATAAAGAAAGTTGTCCAGAAATTTTGA
*
363063 TTCGAACAGTGAGTTTAGAAATTTACTATAAATATGAAGAATTGATTAGAGGGTGATTTATATTG
66 TTCGAACAGTGAGTTTAGAAATTTACTATAAATATGAAGAATTGATTAGAGGGTGATTTATATCG
* *
363128 TTGGATTTGTATGTCAGTCTAGTTTTATTTACAACAGACAACTATTGATTTTGATCTGTATACGA
131 TTGGATTCGTATGTCAGTCTAGTTTTATTTACAACAGACAACTACTGATTTTGATCTGTATACGA
** ** * *
363193 AAAGATATTAAATTTTAATCGAGAATAGATCATAAAACA
196 AAAGATAAAAAAAATTAATCGAGAATAGATAAGAAAACA
* *
363232 GTAAGCTTATAGAATTATGGAATTAGTTAAGGATGCTAATAAAGAAAGTTGTCTAGAAATTTTGA
1 GTAAGCTTATAGAATTATGGAATGAGTTAAGGATGCTAATAAAGAAAGTTGTCCAGAAATTTTGA
363297 TTCGAACAGTGAGTTTAGAAATTTACTATAAATTATGAAGAATTGATTAGAGGGTGATTTTATAT
66 TTCGAACAGTGAGTTTAGAAATTTACTATAAA-TATGAAGAATTGATTAGAGGGTGA-TTTATAT
* *
363362 CGTTGGATTCGTATGTCAGTCTAGTTTTATTTACAATAGACAACTACTGATTTTGATGTGTATAC
129 CGTTGGATTCGTATGTCAGTCTAGTTTTATTTACAACAGACAACTACTGATTTTGATCTGTATAC
363427 GAAAAGATAAAAAAAATTAATCGAGAATAGATAAGAAAACA
194 GAAAAGATAAAAAAAATTAATCGAGAATAGATAAGAAAACA
363468 G
1 G
363469 GACAACAAAT
Statistics
Matches: 222, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
234 95 0.43
235 24 0.11
236 103 0.46
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (234 bp):
GTAAGCTTATAGAATTATGGAATGAGTTAAGGATGCTAATAAAGAAAGTTGTCCAGAAATTTTGA
TTCGAACAGTGAGTTTAGAAATTTACTATAAATATGAAGAATTGATTAGAGGGTGATTTATATCG
TTGGATTCGTATGTCAGTCTAGTTTTATTTACAACAGACAACTACTGATTTTGATCTGTATACGA
AAAGATAAAAAAAATTAATCGAGAATAGATAAGAAAACA
Found at i:366381 original size:13 final size:13
Alignment explanation
Indices: 366363--366399 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
366353 GATTTCAGTT
366363 CCACTCTTTTTAG
1 CCACTCTTTTTAG
366376 CCACTCTTTTTAG
1 CCACTCTTTTTAG
366389 CCACTCTTTTT
1 CCACTCTTTTT
366400 TATATAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.14, C:0.32, G:0.05, T:0.49
Consensus pattern (13 bp):
CCACTCTTTTTAG
Found at i:381639 original size:15 final size:16
Alignment explanation
Indices: 381614--381645 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
381604 ACTGGTTATC
381614 AAATGCGATTTAATAA
1 AAATGCGATTTAATAA
381630 AAAT-CGATTTAATAA
1 AAATGCGATTTAATAA
381645 A
1 A
381646 CTGGGAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.31
Consensus pattern (16 bp):
AAATGCGATTTAATAA
Found at i:383144 original size:27 final size:27
Alignment explanation
Indices: 383110--383176 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
383100 AATAATGACT
* * *
383110 CTGAATCATTCATAATGTATTTCTGTG
1 CTGAATCATTCAGAATGTATTTATGTA
383137 CTGAATCATTCAGAATGTATTTATGTA
1 CTGAATCATTCAGAATGTATTTATGTA
383164 CTGAATCATTCAG
1 CTGAATCATTCAG
383177 CACTGTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTATTTATGTA
Found at i:383643 original size:26 final size:26
Alignment explanation
Indices: 383614--383696 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 26
383604 ATGTTTTATA
* *
383614 TTTAATTTTATATTATAGATATTAAT
1 TTTAATATTATATTATAAATATTAAT
* *
383640 TTTAA-ATTA-AATAT-TA-ATT--T
1 TTTAATATTATATTATAAATATTAAT
383660 TTTAATATTATATTATAAATATTAAT
1 TTTAATATTATATTATAAATATTAAT
383686 TTTAATATTAT
1 TTTAATATTAT
383697 TGTTTTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 6 0.13
21 4 0.09
22 7 0.15
23 2 0.04
24 7 0.15
25 3 0.07
26 17 0.37
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (26 bp):
TTTAATATTATATTATAAATATTAAT
Found at i:383655 original size:18 final size:20
Alignment explanation
Indices: 383615--383660 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
383605 TGTTTTATAT
*
383615 TTAATTTTATATTATAGATA
1 TTAATTTTAAATTATAGATA
383635 TTAATTTTAAATTA-A-ATA
1 TTAATTTTAAATTATAGATA
383653 TTAATTTT
1 TTAATTTT
383661 TTAATATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTAATTTTAAATTATAGATA
Found at i:383668 original size:14 final size:14
Alignment explanation
Indices: 383649--383733 Score: 51
Period size: 14 Copynumber: 6.5 Consensus size: 14
383639 TTTTAAATTA
383649 AATATTAATTTTTT
1 AATATTAATTTTTT
* *
383663 AATATT-ATATTATA
1 AATATTAAT-TTTTT
383677 AATATTAA--TTTT
1 AATATTAATTTTTT
*
383689 AATATTATTGTTTTT
1 AATATTAAT-TTTTT
* *
383704 AA-A-TAA--ATTA
1 AATATTAATTTTTT
383714 AATATT-ATTTTTT
1 AATATTAATTTTTT
383727 AATATTA
1 AATATTA
383734 TATTATAGAT
Statistics
Matches: 51, Mismatches: 10, Indels: 20
0.63 0.12 0.25
Matches are distributed among these distances:
10 4 0.08
11 2 0.04
12 10 0.20
13 12 0.24
14 16 0.31
15 7 0.14
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (14 bp):
AATATTAATTTTTT
Found at i:383799 original size:20 final size:20
Alignment explanation
Indices: 383768--383823 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
383758 CATATAAATT
383768 ATTTTATA--TATTATTAA-A
1 ATTTTATATTTATT-TTAATA
*
383786 ATTTTATATTTATTTTAATT
1 ATTTTATATTTATTTTAATA
383806 ATTTTA-ATTTAATTTTAA
1 ATTTTATATTT-ATTTTAA
383824 ATATAATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.24
19 8 0.24
20 17 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTATATTTATTTTAATA
Found at i:384111 original size:25 final size:25
Alignment explanation
Indices: 384047--384116 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
384037 AAATATTTTC
*
384047 TAAAAATATCATATAATTATAAAAA
1 TAAAAATATTATATAATTATAAAAA
* * *
384072 TAAATTATGAATATATATTTA-AAAAA
1 TAAA-AAT-ATTATATAATTATAAAAA
384098 TTAAAAATATTATATAATT
1 -TAAAAATATTATATAATT
384117 GCATATTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
25 13 0.37
26 9 0.26
27 13 0.37
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (25 bp):
TAAAAATATTATATAATTATAAAAA
Found at i:384458 original size:31 final size:31
Alignment explanation
Indices: 384423--384482 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
384413 TAGTTGTATG
* *
384423 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
384454 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
384483 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:384634 original size:23 final size:23
Alignment explanation
Indices: 384604--384653 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
384594 TCTTCTACTA
384604 CAGATGCCTACAGATGTAATCCG
1 CAGATGCCTACAGATGTAATCCG
* * *
384627 CAGATGCCTGCATATGTAATTCG
1 CAGATGCCTACAGATGTAATCCG
384650 CAGA
1 CAGA
384654 CTGTAAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
CAGATGCCTACAGATGTAATCCG
Found at i:384721 original size:18 final size:18
Alignment explanation
Indices: 384698--384752 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
384688 TAGTGCTGAA
384698 ATTCCAACTTCTCTCACT
1 ATTCCAACTTCTCTCACT
384716 ATTCCAACTTCTC-C-C-
1 ATTCCAACTTCTCTCACT
384731 A---CAACTTCTCTCACT
1 ATTCCAACTTCTCTCACT
384746 ATTCCAA
1 ATTCCAA
384753 GATTTGGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
12 9 0.29
13 1 0.03
14 1 0.03
15 2 0.06
16 1 0.03
17 1 0.03
18 16 0.52
ACGTcount: A:0.25, C:0.40, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTCCAACTTCTCTCACT
Found at i:386083 original size:44 final size:44
Alignment explanation
Indices: 386019--386156 Score: 161
Period size: 44 Copynumber: 3.0 Consensus size: 44
386009 CACTTAACAC
*
386019 ATACTTACACCGGTGTAAGTGAATAAAACAAAAAAGTGTAGCACT
1 ATAC-TACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACT
* *
386064 ATACTACAACGGTGTAAGTGAATAAAATAAAAAAGTGTAGTACTTAACAC
1 ATACTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAG--C---AC-T
* *
386114 ATATTACACCGGTATAAGTGAATAAAATAAAAAA-TGTAGCACT
1 ATACTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACT
386157 TAACACATAC
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
44 36 0.45
45 4 0.05
46 1 0.01
47 1 0.01
49 7 0.09
50 31 0.39
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (44 bp):
ATACTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACT
Found at i:386134 original size:50 final size:51
Alignment explanation
Indices: 385997--386226 Score: 298
Period size: 50 Copynumber: 4.7 Consensus size: 51
385987 TTCATACTAC
*
385997 AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAC
1 AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* *
386048 AAAAAAGTGTAGCAC-T-----ATAC-TACAACGGTGTAAGTGAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * *
386092 AAAAAAGTGTAGTACTTAACACATA-TTACACCGGTATAAGTGAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
** *
386142 -AAAAAATGTAGCACTTAACACATACTTACAATGGTGTAAGTAAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
*
386192 AAAAAATATATAGCACTTAACACATACTTACACCG
1 AAAAAA-ATGTAGCACTTAACACATACTTACACCG
386227 ACGTAAGTAT
Statistics
Matches: 154, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
44 36 0.23
45 5 0.03
49 22 0.14
50 47 0.31
51 19 0.12
52 25 0.16
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (51 bp):
AAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
Found at i:386459 original size:71 final size:71
Alignment explanation
Indices: 386323--386469 Score: 167
Period size: 71 Copynumber: 2.1 Consensus size: 71
386313 AGAAACAAAA
* * *
386323 AAATTAAAAATAATAAAAAATATATATTAAGTTATTTGTATATAAATTTTATTAAATATACATAT
1 AAATTAAAAATAATAAAAAATATATATTAAGTTATTTGTATATAAATTATAATAAATATAAATAT
386388 AAATTAT
66 -AATTAT
* * *
386395 AAATTATAAATAAT-AGAAATTTATATTAAGTTATTTACGTA-A-AAA-TATAATAAATTATAAA
1 AAATTAAAAATAATAAAAAATATATATTAAGTTATTT--GTATATAAATTATAATAAA-TATAAA
*
386456 TATAGTTAT
63 TATAATTAT
386465 AAATT
1 AAATT
386470 TAATTTTTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
70 17 0.26
71 31 0.48
72 14 0.22
73 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (71 bp):
AAATTAAAAATAATAAAAAATATATATTAAGTTATTTGTATATAAATTATAATAAATATAAATAT
AATTAT
Found at i:386687 original size:24 final size:24
Alignment explanation
Indices: 386633--386688 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
386623 CCAATCACCA
*
386633 ACAAAACCTAAGAACAACCTACTT
1 ACAAAATCTAAGAACAACCTACTT
386657 ACAAAATCTAAGAACAACCTACTT
1 ACAAAATCTAAGAACAACCTACTT
386681 ACAAAATC
1 ACAAAATC
386689 AATTGATCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.52, C:0.27, G:0.04, T:0.18
Consensus pattern (24 bp):
ACAAAATCTAAGAACAACCTACTT
Found at i:392615 original size:27 final size:25
Alignment explanation
Indices: 392553--392627 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
392543 TATCTATATA
** *
392553 TAACTTAAAAAATAT-TTTTATATGT
1 TAACTTATTAAATATATTTTAT-TAT
392578 TAACTTATTAAATATATTTTATTAT
1 TAACTTATTAAATATATTTTATTAT
*
392603 TAACTTTATTTAAAAATATTTTATT
1 TAAC-TTA-TTAAATATATTTTATT
392628 TTTATTTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.44
26 9 0.21
27 15 0.35
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (25 bp):
TAACTTATTAAATATATTTTATTAT
Found at i:392640 original size:27 final size:26
Alignment explanation
Indices: 392585--392661 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 26
392575 TGTTAACTTA
* * *
392585 TTAAATATATTTTATTATTAACTTTAT
1 TTAAAAATATTTTATT-TTTATTTTAT
392612 TTAAAAATATTTTATTTTTATTTTCAT
1 TTAAAAATATTTTATTTTTATTTT-AT
*
392639 TTAAAAATA-TATA-TTTTATTTTA
1 TTAAAAATATTTTATTTTTATTTTA
392662 AAATTTATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
24 1 0.02
25 9 0.20
26 9 0.20
27 26 0.58
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (26 bp):
TTAAAAATATTTTATTTTTATTTTAT
Found at i:392672 original size:31 final size:29
Alignment explanation
Indices: 392587--392675 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 29
392577 TTAACTTATT
*
392587 AAATATATTTTATTATTAACTTTATTT--A
1 AAATATATTTTATT-TTAAATTTATTTAAA
* *
392615 AAA-ATATTTTATTTTTATTTTCATTTAAA
1 AAATATATTTTATTTTAAATTT-ATTTAAA
392644 AATATATATTTTATTTTAAAATTTATTTAAA
1 AA-ATATATTTTATTTT-AAATTTATTTAAA
392675 A
1 A
392676 GTTTTATTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
26 6 0.12
27 14 0.27
28 3 0.06
29 3 0.06
30 1 0.02
31 20 0.39
32 4 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
AAATATATTTTATTTTAAATTTATTTAAA
Found at i:396648 original size:35 final size:34
Alignment explanation
Indices: 396563--396649 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
396553 AATATAATTT
*
396563 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
396597 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
396635 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
396650 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:398970 original size:17 final size:18
Alignment explanation
Indices: 398950--398990 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
398940 AAATTATATT
398950 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
398967 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
398985 ATTAAA
1 AGTAAA
398991 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:403993 original size:51 final size:51
Alignment explanation
Indices: 403928--404025 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
403918 CGAATGAAAA
* * *
403928 TATGGTTACCGAAGATAAGCCAATGCAAACAGATCATGTAAAAGGTGGAAG
1 TATGGTTACAGAAGATAAGCCAATGCAAACAGATAATGCAAAAGGTGGAAG
* * *
403979 TATGGTTACAGAAGATAAGTCAATGCAAATAGGTAATGCAAAAGGTG
1 TATGGTTACAGAAGATAAGCCAATGCAAACAGATAATGCAAAAGGTG
404026 ATGAAGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (51 bp):
TATGGTTACAGAAGATAAGCCAATGCAAACAGATAATGCAAAAGGTGGAAG
Found at i:407178 original size:29 final size:30
Alignment explanation
Indices: 407115--407179 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
407105 TACTAATAAT
* * *
407115 TATATTTTTTTCTGATTATAATATTGTACTT
1 TATATTTTTTTCTGATCAT-ATATTATACTA
407146 TATATTTTTTTCTGATCAT-TATTAATA-TA
1 TATATTTTTTTCTGATCATATATT-ATACTA
407175 TATAT
1 TATAT
407180 ATATATCGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 2 0.07
31 18 0.60
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (30 bp):
TATATTTTTTTCTGATCATATATTATACTA
Found at i:407181 original size:31 final size:29
Alignment explanation
Indices: 407108--407181 Score: 69
Period size: 31 Copynumber: 2.4 Consensus size: 29
407098 AGTTAAGTAC
*
407108 TAATA-ATTATATTTTTTTCTGATTATAA
1 TAATATATTATATTTTTTTCTGATCATAA
* * *
407136 TATTGTACTTTATATTTTTTTCTGATCATTAT
1 TAATATA--TTATATTTTTTTCTGATCA-TAA
407168 TAATATATATATAT
1 TAATATAT-TATAT
407182 ATATCGCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
28 3 0.09
29 1 0.03
30 1 0.03
31 23 0.66
32 7 0.20
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.58
Consensus pattern (29 bp):
TAATATATTATATTTTTTTCTGATCATAA
Found at i:407818 original size:10 final size:10
Alignment explanation
Indices: 407798--407836 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
407788 ATGTTGAGAA
407798 AAAAGAAAAGG
1 AAAA-AAAAGG
407809 AAAAAAAAGG
1 AAAAAAAAGG
*
407819 AAAAAAAGAAG
1 AAAAAAA-AGG
407830 AAAAAAA
1 AAAAAAA
407837 TGTTTTATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:411792 original size:12 final size:12
Alignment explanation
Indices: 411775--411799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
411765 GGTTGGATTC
411775 ATTTGTTTTTGG
1 ATTTGTTTTTGG
411787 ATTTGTTTTTGG
1 ATTTGTTTTTGG
411799 A
1 A
411800 ATTGAAACAG
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:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (12 bp):
ATTTGTTTTTGG
Found at i:420111 original size:13 final size:13
Alignment explanation
Indices: 420093--420120 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
420083 CATCGTTGAA
420093 CAGTCTTCATATG
1 CAGTCTTCATATG
420106 CAGTCTTCATATG
1 CAGTCTTCATATG
420119 CA
1 CA
420121 CGTATGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:421022 original size:20 final size:21
Alignment explanation
Indices: 420999--421042 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
420989 CTTAGGTTCT
420999 TGAAAC-AATCCTTTGAGGGG
1 TGAAACGAATCCTTTGAGGGG
**
421019 TG-AACGTGTCCTTTGAGGGG
1 TGAAACGAATCCTTTGAGGGG
421039 TGAA
1 TGAA
421043 CATGTCCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 3 0.15
20 16 0.80
21 1 0.05
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.27
Consensus pattern (21 bp):
TGAAACGAATCCTTTGAGGGG
Found at i:421043 original size:20 final size:20
Alignment explanation
Indices: 421007--421051 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
420997 CTTGAAACAA
*
421007 TCCTTTGAGGGGTGAACGTG
1 TCCTTTGAGGGGTGAACATG
421027 TCCTTTGAGGGGTGAACATG
1 TCCTTTGAGGGGTGAACATG
421047 TCCTT
1 TCCTT
421052 CGATGCATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (20 bp):
TCCTTTGAGGGGTGAACATG
Found at i:423908 original size:55 final size:57
Alignment explanation
Indices: 423828--424042 Score: 179
Period size: 56 Copynumber: 3.8 Consensus size: 57
423818 AAAAATAATA
*
423828 TTTTGATATATTACAATAAAGACCAAAAC-TTTTATAAATTACAAACAAATGCCAAAC
1 TTTTGATAAATTACAATAAAGACCAAAACTTTTTATAAATTAC-AACAAATGCCAAAC
* *
423885 TTTT-ATAAATTACAA-AAATACCAAAACTTTTTATAAATTACAACAAATGCCAAAAA
1 TTTTGATAAATTACAATAAAGACCAAAACTTTTTATAAATTACAACAAATGCC-AAAC
** * * * ** *** * **
423941 AATT-AAAAATTACTACAAATTCCAATTGTTTTTATAAATTACAACAAATTCCAATTG
1 TTTTGATAAATTACAATAAAGACCAAAACTTTTTATAAATTACAACAAATGCCAA-AC
* * * *
423998 TTTTTATAAATTACAATCAAAGA-AAAAACTTCTAATAAATTACAA
1 TTTTGATAAATTACAAT-AAAGACCAAAACTTTTTATAAATTACAA
424043 TAATGACTTG
Statistics
Matches: 125, Mismatches: 27, Indels: 11
0.77 0.17 0.07
Matches are distributed among these distances:
55 21 0.17
56 39 0.31
57 37 0.30
58 25 0.20
59 3 0.02
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (57 bp):
TTTTGATAAATTACAATAAAGACCAAAACTTTTTATAAATTACAACAAATGCCAAAC
Found at i:423923 original size:56 final size:56
Alignment explanation
Indices: 423828--423938 Score: 172
Period size: 55 Copynumber: 2.0 Consensus size: 56
423818 AAAAATAATA
*
423828 TTTTGATATATTACAATAAAGACCAAAACTTTTATAAATTACAAACAAATGCCAAAC
1 TTTTGATAAATTACAATAAAGACCAAAACTTTTATAAATTAC-AACAAATGCCAAAC
*
423885 TTTT-ATAAATTACAA-AAATACCAAAACTTTTTATAAATTACAACAAATGCCAAA
1 TTTTGATAAATTACAATAAAGACCAAAAC-TTTTATAAATTACAACAAATGCCAAA
423939 AAAATTAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
55 24 0.47
56 23 0.45
57 4 0.08
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (56 bp):
TTTTGATAAATTACAATAAAGACCAAAACTTTTATAAATTACAACAAATGCCAAAC
Found at i:423983 original size:57 final size:56
Alignment explanation
Indices: 423837--423994 Score: 176
Period size: 57 Copynumber: 2.8 Consensus size: 56
423827 ATTTTGATAT
* *** *
423837 ATTACAATAAAGACCAAAAC-TTTTATAAATTACAAACAAATGCC-AAACTTTTATAA
1 ATTACAA-AAATACCAAAACTTTTTATAAATTAC-AACAAATGCCAAAAAAATTAAAA
423893 ATTACAAAAATACCAAAACTTTTTATAAATTACAACAAATGCCAAAAAAATTAAAA
1 ATTACAAAAATACCAAAACTTTTTATAAATTACAACAAATGCCAAAAAAATTAAAA
* * *** *
423949 ATTACTACAAATTCCAATTGTTTTTATAAATTACAACAAATTCCAA
1 ATTAC-AAAAATACCAAAACTTTTTATAAATTACAACAAATGCCAA
423995 TTGTTTTTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
55 21 0.24
56 33 0.38
57 34 0.39
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.30
Consensus pattern (56 bp):
ATTACAAAAATACCAAAACTTTTTATAAATTACAACAAATGCCAAAAAAATTAAAA
Found at i:423987 original size:29 final size:28
Alignment explanation
Indices: 423827--424018 Score: 156
Period size: 28 Copynumber: 6.8 Consensus size: 28
423817 TAAAAATAAT
* * *
423827 ATTTTGATATATTACAATAAA-GACCAAA
1 ATTTTTATAAATTACAACAAATG-CCAAA
*
423855 ACTTTTATAAATTACAAACAAATGCC-AA
1 ATTTTTATAAATTAC-AACAAATGCCAAA
* *
423883 ACTTTTATAAATTACAA-AAATACCAAA
1 ATTTTTATAAATTACAACAAATGCCAAA
423910 ACTTTTTATAAATTACAACAAATGCCAAA
1 A-TTTTTATAAATTACAACAAATGCCAAA
*** * * * *
423939 AAAATTAAAAATTACTACAAATTCCAATT
1 ATTTTTATAAATTACAACAAATGCCAA-A
* * *
423968 GTTTTTATAAATTACAACAAATTCCAATT
1 ATTTTTATAAATTACAACAAATGCCAA-A
*
423997 GTTTTTATAAATTACAATCAAA
1 ATTTTTATAAATTACAA-CAAA
424019 GAAAAAACTT
Statistics
Matches: 137, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
26 6 0.04
27 5 0.04
28 64 0.47
29 57 0.42
30 5 0.04
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.33
Consensus pattern (28 bp):
ATTTTTATAAATTACAACAAATGCCAAA
Found at i:438054 original size:17 final size:18
Alignment explanation
Indices: 438011--438061 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
438001 GGAATGTTTC
*
438011 TGAAGGAATTAGAATCTG
1 TGAAGGAATTGGAATCTG
438029 TGAAGGAATTGGAATCTG
1 TGAAGGAATTGGAATCTG
*
438047 T-CAGGAATTGGAATC
1 TGAAGGAATTGGAATC
438062 CAATTCCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.27
Consensus pattern (18 bp):
TGAAGGAATTGGAATCTG
Found at i:438131 original size:32 final size:27
Alignment explanation
Indices: 438071--438126 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
438061 CCAATTCCAT
438071 ATTCAGTTTGGTTGGCAGGAAATTGGA
1 ATTCAGTTTGGTTGGCAGGAAATTGGA
438098 ATTCAGTTTGGTTGGCAGGAAATT-GA
1 ATTCAGTTTGGTTGGCAGGAAATTGGA
438124 ATT
1 ATT
438127 GGAATCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.27, C:0.07, G:0.30, T:0.36
Consensus pattern (27 bp):
ATTCAGTTTGGTTGGCAGGAAATTGGA
Found at i:442700 original size:26 final size:26
Alignment explanation
Indices: 442671--442720 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
442661 ATATATACAC
*
442671 AAATAAATTTATAAAATTTGAAGAAA
1 AAATAAATTCATAAAATTTGAAGAAA
* *
442697 AAATGAATTCATAAAATTTTAAGA
1 AAATAAATTCATAAAATTTGAAGA
442721 TACATTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (26 bp):
AAATAAATTCATAAAATTTGAAGAAA
Found at i:447076 original size:46 final size:46
Alignment explanation
Indices: 447010--447118 Score: 146
Period size: 46 Copynumber: 2.3 Consensus size: 46
447000 TATAAATGAT
* *
447010 CGAAACCGACTCTAGTTGTTACACAGTCAAGAATTGCTAGAGGTGCC
1 CGAAACAG-CTCTAGTTGTTACACAGTCAAGAATCGCTAGAGGTGCC
** *
447057 CGAAACAGCTCTAGTTGTTATTCATTCAAGAATCGCTAGAGGTGCC
1 CGAAACAGCTCTAGTTGTTACACAGTCAAGAATCGCTAGAGGTGCC
*
447103 CGAAATCGGCTCTAGT
1 CGAAA-CAGCTCTAGT
447119 CAACAAAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 39 0.71
47 16 0.29
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (46 bp):
CGAAACAGCTCTAGTTGTTACACAGTCAAGAATCGCTAGAGGTGCC
Found at i:450923 original size:20 final size:19
Alignment explanation
Indices: 450884--450925 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
450874 GTAACTTCAA
*
450884 TCCATTTTCATTTCTTTAT
1 TCCATTTTCATTTATTTAT
*
450903 TCCATTCTTCCTTTATTTAT
1 TCCATT-TTCATTTATTTAT
450923 TCC
1 TCC
450926 TTATACACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (19 bp):
TCCATTTTCATTTATTTAT
Found at i:452990 original size:30 final size:30
Alignment explanation
Indices: 452922--453015 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
452912 GAAGGACCTA
* * *
452922 TCCAGAGGTCACAAAG-ACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCTCGGAAACTG
* *
452951 TCCAGAGGTCATAAAGAACCTCGGCAACTG
1 TCCAGAGGTCACAAAGAACCTCGGAAACTG
* * *
452981 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGAACCTCGG-AAACTG
453012 TCCA
1 TCCA
453016 TATGTTCCTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.28
30 30 0.56
31 9 0.17
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCTCGGAAACTG
Found at i:453030 original size:31 final size:31
Alignment explanation
Indices: 452976--453070 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 31
452966 GAACCTCGGC
* *
452976 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* ** *
453007 AACTGTCCATATGTTCCTTAGAACATATGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* * *
453038 TACTATCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
453069 AA
1 AA
453071 ACCCTCGACT
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
31 46 0.94
32 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:457964 original size:2 final size:2
Alignment explanation
Indices: 457957--457981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
457947 TATGTGTATG
457957 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 T
457982 GTATGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:457986 original size:4 final size:4
Alignment explanation
Indices: 457979--458036 Score: 80
Period size: 4 Copynumber: 14.5 Consensus size: 4
457969 TATATATATA
* * * *
457979 TATG TATG TGTG TATG CATG CATG TATG TATG CATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
458027 TATG TATG TA
1 TATG TATG TA
458037 GCTTTAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:458871 original size:15 final size:16
Alignment explanation
Indices: 458833--458873 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
458823 ACAGAGCCTC
*
458833 TGAATCATTCGGCATT
1 TGAATCATTCGGCACT
*
458849 TGAATCATTCGGCGCT
1 TGAATCATTCGGCACT
458865 T-AATCATTC
1 TGAATCATTC
458874 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (16 bp):
TGAATCATTCGGCACT
Found at i:477338 original size:28 final size:29
Alignment explanation
Indices: 477306--477377 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
477296 TTAACTTTTA
* *
477306 GTGCAATTAGGTA-ATTAACTTTT-TAATG
1 GTGCAATTAGGTATA-GAACTTTTAAAATG
*
477334 GTGCATTTAGGTATAGAACTTTTAAAAATG
1 GTGCAATTAGGTATAGAACTTTT-AAAATG
*
477364 GTGCAATTATGTAT
1 GTGCAATTAGGTAT
477378 CTATTTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 19 0.53
29 1 0.03
30 16 0.44
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (29 bp):
GTGCAATTAGGTATAGAACTTTTAAAATG
Found at i:477802 original size:54 final size:54
Alignment explanation
Indices: 477720--477837 Score: 236
Period size: 54 Copynumber: 2.2 Consensus size: 54
477710 AATATGTTAT
477720 CTAAACTTAAGCTCAAGATTCAATTTATTGCCTATTTTTGTATTCAATTAGGTA
1 CTAAACTTAAGCTCAAGATTCAATTTATTGCCTATTTTTGTATTCAATTAGGTA
477774 CTAAACTTAAGCTCAAGATTCAATTTATTGCCTATTTTTGTATTCAATTAGGTA
1 CTAAACTTAAGCTCAAGATTCAATTTATTGCCTATTTTTGTATTCAATTAGGTA
477828 CTAAACTTAA
1 CTAAACTTAA
477838 ACATCAAATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (54 bp):
CTAAACTTAAGCTCAAGATTCAATTTATTGCCTATTTTTGTATTCAATTAGGTA
Found at i:487291 original size:13 final size:13
Alignment explanation
Indices: 487273--487297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
487263 ATTTATGTTT
487273 GAAGATCTTCATG
1 GAAGATCTTCATG
487286 GAAGATCTTCAT
1 GAAGATCTTCAT
487298 CGATCAAGTA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
GAAGATCTTCATG
Found at i:502777 original size:18 final size:18
Alignment explanation
Indices: 502754--502788 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
502744 TAGTTGATAA
502754 TATATGTTAAATCTGAAG
1 TATATGTTAAATCTGAAG
*
502772 TATATGTTAAATTTGAA
1 TATATGTTAAATCTGAA
502789 AGACTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (18 bp):
TATATGTTAAATCTGAAG
Found at i:509439 original size:13 final size:13
Alignment explanation
Indices: 509421--509445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
509411 GACAATAAGA
509421 AGAAAATAAAAAG
1 AGAAAATAAAAAG
509434 AGAAAATAAAAA
1 AGAAAATAAAAA
509446 TAAAAAATCC
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:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (13 bp):
AGAAAATAAAAAG
Found at i:518528 original size:35 final size:35
Alignment explanation
Indices: 518482--518550 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
518472 CTAATTTTAT
518482 TAAAAATAGAAAACATTGAATTACAATATGAACAC
1 TAAAAATAGAAAACATTGAATTACAATATGAACAC
518517 TAAAAATAGAAAACATTGAATTACAATATGAACA
1 TAAAAATAGAAAACATTGAATTACAATATGAACA
518551 TTCAGAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.58, C:0.10, G:0.09, T:0.23
Consensus pattern (35 bp):
TAAAAATAGAAAACATTGAATTACAATATGAACAC
Found at i:518574 original size:12 final size:12
Alignment explanation
Indices: 518557--518582 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
518547 AACATTCAGA
518557 ATTACAATATTC
1 ATTACAATATTC
518569 ATTACAATATTC
1 ATTACAATATTC
518581 AT
1 AT
518583 AATTACAATA
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:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTACAATATTC
Found at i:518587 original size:15 final size:14
Alignment explanation
Indices: 518550--518592 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
518540 CAATATGAAC
518550 ATTCAGAATTACAAT
1 ATTCA-AATTACAAT
518565 ATTC--ATTACAAT
1 ATTCAAATTACAAT
518577 ATTCATAATTACAAT
1 ATTCA-AATTACAAT
518592 A
1 A
518593 CGAAGATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.48
15 13 0.52
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (14 bp):
ATTCAAATTACAAT
Found at i:518953 original size:118 final size:118
Alignment explanation
Indices: 518816--519047 Score: 437
Period size: 118 Copynumber: 2.0 Consensus size: 118
518806 AACATGTATC
518816 CAAATCAATCTGAGGATTCAATGCATAGAAAATCAACATGATAATAAGCATCATATTGATCAGTC
1 CAAATCAATCTGAGGATTCAATGCATAGAAAATCAACATGATAATAAGCATCATATTGATCAGTC
518881 GTCACGATATCAAATCCAACATTAAGAAGAAAAAAATAAATGAAAACAACAGT
66 GTCACGATATCAAATCCAACATTAAGAAGAAAAAAATAAATGAAAACAACAGT
*
518934 CAAATCAATCTGAGGATTCAATGCATAGAAAATCAACATGATAATAAGCGTCATATTGATCAGTC
1 CAAATCAATCTGAGGATTCAATGCATAGAAAATCAACATGATAATAAGCATCATATTGATCAGTC
* *
518999 GTCACGATATCAAATCCAATATTAAGAAGAAAAAGATAAATGAAAACAA
66 GTCACGATATCAAATCCAACATTAAGAAGAAAAAAATAAATGAAAACAA
519048 TAACCAAACG
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 111 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (118 bp):
CAAATCAATCTGAGGATTCAATGCATAGAAAATCAACATGATAATAAGCATCATATTGATCAGTC
GTCACGATATCAAATCCAACATTAAGAAGAAAAAAATAAATGAAAACAACAGT
Found at i:519102 original size:17 final size:17
Alignment explanation
Indices: 519082--519116 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
519072 AAAGATAGAA
*
519082 ATAAACGTGTCATAAAG
1 ATAAACATGTCATAAAG
*
519099 ATAAATATGTCATAAAG
1 ATAAACATGTCATAAAG
519116 A
1 A
519117 CATAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (17 bp):
ATAAACATGTCATAAAG
Found at i:519451 original size:13 final size:14
Alignment explanation
Indices: 519423--519452 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
519413 ATATCTTATC
519423 TTTTCATTTATAAT
1 TTTTCATTTATAAT
519437 TTTTCATTTAT-AT
1 TTTTCATTTATAAT
519450 TTT
1 TTT
519453 CAACATGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTCATTTATAAT
Found at i:521591 original size:36 final size:38
Alignment explanation
Indices: 521520--521591 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
521510 AGTTGGAAAA
* *
521520 TATATATATTTTTCTTTAAAAATTTAAATTCATAAATT
1 TATATATATTTTTCTTTAAAAATTGAAAATCATAAATT
521558 TATATA-ATTTTT-TTTACAAAATTGAAAAT-ATAAA
1 TATATATATTTTTCTTTA-AAAATTGAAAATCATAAA
521592 AAGGTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 9 0.29
37 16 0.52
38 6 0.19
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (38 bp):
TATATATATTTTTCTTTAAAAATTGAAAATCATAAATT
Found at i:522475 original size:13 final size:13
Alignment explanation
Indices: 522457--522483 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
522447 ATGTATTGAT
522457 CATTAATAATTAG
1 CATTAATAATTAG
522470 CATTAATAATTAG
1 CATTAATAATTAG
522483 C
1 C
522484 GGTTTCATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (13 bp):
CATTAATAATTAG
Found at i:527495 original size:2 final size:2
Alignment explanation
Indices: 527488--527520 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
527478 CCAACATCTT
527488 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
527521 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:527568 original size:2 final size:2
Alignment explanation
Indices: 527520--527553 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
527510 TCTCTCTCTC
527520 TA TA TA TA TA TA 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
527554 AAAGTTTGTA
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):
TA
Found at i:528237 original size:23 final size:23
Alignment explanation
Indices: 528204--528259 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
528194 TTATATTTAG
528204 TATTTTGTTAATAATTTATTTAAC
1 TATTTT-TTAATAATTTATTTAAC
* *
528228 TATTTTTTAATATTTTATTTAAT
1 TATTTTTTAATAATTTATTTAAC
528251 TAATTTTTT
1 T-ATTTTTT
528260 TACAGATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTTTTTAATAATTTATTTAAC
Found at i:528248 original size:12 final size:12
Alignment explanation
Indices: 528192--528250 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
528182 AGGTGTATTT
* *
528192 TATTATATTTAG
1 TATTTTATTTAA
*
528204 TATTTT-GTTAA
1 TATTTTATTTAA
*
528215 TAATTTATTTAA
1 TATTTTATTTAA
528227 CTA-TTT-TTTAA
1 -TATTTTATTTAA
528238 TATTTTATTTAA
1 TATTTTATTTAA
528250 T
1 T
528251 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
10 2 0.05
11 16 0.42
12 18 0.47
13 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:529158 original size:20 final size:20
Alignment explanation
Indices: 529133--529194 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
529123 CCCCTACAGA
*
529133 CAAATTCTCGTTGCGATAGT
1 CAAATTCGCGTTGCGATAGT
529153 CAAATTCGCGTTGCGATAGT
1 CAAATTCGCGTTGCGATAGT
**
529173 CATTTTCGCGTTGCGATAGT
1 CAAATTCGCGTTGCGATAGT
529193 CA
1 CA
529195 TTCATGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (20 bp):
CAAATTCGCGTTGCGATAGT
Found at i:529205 original size:18 final size:18
Alignment explanation
Indices: 529136--529207 Score: 81
Period size: 20 Copynumber: 3.8 Consensus size: 18
529126 CTACAGACAA
*
529136 ATTCTCGTTGCGATAGTC
1 ATTCGCGTTGCGATAGTC
529154 AAATTCGCGTTGCGATAGTC
1 --ATTCGCGTTGCGATAGTC
529174 ATTTTCGCGTTGCGATAGTC
1 A--TTCGCGTTGCGATAGTC
**
529194 ATTCATGTTGCGAT
1 ATTCGCGTTGCGAT
529208 TTTAAGTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 12 0.26
20 35 0.74
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (18 bp):
ATTCGCGTTGCGATAGTC
Found at i:529788 original size:21 final size:20
Alignment explanation
Indices: 529697--529801 Score: 59
Period size: 21 Copynumber: 5.0 Consensus size: 20
529687 GACTCACCTG
529697 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* * *
529717 CCTATCGTTCAAGATGACCCTA
1 TC-ATCGTTCAAGA-GGCCCTC
** *
529739 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-GCCCTC
* * *
529760 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
529781 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGG-CCCTC
529802 CCAACATTCT
Statistics
Matches: 61, Mismatches: 18, Indels: 11
0.68 0.20 0.12
Matches are distributed among these distances:
20 4 0.07
21 50 0.82
22 4 0.07
23 3 0.05
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:531420 original size:20 final size:20
Alignment explanation
Indices: 531367--531420 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
531357 AGGTACACTT
* **
531367 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
**
531387 TCGCAATACGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
531407 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
531421 TCAATTCGCT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:531456 original size:20 final size:20
Alignment explanation
Indices: 531414--531653 Score: 245
Period size: 20 Copynumber: 12.7 Consensus size: 20
531404 AAATCGCAAC
* *
531414 GCGAAAGTC-AATTCGCTTT
1 GCGATAGTCAAATTCGCGTT
* *
531433 GCGATAGTCAAATACTCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
531453 GCGATAATCAAATTTGCATT
1 GCGATAGTCAAATTCGCGTT
531473 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
531493 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
531513 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
531527 GCGATAGTCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
*
531547 GCGATAGACAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
531567 GCGATAGTCATATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
531587 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
531607 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
*
531621 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
531641 GCGATATTCAAAT
1 GCGATAGTCAAAT
531654 GAATGTGTAA
Statistics
Matches: 182, Mismatches: 26, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
14 23 0.13
16 2 0.01
18 2 0.01
19 8 0.04
20 147 0.81
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:531538 original size:74 final size:74
Alignment explanation
Indices: 531447--531591 Score: 227
Period size: 74 Copynumber: 2.0 Consensus size: 74
531437 TAGTCAAATA
** *
531447 CTCGTTGCGATAATCAAATTTGCATTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGT
1 CTCGTTGCGATAATCAAATTCACATTGCGATAGACAAATTCGCGTTGCGATAGTCAAATTCGCGT
531512 TGCGATTTT
66 TGCGATTTT
* * * *
531521 CTCGTTGCGATAGTCAAATTCACGTTGCGATAGACAAATTCGCGTTGCGATAGTCATATTCGTGT
1 CTCGTTGCGATAATCAAATTCACATTGCGATAGACAAATTCGCGTTGCGATAGTCAAATTCGCGT
531586 TGCGAT
66 TGCGAT
531592 AGTCAAATTC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (74 bp):
CTCGTTGCGATAATCAAATTCACATTGCGATAGACAAATTCGCGTTGCGATAGTCAAATTCGCGT
TGCGATTTT
Found at i:531592 original size:94 final size:94
Alignment explanation
Indices: 531431--531653 Score: 324
Period size: 94 Copynumber: 2.4 Consensus size: 94
531421 TCAATTCGCT
* * *
531431 TTGCGATAGTCAAATACTCGTTGCGATAATCAAATTTGCATTGCGATAGTCAAATTCGCGTTGCG
1 TTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCG
*
531496 ATAGTCAAATTCGCGTTGCGATTTTCT-CG
66 ATAGTCAAATTCGCGTTGCGATTTT-TGAG
* * *
531525 TTGCGATAGTCAAATTCACGTTGCGATAGA-CAAATTCGCGTTGCGATAGTCATATTCGTGTTGC
1 TTGCGATAGTCAAATTCACGTTGCGATA-ATCAAATTCGCATTGCGATAGTCAAATTCGCGTTGC
531589 GATAGTCAAATTCGCGTTGCGATTTTTGAG
65 GATAGTCAAATTCGCGTTGCGATTTTTGAG
* * *
531619 TTGCGATAATCAAATTCGCGTTGCGATATTCAAAT
1 TTGCGATAGTCAAATTCACGTTGCGATAATCAAAT
531654 GAATGTGTAA
Statistics
Matches: 116, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
93 1 0.01
94 114 0.98
95 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (94 bp):
TTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCG
ATAGTCAAATTCGCGTTGCGATTTTTGAG
Found at i:531880 original size:140 final size:140
Alignment explanation
Indices: 531628--531893 Score: 505
Period size: 140 Copynumber: 1.9 Consensus size: 140
531618 GTTGCGATAA
* *
531628 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAAAAACTGAACAGATCATAGC
531693 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
531758 CACATAATAG
131 CACATAATAG
*
531768 TCAAATTCGCGTTGTGATATTCAAATGAATGTGTAATAAGTGATAAAAACTGAACAGATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAAAAACTGAACAGATCATAGC
531833 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
531894 TACAACGTTT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 123 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAAAAACTGAACAGATCATAGC
AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
CACATAATAG
Found at i:531976 original size:18 final size:18
Alignment explanation
Indices: 531953--531987 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
531943 AAGCCGGTTG
*
531953 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
531971 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
531988 GTCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:533618 original size:20 final size:20
Alignment explanation
Indices: 533552--533682 Score: 106
Period size: 20 Copynumber: 6.5 Consensus size: 20
533542 AAATTCAGTG
* * *
533552 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
* *
533572 TTGCGACAGTCAGAATCGCA
1 TTGCGATAGTCATAATCGCA
533592 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
533612 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
* * *
533632 TTGCTAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
* *
533652 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
533672 TTGCGATAGTC
1 TTGCGATAGTC
533683 GGAAAATCTC
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 99 0.98
21 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Done.