Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001132.1 Hibiscus syriacus cultivar Beakdansim tig00002255_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: 95412
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:491 original size:13 final size:12
Alignment explanation
Indices: 475--520 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
465 AAACTATATT
475 AAAAAAATAAAG
1 AAAAAAATAAAG
487 AAAAAAATAAAG
1 AAAAAAATAAAG
* *
499 AAAAAAACAAAC
1 AAAAAAATAAAG
*
511 AAAATAATAA
1 AAAAAAATAA
521 TAATTTTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.09
Consensus pattern (12 bp):
AAAAAAATAAAG
Found at i:4579 original size:73 final size:72
Alignment explanation
Indices: 4480--4627 Score: 224
Period size: 73 Copynumber: 2.0 Consensus size: 72
4470 GCCTCTTTAG
* **
4480 AGATAGTTTCCCTTGAAGTAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
1 AGATAGTTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
*
4545 TCCCTTT
66 TCCCATT
* * *
4552 AGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGT
1 AGATAGTTTCCCTTAAAACAAA-TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTAT
4617 CTCCCATT
65 CTCCCATT
4625 AGA
1 AGA
4628 CAGTCTCTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
72 19 0.28
73 49 0.72
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (72 bp):
AGATAGTTTCCCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATC
TCCCATT
Found at i:4601 original size:37 final size:36
Alignment explanation
Indices: 4419--4621 Score: 228
Period size: 36 Copynumber: 5.6 Consensus size: 36
4409 AGTTATCACG
** * **
4419 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTG
1 TTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCC
* * * *
4455 TGGAAATAAAGTTTTGCCT-CTTTAGAGATAGTTTCCC
1 TTGAAACAAA-TTTTGTCTCCCTT-GAGATAGTTTCCC
** *
4492 TTGAAGTAAATTTTGTCTCCCTTGAGACAGTTTCCC
1 TTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCC
* *
4528 TTGAAACAAATTTTATCTCCCTTTAGATAGTTTCCC
1 TTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCC
* *
4564 TTAAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCC
1 TTGAAACAAA-TTTTGTCTCCCTTGAGATAGTTTCCC
4601 TTGAAACAAATTTTGTCTCCC
1 TTGAAACAAATTTTGTCTCCC
4622 ATTAGACAGT
Statistics
Matches: 138, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
36 80 0.58
37 58 0.42
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCC
Found at i:4612 original size:109 final size:109
Alignment explanation
Indices: 4419--4640 Score: 295
Period size: 109 Copynumber: 2.0 Consensus size: 109
4409 AGTTATCACG
** * *
4419 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTGTGGAAATAAAGTTTTGCCTCTTTAGAGAT
1 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGAAAACAAAGTTTTGCCTCTTTAGAGAT
** *
4484 AGTTTCCCTTGAAGTAAATTTTGTCTCCC-TTGAGACAGTTTCCC
66 AGTTTCCCTTGAAACAAATTTTGTCTCCCATT-AGACAGTCTCCC
* * * * *
4528 TTGAAACAAATTTTATCTCCCTTTAGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTT-GAGA
1 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGAAAACAAAGTTTTGCCTCT-TTAGAGA
*
4592 TAGTTTCCCTTGAAACAAATTTTGTCTCCCATTAGACAGTCTCTC
65 TAGTTTCCCTTGAAACAAATTTTGTCTCCCATTAGACAGTCTCCC
4637 TTGA
1 TTGA
4641 GATAGTTTCC
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
109 94 0.96
110 4 0.04
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (109 bp):
TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTGAAAACAAAGTTTTGCCTCTTTAGAGAT
AGTTTCCCTTGAAACAAATTTTGTCTCCCATTAGACAGTCTCCC
Found at i:4662 original size:124 final size:123
Alignment explanation
Indices: 4506--4763 Score: 365
Period size: 124 Copynumber: 2.1 Consensus size: 123
4496 AGTAAATTTT
* *
4506 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCCCTTTAGATAGTTTCCCTTAAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTACCTTGAGATAGTTTCCCTTAAAAC
* * *
4571 AAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCATTAGACA
66 AAA-TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCATTAGACA
* * * * *
4630 GTCTCTCTTGAGATAGTTTCCTTTGAAACAAATTTTGTCTACCTTGAGATAGTTTCCCTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTACCTTGAGATAGTTTCCCTTAAAAC
* * *
4695 AAATTTTGTCTCCCTTGAGACAATTTCCCTTTAAATAAATTTTGTCTCTC-TTAAGACA
66 AAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCATT-AGACA
*
4753 GTTTCCCTTGA
1 GTCTCCCTTGA
4764 AACAACCTTA
Statistics
Matches: 118, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
122 2 0.02
123 55 0.47
124 61 0.52
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (123 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTACCTTGAGATAGTTTCCCTTAAAAC
AAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCATTAGACA
Found at i:4683 original size:36 final size:35
Alignment explanation
Indices: 4630--4768 Score: 179
Period size: 36 Copynumber: 3.9 Consensus size: 35
4620 CCATTAGACA
* *
4630 GTCTCTCTTGAGATAGTTTCCTTTGAAACAAATTTT
1 GTCTC-CTTGAGACAGTTTCCCTTGAAACAAATTTT
*
4666 GTCTACCTTGAGATAGTTTCCCTTGAAACAAATTTT
1 GTCT-CCTTGAGACAGTTTCCCTTGAAACAAATTTT
* * *
4702 GTCTCCCTTGAGACAATTTCCCTTTAAATAAATTTT
1 GTCT-CCTTGAGACAGTTTCCCTTGAAACAAATTTT
*
4738 GTCTCTCTTAAGACAGTTTCCCTTGAAACAA
1 GTCTC-CTTGAGACAGTTTCCCTTGAAACAA
4769 CCTTAGCTTG
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
35 1 0.01
36 89 0.98
37 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (35 bp):
GTCTCCTTGAGACAGTTTCCCTTGAAACAAATTTT
Found at i:4689 original size:87 final size:88
Alignment explanation
Indices: 4543--4725 Score: 273
Period size: 87 Copynumber: 2.1 Consensus size: 88
4533 ACAAATTTTA
*
4543 TCTCCCTTTAGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
1 TCTCCCTTGAGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
4608 AAATTTTGTCTCCCATT-AGACAG
66 AAATTTTGTCTCCC-TTGAGACAG
* * *
4631 TCTCTCTTGAGATAGTTTCCTTTGAAACAAA-TTTTGTCTAC-CTTGAGATAGTTTCCCTTGAAA
1 TCTCCCTTGAGATAGTTTCCCTTAAAACAAAGTTTTGTCT-CTCTTGAGATAGTTTCCCTTGAAA
*
4694 CAAATTTTGTCTCCCTTGAGACAA
65 CAAATTTTGTCTCCCTTGAGACAG
*
4718 TTTCCCTT
1 TCTCCCTT
4726 TAAATAAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
86 2 0.02
87 56 0.65
88 28 0.33
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (88 bp):
TCTCCCTTGAGATAGTTTCCCTTAAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
AAATTTTGTCTCCCTTGAGACAG
Found at i:4691 original size:51 final size:51
Alignment explanation
Indices: 4579--4691 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
4569 ACAAAGTTTT
* *
4579 GTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCATTAGACA
1 GTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTACCATTAGACA
* * *
4630 GTCTCTCTTGAGATAGTTTCCTTTGAAACAAATTTTGTCTACC-TTGAGATA
1 GTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTACCATT-AGACA
*
4681 GTTTCCCTTGA
1 GTCTCCCTTGA
4692 AACAAATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 2 0.04
51 54 0.96
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (51 bp):
GTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTACCATTAGACA
Found at i:13319 original size:26 final size:26
Alignment explanation
Indices: 13288--13338 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
13278 TGAAAAATTA
*
13288 AAATCCACCGAAAGGTGGCATTAAAC
1 AAATCCACCGAAAGGTGGAATTAAAC
13314 AAATCCACCGAAAGGTGGAATTAAA
1 AAATCCACCGAAAGGTGGAATTAAA
13339 TCCACCGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.16
Consensus pattern (26 bp):
AAATCCACCGAAAGGTGGAATTAAAC
Found at i:13342 original size:22 final size:23
Alignment explanation
Indices: 13283--13348 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 23
13273 ATTGTTGAAA
13283 AATTAAAATCCACCGAAAGGTGG
1 AATTAAAATCCACCGAAAGGTGG
*
13306 CATTAAACAAATCCACCGAAAGGTGG
1 AATT--A-AAATCCACCGAAAGGTGG
13332 AATT-AAATCCACCGAAA
1 AATTAAAATCCACCGAAA
13349 ATAATAAGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
22 13 0.34
23 3 0.08
25 1 0.03
26 21 0.55
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (23 bp):
AATTAAAATCCACCGAAAGGTGG
Found at i:15503 original size:15 final size:16
Alignment explanation
Indices: 15476--15508 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
15466 TAATATAAAA
15476 ATAAAATTTAAAAGTT
1 ATAAAATTTAAAAGTT
*
15492 ATAAAA-TTAAAATTT
1 ATAAAATTTAAAAGTT
15507 AT
1 AT
15509 GTATGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
ATAAAATTTAAAAGTT
Found at i:15721 original size:20 final size:20
Alignment explanation
Indices: 15681--15720 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
15671 AATAATAATA
15681 TATATTTATTTTTAATATTT
1 TATATTTATTTTTAATATTT
15701 TATATTTATTTTTAA-ATTT
1 TATATTTATTTTTAATATTT
15720 T
1 T
15721 TTATAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATATTTATTTTTAATATTT
Found at i:15736 original size:22 final size:23
Alignment explanation
Indices: 15694--15748 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
15684 ATTTATTTTT
* *
15694 AATA-TTTTATATTT-ATTTTTA
1 AATATTTTTATATTTAAATTTAA
15715 AAT-TTTTTATAATTTAAATTTAA
1 AATATTTTTAT-ATTTAAATTTAA
15738 AATATTTTTAT
1 AATATTTTTAT
15749 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 9 0.32
22 4 0.14
23 8 0.29
24 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
AATATTTTTATATTTAAATTTAA
Found at i:17155 original size:38 final size:38
Alignment explanation
Indices: 17111--17195 Score: 161
Period size: 38 Copynumber: 2.2 Consensus size: 38
17101 CTAATTCATC
17111 GATCGATTTCATTTCTATAATGAATACCCCTACGGAGG
1 GATCGATTTCATTTCTATAATGAATACCCCTACGGAGG
17149 GATCGATTTCATTTCTATAATGAATACCCCTACGGAGG
1 GATCGATTTCATTTCTATAATGAATACCCCTACGGAGG
*
17187 GCTCGATTT
1 GATCGATTT
17196 TTATATTCGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (38 bp):
GATCGATTTCATTTCTATAATGAATACCCCTACGGAGG
Found at i:17613 original size:21 final size:21
Alignment explanation
Indices: 17589--17630 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17579 CATTTGACCA
*
17589 TTACAATGCTGACATGACAGT
1 TTACAATACTGACATGACAGT
*
17610 TTACAATATTGACATGACAGT
1 TTACAATACTGACATGACAGT
17631 CAATCTGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (21 bp):
TTACAATACTGACATGACAGT
Found at i:20859 original size:23 final size:23
Alignment explanation
Indices: 20833--20894 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
20823 ACTTCTGTGC
*
20833 TGAATCATTCAGCACTGTTTTGT
1 TGAATCAGTCAGCACTGTTTTGT
* * *
20856 TGAATCGGTCAACATTGTTTTGT
1 TGAATCAGTCAGCACTGTTTTGT
20879 TGAATCAGTCAGCACT
1 TGAATCAGTCAGCACT
20895 TAATCATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (23 bp):
TGAATCAGTCAGCACTGTTTTGT
Found at i:21423 original size:2 final size:2
Alignment explanation
Indices: 21416--21450 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21406 CGGCAACAAA
21416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21451 AAAGGTGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22322 original size:77 final size:77
Alignment explanation
Indices: 22236--22379 Score: 207
Period size: 77 Copynumber: 1.9 Consensus size: 77
22226 CCTAATATGT
* * * * * * *
22236 CATGATTAACTAAGAAATATGTTGTGATTTGTAATGTTAATATTTTTATTAATAAAATAGGTTGT
1 CATGATTAACTAAAAAACATGTTGCGATATGGAATCTTAATATTTTTAATAATAAAATAGGTTGT
22301 GCCGAAGAAAGC
66 GCCGAAGAAAGC
* *
22313 CATGGTTAACTAAAAAACATGTTGCGATATGGAATCTTAATATTTTTAATAATAAAATGGGTTGT
1 CATGATTAACTAAAAAACATGTTGCGATATGGAATCTTAATATTTTTAATAATAAAATAGGTTGT
22378 GC
66 GC
22380 ATAAAATGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 58 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.37
Consensus pattern (77 bp):
CATGATTAACTAAAAAACATGTTGCGATATGGAATCTTAATATTTTTAATAATAAAATAGGTTGT
GCCGAAGAAAGC
Found at i:23453 original size:73 final size:72
Alignment explanation
Indices: 23371--23577 Score: 195
Period size: 73 Copynumber: 2.8 Consensus size: 72
23361 TATTAATATT
23371 GATAATTTTAAATATTGAAAAAGTTAAAGATAAGATCGAAAGTTAAAATATCGATACTTATGCGG
1 GATAATTTTAAATATTGAAAAAGTTAAAGA-AAGATCGAAAGTTAAAATATCGATACTTATGC-G
23436 A-AATGATC
64 ATAATGATC
* * * * * *
23444 GATACTTTTAAA-ATTTGAAAAAACTGATAA-AAATATCAAAATTTAAAATATCGATACTTATGC
1 GATAATTTTAAATA-TTG-AAAAAGTTA-AAGAAAGATCGAAAGTTAAAATATCGATACTTATGC
*
23507 GATGATGATC
63 GATAATGATC
* * * * * * * * * *
23517 AATATTTTTAGATATTGAACAAGTTGATGAATGATCGACAGTTAAAATATCAATACATATG
1 GATAATTTTAAATATTGAAAAAGTTAAAGAAAGATCGAAAGTTAAAATATCGATACTTATG
23578 TCATGAGGTT
Statistics
Matches: 106, Mismatches: 22, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
71 1 0.01
72 33 0.31
73 61 0.58
74 9 0.08
75 2 0.02
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.32
Consensus pattern (72 bp):
GATAATTTTAAATATTGAAAAAGTTAAAGAAAGATCGAAAGTTAAAATATCGATACTTATGCGAT
AATGATC
Found at i:29624 original size:35 final size:34
Alignment explanation
Indices: 29539--29625 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
29529 AATATAATTT
*
29539 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
29573 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
29611 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
29626 AACAAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:29908 original size:12 final size:12
Alignment explanation
Indices: 29891--29916 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29881 GTCATCACCA
29891 TCATCGTCGTCG
1 TCATCGTCGTCG
29903 TCATCGTCGTCG
1 TCATCGTCGTCG
29915 TC
1 TC
29917 GTCCTGAGTA
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:0.08, C:0.35, G:0.23, T:0.35
Consensus pattern (12 bp):
TCATCGTCGTCG
Found at i:31967 original size:17 final size:18
Alignment explanation
Indices: 31949--31981 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
31939 TAATTAAATA
31949 AAATA-TTAAA-AAATTT
1 AAATACTTAAATAAATTT
31965 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
31982 ACAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATACTTAAATAAATTT
Found at i:34886 original size:47 final size:49
Alignment explanation
Indices: 34759--34888 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 49
34749 ATATAAATTT
* *
34759 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA--TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* ** *
34805 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* **
34855 CTTGCCA-TT-ATTCTGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
34889 GTATGGTTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
46 6 0.09
47 25 0.36
48 20 0.29
49 2 0.03
50 17 0.24
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (49 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
Found at i:37582 original size:14 final size:14
Alignment explanation
Indices: 37563--37596 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
37553 GTTGTTATAT
37563 TTTTTAAAAAATAA
1 TTTTTAAAAAATAA
37577 TTTTT-AAAAATAA
1 TTTTTAAAAAATAA
37590 TATTTTA
1 T-TTTTA
37597 TTTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTTAAAAAATAA
Found at i:37585 original size:13 final size:13
Alignment explanation
Indices: 37563--37596 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
37553 GTTGTTATAT
37563 TTTTTAAAAAATAA
1 TTTTT-AAAAATAA
37577 TTTTTAAAAATAA
1 TTTTTAAAAATAA
37590 TATTTTA
1 T-TTTTA
37597 TTTTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTTAAAAATAA
Found at i:37627 original size:23 final size:22
Alignment explanation
Indices: 37573--37629 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
37563 TTTTTAAAAA
*
37573 ATAATTTTTAAAAATAATATTTT
1 ATAATTATT-AAAATAATATTTT
**
37596 ATTTTTTATTAAAATAATATTTAT
1 A-TAATTATTAAAATAATATTT-T
37620 ATAATTATTA
1 ATAATTATTA
37630 TTTATTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATTATTAAAATAATATTTT
Found at i:37632 original size:38 final size:34
Alignment explanation
Indices: 37560--37636 Score: 82
Period size: 37 Copynumber: 2.1 Consensus size: 34
37550 ATAGTTGTTA
37560 TATTTTTTAAAAAATAATTTTTAAAAATAATATTT
1 TATTTTTTAAAAAATAATTTTTAAAAATAATA-TT
* * * *
37595 TATTTTTTATTAAAATAATATTTATATAATTATTATT
1 TATTTTTTA-AAAAATAAT-TTT-TAAAAATAATATT
37632 TATTT
1 TATTT
37637 AAATTTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 9 0.26
36 8 0.23
37 10 0.29
38 8 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TATTTTTTAAAAAATAATTTTTAAAAATAATATT
Found at i:37644 original size:25 final size:24
Alignment explanation
Indices: 37614--37660 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
37604 TTAAAATAAT
37614 ATTTATATAATT-ATTATTTATTTAA
1 ATTTAT-TAATTAATTA-TTATTTAA
37639 ATTTATTAATTAATTATTATTT
1 ATTTATTAATTAATTATTATTT
37661 GTGCTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTATTAATTAATTATTATTTAA
Found at i:38811 original size:17 final size:17
Alignment explanation
Indices: 38789--38824 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
38779 GCTTGATATA
38789 ATTAGAA-TATTATATTT
1 ATTAGAATTA-TATATTT
38806 ATTAGAATTATATATTT
1 ATTAGAATTATATATTT
38823 AT
1 AT
38825 GTTTCAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTAGAATTATATATTT
Found at i:39444 original size:42 final size:42
Alignment explanation
Indices: 39397--39486 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
39387 ATGTCCAGCA
**
39397 CACCAGTTCAGATGTCATCTCCGCAAGGG-TATATGCCAAGCC
1 CACCAGTTCAGATACCATCTCCGC-AGGGTTATATGCCAAGCC
* * *
39439 CACCAGTTCATATACCATCTCCGCAGGGTTATATTCCTAGCC
1 CACCAGTTCAGATACCATCTCCGCAGGGTTATATGCCAAGCC
39481 CACCAG
1 CACCAG
39487 GTTACATGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (42 bp):
CACCAGTTCAGATACCATCTCCGCAGGGTTATATGCCAAGCC
Found at i:39510 original size:21 final size:21
Alignment explanation
Indices: 39459--39510 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
39449 TATACCATCT
* * *
39459 CCGCAGGGTTATATTCCTAGC
1 CCGCAGGGTTACATGCCCAGC
*
39480 CCACCA-GGTTACATGCCCAGC
1 CC-GCAGGGTTACATGCCCAGC
39501 CCGCAGGGTT
1 CCGCAGGGTT
39511 TTATGACACT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCCAGC
Found at i:40744 original size:136 final size:135
Alignment explanation
Indices: 40536--41537 Score: 1326
Period size: 136 Copynumber: 7.4 Consensus size: 135
40526 AAATTTCAAG
* * * * *
40536 CATAATAGGGCAATTATAACCTATTAGT-TGGAAAAAAAAAGAAAGGCGCTCCCCCTGAAACACG
1 CATAATAGGGCAATTATAACATATT-CTCT-GACAAAAAAGGGAAGGCGC-CCCCCTGAAACACG
* * * * *
40600 CTTTCACCACATTATTACGTCCCCGCAAACATGATAGGTACTGACATGAATAGTGCCCCCAGGAG
63 CTTTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGG
40665 ACATCACA
128 ACATCACA
* * **
40673 CATAATAGGGTAATTATAACATATTCTCTGACAAAAAAAAGGGAAGGTG-CCCCCTGAAATGCGC
1 CATAATAGGGCAATTATAACATATTCTCTGAC--AAAAAAGGGAAGGCGCCCCCCTGAAACACGC
* * * *
40737 TTTCACCACTTTGTTGCATCCCCTCAAACATGATAGGTACTGATATGAATAGTACCCCCGGGGGA
64 TTTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGA
*
40802 CATCAAA
129 CATCACA
* * *
40809 CATAATAGGGCACTTATAACATAATCTCTAACAAAAAAAGGGAAGGCGCCCCCCCTGAAACACGC
1 CATAATAGGGCAATTATAACATATTCTCTGAC-AAAAAAGGGAAGGCG-CCCCCCTGAAACACGC
*
40874 TTTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGACTAGTGCCCCCGGGGGA
64 TTTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGA
40939 CATCACA
129 CATCACA
* * * *
40946 CATAATAGGGAAATTATAACATATTCTCTGACAAAAAATGGAAGGCGCCCCCCTAAAACACGTTT
1 CATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGGAAGGCGCCCCCCTGAAACACGCTT
* * * * *
41011 TCACCACTTTGTTGCGTCCCCTTAAACATGATAGGTACTGACATGAATAGTTCCCCCAGGGGAAA
66 TCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGACA
41076 TCACA
131 TCACA
* * * * * *
41081 CATAATAGGGCAATTATAACATATTCTCTGACAAAAAATGTAAGACACGCCCCCTGAAACGCACT
1 CATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGGAAGGCGC-CCCCCTGAAACACGCT
* *
41146 TTCACCACTTTGA-TGCGTCTCCTCAAACATGATAGGTACTGATATGAATAGTGCCCCCGGGGGA
65 TTCACCACTTT-ATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGA
41210 CATCACA
129 CATCACA
* * * * *
41217 CATAATATGACAATTATAATATATTCTCTGAGAAAAAAAGGGAAGGCACGCCCCCTGAAACACGC
1 CATAATAGGGCAATTATAACATATTCTCTGA-CAAAAAAGGGAAGGCGC-CCCCCTGAAACACGC
* * * *
41282 TTTCACCACTTTATTGTGTCCCCTCAAACATGATAGGTATTGGCATGAATAGTGACCCCGGGGGA
64 TTTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGA
41347 CATCACA
129 CATCACA
* * * * * *
41354 CATAATAGGGCAATTAAAACATATTCTCTGACAAAAAATGTAAGGTGCTCCCCCTGAAACGCTCT
1 CATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGGAAGGCGC-CCCCCTGAAACACGCT
* * * *
41419 TTCACCACTTTGTTGTGTCCCCTCAAACATGATAGGTACTAACATGAATAGTGCCCCCGGGGGAT
65 TTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGAC
41484 ATCACA
130 ATCACA
* *
41490 CATAATAGGGCAATTATAACATATTCTCTTATAAAAAAGGGAAGGCGC
1 CATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGGAAGGCGC
41538 GTGTAACACC
Statistics
Matches: 757, Mismatches: 99, Indels: 19
0.87 0.11 0.02
Matches are distributed among these distances:
135 139 0.18
136 357 0.47
137 249 0.33
138 12 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (135 bp):
CATAATAGGGCAATTATAACATATTCTCTGACAAAAAAGGGAAGGCGCCCCCCTGAAACACGCTT
TCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGACA
TCACA
Found at i:41134 original size:273 final size:270
Alignment explanation
Indices: 40536--41537 Score: 1348
Period size: 273 Copynumber: 3.7 Consensus size: 270
40526 AAATTTCAAG
* * * * *
40536 CATAATAGGGCAATTATAACCTATTAGT-TGGAAAAAAAAAGAAAGGCGCTCCCCCTGAAACACG
1 CATAATAGGGCAATTATAACATATT-CTCT-GACAAAAAATGTAAGGCGC-CCCCCTGAAACACG
* * * * *
40600 CTTTCACCACATTATTACGTCCCCGCAAACATGATAGGTACTGACATGAATAGTGCCCCCAGGAG
63 CTTTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGG
* *
40665 ACATCACACATAATAGGGTAATTATAACATATTCTCTGACAAAAAAAAGGGAAGGTG-CCCCCTG
128 ACATCACACATAATAGGGAAATTATAACATATTCTCTGAC--AAAAAAGGGAAGGCGCCCCCCTG
** * *
40729 AAATGCGCTTTCACCACTTTGTTGCATCCCCTCAAACATGATAGGTACTGATATGAATAGTACCC
191 AAACACGCTTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTACCC
*
40794 CCGGGGGACATCAAA
256 CCGGGGGACATCACA
* * * * *
40809 CATAATAGGGCACTTATAACATAATCTCTAACAAAAAAAGGGAAGGCGCCCCCCCTGAAACACGC
1 CATAATAGGGCAATTATAACATATTCTCTGAC-AAAAAATGTAAGGCG-CCCCCCTGAAACACGC
*
40874 TTTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGACTAGTGCCCCCGGGGGA
64 TTTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGA
* *
40939 CATCACACATAATAGGGAAATTATAACATATTCTCTGACAAAAAATGGAAGGCGCCCCCCTAAAA
129 CATCACACATAATAGGGAAATTATAACATATTCTCTGACAAAAAAGGGAAGGCGCCCCCCTGAAA
* * * *
41004 CACGTTTTCACCACTTTGTTGCGTCCCCTTAAACATGATAGGTACTGACATGAATAGTTCCCCCA
194 CACGCTTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTACCCCCG
*
41069 GGGGAAATCACA
259 GGGGACATCACA
* * * *
41081 CATAATAGGGCAATTATAACATATTCTCTGACAAAAAATGTAAGACACGCCCCCTGAAACGCACT
1 CATAATAGGGCAATTATAACATATTCTCTGACAAAAAATGTAAGGCGC-CCCCCTGAAACACGCT
* *
41146 TTCACCACTTTGA-TGCGTCTCCTCAAACATGATAGGTACTGATATGAATAGTGCCCCCGGGGGA
65 TTCACCACTTT-ATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGA
* * * *
41210 CATCACACATAATA-TGACAATTATAATATATTCTCTGAGAAAAAAAGGGAAGGCACGCCCCCTG
129 CATCACACATAATAGGGA-AATTATAACATATTCTCTGA-CAAAAAAGGGAAGGCGC-CCCCCTG
* * * *
41274 AAACACGCTTTCACCACTTTATTGTGTCCCCTCAAACATGATAGGTATTGGCATGAATAGTGA-C
191 AAACACGCTTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGT-ACC
41338 CCCGGGGGACATCACA
255 CCCGGGGGACATCACA
* * * *
41354 CATAATAGGGCAATTAAAACATATTCTCTGACAAAAAATGTAAGGTGCTCCCCCTGAAACGCTCT
1 CATAATAGGGCAATTATAACATATTCTCTGACAAAAAATGTAAGGCGC-CCCCCTGAAACACGCT
* * * *
41419 TTCACCACTTTGTTGTGTCCCCTCAAACATGATAGGTACTAACATGAATAGTGCCCCCGGGGGAT
65 TTCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGAC
* * *
41484 ATCACACATAATAGGGCAATTATAACATATTCTCTTATAAAAAAGGGAAGGCGC
130 ATCACACATAATAGGGAAATTATAACATATTCTCTGACAAAAAAGGGAAGGCGC
41538 GTGTAACACC
Statistics
Matches: 644, Mismatches: 73, Indels: 25
0.87 0.10 0.03
Matches are distributed among these distances:
270 3 0.00
271 130 0.20
272 137 0.21
273 372 0.58
274 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (270 bp):
CATAATAGGGCAATTATAACATATTCTCTGACAAAAAATGTAAGGCGCCCCCCTGAAACACGCTT
TCACCACTTTATTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTGCCCCCGGGGGACA
TCACACATAATAGGGAAATTATAACATATTCTCTGACAAAAAAGGGAAGGCGCCCCCCTGAAACA
CGCTTTCACCACTTTGTTGCGTCCCCTCAAACATGATAGGTACTGACATGAATAGTACCCCCGGG
GGACATCACA
Found at i:41732 original size:19 final size:21
Alignment explanation
Indices: 41708--41755 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
41698 ATATACGTTT
* *
41708 TATGAATAGT-AA-AATATGG
1 TATGAACAGTGAACAATATCG
41727 TATGAACAGTGAACAATATCG
1 TATGAACAGTGAACAATATCG
41748 TATGAACA
1 TATGAACA
41756 ATAATGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 14 0.56
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (21 bp):
TATGAACAGTGAACAATATCG
Found at i:42475 original size:31 final size:31
Alignment explanation
Indices: 42437--42592 Score: 174
Period size: 31 Copynumber: 5.0 Consensus size: 31
42427 CCCGAAGGAC
* * *
42437 CAGTCCATAGATTCCGAAGAACCTAGGTAAT
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
* *
42468 CAGTCCATATG-TCCTGAATAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
* * *
42499 CAATTCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAAA
*
42530 CAGTCCATATG-TCCCGAAGAACATAGGTAAG
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
*
42561 CAGTCCATATG-TCCCGAAAAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAAA
42592 C
1 C
42593 CCTTGACCCT
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
31 105 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (31 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAAA
Found at i:42553 original size:62 final size:62
Alignment explanation
Indices: 42440--42592 Score: 207
Period size: 62 Copynumber: 2.5 Consensus size: 62
42430 GAAGGACCAG
* * * * * *
42440 TCCATAGATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCTGAATAACATAGGTAAACAA
1 TCCATATATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAA
* * *
42502 TTCATATATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAGCAG
1 TCCATATATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAA
* *
42564 TCCATATGTCCCGAAAAACATAGGTAAAC
1 TCCATATATCCCGAAGAACATAGGTAAAC
42593 CCTTGACCCT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 79 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (62 bp):
TCCATATATCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAA
Found at i:48141 original size:29 final size:29
Alignment explanation
Indices: 48108--48177 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
48098 TCCCCAAGCA
*
48108 TAGGTCGTCATGCCCTCCGGGAGACCTTG
1 TAGGTCGTCATGCCCTCCAGGAGACCTTG
** *
48137 TAGGTC-TCCATGCTTTCCAGGCGACCTTG
1 TAGGTCGT-CATGCCCTCCAGGAGACCTTG
48166 TAGGTCG-CATGC
1 TAGGTCGTCATGC
48178 ACTACTGGCG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.14, C:0.30, G:0.29, T:0.27
Consensus pattern (29 bp):
TAGGTCGTCATGCCCTCCAGGAGACCTTG
Found at i:48272 original size:14 final size:14
Alignment explanation
Indices: 48250--48310 Score: 88
Period size: 14 Copynumber: 4.4 Consensus size: 14
48240 CCTCGCATAG
*
48250 CTCGCTCGGATAG-C
1 CTCGGTCGGAT-GCC
48264 CTCGGTCGGATGCC
1 CTCGGTCGGATGCC
*
48278 CTAGGTCGGATGCC
1 CTCGGTCGGATGCC
48292 CTCGGTCGGATGCC
1 CTCGGTCGGATGCC
48306 CTCGG
1 CTCGG
48311 ATGCTCAGCG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
13 1 0.02
14 42 0.98
ACGTcount: A:0.10, C:0.34, G:0.34, T:0.21
Consensus pattern (14 bp):
CTCGGTCGGATGCC
Found at i:49662 original size:23 final size:23
Alignment explanation
Indices: 49611--49656 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
49601 TATTTTTGTG
49611 TTAAGTCTTTTTAATAATAAAAATA
1 TTAAGTC-TTTT-ATAATAAAAATA
*
49636 TTAAGTCTTTTATTATAAAAA
1 TTAAGTCTTTTATAATAAAAA
49657 GTTTAACGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (23 bp):
TTAAGTCTTTTATAATAAAAATA
Found at i:49669 original size:23 final size:22
Alignment explanation
Indices: 49618--49670 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
49608 GTGTTAAGTC
49618 TTTTTAATAATAAAAATATTAAG
1 TTTTT-ATAATAAAAATATTAAG
*
49641 TCTTTTATTATAAAAAGT-TTAACG
1 T-TTTTATAATAAAAA-TATTAA-G
49665 TTTTTA
1 TTTTTA
49671 GACATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (22 bp):
TTTTTATAATAAAAATATTAAG
Found at i:50070 original size:14 final size:14
Alignment explanation
Indices: 50049--50085 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
50039 AGTCACAGAC
50049 CGACGGTGGTCGAT
1 CGACGGTGGTCGAT
*
50063 CTACGGTGGTCGAT
1 CGACGGTGGTCGAT
50077 CGACGGTGG
1 CGACGGTGG
50086 AAGAAGTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.22, G:0.43, T:0.22
Consensus pattern (14 bp):
CGACGGTGGTCGAT
Found at i:50753 original size:21 final size:21
Alignment explanation
Indices: 50727--50781 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
50717 CATAGCTTTC
50727 TCTCTTTCTTCCCTCCCATTT
1 TCTCTTTCTTCCCTCCCATTT
*
50748 TCTCTTTCTTCCCTCCCCTTT
1 TCTCTTTCTTCCCTCCCATTT
50769 TCTCTTTCTTCCC
1 TCTCTTTCTTCCC
50782 ACTTTTGTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (21 bp):
TCTCTTTCTTCCCTCCCATTT
Found at i:54970 original size:28 final size:29
Alignment explanation
Indices: 54932--54993 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
54922 TGGATCATGT
*
54932 TGTTTGAAGCT-GTTTAGGATCATTTTAC
1 TGTTTGAAGCTAGTTTAGGATCATGTTAC
* * * *
54960 TGTTTGGAGCTATTTTTGGATCATGTTGC
1 TGTTTGAAGCTAGTTTAGGATCATGTTAC
54989 TGTTT
1 TGTTT
54994 TGAATGTGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.16, C:0.10, G:0.24, T:0.50
Consensus pattern (29 bp):
TGTTTGAAGCTAGTTTAGGATCATGTTAC
Found at i:54991 original size:29 final size:27
Alignment explanation
Indices: 54920--54993 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 27
54910 TGCAGTGGAC
54920 TTTGGATCATG-T-TGTTTGAAGCTGT
1 TTTGGATCATGTTCTGTTTGAAGCTGT
* * * *
54945 TTAGGATCATTTTACTGTTTGGAGCTATT
1 TTTGGATCATGTT-CTGTTTGAAGCT-GT
54974 TTTGGATCATGTTGCTGTTT
1 TTTGGATCATGTT-CTGTTT
54994 TGAATGTGCT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 9 0.24
26 1 0.03
28 10 0.26
29 18 0.47
ACGTcount: A:0.16, C:0.09, G:0.24, T:0.50
Consensus pattern (27 bp):
TTTGGATCATGTTCTGTTTGAAGCTGT
Found at i:62236 original size:32 final size:31
Alignment explanation
Indices: 62200--62276 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
62190 CGGGGCCGTG
*
62200 GGGCCTACCTAAGAACACATCTTAGGGCCACA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
** ** *
62232 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
62263 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
62277 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:63187 original size:5 final size:5
Alignment explanation
Indices: 63177--63230 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
63167 TGGGTCAACA
** *
63177 GTCGG GTCGG GTCGG GTCAACA GTCGG GTCGG GTCGG GTC-A GTCGG GTCGG
1 GTCGG GTCGG GTCGG GTC--GG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG
63228 GTC
1 GTC
63231 AACCCGGTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 34 0.85
7 3 0.08
ACGTcount: A:0.07, C:0.22, G:0.50, T:0.20
Consensus pattern (5 bp):
GTCGG
Found at i:63193 original size:22 final size:22
Alignment explanation
Indices: 63159--63230 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
63149 AACGGTCAAC
* *
63159 GGTCAGGTTGGGTCAACAGTCG
1 GGTCGGGTCGGGTCAACAGTCG
63181 GGTCGGGTCGGGTCAACAGTCG
1 GGTCGGGTCGGGTCAACAGTCG
63203 GGTCGGGTCGGGT---CAGTCG
1 GGTCGGGTCGGGTCAACAGTCG
63222 GGTCGGGTC
1 GGTCGGGTC
63231 AACCCGGTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 15 0.31
22 33 0.69
ACGTcount: A:0.11, C:0.21, G:0.47, T:0.21
Consensus pattern (22 bp):
GGTCGGGTCGGGTCAACAGTCG
Found at i:63223 original size:14 final size:14
Alignment explanation
Indices: 63204--63231 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
63194 CAACAGTCGG
63204 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
63218 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
63232 ACCCGGTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.50, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:63261 original size:10 final size:10
Alignment explanation
Indices: 63229--63278 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
63219 TCGGGTCGGG
*
63229 TCAACCCGGT
1 TCAAACCGGT
*
63239 TCAGACCGG-
1 TCAAACCGGT
63248 TCAAACCGGT
1 TCAAACCGGT
*
63258 TCAAAACTGG-
1 TC-AAACCGGT
63268 TCAAACCGGT
1 TCAAACCGGT
63278 T
1 T
63279 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:63269 original size:20 final size:19
Alignment explanation
Indices: 63227--63278 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
63217 AGTCGGGTCG
* *
63227 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
63246 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
63266 GGTCAAACCGGTT
1 GGTCAAACCGGTT
63279 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:68243 original size:32 final size:31
Alignment explanation
Indices: 68207--68283 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
68197 CGGGGCCGTG
*
68207 GGGCCTACCTAAGAACACATCTTAGGGCCACA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
** ** *
68239 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
68270 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
68284 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:68266 original size:63 final size:63
Alignment explanation
Indices: 68162--68283 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
68152 CTAAGGGAAT
* * ** *
68162 ATCTTAGGGCCTAAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAACAC
1 ATCTTAGGGCCTAAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAACAC
* *
68225 ATCTTAGGGCC-ACAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ATCTTAGGGCCTA-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
68284 GTCACATTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ATCTTAGGGCCTAAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAACAC
Found at i:69195 original size:5 final size:5
Alignment explanation
Indices: 69187--69240 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
69177 CGGGTCAACA
** *
69187 GTCGG GTCGG GTCGG GTCAACA GTCGG GTCGG GTCGG GTC-A GTCGG GTCGG
1 GTCGG GTCGG GTCGG GTC--GG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG
69238 GTC
1 GTC
69241 AACCCGGTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 34 0.85
7 3 0.08
ACGTcount: A:0.07, C:0.22, G:0.50, T:0.20
Consensus pattern (5 bp):
GTCGG
Found at i:69202 original size:22 final size:22
Alignment explanation
Indices: 69174--69240 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
69164 AACGGTCAAC
69174 GGTCGGGTCAACAGTCGGGTCG
1 GGTCGGGTCAACAGTCGGGTCG
69196 GGTCGGGTCAACAGTCGGGTCG
1 GGTCGGGTCAACAGTCGGGTCG
69218 GGTCGGGT---CAGTCGGGTCG
1 GGTCGGGTCAACAGTCGGGTCG
69237 GGTC
1 GGTC
69241 AACCCGGTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.33
22 30 0.67
ACGTcount: A:0.10, C:0.22, G:0.48, T:0.19
Consensus pattern (22 bp):
GGTCGGGTCAACAGTCGGGTCG
Found at i:69233 original size:14 final size:14
Alignment explanation
Indices: 69214--69241 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
69204 CAACAGTCGG
69214 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
69228 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
69242 ACCCGGTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.50, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:69271 original size:10 final size:10
Alignment explanation
Indices: 69239--69288 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
69229 TCGGGTCGGG
*
69239 TCAACCCGGT
1 TCAAACCGGT
*
69249 TCAGACCGG-
1 TCAAACCGGT
69258 TCAAACCGGT
1 TCAAACCGGT
*
69268 TCAAAACTGG-
1 TC-AAACCGGT
69278 TCAAACCGGT
1 TCAAACCGGT
69288 T
1 T
69289 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:69279 original size:20 final size:19
Alignment explanation
Indices: 69237--69288 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
69227 AGTCGGGTCG
* *
69237 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
69256 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
69276 GGTCAAACCGGTT
1 GGTCAAACCGGTT
69289 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:70679 original size:2 final size:2
Alignment explanation
Indices: 70668--70752 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
70658 ACACACACAC
*
70668 AG AG AC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
70710 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
70752 A
1 A
70753 TCATTCTCCT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.01, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:71986 original size:2 final size:2
Alignment explanation
Indices: 71979--72003 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71969 ATTTTCCTAT
71979 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
72004 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72075 original size:2 final size:2
Alignment explanation
Indices: 72068--72094 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
72058 TTCCTAACGT
72068 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
72095 TCTTACTTCA
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:72249 original size:26 final size:26
Alignment explanation
Indices: 72205--72278 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 26
72195 TATTATTTTA
* *
72205 TTATATTATACATACATTTTTA-TAT
1 TTATATTATATATATATTTTTATTAT
72230 TTATA-TATATATATATATTTTATTAT
1 TTATATTATATATATAT-TTTTATTAT
72256 TT-TATT-TATACTAT-TTATTTATT
1 TTATATTATATA-TATATT-TTTATT
72279 TTCATTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
24 10 0.24
25 23 0.55
26 9 0.21
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (26 bp):
TTATATTATATATATATTTTTATTAT
Found at i:73576 original size:19 final size:20
Alignment explanation
Indices: 73540--73577 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
73530 ACCTTACTAA
*
73540 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
73560 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
73578 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Found at i:76856 original size:16 final size:15
Alignment explanation
Indices: 76831--76872 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
76821 CAAAAAGGCC
*
76831 AAAAATAAAAAAGAA
1 AAAAACAAAAAAGAA
76846 AAGAAACAAAAAAGAA
1 AA-AAACAAAAAAGAA
*
76862 GAAAACAAAAA
1 AAAAACAAAAA
76873 TTAAACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.02
Consensus pattern (15 bp):
AAAAACAAAAAAGAA
Found at i:77516 original size:22 final size:22
Alignment explanation
Indices: 77488--77542 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
77478 GCTACCCCAT
*
77488 CAAACCTTTGAGCATTAAATGC
1 CAAACCTTTGAGCATCAAATGC
77510 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
77532 CAAACCTTTGA
1 CAAACCTTTGA
77543 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:77982 original size:18 final size:19
Alignment explanation
Indices: 77956--77992 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
77946 TCAACATCAA
77956 ATATGGGGGCATT-TTTGG
1 ATATGGGGGCATTATTTGG
*
77974 ATATTGGGGCATTATTTGG
1 ATATGGGGGCATTATTTGG
77993 GGATTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.19, C:0.05, G:0.35, T:0.41
Consensus pattern (19 bp):
ATATGGGGGCATTATTTGG
Found at i:79525 original size:106 final size:106
Alignment explanation
Indices: 78367--79524 Score: 1703
Period size: 106 Copynumber: 11.0 Consensus size: 106
78357 ATATCGTGTC
* * * * * *
78367 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGACAAC-AACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
** * *
78431 AATTTTGGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
78472 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
78537 AA-ATCAGAGTCAATTTCAACTTTACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
78577 ACT--------C-CAAGTTCAACTTCACGAC-AAGGGACCGTTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
78632 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
78673 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
78738 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
78779 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
78844 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
78885 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAATCAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
78950 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
78991 ACTCCAGACAACGCAAGTTCAACTTCACAAAGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
79056 AATTTCGGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* **
79097 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTATC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
79162 AATTTCAGAGCCAATTTCAACTTTACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
79203 ACTCTAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
79268 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
79309 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
79374 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
79415 ACTCGAGATAACACAAGTTCAACTTCACAACGAATGGA-CGATTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCC
* * * *
79479 CGATTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
79521 ACTC
1 ACTC
79525 GGAACAATGC
Statistics
Matches: 954, Mismatches: 86, Indels: 25
0.90 0.08 0.02
Matches are distributed among these distances:
95 30 0.03
96 54 0.06
97 1 0.00
104 1 0.00
105 101 0.11
106 767 0.80
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:79938 original size:37 final size:37
Alignment explanation
Indices: 79852--79952 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 37
79842 TTCGTCCTAT
* * * *
79852 TAGGATTCGAACTCCTAAAAATATGATAGAATTTTGC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
* *
79889 TAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTAT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
** * *
79926 TATTATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
79953 CCACAAACAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
Found at i:80493 original size:2 final size:2
Alignment explanation
Indices: 80486--80516 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
80476 ATTTTCCTAT
80486 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
80517 TATTTTTTAT
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:80572 original size:95 final size:92
Alignment explanation
Indices: 80392--80574 Score: 199
Period size: 93 Copynumber: 1.9 Consensus size: 92
80382 CCCTTATTAT
* * *
80392 TTATATGTATATAAATATATATATATTAATTATATTTTATTTATTTATTATAGTTTTTTTTTTCA
1 TTATATATATATAAATATATATATATTAATTATATTTTATTTATTTATTATA-TTATTTTTTACA
* * *
80457 TTTTTTTGCGTTATATTATATTTTCCTA
65 TATTTTTCCATTATATTATATTTTCCTA
* * *
80485 TTATATATATATATATATATATATATATATATTATTTTTTATCTATGTTTACTTAT-TTATTTTT
1 TTATATATATATAAATATATATATAT-TA-ATTATATTTTAT-T-TATTTA-TTATATTATTTTT
80549 TAC-TATTTTTCCTATTATATATATAT
61 TACATATTTTTCC-ATTATAT-TATAT
80575 ATATTCTTAC
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
93 24 0.32
94 2 0.03
95 18 0.24
96 16 0.22
97 10 0.14
98 4 0.05
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (92 bp):
TTATATATATATAAATATATATATATTAATTATATTTTATTTATTTATTATATTATTTTTTACAT
ATTTTTCCATTATATTATATTTTCCTA
Found at i:80680 original size:21 final size:21
Alignment explanation
Indices: 80650--80759 Score: 77
Period size: 22 Copynumber: 4.9 Consensus size: 21
80640 TTTATTTTTC
80650 ATTTATTTATTATTATTATACT
1 ATTTA-TTATTATTATTATACT
80672 ATTTATTATTTTATTATATATACAT
1 ATTTATTA--TTATTAT-TATAC-T
80697 ACATTT-TTA-TATTATATATA-T
1 --ATTTATTATTATTAT-TATACT
80718 ATATTATTATT-TTATTTATACT
1 AT-TTATTATTATTA-TTATACT
80740 ATTTATTTATT-TTCATTATA
1 ATTTA-TTATTATT-ATTATA
80760 TTTTTAGTTT
Statistics
Matches: 75, Mismatches: 0, Indels: 26
0.74 0.00 0.26
Matches are distributed among these distances:
19 2 0.03
20 2 0.03
21 17 0.23
22 22 0.29
23 19 0.25
24 5 0.07
25 1 0.01
26 3 0.04
27 4 0.05
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTATTATTATTATTATACT
Found at i:80860 original size:20 final size:21
Alignment explanation
Indices: 80837--80883 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
80827 TGTATATATA
80837 TTTATCTTC-ATTT-ATTTTAT
1 TTTAT-TTCAATTTCATTTTAT
80857 TTTA-TTCAATTTCATTTTAT
1 TTTATTTCAATTTCATTTTAT
80877 TTTATTT
1 TTTATTT
80884 TTTTTGTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 15 0.62
21 2 0.08
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATTTCAATTTCATTTTAT
Found at i:80885 original size:6 final size:5
Alignment explanation
Indices: 80847--80888 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
80837 TTTATCTTCA
** *
80847 TTTAT TTTAT TTTAT TCAAT TTCAT TTTAT TTTAT TTT-T TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
80889 GTTTCATCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:90176 original size:14 final size:14
Alignment explanation
Indices: 90134--90183 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
90124 TTAACGAAAT
90134 TAATATTTTTAGTAAA
1 TAATA-TTTTA-TAAA
90150 -AATATATTT-TAAA
1 TAATAT-TTTATAAA
90163 TAATATTTTATAAA
1 TAATATTTTATAAA
*
90177 AAATATT
1 TAATATT
90184 AATATTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 7 0.23
14 16 0.53
15 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TAATATTTTATAAA
Found at i:90207 original size:21 final size:20
Alignment explanation
Indices: 90163--90203 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
90153 ATATTTTAAA
90163 TAATATTTTATAAAAAATAT
1 TAATATTTTATAAAAAATAT
90183 TAATATTTT-TAATAAAATAT
1 TAATATTTTATAA-AAAATAT
90203 T
1 T
90204 TAATTAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATTTTATAAAAAATAT
Found at i:90272 original size:3 final size:3
Alignment explanation
Indices: 90254--90297 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
90244 TATTTATTTT
90254 TTA TT- TTA TT- TTA TTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
90298 CATTTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:90288 original size:19 final size:18
Alignment explanation
Indices: 90259--90294 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
90249 ATTTTTTATT
90259 TTATTTTATTATTATTAA
1 TTATTTTATTATTATTAA
90277 TTATTATTATTATTATTA
1 TTATT-TTATTATTATTA
90295 TTACATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTTATTATTATTAA
Found at i:90381 original size:37 final size:37
Alignment explanation
Indices: 90338--90437 Score: 200
Period size: 37 Copynumber: 2.7 Consensus size: 37
90328 AGATTACAAA
90338 GGCCCAATCCCGGAGCCCAACAACCCGAAGCCCAATT
1 GGCCCAATCCCGGAGCCCAACAACCCGAAGCCCAATT
90375 GGCCCAATCCCGGAGCCCAACAACCCGAAGCCCAATT
1 GGCCCAATCCCGGAGCCCAACAACCCGAAGCCCAATT
90412 GGCCCAATCCCGGAGCCCAACAACCC
1 GGCCCAATCCCGGAGCCCAACAACCC
90438 ATCAGATTAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.29, C:0.45, G:0.19, T:0.07
Consensus pattern (37 bp):
GGCCCAATCCCGGAGCCCAACAACCCGAAGCCCAATT
Found at i:90391 original size:22 final size:22
Alignment explanation
Indices: 90361--90431 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
90351 AGCCCAACAA
90361 CCCGAAGCCCAATTGGCCCAAT
1 CCCGAAGCCCAATTGGCCCAAT
*
90383 CCCGGAGCCCAA------CAA-
1 CCCGAAGCCCAATTGGCCCAAT
90398 CCCGAAGCCCAATTGGCCCAAT
1 CCCGAAGCCCAATTGGCCCAAT
*
90420 CCCGGAGCCCAA
1 CCCGAAGCCCAA
90432 CAACCCATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
15 11 0.28
16 3 0.08
21 3 0.08
22 22 0.56
ACGTcount: A:0.28, C:0.44, G:0.20, T:0.08
Consensus pattern (22 bp):
CCCGAAGCCCAATTGGCCCAAT
Found at i:90467 original size:25 final size:25
Alignment explanation
Indices: 90438--90512 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
90428 CCAACAACCC
90438 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
90463 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* *
90488 AACAAATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
90513 TCCCCTACTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:92073 original size:17 final size:17
Alignment explanation
Indices: 92051--92090 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
92041 CTTATAGAAA
*
92051 TTATTTTTATTG-TTATT
1 TTATTTTT-TTGATTAAT
92068 TTATTTTTTTGATTAAT
1 TTATTTTTTTGATTAAT
92085 TTATTT
1 TTATTT
92091 GATGTTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (17 bp):
TTATTTTTTTGATTAAT
Found at i:93675 original size:13 final size:13
Alignment explanation
Indices: 93657--93681 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93647 CCCTAACCTT
93657 TTTATTTATTTTA
1 TTTATTTATTTTA
93670 TTTATTTATTTT
1 TTTATTTATTTT
93682 TGAGTATGTA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTATTTTA
Done.