Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009070.1 Hibiscus syriacus cultivar Beakdansim tig00112498_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: 2268343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:315608 original size:40 final size:40
Alignment explanation
Indices: 315575--315828 Score: 309
Period size: 40 Copynumber: 6.3 Consensus size: 40
315565 CGATAGTCAG
* *
315575 AATCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGT
1 AATCTCGTTGCGATTTACGGATACGCATTGCGATTTACGT
* * * *
315615 ATTCGCATTGCGATTTACGTA-ATCGCATTGCGATTTACGT
1 AATCTCGTTGCGATTTACGGATA-CGCATTGCGATTTACGT
*
315655 AA--TCGTTGCGATTTACGGATACACATTGCGATTTACGT
1 AATCTCGTTGCGATTTACGGATACGCATTGCGATTTACGT
* * *
315693 ATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGT
1 AATCTCGTTGCGATTTACGGATACGCATTGCGATTTACGT
* *
315733 ATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGT
1 AATCTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGT
* *
315774 ATTGTCGTTGCGATTTACGGATACGCATTGCGATTTTACG-
1 AATCTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGT
*
315814 GATACTCGTTGCGAT
1 AAT-CTCGTTGCGAT
315829 AGTCAGAATC
Statistics
Matches: 187, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
38 31 0.17
39 1 0.01
40 100 0.53
41 55 0.29
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (40 bp):
AATCTCGTTGCGATTTACGGATACGCATTGCGATTTACGT
Found at i:315887 original size:21 final size:21
Alignment explanation
Indices: 315863--315932 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
315853 ATGTTCGCGT
*
315863 TGCGATTCTGGAAAATCGCAA
1 TGCGATTCTGCAAAATCGCAA
* ** *
315884 TGCGAATT-TGTACTATCGCAT
1 TGCG-ATTCTGCAAAATCGCAA
* *
315905 TGCGATTCTTCATAATCGCAA
1 TGCGATTCTGCAAAATCGCAA
*
315926 CGCGATT
1 TGCGATT
315933 ATGGGAATTG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
20 3 0.08
21 31 0.84
22 3 0.08
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (21 bp):
TGCGATTCTGCAAAATCGCAA
Found at i:322173 original size:15 final size:16
Alignment explanation
Indices: 322140--322181 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
322130 TTTCATTTCA
322140 TTTCATTTTATTTAAT
1 TTTCATTTTATTTAAT
*
322156 TTTC-TTTTCTTTAAT
1 TTTCATTTTATTTAAT
*
322171 TTTGATTTTAT
1 TTTCATTTTAT
322182 ATCAAAAGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTCATTTTATTTAAT
Found at i:323020 original size:3 final size:3
Alignment explanation
Indices: 323012--323036 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
323002 GTCCTCCAAG
323012 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
323037 CACCCATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:325739 original size:74 final size:75
Alignment explanation
Indices: 325557--325764 Score: 260
Period size: 75 Copynumber: 2.8 Consensus size: 75
325547 CAAAGCCAAA
** * **
325557 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGA-TGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
325621 TTTGGCTCCGAG
64 TTTGGCTCCGAG
*
325633 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
325697 TTTGTTCCGAG
65 TTGGCTCCGAG
* * *
325708 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
325765 TGTACAACGG
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
74 21 0.18
75 64 0.55
76 30 0.26
77 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:331559 original size:20 final size:20
Alignment explanation
Indices: 331534--331597 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
331524 TTTTGGTGCA
331534 GAGGGAATCGATCCCCCCCT
1 GAGGGAATCGATCCCCCCCT
* **
331554 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGA-TCCCCCCCT
*
331575 GAAGGGGAATCGATACCCCCCT
1 G-A-GGGAATCGATCCCCCCCT
331597 G
1 G
331598 GGGTTCTGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 8 0.24
23 8 0.24
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.17
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCCT
Found at i:331588 original size:23 final size:21
Alignment explanation
Indices: 331534--331595 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
331524 TTTTGGTGCA
331534 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAATCGATTCCCCCCCT
* **
331554 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCCT
*
331575 GAAGGGGAATCGATACCCCCC
1 G-A-GGGAATCGATTCCCCCC
331596 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 10 0.30
21 8 0.24
22 1 0.03
23 14 0.42
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCCT
Found at i:333915 original size:53 final size:53
Alignment explanation
Indices: 333835--333941 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
333825 GAATAAGTTA
333835 AGTGTTAAATGTTTTACATAATAAATTGAAGAAGTGTTAAAGTAAGGGGGAGT
1 AGTGTTAAATGTTTTACATAATAAATTGAAGAAGTGTTAAAGTAAGGGGGAGT
333888 AGTGTTAAATGTTTTACATAATAAATTGAAGAAGTGTTAAAGTAAGGGGGAGT
1 AGTGTTAAATGTTTTACATAATAAATTGAAGAAGTGTTAAAGTAAGGGGGAGT
333941 A
1 A
333942 ATTTCAAAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.32
Consensus pattern (53 bp):
AGTGTTAAATGTTTTACATAATAAATTGAAGAAGTGTTAAAGTAAGGGGGAGT
Found at i:334387 original size:75 final size:75
Alignment explanation
Indices: 334237--334444 Score: 276
Period size: 75 Copynumber: 2.8 Consensus size: 75
334227 CAAAGCCAAA
* ** * **
334237 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
334302 TTGGCTCCGAG
65 TTGGCTCCGAG
*
334313 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
334378 TTGTTCCGAG
66 TGGCTCCGAG
* *
334388 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGG-GGATACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGA-ACCGATTCCCCCCT
334445 TGTACACCGG
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
74 3 0.03
75 84 0.71
76 31 0.26
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:338839 original size:16 final size:16
Alignment explanation
Indices: 338818--338878 Score: 122
Period size: 16 Copynumber: 3.8 Consensus size: 16
338808 GGGTCTCCAA
338818 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
338834 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
338850 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
338866 CGTTTATGTTCGT
1 CGTTTATGTTCGT
338879 TTATTTATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.07, C:0.13, G:0.25, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:338845 original size:10 final size:10
Alignment explanation
Indices: 338830--338882 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
338820 TTTATGTTCG
338830 TGTTCGTTTA
1 TGTTCGTTTA
338840 TGTTCG----
1 TGTTCGTTTA
338846 TGTTCGTTTA
1 TGTTCGTTTA
338856 TGTTCG----
1 TGTTCGTTTA
338862 TGTTCGTTTA
1 TGTTCGTTTA
338872 TGTTCGTTTA
1 TGTTCGTTTA
338882 T
1 T
338883 TTATTAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
6 12 0.34
10 23 0.66
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:342547 original size:19 final size:20
Alignment explanation
Indices: 342523--342570 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
342513 AATGATTTTC
342523 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAGA
* * *
342542 TTTTGAAATCCAAAATGATA
1 TTTTGAAAACAAAAATGAGA
342562 TTTTGAAAA
1 TTTTGAAAA
342571 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.33
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAGA
Found at i:344061 original size:42 final size:39
Alignment explanation
Indices: 343973--344070 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 39
343963 AATCAGATTA
* **
343973 CCCA-GGGGTACAGATTCCCCCTTAGGAGAACAGATTCC
1 CCCAGGGGGTACCGATTCCCCCCCAGGAGAACAGATTCC
* *
344011 CCCCGGGGGTACCGATTCCCCACCCAGGGGAACAGATTTTCC
1 CCCAGGGGGTACCGATTCCCC-CCCAGGAGAACAGA--TTCC
344053 CCCAGGGGGTACCGATTC
1 CCCAGGGGGTACCGATTC
344071 TCCCTGTCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
38 3 0.06
39 15 0.30
40 11 0.22
42 21 0.42
ACGTcount: A:0.21, C:0.35, G:0.27, T:0.17
Consensus pattern (39 bp):
CCCAGGGGGTACCGATTCCCCCCCAGGAGAACAGATTCC
Found at i:344069 original size:21 final size:21
Alignment explanation
Indices: 344005--344074 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
343995 TAGGAGAACA
344005 GATTC-CCCCC-GGGGGTACC
1 GATTCTCCCCCAGGGGGTACC
* * *
344024 GATTCCCCACCCA-GGGGAACA
1 GATTCTCC-CCCAGGGGGTACC
*
344045 GATTTTCCCCCAGGGGGTACC
1 GATTCTCCCCCAGGGGGTACC
344066 GATTCTCCC
1 GATTCTCCC
344075 TGTCTAACGG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
19 5 0.12
20 6 0.15
21 29 0.73
ACGTcount: A:0.17, C:0.39, G:0.26, T:0.19
Consensus pattern (21 bp):
GATTCTCCCCCAGGGGGTACC
Found at i:344447 original size:34 final size:34
Alignment explanation
Indices: 344408--344491 Score: 141
Period size: 34 Copynumber: 2.5 Consensus size: 34
344398 AAGGGAAAAA
344408 GTTCTAGCTTAGCCCGTGTAAAAGCTAGAGAAAT
1 GTTCTAGCTTAGCCCGTGTAAAAGCTAGAGAAAT
*
344442 GTTCTAGCTTAGCCCGTGTAAAAGCTAGGGAAAT
1 GTTCTAGCTTAGCCCGTGTAAAAGCTAGAGAAAT
* *
344476 ATTCTAGTTTAGCCCG
1 GTTCTAGCTTAGCCCG
344492 AAAAAACTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (34 bp):
GTTCTAGCTTAGCCCGTGTAAAAGCTAGAGAAAT
Found at i:349333 original size:21 final size:21
Alignment explanation
Indices: 349296--349335 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
349286 TATCATTAAA
*
349296 TTAAATATATATCTTTATTAC
1 TTAAATATATATATTTATTAC
349317 TTAAATAGTA-ATATTTATT
1 TTAAATA-TATATATTTATT
349336 TAATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TTAAATATATATATTTATTAC
Found at i:349697 original size:29 final size:29
Alignment explanation
Indices: 349655--349714 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
349645 ATTAAATTGG
349655 AATTTTATCATTCTAAGGGATCAAAATAC
1 AATTTTATCATTCTAAGGGATCAAAATAC
* * *
349684 AATTTTATCATTCTATGGGGTTAAAATAC
1 AATTTTATCATTCTAAGGGATCAAAATAC
349713 AA
1 AA
349715 CTTATTATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (29 bp):
AATTTTATCATTCTAAGGGATCAAAATAC
Found at i:350158 original size:32 final size:32
Alignment explanation
Indices: 350095--350158 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
350085 AATAGTATCA
* *
350095 GAGAGCTCTCAAAGCAAGCTTCTGTCTAGGAG
1 GAGAGCTCTCAAAGCAAGCTTCTGACAAGGAG
**
350127 GAGAGCTCTCGGAGCAAGCTTCTGACAAGGAG
1 GAGAGCTCTCAAAGCAAGCTTCTGACAAGGAG
350159 ACAAGCAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (32 bp):
GAGAGCTCTCAAAGCAAGCTTCTGACAAGGAG
Found at i:361433 original size:12 final size:13
Alignment explanation
Indices: 361404--361436 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
361394 TAGATGAAAA
361404 CATTTTTAATTAT
1 CATTTTTAATTAT
*
361417 TATTTTTAATT-T
1 CATTTTTAATTAT
361429 CATTTTTA
1 CATTTTTA
361437 TCTTTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (13 bp):
CATTTTTAATTAT
Found at i:361491 original size:16 final size:17
Alignment explanation
Indices: 361450--361493 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
361440 TTATTTATTC
361450 ATAATTTAA-ATAAATA
1 ATAATTTAATATAAATA
*
361466 AAAATATTAATATAAA-A
1 ATAAT-TTAATATAAATA
361483 ATAATTTAATA
1 ATAATTTAATA
361494 AATCAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.42
17 9 0.38
18 5 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATTTAATATAAATA
Found at i:361501 original size:16 final size:16
Alignment explanation
Indices: 361458--361510 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
361448 TCATAATTTA
*
361458 AATAAATAAAAATATT
1 AATAAATAATAATATT
*
361474 AATATAAAAATAAT-TT
1 AATA-AATAATAATATT
361490 AATAAATCAAT-ATATT
1 AATAAAT-AATAATATT
361506 AATAA
1 AATAA
361511 TAGGACAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 20 0.65
17 7 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAAATAATAATATT
Found at i:362057 original size:31 final size:30
Alignment explanation
Indices: 362016--362091 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 30
362006 AGTTACATCA
362016 GGGACTATATTGCAAACGGACTAAATGTTGG
1 GGGACTATATTGCAAACGGACTAAATG-TGG
* *
362047 GGGACCATATTACAAACGGACTAAATGTGG
1 GGGACTATATTGCAAACGGACTAAATGTGG
*
362077 GGGACTGTATTGCAA
1 GGGACTATATTGCAA
362092 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 15 0.38
31 25 0.62
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (30 bp):
GGGACTATATTGCAAACGGACTAAATGTGG
Found at i:364441 original size:31 final size:31
Alignment explanation
Indices: 364403--364461 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
364393 TTACGTCAGT
364403 GACCATATTGCAAACGGACTAAATGTTGAGG
1 GACCATATTGCAAACGGACTAAATGTTGAGG
364434 GACCATATTGCAAACGGACTAAATGTTG
1 GACCATATTGCAAACGGACTAAATGTTG
364462 GGAGACTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (31 bp):
GACCATATTGCAAACGGACTAAATGTTGAGG
Found at i:372146 original size:2 final size:2
Alignment explanation
Indices: 372093--372135 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
372083 TATTTTTTTA
372093 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
372135 A
1 A
372136 GATGAATATA
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:374746 original size:2 final size:2
Alignment explanation
Indices: 374739--374769 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
374729 AAAACAAAAT
374739 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 T
374770 TTTAATTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:377728 original size:11 final size:12
Alignment explanation
Indices: 377701--377740 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
377691 ACAGCAGCCC
377701 CCCCCTTAGCAG
1 CCCCCTTAGCAG
*
377713 CCCCCTTATCAG
1 CCCCCTTAGCAG
377725 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
377738 CCC
1 CCC
377741 ATGTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.15, C:0.55, G:0.12, T:0.17
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:377729 original size:13 final size:13
Alignment explanation
Indices: 377700--377740 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
377690 TACAGCAGCC
377700 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
*
377713 -CCCCCTTATCAG
1 CCCCCCTTAGCAG
377725 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
377738 CCC
1 CCC
377741 ATGTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.15, C:0.56, G:0.12, T:0.17
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:381030 original size:15 final size:16
Alignment explanation
Indices: 381002--381033 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
380992 AAAATCTTTC
381002 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
381018 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
381033 T
1 T
381034 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:381808 original size:16 final size:16
Alignment explanation
Indices: 381784--381817 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
381774 TATCGCCGAC
*
381784 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
381800 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
381816 CG
1 CG
381818 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:382248 original size:13 final size:13
Alignment explanation
Indices: 382213--382272 Score: 104
Period size: 13 Copynumber: 4.6 Consensus size: 13
382203 AAAAAATTAC
382213 AGCAGCCCCCCCTT
1 AGCAG-CCCCCCTT
382227 AGCAG-CCCCCTT
1 AGCAGCCCCCCTT
382239 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
382252 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
382265 AGCAGCCC
1 AGCAGCCC
382273 ATGTGTTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.27
13 28 0.62
14 5 0.11
ACGTcount: A:0.17, C:0.53, G:0.17, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:384396 original size:23 final size:23
Alignment explanation
Indices: 384370--384416 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
384360 AACGAGTCGA
384370 ACAAATCAAAACAATAGTTGGAT
1 ACAAATCAAAACAATAGTTGGAT
*
384393 ACAAATCAAAGCAATAGTTGGAT
1 ACAAATCAAAACAATAGTTGGAT
384416 A
1 A
384417 ATTACATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (23 bp):
ACAAATCAAAACAATAGTTGGAT
Found at i:391744 original size:21 final size:21
Alignment explanation
Indices: 391720--391772 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
391710 ATTCTGACTA
391720 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
391741 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
391762 TCGCAATGCGA
1 TCGCATTGCGA
391773 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:391787 original size:20 final size:20
Alignment explanation
Indices: 391762--391834 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
391752 TTTTCCTAAT
391762 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
391782 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
391802 TCGCAATGC-AATTACGTAAA
1 TCGCAATGCGAA-TACGTAAA
*
391822 TCGTAATGCGAAT
1 TCGCAATGCGAAT
391835 CTGACTATCG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.93
21 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:392447 original size:20 final size:20
Alignment explanation
Indices: 392422--392469 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
392412 CAACGAGTGA
392422 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
** **
392442 ATCGCAATGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
392462 ATCGCAAC
1 ATCGCAAC
392470 GAGAGAATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:392537 original size:20 final size:20
Alignment explanation
Indices: 392512--392561 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
392502 TGCGATTCTT
*
392512 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAATCAAATTC
* **
392532 GCGTTGCAATAATCATTTTC
1 GCGTTGCGATAATCAAATTC
*
392552 GTGTTGCGAT
1 GCGTTGCGAT
392562 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAATCAAATTC
Found at i:392567 original size:20 final size:20
Alignment explanation
Indices: 392544--392583 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
392534 GTTGCAATAA
392544 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
392564 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
392584 AAAGTTTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.55
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:392591 original size:20 final size:20
Alignment explanation
Indices: 392548--392591 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
392538 CAATAATCAT
** *
392548 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
392568 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
392588 TTTC
1 TTTC
392592 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:394480 original size:20 final size:20
Alignment explanation
Indices: 394455--394585 Score: 193
Period size: 20 Copynumber: 6.8 Consensus size: 20
394445 AGAATAGTTT
394455 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
394475 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
394491 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
394509 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
394529 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
394549 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
394569 ACTATCGCAATGCGAAA
1 ACTATCGCAATGCGAAA
394586 TGAAAATCGC
Statistics
Matches: 100, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
14 7 0.07
16 4 0.04
17 4 0.04
18 4 0.04
20 81 0.81
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:394536 original size:40 final size:40
Alignment explanation
Indices: 394455--394602 Score: 193
Period size: 40 Copynumber: 3.9 Consensus size: 40
394445 AGAATAGTTT
*
394455 ACTATCGCAATGCGAAAATGACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
394491 A--ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
**
394529 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
394569 ACTATCGCAATGCG-AAATGAAAATCGCATTGCGA
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGA
394603 TTCTCTCGTT
Statistics
Matches: 100, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
34 27 0.27
36 3 0.03
37 2 0.02
38 2 0.02
39 17 0.17
40 49 0.49
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
Found at i:394723 original size:20 final size:20
Alignment explanation
Indices: 394698--394764 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
394688 GATTCTCTCG
**
394698 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCATTTTCACA
*
394718 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCACA
*
394738 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCACA
394758 TTGCGAT
1 TTGCGAT
394765 TTTAAGTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCACA
Found at i:395339 original size:21 final size:21
Alignment explanation
Indices: 395248--395352 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
395238 AACTCACCTG
*
395248 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
395270 T-ATCGTTGAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
395290 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
395311 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
395332 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
395353 CCAACATTCT
Statistics
Matches: 61, Mismatches: 21, Indels: 3
0.72 0.25 0.04
Matches are distributed among these distances:
20 3 0.05
21 57 0.93
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:395345 original size:42 final size:42
Alignment explanation
Indices: 395245--395355 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
395235 CCCAACTCAC
* * * * *
395245 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTGAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
395287 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
395329 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
395356 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:396741 original size:14 final size:14
Alignment explanation
Indices: 396707--396745 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
396697 TTGATTGTTT
396707 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
396721 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
396735 TGTTGATTTGT
1 AATTGATTTGT
396746 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:396911 original size:33 final size:34
Alignment explanation
Indices: 396867--396942 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
396857 GGAAATGACT
* *
396867 ATCGTAACGAGAGAATCGCAATACG-AAACGAGA
1 ATCGCAACGAGAGAATCGCAATACGAAAACGAAA
* *
396900 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATACGAAAACGAAA
396934 ATCGCAACG
1 ATCGCAACG
396943 CGAAACTAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 23 0.61
34 15 0.39
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATACGAAAACGAAA
Found at i:396915 original size:14 final size:14
Alignment explanation
Indices: 396867--396920 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
396857 GGAAATGACT
*
396867 ATCGTAACGAGAGA
1 ATCGCAACGAGAGA
396881 ATCGCAATACGAAACGAGA
1 ATCGC-A-ACG--A-GAGA
396900 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
396914 ATCGCAA
1 ATCGCAA
396921 TGCGAAAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 15 0.44
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 9 0.26
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:397003 original size:34 final size:34
Alignment explanation
Indices: 396959--397052 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
396949 TAAGTTCGCA
*
396959 TTGCGCTTTTCATTTTCGCATTGCGATTCACTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
*
396993 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
** * *
397026 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
397053 AGTCAATTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.57
34 23 0.43
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
Found at i:397049 original size:20 final size:20
Alignment explanation
Indices: 397024--397112 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
397014 GCGATTCTCT
397024 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
397044 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
397064 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
397084 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
397104 CGTTGCGAT
1 CGTTGCGAT
397113 TTCCGCGTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:400459 original size:20 final size:20
Alignment explanation
Indices: 400436--400495 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
400426 CAGAATCTCG
*
400436 TTGCGATTTACAG-ATTTGCA
1 TTGCGATTTAC-GTATTCGCA
400456 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
400476 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
400496 ACGCAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:401212 original size:21 final size:22
Alignment explanation
Indices: 401188--401247 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
401178 AAATAATACA
401188 TTTATTAAAAAAAATATTAT-T
1 TTTATTAAAAAAAATATTATAT
* *
401209 TTTATTCAATAAAATA-TATAT
1 TTTATTAAAAAAAATATTATAT
*
401230 TTAATTAAAAAAACATAT
1 TTTATTAAAAAAA-ATAT
401248 AGAGTGACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 3 0.10
21 25 0.81
22 3 0.10
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTATTAAAAAAAATATTATAT
Found at i:401242 original size:20 final size:18
Alignment explanation
Indices: 401182--401248 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 18
401172 GACTTGAAAT
*
401182 AATACATTTATTAAAAAA
1 AATATATTTATTAAAAAA
401200 AATATTATTTTTATTCAATAAAA
1 AATA-TA--TTTATT-AA-AAAA
*
401223 TATATATTTAATTAAAAAA
1 AATATATTT-ATTAAAAAA
401242 ACATATA
1 A-ATATA
401249 GAGTGACATT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
18 4 0.10
19 5 0.13
20 10 0.26
21 9 0.23
22 4 0.10
23 7 0.18
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATATTTATTAAAAAA
Found at i:402205 original size:11 final size:11
Alignment explanation
Indices: 402189--402213 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
402179 TAGATCATTG
402189 TATGTATTTTA
1 TATGTATTTTA
402200 TATGTATTTTA
1 TATGTATTTTA
402211 TAT
1 TAT
402214 TAAAAACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TATGTATTTTA
Found at i:405523 original size:21 final size:19
Alignment explanation
Indices: 405492--405544 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
405482 TGTATTTTCG
* *
405492 TTTTTTAAAAATATTTAATTT
1 TTTTTT-AAAAT-TTTAAATA
405513 TATTTTTAAAATTTTAAATA
1 T-TTTTTAAAATTTTAAATA
405533 TTTTTTAAAATT
1 TTTTTTAAAATT
405545 ACTAAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 7 0.24
21 6 0.21
22 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTTAAAATTTTAAATA
Found at i:408724 original size:25 final size:25
Alignment explanation
Indices: 408695--408745 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
408685 GAATGTCGGT
408695 ATTCAATTTGTGATAAGAGAATGAA
1 ATTCAATTTGTGATAAGAGAATGAA
408720 ATTCAATTTGTGATAAGAGAATGAA
1 ATTCAATTTGTGATAAGAGAATGAA
408745 A
1 A
408746 CATATGGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (25 bp):
ATTCAATTTGTGATAAGAGAATGAA
Found at i:420073 original size:37 final size:37
Alignment explanation
Indices: 420023--420099 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
420013 AAATTGTTTT
420023 TATTTGAATGATGCAACTCAATGGTTGGGGTATTTGC
1 TATTTGAATGATGCAACTCAATGGTTGGGGTATTTGC
420060 TATTTGAATGATGCAACTCAATGGTTGGGGTATTTGC
1 TATTTGAATGATGCAACTCAATGGTTGGGGTATTTGC
420097 TAT
1 TAT
420100 GAAAAGTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.25, C:0.10, G:0.26, T:0.39
Consensus pattern (37 bp):
TATTTGAATGATGCAACTCAATGGTTGGGGTATTTGC
Found at i:420670 original size:15 final size:15
Alignment explanation
Indices: 420647--420682 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
420637 TAATTATATG
*
420647 TTTAGTATTTTATAA
1 TTTAATATTTTATAA
420662 TTTAATATTTTATAA
1 TTTAATATTTTATAA
*
420677 ATTAAT
1 TTTAAT
420683 TTTACGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTAATATTTTATAA
Found at i:426661 original size:16 final size:16
Alignment explanation
Indices: 426640--426670 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
426630 TAATAAATAA
426640 ACGAACATAAACGAAT
1 ACGAACATAAACGAAT
*
426656 ACGAACATAATCGAA
1 ACGAACATAAACGAA
426671 CAAATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (16 bp):
ACGAACATAAACGAAT
Found at i:426763 original size:16 final size:16
Alignment explanation
Indices: 426734--426800 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
426724 CGTTCATTTA
426734 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
426748 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
426764 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
426780 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
426796 ATAAA
1 ATAAA
426801 AGTTGGAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 41 0.84
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:427885 original size:10 final size:10
Alignment explanation
Indices: 427870--427920 Score: 57
Period size: 10 Copynumber: 4.7 Consensus size: 10
427860 AACATAAATG
427870 AACGAACATA
1 AACGAACATA
427880 AACGAACATAACCA
1 AACGAACAT----A
427894 AACGAACATA
1 AACGAACATA
427904 AACGAACATA
1 AACGAACATA
*
427914 ACCGAAC
1 AACGAAC
427921 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 26 0.72
14 10 0.28
ACGTcount: A:0.57, C:0.25, G:0.10, T:0.08
Consensus pattern (10 bp):
AACGAACATA
Found at i:427897 original size:24 final size:24
Alignment explanation
Indices: 427870--427921 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
427860 AACATAAATG
427870 AACGAACATAAACGAACATAACCA
1 AACGAACATAAACGAACATAACCA
*
427894 AACGAACATAAACGAACATAACCG
1 AACGAACATAAACGAACATAACCA
427918 AACG
1 AACG
427922 TTCACGAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.08
Consensus pattern (24 bp):
AACGAACATAAACGAACATAACCA
Found at i:448583 original size:13 final size:13
Alignment explanation
Indices: 448565--448589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
448555 TGGCTGCTGC
448565 GGAGAAGAGAAAA
1 GGAGAAGAGAAAA
448578 GGAGAAGAGAAA
1 GGAGAAGAGAAA
448590 TCCCTAAAAT
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:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (13 bp):
GGAGAAGAGAAAA
Found at i:451192 original size:25 final size:25
Alignment explanation
Indices: 451163--451214 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
451153 TGTACAATTA
451163 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
451188 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
451213 TT
1 TT
451215 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGCCGG
Found at i:451255 original size:23 final size:23
Alignment explanation
Indices: 451227--451272 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
451217 AAAAGAAAGA
451227 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
**
451250 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
451273 CCGAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.35, T:0.13
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:451287 original size:25 final size:23
Alignment explanation
Indices: 451227--451287 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
451217 AAAAGAAAGA
**
451227 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
451250 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
451273 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
451288 AGTGAGAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 21 0.68
25 10 0.32
ACGTcount: A:0.51, C:0.07, G:0.33, T:0.10
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:451301 original size:21 final size:21
Alignment explanation
Indices: 451277--451329 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
451267 TTGCAGCCGA
*
451277 GAAAGAAAGAAAGTGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
451298 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
451319 GAAAGTAAGAA
1 GAAAGAAAGAA
451330 GAAGAAAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.04
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:451323 original size:17 final size:16
Alignment explanation
Indices: 451275--451306 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
451265 GATTGCAGCC
451275 GAGAAAGAAAGAAAGT
1 GAGAAAGAAAGAAAGT
451291 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
451307 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.03
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGT
Found at i:451585 original size:45 final size:48
Alignment explanation
Indices: 451536--451626 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 48
451526 TTATATAGTT
*
451536 AAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
* *
451581 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
451627 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 20 0.50
46 5 0.12
47 7 0.17
48 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:451825 original size:15 final size:16
Alignment explanation
Indices: 451802--451841 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
451792 GTTTGTTAGT
*
451802 TTATTAGTTTA-TATA
1 TTATAAGTTTATTATA
451817 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
451832 TTA-AAGTTTA
1 TTATAAGTTTA
451842 GTGTTGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:454012 original size:17 final size:17
Alignment explanation
Indices: 453990--454022 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
453980 CAATGATTTT
*
453990 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
454007 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
454023 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:454039 original size:24 final size:22
Alignment explanation
Indices: 454007--454075 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
453997 AAATCATTAC
454007 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
454029 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
454054 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
454076 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:454251 original size:14 final size:14
Alignment explanation
Indices: 454232--454271 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
454222 TAGTAATAAT
454232 TATTAAATCATTAG
1 TATTAAATCATTAG
*
454246 TATTAAATCATTAT
1 TATTAAATCATTAG
*
454260 TA-TAAATAATTA
1 TATTAAATCATTA
454272 CTAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:454259 original size:38 final size:37
Alignment explanation
Indices: 454217--454311 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 37
454207 GTATTCTATA
* *
454217 ATTATTAGTAATAATTATTAAATCATTAGTATTAAATC
1 ATTATTA-TAATAATTATTAAATAATTAGTATAAAATC
* *
454255 ATTATTATAAATAATTACTAAATAATTATTATAAAATC
1 ATTATTAT-AATAATTATTAAATAATTAGTATAAAATC
*
454293 ATTATTATAATGATTATTA
1 ATTATTATAATAATTATTA
454312 TCAAATCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
37 10 0.20
38 40 0.80
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (37 bp):
ATTATTATAATAATTATTAAATAATTAGTATAAAATC
Found at i:454291 original size:14 final size:13
Alignment explanation
Indices: 454214--454694 Score: 101
Period size: 12 Copynumber: 38.5 Consensus size: 13
454204 TTAGTATTCT
454214 ATAATTATTAGT-A
1 ATAATTATTA-TAA
454227 ATAATTA-T-TAA
1 ATAATTATTATAA
* *
454238 ATCATTAGTATTAA
1 ATAATTATTA-TAA
*
454252 ATCATTATTATAA
1 ATAATTATTATAA
*
454265 ATAATTA--CTAA
1 ATAATTATTATAA
454276 ATAATTATTATAAA
1 ATAATTATTAT-AA
*
454290 ATCATTATTAT-A
1 ATAATTATTATAA
*
454302 ATGATTATTATCAA
1 ATAATTATTAT-AA
* *
454316 ATCATTA--CTAA
1 ATAATTATTATAA
* * * *
454327 ATCATCA-AATCA
1 ATAATTATTATAA
* *
454339 TTAAATATT-TAA
1 ATAATTATTATAA
*
454351 ATCATTA-T-TAA
1 ATAATTATTATAA
* *
454362 ATCATTTTTAT-A
1 ATAATTATTATAA
*
454374 ATGATTATTACTAA
1 ATAATTATTA-TAA
*
454388 ATCATTATTAT-A
1 ATAATTATTATAA
454400 ATAATTATTATCAA
1 ATAATTATTAT-AA
* *
454414 ATCATTACTAT-A
1 ATAATTATTATAA
*
454426 ATGATTATTATCAA
1 ATAATTATTAT-AA
* *
454440 ATCATTA--CTAA
1 ATAATTATTATAA
* * * *
454451 ATCATCA-AATCA
1 ATAATTATTATAA
* *
454463 TTAAATATT-TAA
1 ATAATTATTATAA
*
454475 ATCATTA-T-TAA
1 ATAATTATTATAA
* *
454486 ATCATTTTTAT-A
1 ATAATTATTATAA
*
454498 ATGATTATTACTAA
1 ATAATTATTA-TAA
*
454512 ATCATTATTAT-A
1 ATAATTATTATAA
*
454524 ATGATTATTATCAA
1 ATAATTATTAT-AA
* *
454538 ATCATTACTAT-A
1 ATAATTATTATAA
*
454550 ATGATTATTATCAA
1 ATAATTATTAT-AA
* *
454564 ATCATTA--CTAA
1 ATAATTATTATAA
* * * *
454575 ATCATCA-AATCA
1 ATAATTATTATAA
* *
454587 TTAAATATT-TAA
1 ATAATTATTATAA
*
454599 ATCATTA-T-TAA
1 ATAATTATTATAA
* *
454610 ATCATTTTTAT-A
1 ATAATTATTATAA
*
454622 ATGATTATTACTAA
1 ATAATTATTA-TAA
*
454636 ATCATTATTAT-A
1 ATAATTATTATAA
*
454648 ATGATTATTATCAA
1 ATAATTATTAT-AA
* *
454662 ATCATTACTAT-A
1 ATAATTATTATAA
*
454674 ATGATTATTATCAA
1 ATAATTATTAT-AA
*
454688 ATCATTA
1 ATAATTA
454695 CTAAATCATC
Statistics
Matches: 352, Mismatches: 77, Indels: 77
0.70 0.15 0.15
Matches are distributed among these distances:
10 1 0.00
11 71 0.20
12 142 0.40
13 26 0.07
14 112 0.32
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (13 bp):
ATAATTATTATAA
Found at i:454317 original size:26 final size:26
Alignment explanation
Indices: 454230--454694 Score: 355
Period size: 26 Copynumber: 18.6 Consensus size: 26
454220 ATTAGTAATA
* * *
454230 ATTATTAAATCATTAGTATTAAATCATT
1 ATTATCAAATCATTATTA-T-AATGATT
* * *
454258 ATTAT-AAATAATTACTA-AATAATT
1 ATTATCAAATCATTATTATAATGATT
*
454282 ATTATAAAATCATTATTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
* * *
454308 ATTATCAAATCATTACTA-AATCATC
1 ATTATCAAATCATTATTATAATGATT
* * * * *
454333 A-AATC-ATTAAATATT-TAA--ATC
1 ATTATCAAATCATTATTATAATGATT
* *
454354 ATTATTAAATCATTTTTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
*
454380 ATTA-CTAAATCATTATTATAATAATT
1 ATTATC-AAATCATTATTATAATGATT
*
454406 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
* * *
454432 ATTATCAAATCATTACTA-AATCATC
1 ATTATCAAATCATTATTATAATGATT
* * * * *
454457 A-AATC-ATTAAATATT-TAA--ATC
1 ATTATCAAATCATTATTATAATGATT
* *
454478 ATTATTAAATCATTTTTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
454504 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTATTATAATGATT
*
454530 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
* * *
454556 ATTATCAAATCATTACTA-AATCATC
1 ATTATCAAATCATTATTATAATGATT
* * * * *
454581 A-AATC-ATTAAATATT-TAA--ATC
1 ATTATCAAATCATTATTATAATGATT
* *
454602 ATTATTAAATCATTTTTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
454628 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTATTATAATGATT
*
454654 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
454680 ATTATCAAATCATTA
1 ATTATCAAATCATTA
454695 CTAAATCATC
Statistics
Matches: 350, Mismatches: 61, Indels: 54
0.75 0.13 0.12
Matches are distributed among these distances:
21 12 0.03
22 6 0.02
23 42 0.12
24 29 0.08
25 28 0.08
26 215 0.61
27 13 0.04
28 5 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATCAAATCATTATTATAATGATT
Found at i:454403 original size:124 final size:124
Alignment explanation
Indices: 454230--454746 Score: 923
Period size: 124 Copynumber: 4.2 Consensus size: 124
454220 ATTAGTAATA
* * * *
454230 ATTATTAAATCATTAGTATTA-AATCATTATTA-TAAATAATTACTA-AATAATTATTATAAAAT
1 ATTATTAAATCATT--T-TTATAATGATTATTACTAAATCATTATTATAATAATTATTATCAAAT
*
454292 CATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
63 CATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
454354 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATAATTATTATCAAATCAT
1 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATAATTATTATCAAATCAT
454419 TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
66 TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
*
454478 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATAATTATTATCAAATCAT
454543 TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
66 TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
*
454602 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCAT
1 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATAATTATTATCAAATCAT
454667 TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
66 TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
454726 ATTATTAAATCATTTTTATAA
1 ATTATTAAATCATTTTTATAA
454747 GAGAAAATCG
Statistics
Matches: 384, Mismatches: 6, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
121 3 0.01
122 11 0.03
123 11 0.03
124 359 0.93
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (124 bp):
ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATAATTATTATCAAATCAT
TACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
Found at i:454637 original size:150 final size:145
Alignment explanation
Indices: 454354--454697 Score: 403
Period size: 150 Copynumber: 2.3 Consensus size: 145
454344 TATTTAAATC
* *
454354 ATTATTAAATCATTTTTATAATGATTATTA-CTAAATCATTATTATAATAATTATTATCAAATCA
1 ATTA-TAAATCATTATTATAATGATTATTATC-AAATCATTACTATAATAATTATTATCAAATCA
* * *
454418 TTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTAT
64 TTACTATAATCATAATCATCAAATCATTA-TAAATCAT---ATCATTAAATATTTAAATCATTAT
*
454483 TAAATCATTTTTATAATGATT
125 TAAATCATTATTATAATGATT
*
454504 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTA-TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATAATTATTATCAAATCAT
* *
454569 TACTA-AATCATCAAATCATTAAAT-ATT-TAAATCAT-T-ATTAAATCATTTTTATAATGATTA
65 TACTATAATCAT--AATCATCAAATCATTATAAATCATATCATTAAAT-A--TTTA-AATCATTA
454629 TTACTAAATCATTATTATAATGATT
124 -T--TAAATCATTATTATAATGATT
*
454654 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA
1 ATTAT-AAATCATTATTATAATGATTATTATCAAATCATTACTA
454698 AATCATCAAA
Statistics
Matches: 172, Mismatches: 11, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
143 7 0.04
144 2 0.01
146 4 0.02
147 7 0.04
148 9 0.05
149 6 0.03
150 128 0.74
151 9 0.05
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (145 bp):
ATTATAAATCATTATTATAATGATTATTATCAAATCATTACTATAATAATTATTATCAAATCATT
ACTATAATCATAATCATCAAATCATTATAAATCATATCATTAAATATTTAAATCATTATTAAATC
ATTATTATAATGATT
Found at i:454854 original size:20 final size:20
Alignment explanation
Indices: 454829--455087 Score: 117
Period size: 20 Copynumber: 12.6 Consensus size: 20
454819 AATGACCAAT
454829 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
454849 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
454869 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
454889 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
454910 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
454933 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
454953 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
454973 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
454993 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
455016 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
455036 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
455056 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
455076 AGAATCGCAACG
1 AAAATCGCAACG
455088 TTGAAAATCG
Statistics
Matches: 187, Mismatches: 41, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
20 144 0.77
21 14 0.07
23 29 0.16
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:454988 original size:40 final size:40
Alignment explanation
Indices: 454931--455085 Score: 184
Period size: 40 Copynumber: 3.8 Consensus size: 40
454921 GCGATTTAGA
*
454931 AGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTT
1 AGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTT
* * * *
454971 ATATAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTT
1 AGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTT
* * *
455011 AGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTG
1 ---AGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTT
* * *
455054 AGAGAATCGCAATGCGATTTATAGAATCGCAA
1 AGAAAATCGCAATGCGATTGAGAGAATCGCAA
455086 CGTTGAAAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
40 63 0.66
43 33 0.34
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (40 bp):
AGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTT
Found at i:455022 original size:63 final size:63
Alignment explanation
Indices: 454955--455074 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 63
454945 CGATTGATAG
* * * * * *
454955 AATCGCAATGCGATTTATATAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGAA
*
455018 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTA
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTA
455075 TAGAATCGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (63 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGAA
Found at i:455024 original size:83 final size:83
Alignment explanation
Indices: 454914--455087 Score: 267
Period size: 83 Copynumber: 2.1 Consensus size: 83
454904 GCTTCCAAGT
* * * * * *
454914 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATATAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
*
454979 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAA
454997 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* *
455062 GCAATGCGATTTATAGAA
66 GCAATGCGATTGAGAGAA
455080 TCGCAACG
1 TCGCAACG
455088 TTGAAAATCG
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGAGAGAA
Found at i:455201 original size:6 final size:6
Alignment explanation
Indices: 455190--455262 Score: 114
Period size: 6 Copynumber: 12.5 Consensus size: 6
455180 GACACGTATT
* *
455190 ACCATG ACCATG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
455238 ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
455263 CGAGACGAGA
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
5 10 0.15
6 56 0.85
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:455969 original size:6 final size:6
Alignment explanation
Indices: 455953--455996 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
455943 TCTCGTCTCG
455953 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
455997 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:456099 original size:20 final size:20
Alignment explanation
Indices: 456074--456117 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
456064 TTTTTAACTA
*
456074 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
456094 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
456114 TTCT
1 TTCT
456118 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:456127 original size:20 final size:20
Alignment explanation
Indices: 456104--456402 Score: 152
Period size: 20 Copynumber: 14.6 Consensus size: 20
456094 TTCTTTTTAA
456104 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
456124 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
456144 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
456164 CATTGCGATTCTCTTAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
456184 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
456204 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
456227 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
456247 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
456267 CATTGCAATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
* *
456287 CATTGTGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
456310 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
456331 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
456349 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
456371 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
456391 CGTTGCGATTTT
1 CGTTGCGATTTT
456403 ATTGGTCATT
Statistics
Matches: 221, Mismatches: 47, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
18 2 0.01
20 172 0.78
21 14 0.06
22 6 0.03
23 27 0.12
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:456150 original size:40 final size:40
Alignment explanation
Indices: 456106--456317 Score: 217
Period size: 40 Copynumber: 5.2 Consensus size: 40
456096 CTTTTTAACG
* * *
456106 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCGCA
* * *
456146 TTGCGATTCTATAAATCGCATTGCGATTCTCTTAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCGCA
* * *
456186 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCATTGCGA--TTC-TCTAAATCGCA
* * *
456229 TTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCGCA
* * * * *
456269 TTGCAATTCTATCAATCGCATTGTGATTTTCTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCATTGCGA--TTC-TCTAAATCGCA
456312 TTGCGA
1 TTGCGA
456318 ACTTGGAAGC
Statistics
Matches: 144, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
40 89 0.62
41 3 0.02
42 6 0.04
43 46 0.32
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTAAATCGCA
Found at i:456253 original size:83 final size:83
Alignment explanation
Indices: 456106--456317 Score: 268
Period size: 83 Copynumber: 2.6 Consensus size: 83
456096 CTTTTTAACG
* * * * * *
456106 TTGCGATTTTCTAAATCGCGTTGCGA--TTC-TCTCAATCGCATTGCGATTCTATAAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
* * *
456168 GCGATTCTCTTAGTCGCA
66 GCGATTCTATAAATCGCA
* * *
456186 TTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATT
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
456251 GCGATTCTATAAATCGCA
66 GCGATTCTATAAATCGCA
* * *
456269 TTGCAATTCTATCAATCGCATTGTGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
456318 ACTTGGAAGC
Statistics
Matches: 113, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
80 22 0.19
82 3 0.03
83 88 0.78
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (83 bp):
TTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTATAAATCGCATT
GCGATTCTATAAATCGCA
Found at i:456521 original size:26 final size:26
Alignment explanation
Indices: 456489--456594 Score: 178
Period size: 26 Copynumber: 4.1 Consensus size: 26
456479 TTTCTCTTTT
*
456489 TATAATGATTATTA-CTAAATCATTAT
1 TATAATGATTATTATC-AAATCATTAC
456515 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTATCAAATCATTAC
*
456541 TATAATGATTATTATTAAATCATTAC
1 TATAATGATTATTATCAAATCATTAC
456567 TATAATGATTATTATCAAATCATTAC
1 TATAATGATTATTATCAAATCATTAC
456593 TA
1 TA
456595 AATCATCAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 75 0.99
27 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (26 bp):
TATAATGATTATTATCAAATCATTAC
Found at i:458201 original size:26 final size:24
Alignment explanation
Indices: 458141--458201 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
458131 TACTAATATT
*
458141 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
458165 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
458192 ATTTAATAAT
1 A-TTAATAAT
458202 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:458588 original size:14 final size:14
Alignment explanation
Indices: 458569--458595 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
458559 CACATACACA
458569 ACAACAAAAAATAG
1 ACAACAAAAAATAG
458583 ACAACAAAAAATA
1 ACAACAAAAAATA
458596 ATAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:458588 original size:17 final size:17
Alignment explanation
Indices: 458566--458598 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
458556 TTACACATAC
458566 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
458583 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
458599 AATTACTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:459029 original size:21 final size:21
Alignment explanation
Indices: 458996--459044 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
458986 AATATAATAT
*
458996 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
459017 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
459038 ATTAACT
1 A-TAACT
459045 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:459516 original size:35 final size:35
Alignment explanation
Indices: 459476--459543 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
459466 TGGATGCAAC
459476 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
459511 GCATGCATGAGTGATACAGTTAAAGCTTGGTCG
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCG
459544 CGATGCAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (35 bp):
GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
Found at i:459600 original size:12 final size:12
Alignment explanation
Indices: 459583--459607 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
459573 TCCATGGCGA
459583 CCTACCACCTAC
1 CCTACCACCTAC
459595 CCTACCACCTAC
1 CCTACCACCTAC
459607 C
1 C
459608 ATGTCGTCGG
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:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCTACCACCTAC
Found at i:459840 original size:31 final size:31
Alignment explanation
Indices: 459805--459869 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
459795 CCCATGCATA
459805 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
1 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
459836 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
1 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
459867 GCA
1 GCA
459870 AAGAACCAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.32, G:0.29, T:0.03
Consensus pattern (31 bp):
GCACCAAAGCAGCATCAGCGAGCAACAGCGG
Found at i:463467 original size:47 final size:47
Alignment explanation
Indices: 463394--463484 Score: 157
Period size: 47 Copynumber: 1.9 Consensus size: 47
463384 CAGAATGCAT
463394 GCCTTTGGCAATTGAAATAAGAAACAGCTGCTTCTTAAATAACACAA
1 GCCTTTGGCAATTGAAATAAGAAACAGCTGCTTCTTAAATAACACAA
*
463441 GCCTTTGGCAATTGAAATGAA-CAACAGCTGCTTCTTAAATAACA
1 GCCTTTGGCAATTGAAAT-AAGAAACAGCTGCTTCTTAAATAACA
463485 ATAAGAATTC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
47 40 0.95
48 2 0.05
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.26
Consensus pattern (47 bp):
GCCTTTGGCAATTGAAATAAGAAACAGCTGCTTCTTAAATAACACAA
Found at i:479517 original size:19 final size:19
Alignment explanation
Indices: 479485--479521 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
479475 ATGACCAACA
* *
479485 AAATCGCAATGCGATCTCT
1 AAATCACAACGCGATCTCT
479504 AAATCACAACGCGATCTC
1 AAATCACAACGCGATCTC
479522 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCACAACGCGATCTCT
Found at i:479651 original size:20 final size:20
Alignment explanation
Indices: 479628--479698 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
479618 GAATATGTAA
479628 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
479648 ATCGCAACGTGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
*
479668 AATCACAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
479689 GTCGCAACGC
1 ATCGCAACGC
479699 TGAATTTTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.05
20 22 0.56
21 13 0.33
22 2 0.05
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:480541 original size:24 final size:24
Alignment explanation
Indices: 480514--480579 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
480504 GTATTCGAAA
480514 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
480538 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
480562 TTTGATCTTGGTCAATAC
1 TTTGATCTTGGTCAATAC
480580 TCAGATTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:482621 original size:20 final size:20
Alignment explanation
Indices: 482572--482638 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
482562 TCTGAAACTC
* *
482572 AAAATCACAACACTAAAATG
1 AAAATCGCAACACGAAAATG
*
482592 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
482612 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
482631 AAAATCGC
1 AAAATCGC
482639 GTTGCGATTT
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 6 0.16
20 31 0.84
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:482956 original size:22 final size:22
Alignment explanation
Indices: 482929--482986 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
482919 GATGGAGATA
482929 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
482951 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
482973 GACGGATGTCGCCG
1 GACGGATTTCGCCG
482987 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.45, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:483288 original size:19 final size:19
Alignment explanation
Indices: 483264--483300 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
483254 TACGATACTG
* *
483264 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
483283 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
483301 TGTTGATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:494681 original size:24 final size:23
Alignment explanation
Indices: 494653--494697 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
494643 TTTCGACTAC
*
494653 AAAATATTTTAAATATTTAAATGA
1 AAAATATTATAAAT-TTTAAATGA
*
494677 AAAATATTATATATTTTAAAT
1 AAAATATTATAAATTTTAAAT
494698 ATTGATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AAAATATTATAAATTTTAAATGA
Found at i:515221 original size:10 final size:9
Alignment explanation
Indices: 515206--515265 Score: 66
Period size: 10 Copynumber: 6.3 Consensus size: 9
515196 CCGGTTTTCA
515206 ACCGGTTCTG
1 ACCGGTT-TG
515216 ACCGGTTTG
1 ACCGGTTTG
*
515225 ACCGGTTTCA
1 ACCGGTTT-G
*
515235 ACCGGTTCG
1 ACCGGTTTG
515244 AACCGGTTTG
1 -ACCGGTTTG
*
515254 ACCGGTCTG
1 ACCGGTTTG
515263 ACC
1 ACC
515266 CGACCAGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
9 21 0.49
10 22 0.51
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:515230 original size:19 final size:19
Alignment explanation
Indices: 515206--515265 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
515196 CCGGTTTTCA
515206 ACCGGTTCTGACCGGTT-TG
1 ACCGGTT-TGACCGGTTCTG
*
515225 ACCGGTTTCAACCGGTTC-G
1 ACCGGTTT-GACCGGTTCTG
515244 AACCGGTTTGACCGG-TCTG
1 -ACCGGTTTGACCGGTTCTG
515263 ACC
1 ACC
515266 CGACCAGACC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 6 0.17
19 21 0.60
20 8 0.23
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.27
Consensus pattern (19 bp):
ACCGGTTTGACCGGTTCTG
Found at i:515238 original size:29 final size:29
Alignment explanation
Indices: 515195--515259 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 29
515185 GCTGCTGGAA
515195 ACCGGTTTTCAACCGGTTCTG-ACCGGTTTG
1 ACCGG-TTTCAACCGGTTC-GAACCGGTTTG
515225 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTTCAACCGGTTCGAACCGGTTTG
515254 ACCGGT
1 ACCGGT
515260 CTGACCCGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.82
30 5 0.15
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.29
Consensus pattern (29 bp):
ACCGGTTTCAACCGGTTCGAACCGGTTTG
Found at i:515291 original size:22 final size:21
Alignment explanation
Indices: 515265--515326 Score: 88
Period size: 22 Copynumber: 2.9 Consensus size: 21
515255 CCGGTCTGAC
*
515265 CCGACCAGACCGTTGACCCGAA
1 CCGACCCGACCGTTGACCCG-A
515287 CCGACCCGACCGTTGACCCGA
1 CCGACCCGACCGTTGACCCGA
*
515308 CCTAACCCGACCGTTGACC
1 CC-GACCCGACCGTTGACC
515327 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 3 0.08
22 34 0.92
ACGTcount: A:0.23, C:0.45, G:0.21, T:0.11
Consensus pattern (21 bp):
CCGACCCGACCGTTGACCCGA
Found at i:523791 original size:17 final size:18
Alignment explanation
Indices: 523769--523807 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
523759 TTATGCTATT
523769 TATTATTTA-TATTATAA
1 TATTATTTATTATTATAA
523786 TATTATTTATTATTATAA
1 TATTATTTATTATTATAA
523804 -ATTA
1 TATTA
523808 AATTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATTTATTATTATAA
Found at i:524393 original size:3 final size:3
Alignment explanation
Indices: 524385--524413 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
524375 TATCTCTCAA
524385 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
524414 CTGTCCTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:526940 original size:14 final size:14
Alignment explanation
Indices: 526921--526947 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
526911 TATTTTAAAA
526921 TTTAATTAATTTTT
1 TTTAATTAATTTTT
526935 TTTAATTAATTTT
1 TTTAATTAATTTT
526948 GATTCGATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAATTAATTTTT
Found at i:533720 original size:50 final size:50
Alignment explanation
Indices: 533665--533769 Score: 210
Period size: 50 Copynumber: 2.1 Consensus size: 50
533655 GTCCGGATAT
533665 TCCTCTCTGATTTTTTATATCAAGAGAGTTCCCATCCCAGAGCCTGTTCC
1 TCCTCTCTGATTTTTTATATCAAGAGAGTTCCCATCCCAGAGCCTGTTCC
533715 TCCTCTCTGATTTTTTATATCAAGAGAGTTCCCATCCCAGAGCCTGTTCC
1 TCCTCTCTGATTTTTTATATCAAGAGAGTTCCCATCCCAGAGCCTGTTCC
533765 TCCTC
1 TCCTC
533770 CTAGTGAATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.36
Consensus pattern (50 bp):
TCCTCTCTGATTTTTTATATCAAGAGAGTTCCCATCCCAGAGCCTGTTCC
Found at i:536839 original size:19 final size:20
Alignment explanation
Indices: 536807--536860 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
536797 TTTCTATTTA
* *
536807 GTAAATTTATATTTTGAAAT
1 GTAATTTTATATTTTAAAAT
*
536827 TTAATTTTA-ATTTTAAAAT
1 GTAATTTTATATTTTAAAAT
*
536846 GTAATTTGATATTTT
1 GTAATTTTATATTTT
536861 TTAAGTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
GTAATTTTATATTTTAAAAT
Found at i:540429 original size:9 final size:9
Alignment explanation
Indices: 540415--540439 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
540405 ACTGTCAATT
540415 TTTTTTTAA
1 TTTTTTTAA
540424 TTTTTTTAA
1 TTTTTTTAA
540433 TTTTTTT
1 TTTTTTT
540440 GGTATAAGCA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:555850 original size:2 final size:2
Alignment explanation
Indices: 555843--555872 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
555833 TATAGATTTA
555843 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
555873 CATAACAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:555956 original size:24 final size:23
Alignment explanation
Indices: 555929--555982 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
555919 TATTCTGTAC
*
555929 TTAAATAATACATAA-ATAATATGA
1 TTAAAT-ATA-ATAACATAAAATGA
*
555953 TTAAAGTATAATAACTTAAAATGA
1 TTAAA-TATAATAACATAAAATGA
555977 TTAAAT
1 TTAAAT
555983 TTAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 20 0.77
25 1 0.04
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (23 bp):
TTAAATATAATAACATAAAATGA
Found at i:556131 original size:17 final size:17
Alignment explanation
Indices: 556094--556131 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
556084 AGTCTTTATT
*
556094 TTTTTAAAATTTTGAAG
1 TTTTTAAAATTTCGAAG
556111 TTTTTAAAATATTCGAA-
1 TTTTTAAAAT-TTCGAAG
556128 TTTT
1 TTTT
556132 GTTGAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (17 bp):
TTTTTAAAATTTCGAAG
Found at i:557770 original size:25 final size:25
Alignment explanation
Indices: 557736--557785 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
557726 TTCAGTTGAA
557736 ATCCTAATGCGCTAATTGATTTTAC
1 ATCCTAATGCGCTAATTGATTTTAC
557761 ATCCTAATGCGCTAATTGATTTTAC
1 ATCCTAATGCGCTAATTGATTTTAC
557786 TGATTCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (25 bp):
ATCCTAATGCGCTAATTGATTTTAC
Found at i:558431 original size:72 final size:75
Alignment explanation
Indices: 558353--558496 Score: 249
Period size: 72 Copynumber: 2.0 Consensus size: 75
558343 TTAGAAAAAA
*
558353 TAAAATAAATTAAAATAAAAAATAAAGTCAAATTATTAATACCATTAATATTATGTT-AT-TTTT
1 TAAAATAAATTAAAATAAAAAATAAAGTCAAATTATTAATACCATTAAAATTATGTTAATCTTTT
558416 T-ATAAACAT
66 TCATAAACAT
*
558425 TAAAATAATTTAAAATAAAAAATAAAGTCAAATTATTAATACCATTAAAATTATGTTAATCTTTT
1 TAAAATAAATTAAAATAAAAAATAAAGTCAAATTATTAATACCATTAAAATTATGTTAATCTTTT
558490 TCATAAA
66 TCATAAA
558497 TTTAAAGTTA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 55 0.82
73 2 0.03
74 5 0.07
75 5 0.07
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (75 bp):
TAAAATAAATTAAAATAAAAAATAAAGTCAAATTATTAATACCATTAAAATTATGTTAATCTTTT
TCATAAACAT
Found at i:559125 original size:21 final size:21
Alignment explanation
Indices: 559099--559150 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
559089 TTACTAAAAA
*
559099 TATTATTATTTCTATCGGTTT
1 TATTATTATTTCTATCGATTT
* *
559120 TATTATTTTTTCTATTGATTT
1 TATTATTATTTCTATCGATTT
559141 TATTATTATT
1 TATTATTATT
559151 GGGTACTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (21 bp):
TATTATTATTTCTATCGATTT
Found at i:561308 original size:20 final size:21
Alignment explanation
Indices: 561283--561375 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
561273 TTTTCCCAAT
*
561283 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
561303 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
561324 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
561344 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
561365 TCGCAATGCGA
1 TCGCAATGCGA
561376 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:561328 original size:41 final size:41
Alignment explanation
Indices: 561283--561375 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
561273 TTTTCCCAAT
561283 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
561324 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
561365 TCGCAATGCGA
1 TCGCAATGCGA
561376 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:561388 original size:41 final size:41
Alignment explanation
Indices: 561302--561436 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
561292 GAATAAGTAA
** *
561302 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
561343 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
561384 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
561425 TTCGCAACGCGA
1 ATCGCAACGCGA
561437 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Done.