Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, 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: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 8 of 29
Found at i:2783079 original size:45 final size:46
Alignment explanation
Indices: 2782984--2783121 Score: 115
Period size: 45 Copynumber: 3.0 Consensus size: 46
2782974 GCCTAGAGAA
* * *
2782984 CAATCATGCAATGCCACAAAAACTAGTTACGCAATGCCCTATCAAG
1 CAATCAAGCAATGCCACAAAAACCAGTTACGCAATGCCCTATCAAC
* * * *
2783030 CAATCAAGCAATGCC-TAAAAACCGGTTATGCAATGTCCTA-CAAAC
1 CAATCAAGCAATGCCACAAAAACCAGTTACGCAATGCCCTATC-AAC
** * *
2783075 CAATCACA-CAATGCC-CTATCAACCAGTCACACAATG-CCTATCAAC
1 CAATCA-AGCAATGCCAC-AAAAACCAGTTACGCAATGCCCTATCAAC
2783120 CA
1 CA
2783122 GTCACGTAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
44 1 0.01
45 44 0.59
46 29 0.39
ACGTcount: A:0.39, C:0.31, G:0.11, T:0.19
Consensus pattern (46 bp):
CAATCAAGCAATGCCACAAAAACCAGTTACGCAATGCCCTATCAAC
Found at i:2783117 original size:22 final size:23
Alignment explanation
Indices: 2783072--2783126 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
2783062 ATGTCCTACA
*
2783072 AACCAATCACACAATGCCCTATC
1 AACCAGTCACACAATGCCCTATC
2783095 AACCAGTCACACAATG-CCTATC
1 AACCAGTCACACAATGCCCTATC
2783117 AACCAGTCAC
1 AACCAGTCAC
2783127 GTAATACCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.38, C:0.38, G:0.07, T:0.16
Consensus pattern (23 bp):
AACCAGTCACACAATGCCCTATC
Found at i:2783136 original size:22 final size:22
Alignment explanation
Indices: 2783089--2783167 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
2783079 CACACAATGC
* *
2783089 CCTATCAACCAGTCACACAATG
1 CCTATCAACCAGTCACGCAATA
*
2783111 CCTATCAACCAGTCACGTAATA
1 CCTATCAACCAGTCACGCAATA
** *
2783133 CCTAAAAACTCA-TCATGCAATA
1 CCTATCAAC-CAGTCACGCAATA
*
2783155 CATATCAACCAGT
1 CCTATCAACCAGT
2783168 TAACAATGAC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 2 0.04
22 41 0.91
23 2 0.04
ACGTcount: A:0.39, C:0.32, G:0.08, T:0.22
Consensus pattern (22 bp):
CCTATCAACCAGTCACGCAATA
Found at i:2783255 original size:23 final size:23
Alignment explanation
Indices: 2783223--2783274 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2783213 ACCTAAAATT
* * *
2783223 AGTCATGCAATGCTCTTTCAACC
1 AGTCACGCAATGCCCTATCAACC
2783246 AGTCACGCAATGCCCTATCAACC
1 AGTCACGCAATGCCCTATCAACC
*
2783269 AATCAC
1 AGTCAC
2783275 ACATTAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.23
Consensus pattern (23 bp):
AGTCACGCAATGCCCTATCAACC
Found at i:2783456 original size:22 final size:22
Alignment explanation
Indices: 2783414--2783457 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2783404 TCAGGGAATG
*
2783414 TCCTAAAAATCAGTTACGTAAT
1 TCCTAAAAATCAGTCACGTAAT
* *
2783436 TCCTAAAAATTAGTCATGTAAT
1 TCCTAAAAATCAGTCACGTAAT
2783458 CCCTCATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (22 bp):
TCCTAAAAATCAGTCACGTAAT
Found at i:2789058 original size:10 final size:10
Alignment explanation
Indices: 2789045--2789118 Score: 85
Period size: 10 Copynumber: 7.3 Consensus size: 10
2789035 TTAGTTTTGC
2789045 TTTTTTCTTT
1 TTTTTTCTTT
2789055 TTTTTTCTTT
1 TTTTTTCTTT
2789065 TTTTTTCTTT
1 TTTTTTCTTT
* *
2789075 TCTCTTTCTGT
1 T-TTTTTCTTT
* *
2789086 TTCTCTCTTT
1 TTTTTTCTTT
*
2789096 TATTTTCTTT
1 TTTTTTCTTT
*
2789106 TTTTTTGTTT
1 TTTTTTCTTT
2789116 TTT
1 TTT
2789119 CTCCCCAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
10 46 0.85
11 8 0.15
ACGTcount: A:0.01, C:0.14, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:2789929 original size:22 final size:23
Alignment explanation
Indices: 2789899--2789941 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2789889 AGAACCAAAA
2789899 AAATGAAAATAAGC-AACTAAATG
1 AAATGAAAAT-AGCAAACTAAATG
2789922 AAAT-AAAATAGCAAACTAAA
1 AAATGAAAATAGCAAACTAAA
2789942 CAGTTTAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 12 0.63
23 4 0.21
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.16
Consensus pattern (23 bp):
AAATGAAAATAGCAAACTAAATG
Found at i:2790394 original size:28 final size:30
Alignment explanation
Indices: 2790326--2790391 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 30
2790316 CTTAAATATA
*
2790326 TTTTTAATGTCATATATTTTATTTTCATTTC
1 TTTTTAATCTCATATATTTTATTTTCA-TTC
*
2790357 TTATTATAATCTTATATATTTTATTTTCATT-
1 TT-TT-TAATCTCATATATTTTATTTTCATTC
2790388 TTTT
1 TTTT
2790392 AATATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 2 0.06
31 4 0.13
32 4 0.13
33 21 0.68
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.67
Consensus pattern (30 bp):
TTTTTAATCTCATATATTTTATTTTCATTC
Found at i:2790410 original size:33 final size:33
Alignment explanation
Indices: 2790337--2790399 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
2790327 TTTTAATGTC
* *
2790337 ATATATTTTATTTTCATTTCTTATTATAATCTT
1 ATATATTTTATTTTCATTTTTTAATATAATCTT
2790370 ATATATTTTATTTTCATTTTTTAATATAAT
1 ATATATTTTATTTTCATTTTTTAATATAAT
2790400 TTTTTGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.63
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTTTTAATATAATCTT
Found at i:2790514 original size:15 final size:15
Alignment explanation
Indices: 2790491--2790522 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2790481 TTCTTTTATT
2790491 ATATATTTTATTTTA
1 ATATATTTTATTTTA
*
2790506 ATATTTTTTATTTTA
1 ATATATTTTATTTTA
2790521 AT
1 AT
2790523 TATAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:2790520 original size:32 final size:32
Alignment explanation
Indices: 2790460--2790526 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
2790450 TTTTATTTTT
*
2790460 TATATTTTATTTAATTTTTAATTCTTTT-ATTA
1 TATATTTTATTTAATTTTT-ATTATTTTAATTA
2790492 TATATTTTATTTTAATATTTT-TTATTTTAATTA
1 TATATTTTA-TTTAAT-TTTTATTATTTTAATTA
2790525 TA
1 TA
2790527 AAATTACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 15 0.48
33 12 0.39
34 4 0.13
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (32 bp):
TATATTTTATTTAATTTTTATTATTTTAATTA
Found at i:2799213 original size:39 final size:38
Alignment explanation
Indices: 2799148--2799227 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 38
2799138 GGGACACAAC
* *
2799148 AGATGGGCCTGTAACTTCTTTTTTAGGGAACAAATATG
1 AGATGAGCCTGTAACTCCTTTTTTAGGGAACAAATATG
2799186 AGATGAGCCTGTTAACTCCTTTTTTAGGGAACAAATATG
1 AGATGAGCCTG-TAACTCCTTTTTTAGGGAACAAATATG
2799225 AGA
1 AGA
2799228 ATGTTAGCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 10 0.26
39 29 0.74
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.33
Consensus pattern (38 bp):
AGATGAGCCTGTAACTCCTTTTTTAGGGAACAAATATG
Found at i:2799555 original size:2 final size:2
Alignment explanation
Indices: 2799548--2799574 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2799538 CTTGATATGA
2799548 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2799575 GCATTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2806007 original size:17 final size:17
Alignment explanation
Indices: 2805987--2806025 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2805977 CATTTTAGAC
* *
2805987 TAAAGCAATATTTAAAG
1 TAAAGCAAAATTTAAAA
2806004 TAAAGCAAAATTTAAAA
1 TAAAGCAAAATTTAAAA
2806021 TAAAG
1 TAAAG
2806026 AAGTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (17 bp):
TAAAGCAAAATTTAAAA
Found at i:2806069 original size:17 final size:17
Alignment explanation
Indices: 2806044--2806077 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2806034 TTCTTTTTGG
* *
2806044 AATTTAAAGTAAACCAA
1 AATTCAAAGCAAACCAA
2806061 AATTCAAAGCAAACCAA
1 AATTCAAAGCAAACCAA
2806078 TGGTTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.18, G:0.06, T:0.18
Consensus pattern (17 bp):
AATTCAAAGCAAACCAA
Found at i:2812545 original size:22 final size:23
Alignment explanation
Indices: 2812520--2812569 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2812510 ATATGAGCTT
2812520 CATAAAAT-TAAAATGAAGTCCA
1 CATAAAATATAAAATGAAGTCCA
* *
2812542 CATAACATATAAAATGGAGTCCA
1 CATAAAATATAAAATGAAGTCCA
2812565 -ATAAA
1 CATAAA
2812570 GAAGTCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.54, C:0.14, G:0.10, T:0.22
Consensus pattern (23 bp):
CATAAAATATAAAATGAAGTCCA
Found at i:2818034 original size:2 final size:2
Alignment explanation
Indices: 2818027--2818075 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2818017 ATTGATTCTC
*
2818027 AT AT AT AT AT AT AT AT AT AT AT CT 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
2818069 AT AT AT A
1 AT AT AT A
2818076 AGATGTGTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2818578 original size:86 final size:83
Alignment explanation
Indices: 2818419--2818588 Score: 286
Period size: 86 Copynumber: 2.0 Consensus size: 83
2818409 CAGTTAGAAA
*
2818419 TGAAGTTTCAAGATTTCACAGAGAAGTAAAACAGAACCAACTGTACCATTGGTCATTAACATTCC
1 TGAAGTTTCAAGATTTCACAGAGAAGTAAAACAGAACCAACTGAACCATTGGTCATTAACATTCC
2818484 AATTGCATTTGCATTTGT
66 AATTGCATTTGCATTTGT
* *
2818502 TGAAGTTTCCAGATTTCACAGAGGAAGTAAAACAGAGCCAACTGAACCATTTTGGTCATTAACAT
1 TGAAGTTTCAAGATTTCACAGA-GAAGTAAAACAGAACCAACTGAACCA--TTGGTCATTAACAT
2818567 TCCAATTGCATTTGCATTTGT
63 TCCAATTGCATTTGCATTTGT
2818588 T
1 T
2818589 AACTAAGTGA
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
83 21 0.26
84 24 0.30
86 36 0.44
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (83 bp):
TGAAGTTTCAAGATTTCACAGAGAAGTAAAACAGAACCAACTGAACCATTGGTCATTAACATTCC
AATTGCATTTGCATTTGT
Found at i:2822082 original size:40 final size:40
Alignment explanation
Indices: 2822038--2822118 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
2822028 GCATTAAAAA
* *
2822038 TGCCTCATCATCCATAGTCGCATAAGTTTGCTATGTCCTT
1 TGCCTCATCATCCACAGTCGCATAAGTTTCCTATGTCCTT
*
2822078 TGCCTCATCATCCACAGTCTCATAAGTTTCCTATGTCCTT
1 TGCCTCATCATCCACAGTCGCATAAGTTTCCTATGTCCTT
2822118 T
1 T
2822119 TGCTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.38
Consensus pattern (40 bp):
TGCCTCATCATCCACAGTCGCATAAGTTTCCTATGTCCTT
Found at i:2839312 original size:44 final size:46
Alignment explanation
Indices: 2839257--2839385 Score: 158
Period size: 44 Copynumber: 2.8 Consensus size: 46
2839247 TGTTCAGCCT
* *
2839257 AATATTATTTATTTTGGATCAGACTAATAGCATAAAAG-CAAA-CC
1 AATATTCTTTATTTTGGATCAGACTAATAGCATAAAAGAAAAACCC
**
2839301 AATATTCTTTATTTTGTTTCAGACTAATAGCATAAAAAGATAAAACCC
1 AATATTCTTTATTTTGGATCAGACTAATAGCAT-AAAAGA-AAAACCC
2839349 AATA-TCATTTATTTT-GATCTAGACTAATAGCATAAAA
1 AATATTC-TTTATTTTGGATC-AGACTAATAGCATAAAA
2839386 AGGCAAATCT
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
44 30 0.41
45 5 0.07
47 11 0.15
48 27 0.37
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (46 bp):
AATATTCTTTATTTTGGATCAGACTAATAGCATAAAAGAAAAACCC
Found at i:2839408 original size:48 final size:46
Alignment explanation
Indices: 2839257--2839415 Score: 164
Period size: 48 Copynumber: 3.4 Consensus size: 46
2839247 TGTTCAGCCT
2839257 AATATTATTTATTTTGGATC-AGACTAATAGCAT-AAAA-GCAAACC
1 AATATTATTTATTTT-GATCTAGACTAATAGCATAAAAAGGCAAACC
* * **
2839301 AATATTCTTTATTTTG-TTTCAGACTAATAGCATAAAAAGATAAAACCC
1 AATATTATTTATTTTGATCT-AGACTAATAGCATAAAAAG-GCAAA-CC
* *
2839349 AATATCATTTATTTTGATCTAGACTAATAGCATAAAAAGGCAAATCTT
1 AATATTATTTATTTTGATCTAGACTAATAGCATAAAAAGGCAAA-C-C
* *
2839397 AATATTTTTTATTCTGATC
1 AATATTATTTATTTTGATC
2839416 CAATCTATTT
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 27 0.29
45 4 0.04
47 7 0.08
48 51 0.55
49 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (46 bp):
AATATTATTTATTTTGATCTAGACTAATAGCATAAAAAGGCAAACC
Found at i:2840795 original size:19 final size:18
Alignment explanation
Indices: 2840765--2840804 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
2840755 TTTTTAGTTA
2840765 TTTTATAATTA-TTTAAT
1 TTTTATAATTATTTTAAT
2840782 TTTTATTAAGTTATTTTAAT
1 TTTTA-TAA-TTATTTTAAT
2840802 TTT
1 TTT
2840805 ATGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 3 0.15
19 3 0.15
20 9 0.45
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTATAATTATTTTAAT
Found at i:2840805 original size:19 final size:17
Alignment explanation
Indices: 2840764--2840806 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
2840754 ATTTTTAGTT
2840764 ATTTTA-TAATTATTTA
1 ATTTTATTAATTATTTA
2840780 ATTTTTATTAAGTTATTTTA
1 A-TTTTATTAA-TTA-TTTA
2840800 ATTTTAT
1 ATTTTAT
2840807 GTTTATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 5 0.22
18 3 0.13
19 9 0.39
20 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTATTAATTATTTA
Found at i:2845162 original size:3 final size:3
Alignment explanation
Indices: 2845154--2845207 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
2845144 CGTTTCTTGC
2845154 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2845202 ATT ATT
1 ATT ATT
2845208 TCCTCTATCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2850380 original size:24 final size:24
Alignment explanation
Indices: 2850321--2850383 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 24
2850311 CTTGATCGTT
*
2850321 CATTTATATATTATTTTATTATTA
1 CATTTAAATATTATTTTATTATTA
2850345 CATTAATAAAATATTATTTTA-TATTGA
1 CATT--T-AAATATTATTTTATTATT-A
*
2850372 TATTTAAATATT
1 CATTTAAATATT
2850384 TTTCAAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 11 0.33
25 1 0.03
26 5 0.15
27 16 0.48
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (24 bp):
CATTTAAATATTATTTTATTATTA
Found at i:2851827 original size:23 final size:22
Alignment explanation
Indices: 2851790--2851833 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2851780 CCCCCTCCCC
2851790 TAATTCTAAAAAAAAAAATTTG
1 TAATTCTAAAAAAAAAAATTTG
2851812 TAATTCTAAAAAAAAAAATTTG
1 TAATTCTAAAAAAAAAAATTTG
2851834 GGAACGTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (22 bp):
TAATTCTAAAAAAAAAAATTTG
Found at i:2853767 original size:18 final size:19
Alignment explanation
Indices: 2853732--2853767 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2853722 CAAACTTAAC
*
2853732 AAATTATTTTCTTTTTATT
1 AAATTATTTTCATTTTATT
2853751 AAATTATTTT-ATTTTAT
1 AAATTATTTTCATTTTAT
2853768 GATCACCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
AAATTATTTTCATTTTATT
Found at i:2862458 original size:68 final size:68
Alignment explanation
Indices: 2862374--2862617 Score: 213
Period size: 68 Copynumber: 3.6 Consensus size: 68
2862364 CTTAATCCTT
* * * * * * *
2862374 TCATATAGTATATGGAATTCACATCATATGCACAAGCTCATAGCATGTATTATTCATACTTATTC
1 TCATATGGTATATGGAATTTACATCATATACACAATCTCAGAGCATGTATCATACATACTTATTC
2862439 ATC
66 ATC
* ** ** * * *
2862442 T-ATTATGGTGTATGGAATTTACAAGATATATGCATTCTCAGAGCATTTATCATACATGCTTATT
1 TCA-TATGGTATATGGAATTTACATCATATACACAATCTCAGAGCATGTATCATACATACTTATT
2862506 CATC
65 CATC
* ** * * * *
2862510 TCATATGGTATATGGAATTTACATCATATACACAATCTCAAAATATTTATTATGCATGCTTAATT
1 TCATATGGTATATGGAATTTACATCATATACACAATCTCAGAGCATGTATCATACATACTT-ATT
2862575 -ATC
65 CATC
* * ** *
2862578 TTATACGGTATATAAAATTTACATCATATACATAATCTCA
1 TCATATGGTATATGGAATTTACATCATATACACAATCTCA
2862618 TGGCATTAAT
Statistics
Matches: 142, Mismatches: 31, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
67 1 0.01
68 137 0.96
69 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (68 bp):
TCATATGGTATATGGAATTTACATCATATACACAATCTCAGAGCATGTATCATACATACTTATTC
ATC
Found at i:2871748 original size:31 final size:33
Alignment explanation
Indices: 2871712--2871788 Score: 81
Period size: 32 Copynumber: 2.4 Consensus size: 33
2871702 TTTTTTTTGT
*
2871712 TTCAATTTAGTCCT-CATA-CACTGAA-TTTTTA
1 TTCAATTTAGTCCTCCATACCA-TAAACTTTTTA
* * *
2871743 TTCAATTAAGT-CTCCGTACCATAAACTTTTTC
1 TTCAATTTAGTCCTCCATACCATAAACTTTTTA
2871775 TTCAATTTAGTCCT
1 TTCAATTTAGTCCT
2871789 TCTAATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
30 2 0.05
31 16 0.43
32 17 0.46
33 2 0.05
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.44
Consensus pattern (33 bp):
TTCAATTTAGTCCTCCATACCATAAACTTTTTA
Found at i:2872976 original size:1 final size:1
Alignment explanation
Indices: 2872970--2873009 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
2872960 GTGTTTGTTG
2872970 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2873010 GCTTGTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2889291 original size:26 final size:27
Alignment explanation
Indices: 2889239--2889293 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
2889229 TCTTTCCTTC
* * *
2889239 TTTATATGTTTATTAGTATTATTTAAA
1 TTTATATGTCTATTAATATTATCTAAA
*
2889266 TTTATATGTCT-TTAATATTCTCTAAA
1 TTTATATGTCTATTAATATTATCTAAA
2889292 TT
1 TT
2889294 GATTAGGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.58
Consensus pattern (27 bp):
TTTATATGTCTATTAATATTATCTAAA
Found at i:2890421 original size:19 final size:20
Alignment explanation
Indices: 2890399--2890446 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
2890389 ATAATAATAT
2890399 TAAAAAATAGT-AATATTTA
1 TAAAAAATAGTCAATATTTA
* * * *
2890418 TAAAAAGTATTCGATTTTTA
1 TAAAAAATAGTCAATATTTA
2890438 TAAAAAATA
1 TAAAAAATA
2890447 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (20 bp):
TAAAAAATAGTCAATATTTA
Found at i:2891488 original size:26 final size:26
Alignment explanation
Indices: 2891440--2891501 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
2891430 AAATCGTCAC
* *
2891440 ACAAGCACAACACAATGAGAAGAACA
1 ACAAACACAACACAATGACAAGAACA
* * * *
2891466 ATAATCACAACACAGTTACAAGAACA
1 ACAAACACAACACAATGACAAGAACA
2891492 ACAAACACAA
1 ACAAACACAA
2891502 TATATATACA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.58, C:0.24, G:0.10, T:0.08
Consensus pattern (26 bp):
ACAAACACAACACAATGACAAGAACA
Found at i:2891546 original size:4 final size:4
Alignment explanation
Indices: 2891539--2891566 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2891529 ATATATATAT
2891539 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2891567 TGCAACATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:2893868 original size:439 final size:416
Alignment explanation
Indices: 2893141--2893989 Score: 1119
Period size: 439 Copynumber: 2.0 Consensus size: 416
2893131 TTTTTTGAAA
*
2893141 TTTTAAAAAATAAAAAGCTATTTTGGTTTCTTTTACTTTTTAGAAAGTTTTTTTTATAATTTTTT
1 TTTTAAAAAATAAAAAGCTATTTTGGTTTCTTGTACTTTTTAGAAAGTTTTTTTTATAATTTTTT
*
2893206 TGAAAAATAAAAATGATCTTTAGTTTTAAAAATTTAAAAATTATTTATGTTTCTTGTTATTCAAT
66 TGAAAAATAAAAATGATCTTTACTTTTAAAAATTTAAAAATTATTTATGTTTCTTGTTATTCAAT
* * *
2893271 TTTAAAAAATTAATTCTCTTCGATAACACAAGTTCACATAAGGAATGCTATTGTATTTAATAAAA
131 TTTAAAAAATTAATTCTCTCCGATAACACAAATTCACATAAGGAATGCTATTATATTTAATAAAA
** * * * * *
2893336 TAGGATAAAATACTCACTTTTCTTAACTTTTAGTTATAATTTTACACGAATTTATTAATTTTTAA
196 TAAAATAAAATACTCAATTTTCTTAACTTTTAATCATAATTTCACACGAATCTATTAATTTTTAA
* * *
2893401 AATAAATAATAAAATTTAAAAATTTAAACATCATTAATAAAAAATATAAAAAAATTAAAATTACT
261 AATAAATAATAAAACTCAAAAATTTAAACATCATTAATAAAAAATATAAAAAAATTAAAA-TACC
* *
2893466 TTTTCTTTC-TCTT-TTTTTTTTCTCAAACAATATGATCAGCTTCCCATTAGCCGATTGACCACC
325 TTTTCTTCCTTCTTGTTTTTTTTCTCAAACAATATGATCAGCTTCCCATTAGCCGATCGACCACC
*
2893529 TCATAGCAAGTGCTCTCCAAAATAGCT
390 TCACAGCAAGTGCTCTCCAAAATAGCT
*
2893556 TTTTAAAACATAAAAAGCTATTTTGGTTTCTTGTACTTTTTAGAAAGTTTTTTGTTTTTTATTTT
1 TTTTAAAAAATAAAAAGCTATTTTGGTTTCTTGTACTTTTTAGAAA-------G---TTT-TTTT
* * *
2893621 TATAATTTTTTTGAAAAATAAAAAAT-ATTTTTACTTTTTAAAATTTAAAAAATTAAAAATTATT
55 TATAATTTTTTTGAAAAAT-AAAAATGATCTTTACTTTTAAAAATTT-AAAAATT----ATT-TA
* * * * *
2893685 TGTTTCTTGTTATTCAATTTTAAAAAATTAATTTTCTCCTATAATATAAATTCACGTAAAGATCA
113 TGTTTCTTGTTATTCAATTTTAAAAAATTAATTCTCTCCGATAACACAAATTCACAT-AAG----
* * * * *
2893750 TGAATGTTATTATATTTAATAAAATAAAATAAAATATTTATATTTTTTTAATTTTTAATCATAAT
173 -GAATGCTATTATATTTAATAAAATAAAATAAAATACTCA-ATTTTCTTAACTTTTAATCATAAT
* *
2893815 TTCACACGAATCTATTAATTTTTAAAATAAATAATAAAACTCAAAAGTTTAAACATTATTAATAA
236 TTCACACGAATCTATTAATTTTTAAAATAAATAATAAAACTCAAAAATTTAAACATCATTAATAA
*
2893880 AAAATATAAAAAAATTAAAATACCTTTTCTTCCTTCTTGTTTTTTTTCTCAAATAATATGATCAG
301 AAAATATAAAAAAATTAAAATACCTTTTCTTCCTTCTTGTTTTTTTTCTCAAACAATATGATCAG
*
2893945 CTTCCCATTAGCCGATCGACCACCTCACGGCAAGTGCTCTCCAAA
366 CTTCCCATTAGCCGATCGACCACCTCACAGCAAGTGCTCTCCAAA
2893990 GGGAGAGGAG
Statistics
Matches: 371, Mismatches: 36, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
415 44 0.12
422 1 0.00
425 3 0.01
426 40 0.11
427 13 0.04
431 3 0.01
432 51 0.14
433 3 0.01
438 44 0.12
439 102 0.27
440 67 0.18
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.43
Consensus pattern (416 bp):
TTTTAAAAAATAAAAAGCTATTTTGGTTTCTTGTACTTTTTAGAAAGTTTTTTTTATAATTTTTT
TGAAAAATAAAAATGATCTTTACTTTTAAAAATTTAAAAATTATTTATGTTTCTTGTTATTCAAT
TTTAAAAAATTAATTCTCTCCGATAACACAAATTCACATAAGGAATGCTATTATATTTAATAAAA
TAAAATAAAATACTCAATTTTCTTAACTTTTAATCATAATTTCACACGAATCTATTAATTTTTAA
AATAAATAATAAAACTCAAAAATTTAAACATCATTAATAAAAAATATAAAAAAATTAAAATACCT
TTTCTTCCTTCTTGTTTTTTTTCTCAAACAATATGATCAGCTTCCCATTAGCCGATCGACCACCT
CACAGCAAGTGCTCTCCAAAATAGCT
Found at i:2894099 original size:30 final size:29
Alignment explanation
Indices: 2894065--2894134 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
2894055 GAGAGAAAAA
* *
2894065 TTTAAAATTATAATTTATATAAAAATAA-TT
1 TTTAAAATTATAA--AAAATAAAAATAATTT
*
2894095 TTTAAAATTAATAAAAAATAAAATTAATTT
1 TTTAAAATT-ATAAAAAATAAAAATAATTT
2894125 TTTAAAATTA
1 TTTAAAATTA
2894135 ATATATCATC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 11 0.31
30 20 0.57
31 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TTTAAAATTATAAAAAATAAAAATAATTT
Found at i:2900188 original size:16 final size:16
Alignment explanation
Indices: 2900164--2900196 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2900154 TATCAACTGG
2900164 TCATACTTTCTTTCTT
1 TCATACTTTCTTTCTT
*
2900180 TCATTCTTTCTTTCTT
1 TCATACTTTCTTTCTT
2900196 T
1 T
2900197 TTCTTTTTGG
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:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (16 bp):
TCATACTTTCTTTCTT
Found at i:2906603 original size:2 final size:2
Alignment explanation
Indices: 2906596--2906626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2906586 ACATACATAC
2906596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2906627 AGAATAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2909663 original size:21 final size:20
Alignment explanation
Indices: 2909638--2909686 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
2909628 ATTGAGTTAT
2909638 TTTAATTTTACGT-TTATTTA
1 TTTAATTTTAC-TATTATTTA
*
2909658 CTTTAATTTGACTATTATTTA
1 -TTTAATTTTACTATTATTTA
2909679 -TTAATTTT
1 TTTAATTTT
2909687 TATGCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 7 0.28
20 1 0.04
21 17 0.68
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTAATTTTACTATTATTTA
Found at i:2912571 original size:18 final size:19
Alignment explanation
Indices: 2912530--2912571 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
2912520 ACAATATGAT
*
2912530 TAAATCCAACAAAAAAATG
1 TAAATCAAACAAAAAAATG
* *
2912549 AAAATCAAAGAAAAAAA-G
1 TAAATCAAACAAAAAAATG
2912567 TAAAT
1 TAAAT
2912572 GAAAAATCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.69, C:0.10, G:0.07, T:0.14
Consensus pattern (19 bp):
TAAATCAAACAAAAAAATG
Found at i:2913883 original size:254 final size:257
Alignment explanation
Indices: 2913540--2914007 Score: 689
Period size: 254 Copynumber: 1.8 Consensus size: 257
2913530 TACAACATAA
* * * * *
2913540 AAAATAAATTTTAATTAATAAAACATTCATAGTTGTTTAAAAATAAATATTTTAAATGGAATTTT
1 AAAATAAATCTTAATTAATAAAACATTCATAATTGTTTAAAAATAAATACTTTAAATGAAACTTT
**
2913605 TAAGAAAAGTTATTAGTGGTAATTTCTTTAAATTTTTCAA-AGTAAAAATGATTGTGGGACCTTA
66 TAAGAAAAGTTACAAGTGGTAATTTCTTTAAATTTTT-AATAGTAAAAATGATTGTGGGACCTTA
* *
2913669 CCATAAATTTTAAGGG-TAATCTCATAAATTATTTTTACAAA-AAGG-TTTATTTTTAAATAATT
130 CCATAAATGTT-AGGGTTAATCTCATAAATTAGTTTTACAAAGAAGGTTTTATTTTTAAATAATT
2913731 ATTGCAAATCTAA-AAATAATAAATCATGGAAATAGAATATGACAAAATAGACCTTACTTATAGG
194 ATTGCAAA-C-AAGAAATAATAAATCATGGAAATAGAATATGACAAAATAGACCTTACTTATAGG
2913795 G
257 G
* * *
2913796 AAAATAAATCTTAATTAATAAAAGATTCATAATTG-TT-AAAATAAATCCTTTAAGTGAAACTTT
1 AAAATAAATCTTAATTAATAAAACATTCATAATTGTTTAAAAATAAATACTTTAAATGAAACTTT
* *
2913859 TAAGGAAAGTTACAAGTGGTAATTTCTTTAAATTTTTAATAGTAAAAATGATTGTGGGATCTTAC
66 TAAGAAAAGTTACAAGTGGTAATTTCTTTAAATTTTTAATAGTAAAAATGATTGTGGGACCTTAC
* * * *
2913924 CATGAGTGTTGGGGTTAATCTCGTAAATTAGTTTTACAAAGAAGGTTTTATTTTTAAATAATTAT
131 CATAAATGTTAGGGTTAATCTCATAAATTAGTTTTACAAAGAAGGTTTTATTTTTAAATAATTAT
2913989 TGCAAACAAGAAATAATAA
196 TGCAAACAAGAAATAATAA
2914008 TAAAACAACT
Statistics
Matches: 189, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
253 5 0.03
254 111 0.59
255 16 0.08
256 57 0.30
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (257 bp):
AAAATAAATCTTAATTAATAAAACATTCATAATTGTTTAAAAATAAATACTTTAAATGAAACTTT
TAAGAAAAGTTACAAGTGGTAATTTCTTTAAATTTTTAATAGTAAAAATGATTGTGGGACCTTAC
CATAAATGTTAGGGTTAATCTCATAAATTAGTTTTACAAAGAAGGTTTTATTTTTAAATAATTAT
TGCAAACAAGAAATAATAAATCATGGAAATAGAATATGACAAAATAGACCTTACTTATAGGG
Found at i:2915318 original size:23 final size:23
Alignment explanation
Indices: 2915275--2915318 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2915265 AAGGACATTT
* *
2915275 TTACCCATCATCTTTTACAAAAA
1 TTACCCATAATCCTTTACAAAAA
2915298 TTACCCATAATACCTTT-CAAA
1 TTACCCATAAT-CCTTTACAAA
2915319 CCTTTCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.34
Consensus pattern (23 bp):
TTACCCATAATCCTTTACAAAAA
Found at i:2915415 original size:33 final size:33
Alignment explanation
Indices: 2915354--2915422 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
2915344 AAGTCTGCTG
* ** * *
2915354 CTTCTTCTCCATTTGCAGTAGACGTTGCTCCTC
1 CTTCATCTCCATTTGCAACAAACATTGCTCCTC
*
2915387 CTTCATCTCCATTTGCAACAAACATTGCTCTTC
1 CTTCATCTCCATTTGCAACAAACATTGCTCCTC
2915420 CTT
1 CTT
2915423 TTTATAGTCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.17, C:0.33, G:0.10, T:0.39
Consensus pattern (33 bp):
CTTCATCTCCATTTGCAACAAACATTGCTCCTC
Found at i:2916824 original size:93 final size:92
Alignment explanation
Indices: 2916665--2916885 Score: 336
Period size: 93 Copynumber: 2.4 Consensus size: 92
2916655 CTACTCTATC
*
2916665 ACATGCACCAAGCAGTAGCATCAACGCTGCAGCGCCACACTCCCACTGCTGCAGCGTTGATGCTA
1 ACATGCACCAAGCAGTGGCATCAACGCTGCAGCGCCACACTCCCACT-CTGCAGCGTTGATGCTA
* * *
2916730 CTACCTTCAGCAAGGGGACAGCGCTGAG
65 CTACCTTCACCAAGGAGACAGCACTGAG
*
2916758 ACATGCACCAACCAGTGGCATCAACGCTGCAGCGCCACACTCCCAACAT-TGCAGCGTTGATGCT
1 ACATGCACCAAGCAGTGGCATCAACGCTGCAGCGCCACACTCCC-AC-TCTGCAGCGTTGATGCT
*
2916822 ACTACCTTCACCAAGGAGACAGCACTGGG
64 ACTACCTTCACCAAGGAGACAGCACTGAG
* *
2916851 ACATGCACCAAGCATTGGCATCAACGCTGTAGCGC
1 ACATGCACCAAGCAGTGGCATCAACGCTGCAGCGC
2916886 ATGCACCAAG
Statistics
Matches: 117, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
93 114 0.97
94 2 0.02
95 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.16
Consensus pattern (92 bp):
ACATGCACCAAGCAGTGGCATCAACGCTGCAGCGCCACACTCCCACTCTGCAGCGTTGATGCTAC
TACCTTCACCAAGGAGACAGCACTGAG
Found at i:2916894 original size:33 final size:33
Alignment explanation
Indices: 2916852--2916918 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
2916842 AGCACTGGGA
* * *
2916852 CATGCACCAAGCATTGGCATCAACGCTGTAGCG
1 CATGCACCAAGCAGTGCCATCAACGCTGCAGCG
2916885 CATGCACCAAGCAGTGCCATCAACGCTGCAGCG
1 CATGCACCAAGCAGTGCCATCAACGCTGCAGCG
2916918 C
1 C
2916919 TGGGAGTGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.34, G:0.24, T:0.15
Consensus pattern (33 bp):
CATGCACCAAGCAGTGCCATCAACGCTGCAGCG
Found at i:2917807 original size:15 final size:15
Alignment explanation
Indices: 2917787--2917860 Score: 112
Period size: 15 Copynumber: 4.9 Consensus size: 15
2917777 TTATCTTCTC
*
2917787 TGCAATTACATTGCT
1 TGCAATCACATTGCT
2917802 TGCAATCACATTGCT
1 TGCAATCACATTGCT
2917817 TGCAATCACATTGCT
1 TGCAATCACATTGCT
* *
2917832 TGCAATCACATTACC
1 TGCAATCACATTGCT
*
2917847 TGTAATCACATTGC
1 TGCAATCACATTGC
2917861 ATTGTAAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (15 bp):
TGCAATCACATTGCT
Found at i:2926039 original size:36 final size:36
Alignment explanation
Indices: 2925987--2926057 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
2925977 TTTCACTGCA
*
2925987 AGATGCAATTTCTAGTTAAATTAGCTCAATCAGATG
1 AGATGCAATTTATAGTTAAATTAGCTCAATCAGATG
2926023 AGATGCAATTTATAGTTAAATTAGCTCAATCAGAT
1 AGATGCAATTTATAGTTAAATTAGCTCAATCAGAT
2926058 TGTCAGCGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (36 bp):
AGATGCAATTTATAGTTAAATTAGCTCAATCAGATG
Found at i:2926352 original size:24 final size:25
Alignment explanation
Indices: 2926315--2926366 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
2926305 TGGTTGAAGG
* *
2926315 AAGAAAAGAAGAAATAGAAGG-AAA
1 AAGAAAAGAAGAAAAAAAAGGCAAA
* *
2926339 AAGAAACGAGGAAAAAAAAGGCAAA
1 AAGAAAAGAAGAAAAAAAAGGCAAA
2926364 AAG
1 AAG
2926367 CTAAAAATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.69, C:0.04, G:0.25, T:0.02
Consensus pattern (25 bp):
AAGAAAAGAAGAAAAAAAAGGCAAA
Found at i:2934566 original size:6 final size:6
Alignment explanation
Indices: 2934555--2934581 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2934545 TGCAAAATAG
2934555 GCTTGA GCTTGA GCTTGA GCTTGA GCT
1 GCTTGA GCTTGA GCTTGA GCTTGA GCT
2934582 GCTTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.33, T:0.33
Consensus pattern (6 bp):
GCTTGA
Found at i:2940231 original size:2 final size:2
Alignment explanation
Indices: 2940224--2940257 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2940214 ATAATTGTAT
2940224 TA TA TA TA TA TA TA TA -A 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 T
2940258 TCTTGAAGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2940245 original size:15 final size:15
Alignment explanation
Indices: 2940225--2940254 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2940215 TAATTGTATT
2940225 ATATATATATATATA
1 ATATATATATATATA
2940240 ATATATATATATATA
1 ATATATATATATATA
2940255 TATTCTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:2940246 original size:17 final size:17
Alignment explanation
Indices: 2940224--2940256 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2940214 ATAATTGTAT
2940224 TATATATATATATATAA
1 TATATATATATATATAA
2940241 TATATATATATATATA
1 TATATATATATATATA
2940257 TTCTTGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAA
Found at i:2941731 original size:18 final size:18
Alignment explanation
Indices: 2941688--2941732 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2941678 TCTCACTATT
* *
2941688 CTCAACAACCTCAATATC
1 CTCAACAGCCTCAACATC
2941706 CTCAACAGCCTCAACATC
1 CTCAACAGCCTCAACATC
*
2941724 TTCAACAGC
1 CTCAACAGC
2941733 AGATCCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.40, G:0.04, T:0.20
Consensus pattern (18 bp):
CTCAACAGCCTCAACATC
Found at i:2943093 original size:2 final size:2
Alignment explanation
Indices: 2943088--2943134 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
2943078 ATGTGTGAAC
* *
2943088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT GT -T AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
2943130 AT AT A
1 AT AT A
2943135 AAAGTAGCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2944481 original size:120 final size:118
Alignment explanation
Indices: 2944258--2944585 Score: 405
Period size: 120 Copynumber: 2.8 Consensus size: 118
2944248 TATTGTGATT
***
2944258 AATTTTGCTTTTATGCTTCTAGATGTTAAAATATTGCGCTCATGTTCATATTTCTTGG-T---TT
1 AATTTTGCTTTTATGCTTCTAGATGTT-AAATATCAAGCTCATGTTCATATTTCTTGGTTAGGTT
* * *
2944319 TGGGTTTAGGACTT-CTATGATATAATTTCTTCATGTTAATATATTTTTTGGTTA
65 TGGGTTTAGGATTTGC-ATGATATAATTTCTTCATGTTAATATATTTCTGGGTTA
* * *
2944373 AATTTTGCTTTTATGCTTCAAGATGTTAAATATCATGCTAATGTTCATATTTCTTGGTTCAGGGT
1 AATTTTGCTTTTATGCTTCTAGATGTTAAATATCAAGCTCATGTTCATATTTCTTGGTT-A-GGT
* * * *
2944438 TTTGGTTTAGGATTTGCATGATATAATTTTTTCATGTTCATATATTTCTGGGTTG
64 TTGGGTTTAGGATTTGCATGATATAATTTCTTCATGTTAATATATTTCTGGGTTA
* * *
2944493 GATTTTGCTTTTATGTTTCTAGATGTTAAATATCAAGCTCATATTCATATTTCTTGGTTTAGAGT
1 AATTTTGCTTTTATGCTTCTAGATGTTAAATATCAAGCTCATGTTCATATTTCTTGG-TTAG-GT
*
2944558 TTAGGGTTTAGGATTTGTATGATATAAT
64 TT-GGGTTTAGGATTTGCATGATATAAT
2944586 ATTTAGGTTG
Statistics
Matches: 183, Mismatches: 20, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
114 26 0.14
115 27 0.15
119 1 0.01
120 103 0.56
121 26 0.14
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.50
Consensus pattern (118 bp):
AATTTTGCTTTTATGCTTCTAGATGTTAAATATCAAGCTCATGTTCATATTTCTTGGTTAGGTTT
GGGTTTAGGATTTGCATGATATAATTTCTTCATGTTAATATATTTCTGGGTTA
Found at i:2947412 original size:35 final size:35
Alignment explanation
Indices: 2947373--2947439 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
2947363 TGTGATGGCA
2947373 ATTTGTTGATATTATGGTTGTCCATATTTGTTGCC
1 ATTTGTTGATATTATGGTTGTCCATATTTGTTGCC
2947408 ATTTGTTGATATTATGGTTGTCCATATTTGTT
1 ATTTGTTGATATTATGGTTGTCCATATTTGTT
2947440 CACCATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.18, C:0.09, G:0.19, T:0.54
Consensus pattern (35 bp):
ATTTGTTGATATTATGGTTGTCCATATTTGTTGCC
Found at i:2961084 original size:34 final size:35
Alignment explanation
Indices: 2960959--2961084 Score: 114
Period size: 34 Copynumber: 3.7 Consensus size: 35
2960949 TTTTTCAAGG
** * *
2960959 GAGCAAGTGAAACCCTTAACAACGCTTTTTCACAA
1 GAGCAAGCAAAACCCTTAACAACACTTTTTCATAA
* * * *
2960994 AAGTAAGCAAAACCCTTAACAACGC-TTTTCATGA
1 GAGCAAGCAAAACCCTTAACAACACTTTTTCATAA
* * * *
2961028 GTGCAAGCGAAA-CCTTTACAACATTTTTTCATAA
1 GAGCAAGCAAAACCCTTAACAACACTTTTTCATAA
*
2961062 GAGCAAACAAAACCCTT-ACAACA
1 GAGCAAGCAAAACCCTTAACAACA
2961085 ATGGTTTTTA
Statistics
Matches: 72, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
33 9 0.12
34 38 0.53
35 25 0.35
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (35 bp):
GAGCAAGCAAAACCCTTAACAACACTTTTTCATAA
Found at i:2966162 original size:20 final size:20
Alignment explanation
Indices: 2966119--2966167 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
2966109 ATACAACAGT
* *
2966119 CTTCTTTTAACTAGTTAACT
1 CTTCCTTTAACTAGTTAACG
2966139 CTTCCTTTAACTAGTTGAA-G
1 CTTCCTTTAACTAGTT-AACG
2966159 CTTCACTTT
1 CTTC-CTTT
2966168 TTTTAACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (20 bp):
CTTCCTTTAACTAGTTAACG
Found at i:2984204 original size:13 final size:14
Alignment explanation
Indices: 2984186--2984215 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2984176 TTTTTGTAGG
2984186 AAAGAAA-AAAGAA
1 AAAGAAATAAAGAA
2984199 AAAGAAATAAAGAA
1 AAAGAAATAAAGAA
2984213 AAA
1 AAA
2984216 AGGCGAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAGAAATAAAGAA
Found at i:2984548 original size:6 final size:6
Alignment explanation
Indices: 2984539--2984563 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2984529 ACAGAGTTAC
2984539 GTTTGG GTTTGG GTTTGG GTTTGG G
1 GTTTGG GTTTGG GTTTGG GTTTGG G
2984564 AGAAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (6 bp):
GTTTGG
Found at i:2985345 original size:30 final size:30
Alignment explanation
Indices: 2985311--2985377 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
2985301 AAGTTTAATC
2985311 AAATTTTTATATTATTATTTTAAATTAAAT
1 AAATTTTTATATTATTATTTTAAATTAAAT
* *
2985341 AAATTATTATATTTTTATTTTAAATTAAAT
1 AAATTTTTATATTATTATTTTAAATTAAAT
2985371 AAATTTT
1 AAATTTT
2985378 AATGACTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
AAATTTTTATATTATTATTTTAAATTAAAT
Found at i:2985524 original size:18 final size:18
Alignment explanation
Indices: 2985501--2985535 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2985491 TAATTAATAA
2985501 TGACATGA-AATGATAATT
1 TGACATGATAAT-ATAATT
2985519 TGACATGATAATATAAT
1 TGACATGATAATATAAT
2985536 CACGTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (18 bp):
TGACATGATAATATAATT
Found at i:2986420 original size:28 final size:28
Alignment explanation
Indices: 2986369--2986444 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
2986359 CATTATTATG
*
2986369 TTAAATCAAATATATATATATTTATTTTAAA
1 TTAAATC-AATATA-A-ATTTTTATTTTAAA
2986400 TTAAATCAATATAAATTTTTATTTTAAA
1 TTAAATCAATATAAATTTTTATTTTAAA
* *
2986428 TTAAATTAACATAAATT
1 TTAAATCAATATAAATT
2986445 AATTATTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.67
29 1 0.02
30 6 0.14
31 7 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
TTAAATCAATATAAATTTTTATTTTAAA
Found at i:2986649 original size:16 final size:16
Alignment explanation
Indices: 2986628--2986660 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2986618 ATAATTAATT
2986628 AATTA-TTAATTATAAA
1 AATTATTTAATT-TAAA
2986644 AATTATTTAATTTAAA
1 AATTATTTAATTTAAA
2986660 A
1 A
2986661 TAAAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTATTTAATTTAAA
Found at i:2987703 original size:5 final size:5
Alignment explanation
Indices: 2987693--2987720 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2987683 ACAACCACTA
2987693 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2987721 TTAGGAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:2988165 original size:29 final size:29
Alignment explanation
Indices: 2988133--2988188 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2988123 ATTTTAAAAA
*
2988133 ATTTAAATAAATCATTATTTTTTTATTAT
1 ATTTAAATAAATCATTATATTTTTATTAT
* **
2988162 ATTTAATTAAATTTTTATATTTTTATT
1 ATTTAAATAAATCATTATATTTTTATT
2988189 TTAAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAATCATTATATTTTTATTAT
Found at i:2993891 original size:66 final size:66
Alignment explanation
Indices: 2993785--2993918 Score: 205
Period size: 66 Copynumber: 2.0 Consensus size: 66
2993775 CTTCAAAACG
** *
2993785 ATTTCAATAGTTGGTTTTTGATTTCTGGTTTTAACAAATCAAGTAACTGACTTGATATTATCATG
1 ATTTCAATAGTTGGTTTTTGATTTCTAATTTTAACAAATCAAGTAACTGACTTGATATCATCATG
2993850 A
66 A
* * * *
2993851 ATTTCAATGGTTGGTTTTTGATTTCTAATTTTAGCAAATCAAGTAAGTGACTTGATATCATGATG
1 ATTTCAATAGTTGGTTTTTGATTTCTAATTTTAACAAATCAAGTAACTGACTTGATATCATCATG
2993916 A
66 A
2993917 AT
1 AT
2993919 CTGTCTATTC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (66 bp):
ATTTCAATAGTTGGTTTTTGATTTCTAATTTTAACAAATCAAGTAACTGACTTGATATCATCATG
A
Found at i:2994049 original size:27 final size:27
Alignment explanation
Indices: 2994017--2994069 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2994007 TATTCTAATT
*
2994017 TCCACTAGAAGTGAATGGATAATTTTA
1 TCCACTAAAAGTGAATGGATAATTTTA
*
2994044 TCCACTAAAAGTGAATGGATACTTTT
1 TCCACTAAAAGTGAATGGATAATTTT
2994070 TACTAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (27 bp):
TCCACTAAAAGTGAATGGATAATTTTA
Found at i:2994088 original size:32 final size:32
Alignment explanation
Indices: 2994043--2994169 Score: 155
Period size: 32 Copynumber: 4.0 Consensus size: 32
2994033 GGATAATTTT
* * * ** *
2994043 ATCCACTAAAAGTGAATGGATACTTTTTACTA
1 ATCCACCAAAAATGAATGGATACCTTCCACTC
* * * *
2994075 ATTCACCAGAAGTGGATGGATACCTTCCACTC
1 ATCCACCAAAAATGAATGGATACCTTCCACTC
2994107 ATCCACCAAAAATGAATGGATACCTTCCACTC
1 ATCCACCAAAAATGAATGGATACCTTCCACTC
*
2994139 ATCCACCAAAAATGAATGGATACCTACCACT
1 ATCCACCAAAAATGAATGGATACCTTCCACT
2994170 AACCTATTAG
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 82 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.25
Consensus pattern (32 bp):
ATCCACCAAAAATGAATGGATACCTTCCACTC
Found at i:2996926 original size:30 final size:31
Alignment explanation
Indices: 2996853--2996928 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
2996843 TGTATTTGTT
2996853 TAAACCCTTATAATTTTATTTTTTGAATCAAA
1 TAAACCCTTATAATTTTA-TTTTTGAATCAAA
* ** * * *
2996885 GAAGTCTTTATACTTTTA-TTTTGAGTCAAA
1 TAAACCCTTATAATTTTATTTTTGAATCAAA
2996915 TAAACCCTTATAAT
1 TAAACCCTTATAAT
2996929 AATAGTTAAC
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
30 20 0.61
32 13 0.39
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (31 bp):
TAAACCCTTATAATTTTATTTTTGAATCAAA
Found at i:3001967 original size:33 final size:33
Alignment explanation
Indices: 3001905--3001967 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
3001895 GTATGCTAAC
* * *
3001905 ATATCATATTTGATAATAATGTGATATATTGAT
1 ATATCATAATTGATAATAATATGACATATTGAT
* *
3001938 ATATCATAATTGATGATGATATGACATATT
1 ATATCATAATTGATAATAATATGACATATT
3001968 AATTTACTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.43
Consensus pattern (33 bp):
ATATCATAATTGATAATAATATGACATATTGAT
Found at i:3003240 original size:15 final size:16
Alignment explanation
Indices: 3003212--3003258 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
3003202 AGTCAGGTCG
*
3003212 GATTATTTTCAATTTA
1 GATTATTTTAAATTTA
*
3003228 GATT-TTTTAAATTTG
1 GATTATTTTAAATTTA
*
3003243 GATTATTTTAGATTTA
1 GATTATTTTAAATTTA
3003259 AGTAATTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (16 bp):
GATTATTTTAAATTTA
Found at i:3006163 original size:24 final size:24
Alignment explanation
Indices: 3006131--3006185 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
3006121 AAATGAGTAG
3006131 TTTTCTAAAGAAGCTTTCTTCTTA
1 TTTTCTAAAGAAGCTTTCTTCTTA
3006155 TTTTCTAAAGAAGCTTTCTTCTTA
1 TTTTCTAAAGAAGCTTTCTTCTTA
3006179 TTTTCTA
1 TTTTCTA
3006186 TTTACCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (24 bp):
TTTTCTAAAGAAGCTTTCTTCTTA
Found at i:3008841 original size:16 final size:16
Alignment explanation
Indices: 3008822--3008911 Score: 76
Period size: 16 Copynumber: 5.6 Consensus size: 16
3008812 TATAAATATG
3008822 TATACATATACATACA
1 TATACATATACATACA
* **
3008838 TATACACATACATATG
1 TATACATATACATACA
*
3008854 TATGCATATACATAC-
1 TATACATATACATACA
* **
3008869 -ATACATATAAATATG
1 TATACATATACATACA
*
3008884 TATGCATATACATACA
1 TATACATATACATACA
3008900 TACATACATATA
1 T--ATACATATA
3008912 AATATGTATG
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
14 11 0.20
16 37 0.66
18 8 0.14
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (16 bp):
TATACATATACATACA
Found at i:3008848 original size:12 final size:10
Alignment explanation
Indices: 3008823--3008911 Score: 65
Period size: 10 Copynumber: 8.9 Consensus size: 10
3008813 ATAAATATGT
3008823 ATACATATAC
1 ATACATATAC
3008833 ATACATATACAC
1 ATACATAT--AC
**
3008845 ATACATATGT
1 ATACATATAC
*
3008855 ATGCATATAC
1 ATACATATAC
* *
3008865 ATACATACAT
1 ATACATATAC
* **
3008875 ATAAATATGT
1 ATACATATAC
*
3008885 ATGCATATAC
1 ATACATATAC
3008895 ATAC--ATAC
1 ATACATATAC
3008903 ATACATATA
1 ATACATATA
3008912 AATATGTATG
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
8 8 0.14
10 41 0.69
12 10 0.17
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.31
Consensus pattern (10 bp):
ATACATATAC
Found at i:3008883 original size:30 final size:30
Alignment explanation
Indices: 3008812--3008905 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
3008802 TGTGTGTATG
*
3008812 TATAAATATGTATACATATACATACATATACA
1 TATAAATATGTATGCATATACATAC--ATACA
* *
3008844 CATACATATGTATGCATATACATACATACA
1 TATAAATATGTATGCATATACATACATACA
3008874 TATAAATATGTATGCATATACATACATACA
1 TATAAATATGTATGCATATACATACATACA
3008904 TA
1 TA
3008906 CATATAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 35 0.61
32 22 0.39
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (30 bp):
TATAAATATGTATGCATATACATACATACA
Found at i:3011088 original size:16 final size:17
Alignment explanation
Indices: 3011069--3011101 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3011059 TTGTAGACAA
3011069 TTAATT-AAAACTAAAT
1 TTAATTAAAAACTAAAT
3011085 TTAATTAGAAAACTAAA
1 TTAATTA-AAAACTAAA
3011102 CTAATTAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAATTAAAAACTAAAT
Found at i:3011108 original size:17 final size:18
Alignment explanation
Indices: 3011075--3011108 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3011065 ACAATTAATT
*
3011075 AAAACTAAATTTAATTAG
1 AAAACTAAATCTAATTAG
3011093 AAAACTAAA-CTAATTA
1 AAAACTAAATCTAATTA
3011109 ACAAAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAACTAAATCTAATTAG
Found at i:3011114 original size:18 final size:19
Alignment explanation
Indices: 3011075--3011120 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
3011065 ACAATTAATT
* *
3011075 AAAACTAAATTTAATTA-G
1 AAAACTAAATCTAATTACA
3011093 AAAACTAAA-CTAATTAACA
1 AAAACTAAATCTAATT-ACA
3011112 AAAACTAAA
1 AAAACTAAA
3011121 AATCCACTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAACTAAATCTAATTACA
Found at i:3031710 original size:119 final size:119
Alignment explanation
Indices: 3031518--3031754 Score: 465
Period size: 119 Copynumber: 2.0 Consensus size: 119
3031508 CACAATGATA
3031518 AGAAATACAAACCATAGCCAATGACAAACCTACTAGAAAACATGTAGTACTGTTGTTTGCAACTA
1 AGAAATACAAACCATAGCCAATGACAAACCTACTAGAAAACATGTAGTACTGTTGTTTGCAACTA
3031583 CACCCCAATCTTTGTAGTAACCACTTCCTCAACTTTCAATCTCTCAATTTATAG
66 CACCCCAATCTTTGTAGTAACCACTTCCTCAACTTTCAATCTCTCAATTTATAG
*
3031637 AGAAATACAAACCATAGCCAATGACAAACCTACTAGAAAACATGTAGTATTGTTGTTTGCAACTA
1 AGAAATACAAACCATAGCCAATGACAAACCTACTAGAAAACATGTAGTACTGTTGTTTGCAACTA
3031702 CACCCCAATCTTTGTAGTAACCACTTCCTCAACTTTCAATCTCTCAATTTATA
66 CACCCCAATCTTTGTAGTAACCACTTCCTCAACTTTCAATCTCTCAATTTATA
3031755 ATGACCACTT
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 117 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (119 bp):
AGAAATACAAACCATAGCCAATGACAAACCTACTAGAAAACATGTAGTACTGTTGTTTGCAACTA
CACCCCAATCTTTGTAGTAACCACTTCCTCAACTTTCAATCTCTCAATTTATAG
Found at i:3033281 original size:246 final size:245
Alignment explanation
Indices: 3032843--3033335 Score: 860
Period size: 246 Copynumber: 2.0 Consensus size: 245
3032833 GCCATAATCT
3032843 AAAATTTTTTTGCTTTTGTTTGTTGCCAAAGCAAAGATTTTAGGAAAACAATGTGCCAATATAAC
1 AAAATTTTTTTGCTTTTGTTTGTTGCCAAAGCAAAGATTTTAGGAAAACAATGTGCCAATATAAC
* *
3032908 CTTGTTAATCCATTCATCATGCCAAAAGACAATATTTTCACCATTACCAACTGCAAAACCAATGT
66 CTTGTTAATCCACTCATCATGCCAAAAGACAATATTTTCACCATTACCAACTACAAAACCAATGT
*
3032973 TAGAAACCACTTGTAAGAAAAATTTGTTAGCAAGGGAAATGCGACTAATAATTTTTTTCCATATT
131 TAGAAACCACTTGTAAGAAAAATTTGTTAGCAAGGGAAATGCGACTAATAATTCTTTTCCATATT
*
3033038 GTTAAAACTTTCTTATTTGCACTTTTGTTTGCCCTCATGTTTGGCAAAAG
196 GTTAAAACTTTCTTATTTGCACTCTTGTTTGCCCTCATGTTTGGCAAAAG
* *
3033088 AAAATTTTTTTTGCTTTTGTTTGTTGCCAATGCAAAGATTTTAGGAAAACAATGTGTCAATATAA
1 AAAA-TTTTTTTGCTTTTGTTTGTTGCCAAAGCAAAGATTTTAGGAAAACAATGTGCCAATATAA
* *
3033153 CCTTGTTAATCCACTCGTCATGCCAAAAGACAATATTTTCACCATTACCAACTACAAAATCAATG
65 CCTTGTTAATCCACTCATCATGCCAAAAGACAATATTTTCACCATTACCAACTACAAAACCAATG
* *
3033218 TTAGAAACCATTTGTAAGAAAAATTTGTTAGCAAGGGAAATGGGACTAATAATTCTTTTCCATAT
130 TTAGAAACCACTTGTAAGAAAAATTTGTTAGCAAGGGAAATGCGACTAATAATTCTTTTCCATAT
* * *
3033283 TGTTAAAACTTTCTTATTTGCACTCTTGTTTGCCTTCGTGTTTGGCAGAAG
195 TGTTAAAACTTTCTTATTTGCACTCTTGTTTGCCCTCATGTTTGGCAAAAG
3033334 AA
1 AA
3033336 TGGAAGGATC
Statistics
Matches: 234, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
245 4 0.02
246 230 0.98
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (245 bp):
AAAATTTTTTTGCTTTTGTTTGTTGCCAAAGCAAAGATTTTAGGAAAACAATGTGCCAATATAAC
CTTGTTAATCCACTCATCATGCCAAAAGACAATATTTTCACCATTACCAACTACAAAACCAATGT
TAGAAACCACTTGTAAGAAAAATTTGTTAGCAAGGGAAATGCGACTAATAATTCTTTTCCATATT
GTTAAAACTTTCTTATTTGCACTCTTGTTTGCCCTCATGTTTGGCAAAAG
Found at i:3034404 original size:25 final size:25
Alignment explanation
Indices: 3034376--3034433 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
3034366 TTAATAAATG
3034376 TAATTATATGA-ATTAGAAATCACCA
1 TAATTATA-GAGATTAGAAATCACCA
* * *
3034401 TAATTATAGAGATTGGGAATCATCA
1 TAATTATAGAGATTAGAAATCACCA
3034426 TAATTATA
1 TAATTATA
3034434 AAAATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 2 0.07
25 27 0.93
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (25 bp):
TAATTATAGAGATTAGAAATCACCA
Found at i:3036266 original size:19 final size:19
Alignment explanation
Indices: 3036242--3036289 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
3036232 TTGCTTGTTC
3036242 AAGTGTATTGACCCCTTTG
1 AAGTGTATTGACCCCTTTG
*
3036261 AAGTGTATGGACCCCTTTG
1 AAGTGTATTGACCCCTTTG
3036280 AAGTGTATTG
1 AAGTGTATTG
3036290 TCGATTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (19 bp):
AAGTGTATTGACCCCTTTG
Found at i:3039117 original size:25 final size:25
Alignment explanation
Indices: 3039059--3039122 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
3039049 TTAATAAACG
* *
3039059 TAATTATAAGAATTAGAAATCACCA
1 TAATTATAGGGATTAGAAATCACCA
*
3039084 TAATTATAGGGATT-GAGAATCATCA
1 TAATTATAGGGATTAGA-AATCACCA
3039109 TAATTATAGGGATT
1 TAATTATAGGGATT
3039123 TTATTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
24 2 0.06
25 33 0.94
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.33
Consensus pattern (25 bp):
TAATTATAGGGATTAGAAATCACCA
Found at i:3040268 original size:40 final size:40
Alignment explanation
Indices: 3040223--3040298 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
3040213 TTGGCTATTT
* *
3040223 TTCACCTTAGTCGGGCTTTCAACCTTGCCAAGATTGATGA
1 TTCACCTTAGTCGGGCTTTCAAACTCGCCAAGATTGATGA
* * *
3040263 TTCACCTTAGTGGGGTTTTCAAACTCGCCACGATTG
1 TTCACCTTAGTCGGGCTTTCAAACTCGCCAAGATTG
3040299 GTGTCATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (40 bp):
TTCACCTTAGTCGGGCTTTCAAACTCGCCAAGATTGATGA
Found at i:3055567 original size:19 final size:20
Alignment explanation
Indices: 3055540--3055578 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3055530 ATTGGTTATT
*
3055540 TAATTAAATC-TATGTTTTA
1 TAATGAAATCATATGTTTTA
3055559 TAATGAAATCATATGTTTTA
1 TAATGAAATCATATGTTTTA
3055579 GTCTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (20 bp):
TAATGAAATCATATGTTTTA
Found at i:3056875 original size:17 final size:16
Alignment explanation
Indices: 3056835--3056877 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3056825 AAATAAGCAT
*
3056835 ATAAAATAAAATAATA
1 ATAAAACAAAATAATA
*
3056851 AAAGAAACAAAATGAATA
1 ATA-AAACAAAAT-AATA
3056869 ATAAAACAA
1 ATAAAACAA
3056878 GGGCTAGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 14 0.64
18 6 0.27
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (16 bp):
ATAAAACAAAATAATA
Found at i:3057084 original size:22 final size:22
Alignment explanation
Indices: 3057056--3057106 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
3057046 AAAACTGGCA
3057056 TTGTTTCACTCTTTTATCTCTT
1 TTGTTTCACTCTTTTATCTCTT
3057078 TTGTTTCACTCTTTTATCTCTT
1 TTGTTTCACTCTTTTATCTCTT
*
3057100 TTCTTTC
1 TTGTTTC
3057107 TCTTGAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.24, G:0.04, T:0.65
Consensus pattern (22 bp):
TTGTTTCACTCTTTTATCTCTT
Found at i:3061843 original size:20 final size:20
Alignment explanation
Indices: 3061797--3061835 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3061787 TGCTTCAAAT
*
3061797 GAATTCTATCGATATATTTAA
1 GAATT-TATCAATATATTTAA
*
3061818 GGATTTATCAATATATTT
1 GAATTTATCAATATATTT
3061836 GAAAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (20 bp):
GAATTTATCAATATATTTAA
Found at i:3065583 original size:35 final size:35
Alignment explanation
Indices: 3065544--3065745 Score: 224
Period size: 35 Copynumber: 5.8 Consensus size: 35
3065534 TGAGGCATTG
* * *
3065544 CTTCACATAGAACAATTAAAATAAGTGAAATACTA
1 CTTCACACAGAACAACTAAAACAAGTGAAATACTA
* * *
3065579 CTTCACACAAAACAATTAGAACAAGTGAAATACTA
1 CTTCACACAGAACAACTAAAACAAGTGAAATACTA
* *
3065614 CTTCACACAGAACAATTAGAACAAGTGAAATACTA
1 CTTCACACAGAACAACTAAAACAAGTGAAATACTA
* * *
3065649 CTTCACACAAAACAACTAAAACAAATGACATACTA
1 CTTCACACAGAACAACTAAAACAAGTGAAATACTA
* * * * *
3065684 TTTTACACAGAACAACGAAAACAACTAAAATACTA
1 CTTCACACAGAACAACTAAAACAAGTGAAATACTA
** * *
3065719 CTTCACGTAGAACAACTAGAATAAGTG
1 CTTCACACAGAACAACTAAAACAAGTG
3065746 GAGCACTACT
Statistics
Matches: 141, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 141 1.00
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.21
Consensus pattern (35 bp):
CTTCACACAGAACAACTAAAACAAGTGAAATACTA
Found at i:3066048 original size:14 final size:14
Alignment explanation
Indices: 3066031--3066072 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3066021 TCTAAACTTA
*
3066031 TTCTTATATAGCTT
1 TTCTTATATACCTT
*
3066045 TTCTTGTATACCTT
1 TTCTTATATACCTT
3066059 TTCTCTAT-TACCTT
1 TTCT-TATATACCTT
3066073 CTACTCAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (14 bp):
TTCTTATATACCTT
Found at i:3066369 original size:18 final size:18
Alignment explanation
Indices: 3066342--3066376 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3066332 GCTTCTCTCT
3066342 CTAATCCTCTTCTATTCC
1 CTAATCCTCTTCTATTCC
* *
3066360 CTAATTCTCTTTTATTC
1 CTAATCCTCTTCTATTC
3066377 TCTTTCACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.51
Consensus pattern (18 bp):
CTAATCCTCTTCTATTCC
Found at i:3075984 original size:26 final size:26
Alignment explanation
Indices: 3075955--3076025 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 26
3075945 TGATTAAAAA
3075955 AATAAATTAATAATTTTAATTAATT-T
1 AATAAATTAATAATTTTAATT-ATTAT
* *
3075981 AATAATTTTAT-ATATTTAATT-TTAT
1 AATAAATTAATAAT-TTTAATTATTAT
3076006 AA-AAA-TAATAA-TTTAATTAT
1 AATAAATTAATAATTTTAATTAT
3076026 CAATAGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
22 7 0.19
23 4 0.11
24 5 0.14
25 5 0.14
26 16 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AATAAATTAATAATTTTAATTATTAT
Found at i:3077196 original size:21 final size:21
Alignment explanation
Indices: 3077148--3077188 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3077138 AACTTAAAAC
3077148 AAAAT-AATAAAATAAAATAA
1 AAAATGAATAAAATAAAATAA
*
3077168 AAAATGAATAAAATTAAATAA
1 AAAATGAATAAAATAAAATAA
3077189 TGGATGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAATGAATAAAATAAAATAA
Found at i:3077956 original size:5 final size:5
Alignment explanation
Indices: 3077942--3077974 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3077932 CGGGCTGCTT
*
3077942 CTCTC CTCTC TTCTC CTCTC CTCTC CTCTC CTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTC
3077975 ACTCTGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (5 bp):
CTCTC
Found at i:3087684 original size:13 final size:14
Alignment explanation
Indices: 3087666--3087695 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3087656 AATTGTTTGG
3087666 TAAATT-TTTTTTA
1 TAAATTCTTTTTTA
3087679 TAAATTCTTTTTTA
1 TAAATTCTTTTTTA
3087693 TAA
1 TAA
3087696 GTTACAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
TAAATTCTTTTTTA
Found at i:3088774 original size:51 final size:51
Alignment explanation
Indices: 3088698--3088801 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
3088688 ATGGCGGAAG
*
3088698 TAACATAGTCTGATATTGACTCTTCAAGCTTAGAAGAAGAAAGAGAGAAAT
1 TAACATAGTCTGATATTGACTCTTCAAGCTTAGAAGAACAAAGAGAGAAAT
3088749 TAACATAGTCTGATATTGACTCTTCAAGCTTAGAAGAACAAAGAGAGAAAT
1 TAACATAGTCTGATATTGACTCTTCAAGCTTAGAAGAACAAAGAGAGAAAT
3088800 TA
1 TA
3088802 GAAGAAAGCG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.26
Consensus pattern (51 bp):
TAACATAGTCTGATATTGACTCTTCAAGCTTAGAAGAACAAAGAGAGAAAT
Found at i:3103898 original size:18 final size:17
Alignment explanation
Indices: 3103872--3103905 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3103862 ATTTTTTCTC
3103872 TCCCCCTAAATACTTTTT
1 TCCCCCTAAATA-TTTTT
*
3103890 TCCCTCTAAATATTTT
1 TCCCCCTAAATATTTT
3103906 CTCTTATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (17 bp):
TCCCCCTAAATATTTTT
Found at i:3105472 original size:21 final size:22
Alignment explanation
Indices: 3105417--3105473 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
3105407 ACTTTAAGTG
*
3105417 AAACAAGAAGAATCGACATCTG
1 AAACAAGAAGAATCGACATCTC
* *
3105439 GAA-AAGCAAGAATCGA-TTCTC
1 AAACAAG-AAGAATCGACATCTC
3105460 AAACAAGAAGAATC
1 AAACAAGAAGAATC
3105474 AACACCTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.14
Consensus pattern (22 bp):
AAACAAGAAGAATCGACATCTC
Found at i:3106005 original size:30 final size:30
Alignment explanation
Indices: 3105969--3106078 Score: 159
Period size: 30 Copynumber: 3.7 Consensus size: 30
3105959 TGTTGTAAAA
* *
3105969 GTTATGCGTGATCCTTTAAAAAGTAGAGAG
1 GTTATGCTTGAGCCTTTAAAAAGTAGAGAG
* *
3105999 GTTATGCTTGA-CCCTTGAAAAGTAGAGAG
1 GTTATGCTTGAGCCTTTAAAAAGTAGAGAG
* *
3106028 GTTATGCTTAAGCCTTTAAAAAGTAGTGAG
1 GTTATGCTTGAGCCTTTAAAAAGTAGAGAG
3106058 GTTATGCTTGAGCCTTTAAAA
1 GTTATGCTTGAGCCTTTAAAA
3106079 CTAGTAAGCA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 26 0.37
30 45 0.63
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (30 bp):
GTTATGCTTGAGCCTTTAAAAAGTAGAGAG
Found at i:3106092 original size:29 final size:30
Alignment explanation
Indices: 3106030--3106097 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
3106020 GTAGAGAGGT
* * * **
3106030 TATGCTTAAGCCTTTAAAAAGTAGTGAGGT
1 TATGCTTGAGCCTTTAAAAACTAGTAAGCA
3106060 TATGCTTGAGCCTTT-AAAACTAGTAAGCA
1 TATGCTTGAGCCTTTAAAAACTAGTAAGCA
3106089 TATGCTTGA
1 TATGCTTGA
3106098 TCCATGAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (30 bp):
TATGCTTGAGCCTTTAAAAACTAGTAAGCA
Found at i:3106093 original size:59 final size:59
Alignment explanation
Indices: 3105981--3106095 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 59
3105971 TATGCGTGAT
* **
3105981 CCTTTAAAAAGTAGAGAGGTTATGCTTGACCCTTGAAAAGTAGAGAGGTTATGCTTAAG
1 CCTTTAAAAAGTAGAGAGGTTATGCTTGACCCTTGAAAACTAGAGAGCATATGCTTAAG
* * *
3106040 CCTTTAAAAAGTAGTGAGGTTATGCTTGAGCCTTTAAAACTAGTA-AGCATATGCTT
1 CCTTTAAAAAGTAGAGAGGTTATGCTTGACCCTTGAAAACTAG-AGAGCATATGCTT
3106096 GATCCATGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 48 0.98
60 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (59 bp):
CCTTTAAAAAGTAGAGAGGTTATGCTTGACCCTTGAAAACTAGAGAGCATATGCTTAAG
Found at i:3106125 original size:28 final size:28
Alignment explanation
Indices: 3106089--3106153 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
3106079 CTAGTAAGCA
* *
3106089 TATGCTTGATCCATGAATAGGCAATAGT
1 TATGCTTGATACATGAACAGGCAATAGT
* * *
3106117 TATGCTTGATACTTGAACAGGCATTGGT
1 TATGCTTGATACATGAACAGGCAATAGT
3106145 TATGCTTGA
1 TATGCTTGA
3106154 ACCTTTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (28 bp):
TATGCTTGATACATGAACAGGCAATAGT
Found at i:3113768 original size:24 final size:24
Alignment explanation
Indices: 3113716--3113769 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
3113706 TTTAATTAGT
*
3113716 TTTTCAATTCTTATTTCTTTATTTC
1 TTTT-AATTCTTATTTCTTTATTGC
3113741 TTTTAATTCTT-TTTCATTTA-TGC
1 TTTTAATTCTTATTTC-TTTATTGC
3113764 ATTTTA
1 -TTTTA
3113770 TAGATGTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 6 0.23
24 16 0.62
25 4 0.15
ACGTcount: A:0.19, C:0.13, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAATTCTTATTTCTTTATTGC
Found at i:3115987 original size:12 final size:12
Alignment explanation
Indices: 3115970--3116004 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
3115960 AAAATTGAAT
3115970 AAACTAAAATTA
1 AAACTAAAATTA
3115982 AAACTAAAATTA
1 AAACTAAAATTA
3115994 AAACTAAAATT
1 AAACTAAAATT
3116005 GAAAGCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.26
Consensus pattern (12 bp):
AAACTAAAATTA
Found at i:3120529 original size:60 final size:60
Alignment explanation
Indices: 3120463--3120579 Score: 191
Period size: 60 Copynumber: 1.9 Consensus size: 60
3120453 ATGAACTTAT
*
3120463 ATGTGAATTTGCTATCATGTATTACGTATTATATTTTGTT-TCATGATTTATTAAATTGAA
1 ATGTGAATTTGCTATCATGTAGTACGTATTATATTTTGTTCT-ATGATTTATTAAATTGAA
* *
3120523 ATGTGAATTTGCTATCATGTAGTATGTATTATATTTTGTTCTTTGATTTATTAAATT
1 ATGTGAATTTGCTATCATGTAGTACGTATTATATTTTGTTCTATGATTTATTAAATT
3120580 AGATTGAACA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
60 52 0.98
61 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (60 bp):
ATGTGAATTTGCTATCATGTAGTACGTATTATATTTTGTTCTATGATTTATTAAATTGAA
Found at i:3121068 original size:28 final size:29
Alignment explanation
Indices: 3121036--3121099 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 29
3121026 ATAAGATTCT
3121036 TTTTAACTCACCATAAGTAAATGAATAC-
1 TTTTAACTCACCATAAGTAAATGAATACA
**
3121064 TTTTAA--C-CCATAAGTGGATGAATACA
1 TTTTAACTCACCATAAGTAAATGAATACA
3121090 TTTTAACTCA
1 TTTTAACTCA
3121100 ATAGAAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 16 0.53
26 7 0.23
28 7 0.23
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (29 bp):
TTTTAACTCACCATAAGTAAATGAATACA
Found at i:3121112 original size:29 final size:25
Alignment explanation
Indices: 3121056--3121116 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 25
3121046 CCATAAGTAA
*
3121056 ATGAATACTTTTAACCCATAAGTGG
1 ATGAATACTTTTAACCAATAAGTGG
*
3121081 ATGAATACATTTTAACTCAATAGAAGTTG
1 ATGAATAC-TTTTAAC-CAAT--AAGTGG
3121110 ATGAATA
1 ATGAATA
3121117 GTGAAGAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 8 0.27
26 7 0.23
27 3 0.10
29 12 0.40
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (25 bp):
ATGAATACTTTTAACCAATAAGTGG
Found at i:3121719 original size:20 final size:20
Alignment explanation
Indices: 3121694--3121731 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3121684 ATGTATTATT
3121694 TTTATTAAATGTTAAAGAAA
1 TTTATTAAATGTTAAAGAAA
* *
3121714 TTTATTAAGTTTTAAAGA
1 TTTATTAAATGTTAAAGA
3121732 TATTAGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (20 bp):
TTTATTAAATGTTAAAGAAA
Found at i:3124998 original size:14 final size:15
Alignment explanation
Indices: 3124978--3125015 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3124968 TTCTTTCATC
3124978 AAGGTTTTT-TTAAT
1 AAGGTTTTTCTTAAT
* *
3124992 TAGGTTTTTCTTAGT
1 AAGGTTTTTCTTAAT
3125007 AAGGTTTTT
1 AAGGTTTTT
3125016 AATGAAACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.58
Consensus pattern (15 bp):
AAGGTTTTTCTTAAT
Found at i:3139209 original size:2 final size:2
Alignment explanation
Indices: 3139202--3139228 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3139192 TAATATTGTT
3139202 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 T
3139229 TTGAAAATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3146404 original size:18 final size:18
Alignment explanation
Indices: 3146361--3146410 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
3146351 TCAAAGACGG
**
3146361 AGAGGGAGAGGGAGAGGG
1 AGAGGGAGAGGGAGAGCA
3146379 AGAGGGAGAGGGAGAGCA
1 AGAGGGAGAGGGAGAGCA
3146397 AGCA-GGAGAGGGAG
1 AG-AGGGAGAGGGAG
3146411 CCAAAGAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 28 0.97
19 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.60, T:0.00
Consensus pattern (18 bp):
AGAGGGAGAGGGAGAGCA
Found at i:3146410 original size:6 final size:6
Alignment explanation
Indices: 3146359--3146394 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
3146349 TGTCAAAGAC
3146359 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG
3146395 CAAGCAGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:3150033 original size:12 final size:12
Alignment explanation
Indices: 3150016--3150041 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3150006 TAAATATAGT
3150016 TACTATTACTAC
1 TACTATTACTAC
3150028 TACTATTACTAC
1 TACTATTACTAC
3150040 TA
1 TA
3150042 GAGATAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (12 bp):
TACTATTACTAC
Found at i:3157436 original size:252 final size:252
Alignment explanation
Indices: 3156940--3157442 Score: 618
Period size: 252 Copynumber: 2.0 Consensus size: 252
3156930 ATAAACTAAC
* *
3156940 AACAATCAGCAATATTTAAGCCTCAAACCTCCATGCTCCAAAATAACCCTAATCACAAAGTTATA
1 AACAATCAGCAATATTTAAGCCTCAAACCTCCACGCTCCAAAATAA-CATAATCACAAAGTTATA
* * * ** *
3157005 TCTACTTTAATGCATGTTAAATATTTTAACTCAAAATCACATGCAAACTTTAAAAAAGCTTAGAA
65 TCTACTTTAATGCATGCTAAAAATTTTAACTCAAAACCACACACAAACTGTAAAAAAGCTTAGAA
* * * *
3157070 AAGAAAAATACCAAAATGCAAAGAAACATTATCGTCATCTAAAGAAAACCTCTGCACAAACAATG
130 AAGAAAAATACCAAAACGCAAAGAAACATTATCATCATCGAAAGAAAACCTCTACACAAACAATG
* *
3157135 CTTTTAGGAAAAAACGTACAAAAAATATTAAAAACCAAAACAAAATTGACAAATTTTT
195 CCTGTAGGAAAAAACGTACAAAAAATATTAAAAACCAAAACAAAATTGACAAATTTTT
* * * *
3157193 AACAAT-ATGCAATATTTAAGCGTTAAACCTTCACGCTCCAAATTCAA-ATAATCACAAAGTTAT
1 AACAATCA-GCAATATTTAAGCCTCAAACCTCCACGCTCCAAAAT-AACATAATCACAAAGTTAT
* ** ** *
3157256 AGT-TACTTTAATGGATGCTAAAAATTTTAACTCAAAACCACACACAGGCTGTGGAAAAGCTTAT
64 A-TCTACTTTAATGCATGCTAAAAATTTTAACTCAAAACCACACACAAACTGTAAAAAAGCTTAG
* * * * * *
3157320 AAAAGAAAAATACCAAGACGTAAAGAAACATTGTCATCAAT-GAGAGAAAACTTCTACACCAACA
128 AAAAGAAAAATACCAAAACGCAAAGAAACATTATCATC-ATCGAAAGAAAACCTCTACACAAACA
* * * * *
3157384 ATGCCTGTAGGAAATAATGTACAAAAGATATTAAAAACCAAAATAGAATTGACAAATTT
192 ATGCCTGTAGGAAAAAACGTACAAAAAATATTAAAAACCAAAACAAAATTGACAAATTT
3157443 AATACATGAA
Statistics
Matches: 211, Mismatches: 35, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
252 169 0.80
253 40 0.19
254 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.25
Consensus pattern (252 bp):
AACAATCAGCAATATTTAAGCCTCAAACCTCCACGCTCCAAAATAACATAATCACAAAGTTATAT
CTACTTTAATGCATGCTAAAAATTTTAACTCAAAACCACACACAAACTGTAAAAAAGCTTAGAAA
AGAAAAATACCAAAACGCAAAGAAACATTATCATCATCGAAAGAAAACCTCTACACAAACAATGC
CTGTAGGAAAAAACGTACAAAAAATATTAAAAACCAAAACAAAATTGACAAATTTTT
Found at i:3157823 original size:20 final size:21
Alignment explanation
Indices: 3157800--3157839 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3157790 TATTTGGAGA
*
3157800 AAACTTATA-ATATTAATATG
1 AAACGTATAGATATTAATATG
*
3157820 AAACGTATAGATATTGATAT
1 AAACGTATAGATATTAATAT
3157840 ATGAGTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
AAACGTATAGATATTAATATG
Found at i:3158000 original size:22 final size:22
Alignment explanation
Indices: 3157949--3158000 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
3157939 TTATACATTA
3157949 ATATATAATATATTATGATTAAC
1 ATATATAA-ATATTATGATTAAC
3157972 ---TATAAATATTAT-ATTATAC
1 ATATATAAATATTATGATTA-AC
3157991 ATATATAAAT
1 ATATATAAAT
3158001 TAAGGTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 5 0.20
22 7 0.28
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATATAAATATTATGATTAAC
Found at i:3160450 original size:15 final size:14
Alignment explanation
Indices: 3160412--3160450 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3160402 TGAGATTCTA
3160412 TTTCTGTTTTATTT
1 TTTCTGTTTTATTT
3160426 TTCTCT-TTTTATTT
1 TT-TCTGTTTTATTT
3160440 TTTCGTGTTTT
1 TTTC-TGTTTT
3160451 GGGCATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.09
14 13 0.59
15 7 0.32
ACGTcount: A:0.05, C:0.10, G:0.08, T:0.77
Consensus pattern (14 bp):
TTTCTGTTTTATTT
Found at i:3164790 original size:14 final size:14
Alignment explanation
Indices: 3164771--3164809 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
3164761 TTTTGAGAAT
3164771 TTTTTTTAAAAAAA
1 TTTTTTTAAAAAAA
*
3164785 TTTTTTT--AAAAT
1 TTTTTTTAAAAAAA
3164797 TTTTTTTAAAAAA
1 TTTTTTTAAAAAA
3164810 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTTTTAAAAAAA
Found at i:3164810 original size:14 final size:14
Alignment explanation
Indices: 3164768--3164810 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
3164758 AGATTTTGAG
3164768 AATTTTTTTTAAAA
1 AATTTTTTTTAAAA
*
3164782 AAATTTTTTT--AA
1 AATTTTTTTTAAAA
3164794 AATTTTTTTTAAAA
1 AATTTTTTTTAAAA
3164808 AAT
1 AAT
3164811 AAAATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 11 0.44
14 14 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATTTTTTTTAAAA
Done.