Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold39
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: 4724573
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 178835 characters in sequence are not A, C, G, or T
File 17 of 27
Found at i:2908323 original size:13 final size:13
Alignment explanation
Indices: 2908305--2908330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2908295 TACACAAAGT
2908305 ATGTATCGATACA
1 ATGTATCGATACA
2908318 ATGTATCGATACA
1 ATGTATCGATACA
2908331 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2908328 original size:32 final size:33
Alignment explanation
Indices: 2908287--2908350 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2908277 TAGCCAAACT
**
2908287 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2908319 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2908351 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2910594 original size:21 final size:21
Alignment explanation
Indices: 2910561--2910610 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2910551 TTGCAAGTTG
*
2910561 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2910583 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
2910604 AAATAAA
1 AAATAAA
2910611 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2920403 original size:1 final size:1
Alignment explanation
Indices: 2920397--2920470 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
2920387 CGTCCTCCAC
* * * * * * * * *
2920397 AAAAAAAAAAGAAAAACAAAACAAAAAACAAAACAAAAAAACAAAAAAAAACAAACAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
2920462 CAAAAAAAA
1 AAAAAAAAA
2920471 GGGGTCCGGA
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.12, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:2920424 original size:13 final size:13
Alignment explanation
Indices: 2920408--2920461 Score: 76
Period size: 13 Copynumber: 4.2 Consensus size: 13
2920398 AAAAAAAAAG
2920408 AAAAACAAAAC-A
1 AAAAACAAAACAA
2920420 AAAAACAAAACAA
1 AAAAACAAAACAA
*
2920433 AAAAACAAAAAAA
1 AAAAACAAAACAA
2920446 AACAAAC-AAACAA
1 AA-AAACAAAACAA
2920459 AAA
1 AAA
2920462 CAAAAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
12 12 0.32
13 22 0.58
14 4 0.11
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAACAA
Found at i:2920433 original size:34 final size:31
Alignment explanation
Indices: 2920395--2920470 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 31
2920385 GGCGTCCTCC
*
2920395 ACAAAAAAAAAAGAAAAACAAAACAAAAAACAAA
1 ACAAAAAAAAAAAAAAAAC-AAAC-AAAAA-AAA
*
2920429 ACAAAAAAACAAAAAAAAACAAACAAACAAAA
1 ACAAAAAAA-AAAAAAAAACAAACAAAAAAAA
2920461 ACAAAAAAAA
1 ACAAAAAAAA
2920471 GGGGTCCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 1 0.03
32 12 0.31
33 4 0.10
34 13 0.33
35 9 0.23
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (31 bp):
ACAAAAAAAAAAAAAAAACAAACAAAAAAAA
Found at i:2920443 original size:31 final size:32
Alignment explanation
Indices: 2920400--2920469 Score: 108
Period size: 31 Copynumber: 2.2 Consensus size: 32
2920390 CCTCCACAAA
*
2920400 AAAAAAAGAAAAACAAAACAAA-AAAC-AAAAC
1 AAAAAAACAAAAA-AAAACAAACAAACAAAAAC
2920431 AAAAAAACAAAAAAAAACAAACAAACAAAAAC
1 AAAAAAACAAAAAAAAACAAACAAACAAAAAC
2920463 AAAAAAA
1 AAAAAAA
2920470 AGGGGTCCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 8 0.22
31 16 0.44
32 12 0.33
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (32 bp):
AAAAAAACAAAAAAAAACAAACAAACAAAAAC
Found at i:2920456 original size:18 final size:19
Alignment explanation
Indices: 2920410--2920466 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 19
2920400 AAAAAAAGAA
2920410 AAACAAAACAAAAAACAAAAC
1 AAAC-AAAC-AAAAACAAAAC
*
2920431 AAAAAAACAAAAA-AAAAC
1 AAACAAACAAAAACAAAAC
2920449 AAACAAACAAAAACAAAA
1 AAACAAACAAAAACAAAA
2920467 AAAAGGGGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 17 0.52
19 9 0.27
20 4 0.12
21 3 0.09
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (19 bp):
AAACAAACAAAAACAAAAC
Found at i:2920469 original size:23 final size:22
Alignment explanation
Indices: 2920395--2920470 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
2920385 GGCGTCCTCC
*
2920395 ACAAAAAAAAAAGAAAAAC-AAA
1 ACAAAAAAAAAA-ACAAACAAAA
*
2920417 ACAAAAAACAAAAC-AA-AAAA
1 ACAAAAAAAAAAACAAACAAAA
2920437 ACAAAAAAAAACAAACAAACAAAA
1 AC-AAAAAAAA-AAACAAACAAAA
2920461 ACAAAAAAAA
1 ACAAAAAAAA
2920471 GGGGTCCGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
20 7 0.15
21 8 0.17
22 15 0.33
23 10 0.22
24 6 0.13
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (22 bp):
ACAAAAAAAAAAACAAACAAAA
Found at i:2921954 original size:29 final size:30
Alignment explanation
Indices: 2921912--2922235 Score: 243
Period size: 30 Copynumber: 10.7 Consensus size: 30
2921902 TCACCCTTCA
2921912 AAAGCCCACAAGTCAGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCC
* *
2921941 AAAGCCCACAAGTCAGTGGCACCCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCC
* **
2921971 AAAGCCCACAAATTGGTGGCAAC-C--TT-C
1 AAAGCCCACAAGTCAGTGGC-ACTCTTTTCC
* *
2921998 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCC
* *
2922028 GAAGCCCACAAGTCGGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCC
* * * *
2922057 AAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTG
1 AAAGCCCACAAGTCAGTGGCACTC-TTTTC----C
* * * *
2922092 TAAGCTCACAACTCTA-TAGCACTCTTTTTCC
1 AAAGCCCACAAGTC-AGTGGCACTC-TTTTCC
* * * *
2922123 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTCA
1 ---AAAGCCCACAAGTCAGTGGCACTCTTTTCC
* *
2922156 AAAGCCCACAAGTTAGTGGCATCTCTTTTCA
1 AAAGCCCACAAGTCAGTGGCA-CTCTTTTCC
* *
2922187 AAAGCCCACAAGTCAGTGGCAATC-TTT-A
1 AAAGCCCACAAGTCAGTGGCACTCTTTTCC
*
2922215 AAAGCCCACAAGTCAATGGCA
1 AAAGCCCACAAGTCAGTGGCA
2922236 ACCTTCAAAA
Statistics
Matches: 243, Mismatches: 34, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
26 2 0.01
27 19 0.08
28 23 0.09
29 50 0.21
30 67 0.28
31 35 0.14
33 6 0.02
34 17 0.07
35 24 0.10
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTCC
Found at i:2921973 original size:59 final size:59
Alignment explanation
Indices: 2921908--2922235 Score: 279
Period size: 59 Copynumber: 5.4 Consensus size: 59
2921898 TTCCTCACCC
2921908 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTT
* ** * * *
2921967 TTCAAAAGCCCACAAATTGGTGGCAAC-CTT-CAAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTT
** * * * * *
2922024 TTCCGAAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAC-CCTT
** * * * * *
2922084 TTCTTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTTCCTTTTAAGCCCACAAGTTAGTGGCAC
1 TTC----AAAAGCCCACAAGTC-AGTGGCA-TC-TTTTCC---AAAGCCCACAAGTCAGTGGCAC
2922148 CCTT
56 CCTT
* * **
2922152 TTCAAAAGCCCACAAGTTAGTGGCATCTCTTTTCAAAAGCCCACAAGTCAGTGGCAATC-T
1 TTCAAAAGCCCACAAGTCAGTGGCA--TCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTT
*
2922212 TT-AAAAGCCCACAAGTCAATGGCA
1 TTCAAAAGCCCACAAGTCAGTGGCA
2922236 ACCTTCAAAA
Statistics
Matches: 213, Mismatches: 41, Indels: 30
0.75 0.14 0.11
Matches are distributed among these distances:
57 48 0.23
58 4 0.02
59 63 0.30
60 9 0.04
61 20 0.09
63 1 0.00
64 34 0.16
65 5 0.02
66 6 0.03
68 6 0.03
69 17 0.08
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCACCCTT
Found at i:2922103 original size:35 final size:34
Alignment explanation
Indices: 2922062--2922136 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
2922052 TTTCCAAAGT
* * *
2922062 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCATAGCACTCTTTTTCCTTT-TAAGC
* *
2922097 TCACAACTCTATAGCACTCTTTTTCCTTTTAAGC
1 CCACAACTCCATAGCACTCTTTTTCCTTTTAAGC
2922131 CCACAA
1 CCACAA
2922137 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (34 bp):
CCACAACTCCATAGCACTCTTTTTCCTTTTAAGC
Found at i:2922226 original size:28 final size:29
Alignment explanation
Indices: 2922127--2922281 Score: 147
Period size: 28 Copynumber: 5.3 Consensus size: 29
2922117 TTTTCCTTTT
* **
2922127 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAATCTTTT-AA
* *
2922157 AAGCCCACAAGTTAGTGGCATCTCTTTTCAA
1 AAGCCCACAAGTCAGTGGCA-ATCTTTT-AA
2922188 AAGCCCACAAGTCAGTGGCAATC-TTTAA
1 AAGCCCACAAGTCAGTGGCAATCTTTTAA
* * *
2922216 AAGCCCACAAGTCAATGGCAA-CCTTCAA
1 AAGCCCACAAGTCAGTGGCAATCTTTTAA
* *
2922244 AAGCACACAAGT-TGAT-GCAATCCTTTTAA
1 AAGCCCACAAGTCAG-TGGCAAT-CTTTTAA
2922273 AAGCCCACA
1 AAGCCCACA
2922282 CAAGTTGGTG
Statistics
Matches: 109, Mismatches: 11, Indels: 11
0.83 0.08 0.08
Matches are distributed among these distances:
27 5 0.05
28 38 0.35
29 16 0.15
30 22 0.20
31 28 0.26
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAATCTTTTAA
Found at i:2922372 original size:52 final size:50
Alignment explanation
Indices: 2922303--2922492 Score: 232
Period size: 52 Copynumber: 3.9 Consensus size: 50
2922293 CGTCTTCTTC
* *
2922303 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT-GTACC-T
* *
2922355 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC----T-CC-
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTACCT
* *
2922399 -AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGT-A-CCT
*
2922450 TAAGTCCTATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
2922493 CATCTTTAAC
Statistics
Matches: 118, Mismatches: 11, Indels: 18
0.80 0.07 0.12
Matches are distributed among these distances:
43 36 0.31
46 2 0.02
47 2 0.02
50 2 0.02
52 76 0.64
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (50 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTACCT
Found at i:2922467 original size:95 final size:95
Alignment explanation
Indices: 2922304--2922491 Score: 317
Period size: 95 Copynumber: 2.0 Consensus size: 95
2922294 GTCTTCTTCT
*
2922304 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTTTAAGTCCAATGTAG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTTTAAGTCCAATATAG
2922369 CTGGCCTTGAATCAGCACATTGGCACCTCC
66 CTGGCCTTGAATCAGCACATTGGCACCTCC
*
2922399 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTT-GTCATCC-TTAAGTCCTATAT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGT-A-CCTTTAAGTCCAATAT
*
2922462 CGCTGGCCTTGAATCAGCACATTGGCACCT
64 AGCTGGCCTTGAATCAGCACATTGGCACCT
2922492 TCATCTTTAA
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
94 2 0.02
95 84 0.95
96 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (95 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTTTAAGTCCAATATAG
CTGGCCTTGAATCAGCACATTGGCACCTCC
Found at i:2923322 original size:13 final size:13
Alignment explanation
Indices: 2923304--2923361 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
2923294 CATAAAGTGT
2923304 TGTATCGATACAA
1 TGTATCGATACAA
2923317 TGTATCGATACATA
1 TGTATCGATACA-A
2923331 TTTTTTTGTATCGATACAA
1 ------TGTATCGATACAA
2923350 TGTATCGATACA
1 TGTATCGATACA
2923362 TATTTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 24 0.63
14 1 0.03
19 1 0.03
20 12 0.32
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2923326 original size:33 final size:33
Alignment explanation
Indices: 2923284--2923382 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
2923274 TTCAACGATT
** *
2923284 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAATTTTTTGTATCGATACAA
*
2923317 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAATTTTTTGTATCGATACAA
2923350 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAATTTTTTGTATCGATACAA
2923382 T
1 T
2923383 TTAAGCTACT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 19 0.31
33 42 0.69
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATAATTTTTTGTATCGATACAA
Found at i:2923512 original size:52 final size:52
Alignment explanation
Indices: 2923456--2923584 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2923446 CACTGATCTT
* *
2923456 TGTATCGATACATGCAGGCAAATTTGTCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
2923508 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2923560 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2923585 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2926925 original size:15 final size:15
Alignment explanation
Indices: 2926905--2926935 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2926895 TAAAAATGTC
*
2926905 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2926920 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2926935 C
1 C
2926936 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2928803 original size:8 final size:8
Alignment explanation
Indices: 2928790--2928821 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
2928780 ATTTGATTAA
2928790 ATTTTGTG
1 ATTTTGTG
2928798 ATTTTGTG
1 ATTTTGTG
2928806 ATTTTGTG
1 ATTTTGTG
2928814 ATTTTGTG
1 ATTTTGTG
2928822 TTGAATGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:2929043 original size:13 final size:13
Alignment explanation
Indices: 2929025--2929061 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2929015 ATTTTTCTTA
2929025 GTATCGATACA-T
1 GTATCGATACACT
2929037 CGTATCGATACACT
1 -GTATCGATACACT
2929051 GTATCGATACA
1 GTATCGATACA
2929062 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 22 0.96
14 1 0.04
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (13 bp):
GTATCGATACACT
Found at i:2929225 original size:20 final size:20
Alignment explanation
Indices: 2929182--2929227 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2929172 AAATCTTTTG
2929182 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2929203 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2929223 CAAAA
1 CAAAA
2929228 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2930723 original size:23 final size:21
Alignment explanation
Indices: 2930681--2930724 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
2930671 GTTTAAAGTT
**
2930681 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
2930702 TTTGCATTGTACTTTGAATTTTA
1 TTTGC-TTG-ACTTTGAATTTTA
2930725 ATCTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:2931633 original size:13 final size:13
Alignment explanation
Indices: 2931615--2931640 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2931605 TACACAAAGT
2931615 ATGTATCGATACA
1 ATGTATCGATACA
2931628 ATGTATCGATACA
1 ATGTATCGATACA
2931641 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2931638 original size:32 final size:33
Alignment explanation
Indices: 2931597--2931660 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2931587 TAGCCAAACT
**
2931597 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2931629 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2931661 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2933015 original size:21 final size:22
Alignment explanation
Indices: 2932971--2933015 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2932961 TTTGGCTTAG
* *
2932971 AATAAATTTTTTAATATTTATA
1 AATAAATCTTTAAATATTTATA
*
2932993 AATAAATCTTTAAAT-TTTCTA
1 AATAAATCTTTAAATATTTATA
2933014 AA
1 AA
2933016 ATTGCAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAAATCTTTAAATATTTATA
Found at i:2933511 original size:17 final size:17
Alignment explanation
Indices: 2933478--2933511 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2933468 TATTGTTAAG
*
2933478 AAAAATCAAACATAATA
1 AAAAATCAAACAAAATA
*
2933495 AAAAATCAAAGAAAATA
1 AAAAATCAAACAAAATA
2933512 GTTCATAGCC
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:0.74, C:0.09, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAAATCAAACAAAATA
Found at i:2934381 original size:16 final size:17
Alignment explanation
Indices: 2934349--2934381 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2934339 TGAGCTGAAT
*
2934349 TTAATTTACTCAAAATA
1 TTAATTTACTAAAAATA
2934366 TTAATTTA-TAAAAATA
1 TTAATTTACTAAAAATA
2934382 ATAAAGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAATTTACTAAAAATA
Found at i:2937612 original size:13 final size:13
Alignment explanation
Indices: 2937572--2937624 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
2937562 CCGTTACAAG
2937572 CAATGTATCGATA
1 CAATGTATCGATA
2937585 CAA--T-TC-AT-
1 CAATGTATCGATA
2937593 C-ATGTATCGATA
1 CAATGTATCGATA
2937605 CAATGTATCGATA
1 CAATGTATCGATA
*
2937618 CATTGTA
1 CAATGTA
2937625 CCATGTATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 20 0.61
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2937612 original size:33 final size:33
Alignment explanation
Indices: 2937572--2937640 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2937562 CCGTTACAAG
*
2937572 CAATGTATCGATACAATT-CATCATGTATCGATA
1 CAATGTATCGATAC-ATTGCACCATGTATCGATA
*
2937605 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGCACCATGTATCGATA
2937638 CAA
1 CAA
2937641 ACAGTGGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACATTGCACCATGTATCGATA
Found at i:2937713 original size:19 final size:19
Alignment explanation
Indices: 2937669--2937724 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
2937659 CTGCCAATCT
* **
2937669 CATGTATTGATACAATTGTC
1 CATGTATCGATACAA-TGAA
2937689 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
2937708 CATGTATCAATACAATG
1 CATGTATCGATACAATG
2937725 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2938303 original size:19 final size:20
Alignment explanation
Indices: 2938279--2938323 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
2938269 AGTTTTCGTT
2938279 TTTCTCCCCCTTAA-AAAAA
1 TTTCTCCCCCTTAACAAAAA
*
2938298 TTTCTCCCCTTTAATCAAAAA
1 TTTCTCCCCCTTAA-CAAAAA
2938319 TTTCT
1 TTTCT
2938324 TCGCTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.57
21 10 0.43
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTCTCCCCCTTAACAAAAA
Found at i:2939692 original size:13 final size:13
Alignment explanation
Indices: 2939662--2939699 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2939652 ATAGTACCCT
2939662 ATGTATCGATAC-
1 ATGTATCGATACA
*
2939674 -TATATCGATACA
1 ATGTATCGATACA
2939686 ATGTATCGATACA
1 ATGTATCGATACA
2939699 A
1 A
2939700 GGAATATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
13 12 0.55
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2939866 original size:18 final size:20
Alignment explanation
Indices: 2939825--2939876 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
2939815 CTATAGACCC
2939825 TAATTCATATCAAACAAGCA
1 TAATTCATATCAAACAAGCA
*
2939845 TAATTCAT-TCACACAA-CA
1 TAATTCATATCAAACAAGCA
**
2939863 TAATAAATATCAAA
1 TAATTCATATCAAA
2939877 ATTCATTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 8 0.30
19 11 0.41
20 8 0.30
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (20 bp):
TAATTCATATCAAACAAGCA
Found at i:2945906 original size:13 final size:13
Alignment explanation
Indices: 2945866--2945918 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
2945856 TCGTTACAAG
2945866 CAATGTATCGATA
1 CAATGTATCGATA
2945879 CAA--T-TC-AT-
1 CAATGTATCGATA
2945887 C-ATGTATCGATA
1 CAATGTATCGATA
2945899 CAATGTATCGATA
1 CAATGTATCGATA
*
2945912 CATTGTA
1 CAATGTA
2945919 CCATGTATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 20 0.61
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2945906 original size:33 final size:33
Alignment explanation
Indices: 2945866--2945934 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2945856 TCGTTACAAG
*
2945866 CAATGTATCGATACAATT-CATCATGTATCGATA
1 CAATGTATCGATAC-ATTGCACCATGTATCGATA
*
2945899 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGCACCATGTATCGATA
2945932 CAA
1 CAA
2945935 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACATTGCACCATGTATCGATA
Found at i:2946006 original size:18 final size:19
Alignment explanation
Indices: 2945963--2946021 Score: 84
Period size: 18 Copynumber: 3.1 Consensus size: 19
2945953 TTGTCAATCT
*
2945963 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGTA
2945983 CATGTATCGATACAATG-A
1 CATGTATCGATACAATGTA
*
2946001 CATGTATCGATACAATATA
1 CATGTATCGATACAATGTA
2946020 CA
1 CA
2946022 AGCATAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 16 0.44
19 5 0.14
20 15 0.42
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGTA
Found at i:2949556 original size:34 final size:34
Alignment explanation
Indices: 2949497--2949569 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 34
2949487 ACTTCAACTC
*
2949497 TTGAGAGAGAAAGAGTTCCTCTTCTA-CTATGAGT
1 TTGAGAGAGAAAGAGTTCCTCTTCTATC-AGGAGT
2949531 TTGAGAGAGGAAA-AGTTCC-CTTTCTATCAGGAGT
1 TTGAGAGA-GAAAGAGTTCCTC-TTCTATCAGGAGT
2949565 TTGAG
1 TTGAG
2949570 GTGAGTCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
33 1 0.03
34 29 0.83
35 5 0.14
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.32
Consensus pattern (34 bp):
TTGAGAGAGAAAGAGTTCCTCTTCTATCAGGAGT
Found at i:2952319 original size:2 final size:2
Alignment explanation
Indices: 2952312--2952344 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2952302 CAAGGACCCC
2952312 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 A
2952345 GTAAAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2952968 original size:23 final size:22
Alignment explanation
Indices: 2952924--2952972 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2952914 ATTTTATTTA
2952924 AATTTTAATTATAAAAATATAT
1 AATTTTAATTATAAAAATATAT
2952946 AATTATTAA-TATAAAAATA-AT
1 AATT-TTAATTATAAAAATATAT
*
2952967 ATTTTT
1 AATTTT
2952973 TTAATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 5 0.20
22 14 0.56
23 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTTTAATTATAAAAATATAT
Found at i:2952976 original size:22 final size:22
Alignment explanation
Indices: 2952926--2952978 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2952916 TTTATTTAAA
2952926 TTTTAATTATAAAAATATATAAT
1 TTTTAA-TATAAAAATATATAAT
* *
2952949 TATTAATATAAAAATA-ATATTT
1 TTTTAATATAAAAATATATA-AT
2952971 TTTTAATA
1 TTTTAATA
2952979 ATATAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.12
22 18 0.69
23 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAATATAAAAATATATAAT
Found at i:2953475 original size:19 final size:20
Alignment explanation
Indices: 2953451--2953495 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
2953441 TTCGGTTTGA
*
2953451 TTATTAAA-ATTTTTAGTTT
1 TTATTAAATATTTTAAGTTT
2953470 TTATTAAATATTTTAAGTTT
1 TTATTAAATATTTTAAGTTT
2953490 TATATT
1 T-TATT
2953496 GTTAAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.35
20 11 0.48
21 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTATTAAATATTTTAAGTTT
Found at i:2954560 original size:19 final size:20
Alignment explanation
Indices: 2954538--2954582 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
2954528 TTTAATTTGA
*
2954538 TTATTA-ATATTTTTAGTTT
1 TTATTAGATATTTTAAGTTT
2954557 TTATTAGATATTTTAAGTTT
1 TTATTAGATATTTTAAGTTT
2954577 TATATT
1 T-TATT
2954583 GTTAAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 13 0.57
21 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TTATTAGATATTTTAAGTTT
Found at i:2956829 original size:24 final size:24
Alignment explanation
Indices: 2956797--2956842 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
2956787 ATTTTATTTT
2956797 TATATATAT-TTAAT-TATAAATA
1 TATATATATATTAATATATAAATA
2956819 TATATATATATTAATATATAAATA
1 TATATATATATTAATATATAAATA
2956843 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 9 0.41
23 5 0.23
24 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATATATATATTAATATATAAATA
Found at i:2957334 original size:16 final size:16
Alignment explanation
Indices: 2957290--2957334 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2957280 GTCCAAACTT
2957290 AAATGACTTGAATCTA
1 AAATGACTTGAATCTA
* *
2957306 AAATTA-TCAGAATCTA
1 AAATGACT-TGAATCTA
2957322 AAATGACTTGAAT
1 AAATGACTTGAAT
2957335 TTGAAATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.04
16 21 0.91
17 1 0.04
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (16 bp):
AAATGACTTGAATCTA
Found at i:2957562 original size:6 final size:6
Alignment explanation
Indices: 2957551--2957579 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2957541 TATATATAAT
2957551 ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
2957580 TATATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:2957587 original size:18 final size:18
Alignment explanation
Indices: 2957551--2957587 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2957541 TATATATAAT
*
2957551 ATTTTAATTTTAATTTTA
1 ATTTTAATTTTAATATTA
*
2957569 ATTTTAATTTTTATATTA
1 ATTTTAATTTTAATATTA
2957587 A
1 A
2957588 ATTAAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTAATTTTAATATTA
Found at i:2957710 original size:3 final size:3
Alignment explanation
Indices: 2957684--2957727 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
2957674 TTTTAATTAG
2957684 ATT ATTT ATT -TT AATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT -ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
2957728 TGAAAAGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.05
3 27 0.73
4 8 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2960991 original size:17 final size:17
Alignment explanation
Indices: 2960953--2961122 Score: 68
Period size: 20 Copynumber: 9.5 Consensus size: 17
2960943 TATATCATTT
2960953 TTTAT-TTTTATA-ATCA
1 TTTATATTTTATATAT-A
2960969 TATTATATTTTATATATA
1 T-TTATATTTTATATATA
2960987 TTTATATAAATTT-TAATATA
1 TTTATAT---TTTAT-ATATA
* *
2961007 TTAATAATTTATAT-TA
1 TTTATATTTTATATATA
*
2961023 --TATATTTTA-ATAAA
1 TTTATATTTTATATATA
* *
2961037 TTTATACATTCATATCATA
1 TTTATA-TTTTATAT-ATA
* *
2961056 TTGTATTATTTTTTATATTT
1 TT-TA-TATTTTATATA-TA
2961076 TATTATATTTTATAT-TA
1 T-TTATATTTTATATATA
2961093 TATTAGTTATTTTTATATCATA
1 T-TTA--TA-TTTTATAT-ATA
2961115 TTTATATT
1 TTTATATT
2961123 ATTTAATTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 44
0.67 0.08 0.25
Matches are distributed among these distances:
13 2 0.02
14 8 0.07
16 7 0.06
17 24 0.21
18 14 0.12
19 21 0.18
20 32 0.27
21 6 0.05
22 3 0.03
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (17 bp):
TTTATATTTTATATATA
Found at i:2960992 original size:10 final size:10
Alignment explanation
Indices: 2960972--2961139 Score: 69
Period size: 9 Copynumber: 17.3 Consensus size: 10
2960962 ATAATCATAT
2960972 TATAT-TTTA
1 TATATATTTA
2960981 TATATATTTA
1 TATATATTTA
*
2960991 TATAAATTT-
1 TATATATTTA
*
2961000 TAATATATTAA
1 T-ATATATTTA
*
2961011 TAATTTATATTA
1 T-ATATAT-TTA
2961023 TATAT-TTTA
1 TATATATTTA
*
2961032 -ATA-AATT-
1 TATATATTTA
* *
2961039 TATACATTCA
1 TATATATTTA
2961049 TATCATATTGTA
1 TAT-ATATT-TA
*
2961061 T-TAT-TTTT
1 TATATATTTA
2961069 TATAT-TTTA
1 TATATATTTA
2961078 T-TATATTT-
1 TATATATTTA
2961086 TATATTATATTA
1 TATA-TAT-TTA
*
2961098 GT-TATTTTTA
1 -TATATATTTA
2961108 TATCATATTTA
1 TAT-ATATTTA
2961119 TAT-TATTTA
1 TATATATTTA
2961128 -AT-TATATTA
1 TATATAT-TTA
2961137 TAT
1 TAT
2961140 CTAAAATTAT
Statistics
Matches: 123, Mismatches: 15, Indels: 41
0.69 0.08 0.23
Matches are distributed among these distances:
8 19 0.15
9 35 0.28
10 33 0.27
11 28 0.23
12 7 0.06
13 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (10 bp):
TATATATTTA
Found at i:2960993 original size:22 final size:22
Alignment explanation
Indices: 2960968--2961124 Score: 84
Period size: 21 Copynumber: 7.3 Consensus size: 22
2960958 TTTTATAATC
2960968 ATATTATATTTTATATATATTT
1 ATATTATATTTTATATATATTT
* *
2960990 ATA-TAAATTTTA-ATATATTA
1 ATATTATATTTTATATATATTT
*
2961010 ATAATT-TATATTATATAT-TTT
1 AT-ATTATATTTTATATATATTT
* * *
2961031 A-A-TA-AATTTATACATTCATATC
1 ATATTATATTTTATATA-T-AT-TT
* * *
2961053 ATATTGTATTATTTTTTATATTT
1 ATATTATATT-TTATATATATTT
2961076 -TATTATATTTTATAT-TATATT
1 ATATTATATTTTATATATAT-TT
*
2961097 A-GTTAT-TTTTATATCATATTT
1 ATATTATATTTTATAT-ATATTT
2961118 ATATTAT
1 ATATTAT
2961125 TTAATTATAT
Statistics
Matches: 98, Mismatches: 20, Indels: 34
0.64 0.13 0.22
Matches are distributed among these distances:
18 8 0.08
19 2 0.02
20 20 0.20
21 31 0.32
22 25 0.26
23 2 0.02
24 3 0.03
25 3 0.03
26 4 0.04
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (22 bp):
ATATTATATTTTATATATATTT
Found at i:2961000 original size:40 final size:38
Alignment explanation
Indices: 2960956--2961067 Score: 102
Period size: 42 Copynumber: 2.9 Consensus size: 38
2960946 ATCATTTTTT
*
2960956 ATTTTTATAATCATATTATATTTTATATATATTTATATAA
1 ATTTTTATATTCATATTATATTTTATATAT-TTTA-ATAA
* *
2960996 ATTTTAATATATTAATAATT-TATATTATATATTTTAATAA
1 ATTTT--TATATTCAT-ATTATATTTTATATATTTTAATAA
* * * *
2961036 ATTTATACATTCATATCATATTGTAT-TATTTT
1 ATTTTTATATTCATATTATATTTTATATATTTT
2961068 TTATATTTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
37 8 0.14
38 13 0.22
40 13 0.22
41 4 0.07
42 18 0.31
43 3 0.05
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (38 bp):
ATTTTTATATTCATATTATATTTTATATATTTTAATAA
Found at i:2961633 original size:15 final size:15
Alignment explanation
Indices: 2961613--2961643 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2961603 AAACATAAAC
2961613 AAAAACAAAACCAAA
1 AAAAACAAAACCAAA
*
2961628 AAAAACAAAGCCAAA
1 AAAAACAAAACCAAA
2961643 A
1 A
2961644 CCAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.19, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAACAAAACCAAA
Found at i:2961633 original size:21 final size:21
Alignment explanation
Indices: 2961609--2961653 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2961599 GGCAAAACAT
2961609 AAACAAAAACAAAACCAAAAA
1 AAACAAAAACAAAACCAAAAA
**
2961630 AAACAAAGCCAAAACCAAAAA
1 AAACAAAAACAAAACCAAAAA
2961651 AAA
1 AAA
2961654 AATTAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.78, C:0.20, G:0.02, T:0.00
Consensus pattern (21 bp):
AAACAAAAACAAAACCAAAAA
Found at i:2962762 original size:27 final size:27
Alignment explanation
Indices: 2962732--2962821 Score: 162
Period size: 27 Copynumber: 3.3 Consensus size: 27
2962722 AGGAGATGCA
2962732 GAAGAGGAAGATTTCGTCTTTTGGAAT
1 GAAGAGGAAGATTTCGTCTTTTGGAAT
2962759 GAAGAGGAAGATTTCGTCTTTTGGAAT
1 GAAGAGGAAGATTTCGTCTTTTGGAAT
*
2962786 GAAGAGGAAGATTTCGTCTTTTGGATT
1 GAAGAGGAAGATTTCGTCTTTTGGAAT
*
2962813 GAAAAGGAA
1 GAAGAGGAA
2962822 AAAGAAATCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.31
Consensus pattern (27 bp):
GAAGAGGAAGATTTCGTCTTTTGGAAT
Found at i:2963498 original size:6 final size:6
Alignment explanation
Indices: 2963487--2963511 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2963477 TTGGGTCTTC
2963487 GCAGAA GCAGAA GCAGAA GCAGAA G
1 GCAGAA GCAGAA GCAGAA GCAGAA G
2963512 AGCTGCCAAG
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:0.48, C:0.16, G:0.36, T:0.00
Consensus pattern (6 bp):
GCAGAA
Found at i:2964811 original size:3 final size:3
Alignment explanation
Indices: 2964805--2964835 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2964795 TTTGATGTTG
2964805 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2964836 CATGTAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2970649 original size:22 final size:22
Alignment explanation
Indices: 2970624--2970666 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2970614 TATGTGCATC
2970624 TAGTAAAAACAATATATACATT
1 TAGTAAAAACAATATATACATT
* *
2970646 TAGTAGAAACAATATGTACAT
1 TAGTAAAAACAATATATACAT
2970667 GTACTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (22 bp):
TAGTAAAAACAATATATACATT
Found at i:2970952 original size:21 final size:21
Alignment explanation
Indices: 2970926--2970970 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2970916 GGCTTAATAA
2970926 TCGGTTCCTTTAATAGAGGAG
1 TCGGTTCCTTTAATAGAGGAG
* *
2970947 TCGGTTCTTTTAATGGAGGAG
1 TCGGTTCCTTTAATAGAGGAG
2970968 TCG
1 TCG
2970971 ATTTCTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.36
Consensus pattern (21 bp):
TCGGTTCCTTTAATAGAGGAG
Found at i:2971508 original size:52 final size:52
Alignment explanation
Indices: 2971413--2972131 Score: 538
Period size: 53 Copynumber: 14.1 Consensus size: 52
2971403 CCCAATACAT
* * *
2971413 ATATACAATATCTTTTAATTTTTATTATTTTTTAAATAGTAATTTGAGATTTA
1 ATATAAAATATTTTTTATTTTTTATTA-TTTTTAAATAGTAATTTGAGATTTA
*** **
2971466 CCCTAAAATATTTTTTATTTTTTATTATTTTTAAATAGTAATTCAAGATTTA
1 ATATAAAATATTTTTTATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
* * * ** *
2971518 ATATAAAATA------AGTTTTCTA--ATTTGTTCATTA-TTTTTTGAGTTTTA
1 ATATAAAATATTTTTTA-TTTTTTATTATTT-TTAAATAGTAATTTGAGATTTA
*
2971563 ATATAAAATATTTTTTA-TTTTTATTATTTTTAAATAGTAGTTTGAGATTTA
1 ATATAAAATATTTTTTATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
* * * * * * *
2971614 ACATAAAACATTTTTTACTTTTGATTTATTTTTAAATAATAATTTAAGATTTT
1 ATATAAAATATTTTTTATTTTTTA-TTATTTTTAAATAGTAATTTGAGATTTA
* * * * * *
2971667 ATATAAAATATTTTTTAAATTTTAATGATTTTTAATTATTAATTCGAGATTTA
1 ATATAAAATATTTTTT-ATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
* * **
2971720 ATATAAAATA---TATATTTTTTAATT-TTTTAAAATAGTAATTCAAGATTTA
1 ATATAAAATATTTTTTATTTTTT-ATTATTTTTAAATAGTAATTTGAGATTTA
* * * * * *
2971769 ATATAAAATCTTAATTTA-ATTTTATTATTTTT-AATAGTGATTTGATATTCA
1 ATATAAAATATT-TTTTATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
* * * * * *
2971820 AAATAAAATATTTTTAATTTTTTTATTA-TTTTAAAAAGTAACTCGAGA-TTG
1 ATATAAAATATTTTTTA-TTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
* *
2971871 ATATAAAATATTTTTT-TATTTTT-TTATTTAATGAAACAGTAATTT-AGAATTTA
1 ATATAAAATATTTTTTAT-TTTTTATTATTT--TTAAATAGTAATTTGAG-ATTTA
* * * *
2971924 ATATATAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAAATGTT-
1 ATATAAAATATTTTTTATTTTTTATTATTTTTAAATAGTAATTTGAGAT-TTA
* * * * *
2971976 GTATAAAATATTTTTTAATATTTTATCATTTTTAATTTGTAATTTGAGATTTA
1 ATATAAAATATTTTTT-ATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
* * ** **
2972029 ATATAAAATATTTTTTAATCTTTTA-T-TTTCTAAATAAAAATTCAAGATTTA
1 ATATAAAATATTTTTT-ATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
* * *
2972080 ATAT--AATTTTTTTTAATTTTTAGTATTTTT-AATAGTAATTTGAGATTTA
1 ATATAAAATATTTTTTATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
2972129 ATA
1 ATA
2972132 AGATTGTTTA
Statistics
Matches: 519, Mismatches: 110, Indels: 78
0.73 0.16 0.11
Matches are distributed among these distances:
45 23 0.04
46 6 0.01
47 6 0.01
48 6 0.01
49 72 0.14
50 23 0.04
51 101 0.19
52 101 0.19
53 168 0.32
54 13 0.03
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (52 bp):
ATATAAAATATTTTTTATTTTTTATTATTTTTAAATAGTAATTTGAGATTTA
Found at i:2971681 original size:104 final size:103
Alignment explanation
Indices: 2971469--2972131 Score: 535
Period size: 104 Copynumber: 6.5 Consensus size: 103
2971459 AGATTTACCC
* **
2971469 TAAAATATTTTTTATTTTTTATTATTTTTAAATAGTAATTCAAGATTTAATATAAAATAAGTTTT
1 TAAAATATTTTTTAATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAAT-A-TTTT
* * * * * *
2971534 CTAATTTGTTCATTATT---T--T--TT-GAG-TTTTAATA
64 TTATTTTATTTATTTTTAAATAATAATTCAAGATTTT-ATA
* * *
2971566 TAAAATATTTTTT-ATTTTTATTATTTTTAAATAGTAGTTTGAGATTTAACATAAAACATTTTTT
1 TAAAATATTTTTTAATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATTTTTT
*
2971630 ACTTTTGATTTATTTTTAAATAATAATTTAAGATTTTATA
66 A-TTTT-ATTTATTTTTAAATAATAATTCAAGATTTTATA
* * * * * * *
2971670 TAAAATATTTTTTAAATTTTAATGATTTTTAATTATTAATTCGAGATTTAATATAAAATATATAT
1 TAAAATATTTTTT-AATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATTTTT
* * * *
2971735 T-TTTTAATT-TTTTAAAATAGTAATTCAAGATTTAATA
65 TATTTTATTTATTTTTAAATAATAATTCAAGATTTTATA
* * * * * *
2971772 TAAAATCTTAATTTAA-TTTTATTATTTTT-AATAGTGATTTGATATTCAAAATAAAATATTTTT
1 TAAAATATT-TTTTAATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATTTTT
* * * *
2971835 AATTTT-TTTATTATTTTAAA-AAGTAACTCGAGA-TTGATA
65 TATTTTATTTA-T-TTTTAAATAA-TAATTCAAGATTTTATA
* * * *
2971874 TAAAATATTTTTTTATTTTT-TTATTTAATGAAACAGTAATTT-AGAATTTAATATATAATATTT
1 TAAAATATTTTTTAATTTTTATTATTT--TTAAATAGTAATTTGAG-ATTTAATATAAAATATTT
* * * * * * *
2971937 TTAATTTTTTATTATTTTTAAATAGTAATTTAAAATGTTGTA
63 TTTATTTTAT-TTATTTTTAAATAATAATTCAAGATTTTATA
* * *
2971979 TAAAATATTTTTTAATATTTTATCATTTTTAATTTGTAATTTGAGATTTAATATAAAATATTTTT
1 TAAAATATTTTTTAAT-TTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATTTTT
* * *
2972044 TAATCT-TTTATTTTCTAAATAAAAATTCAAGA-TTTA-A
65 TATTTTATTTATTTT-TAAATAATAATTCAAGATTTTATA
* * *
2972081 TATAATTTTTTTTAATTTTTAGTATTTTT-AATAGTAATTTGAGATTTAATA
1 TAAAATATTTTTTAATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATA
2972132 AGATTGTTTA
Statistics
Matches: 447, Mismatches: 87, Indels: 61
0.75 0.15 0.10
Matches are distributed among these distances:
94 6 0.01
95 4 0.01
96 45 0.10
97 13 0.03
99 1 0.00
100 47 0.11
101 37 0.08
102 68 0.15
103 33 0.07
104 81 0.18
105 57 0.13
106 50 0.11
107 5 0.01
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (103 bp):
TAAAATATTTTTTAATTTTTATTATTTTTAAATAGTAATTTGAGATTTAATATAAAATATTTTTT
ATTTTATTTATTTTTAAATAATAATTCAAGATTTTATA
Found at i:2971984 original size:309 final size:307
Alignment explanation
Indices: 2971563--2972122 Score: 740
Period size: 309 Copynumber: 1.8 Consensus size: 307
2971553 TTGAGTTTTA
* * *
2971563 ATATAAAATATTTTTTATTTTTATTATTTTTAAATAGTAGTTTGAGATTTAACATAAAACATTTT
1 ATATAAAATATTTTTTATTTTTATTATTTTGAAACAGTAATTTGAGATTTAACATAAAACATTTT
* * *
2971628 TTACTTTTGATTTATTTTTAAATAATAATTTAAGATTTTATATAAAATATTTTTTAA-ATTTTAA
66 TAACTTTTGATTTATTTTTAAATAATAATTTAAAATGTTATATAAAATATTTTTTAATATTTT-A
* *
2971692 TGATTTTTAATTAT-TAATTCGAGATTTAATATAAAATATATATT-T-TTTAATTTTTTAAAATA
130 TCATTTTTAATT-TGTAATTCGAGATTTAATATAAAATATATATTATCTTTAATTTTCT-AAATA
** * *
2971754 GTAATTCAAGATTTAATATAAAATCTTAATTTAA-TTTTATTATTTTTAATAGTGATTTGATATT
193 AAAATTCAAGATTTAATAT--AAT-TTAATTTAATTTTTAGTATTTTTAATAGTAATTTGATATT
2971818 CAAAATAAAATATTTTTAATTTTTTTATTATTTTAAAAAGTAACTCGAGATTG
255 CAAAATAAAATATTTTTAATTTTTTTATTATTTTAAAAAGTAACTCGAGATTG
* * *
2971871 ATATAAAATATTTTTTTATTTTT-TTATTTAATGAAACAGTAATTT-AGAATTTAATATATAATA
1 ATATAAAATA-TTTTTTATTTTTATTATTT--TGAAACAGTAATTTGAG-ATTTAACATAAAACA
* * * *
2971934 TTTTTAATTTTTTA-TTATTTTTAAATAGTAATTTAAAATGTTGTATAAAATATTTTTTAATATT
62 TTTTTAACTTTTGATTTATTTTTAAATAATAATTTAAAATGTTATATAAAATATTTTTTAATATT
* * * *
2971998 TTATCATTTTTAATTTGTAATTTGAGATTTAATATAAAATATTTTTTAATCTTTTATTTTCTAAA
127 TTATCATTTTTAATTTGTAATTCGAGATTTAATATAAAATATATATT-ATCTTTAATTTTCTAAA
**
2972063 TAAAAATTCAAGATTTAATATAATTTTTTTTAATTTTTAGTATTTTTAATAGTAATTTGA
191 TAAAAATTCAAGATTTAATATAATTTAATTTAATTTTTAGTATTTTTAATAGTAATTTGA
2972123 GATTTAATAA
Statistics
Matches: 217, Mismatches: 25, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
308 24 0.11
309 122 0.56
310 39 0.18
311 23 0.11
312 9 0.04
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (307 bp):
ATATAAAATATTTTTTATTTTTATTATTTTGAAACAGTAATTTGAGATTTAACATAAAACATTTT
TAACTTTTGATTTATTTTTAAATAATAATTTAAAATGTTATATAAAATATTTTTTAATATTTTAT
CATTTTTAATTTGTAATTCGAGATTTAATATAAAATATATATTATCTTTAATTTTCTAAATAAAA
ATTCAAGATTTAATATAATTTAATTTAATTTTTAGTATTTTTAATAGTAATTTGATATTCAAAAT
AAAATATTTTTAATTTTTTTATTATTTTAAAAAGTAACTCGAGATTG
Found at i:2973719 original size:22 final size:20
Alignment explanation
Indices: 2973694--2973750 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2973684 GCTATGGAAA
2973694 TGTATCGATACATGCTTATAAT
1 TGTATCGATACAT--TTATAAT
* * *
2973716 TGTATCGATGCATTTCTCAT
1 TGTATCGATACATTTATAAT
2973736 TGTATCGATACATTT
1 TGTATCGATACATTT
2973751 TTGGGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 19 0.61
22 12 0.39
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTTATAAT
Found at i:2975403 original size:10 final size:9
Alignment explanation
Indices: 2975375--2975399 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2975365 CATTCCTTCC
2975375 CATAAAACA
1 CATAAAACA
2975384 CATAAAACA
1 CATAAAACA
2975393 CATAAAA
1 CATAAAA
2975400 ACACTTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.20, G:0.00, T:0.12
Consensus pattern (9 bp):
CATAAAACA
Found at i:2979671 original size:26 final size:27
Alignment explanation
Indices: 2979614--2979671 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
2979604 CACCATCGGG
*
2979614 GATACTCTAACCTCGTTATTTTTGAAAG
1 GATACTCTAACCTCG-TATTTTTGAAAA
2979642 GATACTCTAACCTCG-ATTTTAT-AAAA
1 GATACTCTAACCTCGTATTTT-TGAAAA
2979668 GATA
1 GATA
2979672 AATCGATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 12 0.43
27 1 0.04
28 15 0.54
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (27 bp):
GATACTCTAACCTCGTATTTTTGAAAA
Found at i:2979757 original size:52 final size:50
Alignment explanation
Indices: 2979690--2979890 Score: 185
Period size: 52 Copynumber: 4.0 Consensus size: 50
2979680 TAGAATTTAA
* *
2979690 TATATAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAAATGTT
1 TATAAAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAGAT-TT
* * * * *
2979741 GTATAAAATATTTTTAATATTTTATCATTTTTAATTTGTAATTTGAGATTT
1 -TATAAAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAGATTT
* ** *
2979792 AATATAAAATATTTTTTAATCTTTTA-T-TTTTTAAATAAAAATTCAAGATTT
1 --TATAAAATA-TTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAGATTT
* * * * *
2979843 AATATAATTTTTTTAA-TTTTTAGTATTTTT-AATAGTAATTTGAGATTT
1 TATAAAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAGATTT
2979891 AATATAGATT
Statistics
Matches: 121, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
47 5 0.04
48 22 0.18
49 11 0.09
51 20 0.17
52 50 0.41
53 13 0.11
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.56
Consensus pattern (50 bp):
TATAAAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAGATTT
Found at i:2979885 original size:99 final size:104
Alignment explanation
Indices: 2979684--2979896 Score: 269
Period size: 99 Copynumber: 2.1 Consensus size: 104
2979674 TCGATTTAGA
* * ** * *
2979684 ATTTAATATATAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAAATGTTGTATAAAA
1 ATTTAATATAAAATATTTTTAATCTTTTATTATTTTTAAATAAAAATTCAAAATGTTGAATAAAA
*
2979749 TATTTTTAATATTTTATCATTTTTAATTTGTAATTTGAG
66 TATTTTTAATATTTTATCATTTTTAATTAGTAATTTGAG
* *
2979788 ATTTAATATAAAATATTTTTTAATCTTTTA-T-TTTTTAAATAAAAATTCAAGAT-TT-AATATA
1 ATTTAATATAAAATA-TTTTTAATCTTTTATTATTTTTAAATAAAAATTCAAAATGTTGAATAAA
*
2979849 ATTTTTTTAAT-TTTTAGT-ATTTTTAA-TAGTAATTTGAG
65 ATATTTTTAATATTTTA-TCATTTTTAATTAGTAATTTGAG
2979887 ATTTAATATA
1 ATTTAATATA
2979897 GATTGTTTAA
Statistics
Matches: 97, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
99 21 0.22
100 13 0.13
101 15 0.15
102 2 0.02
103 18 0.19
104 15 0.15
105 13 0.13
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (104 bp):
ATTTAATATAAAATATTTTTAATCTTTTATTATTTTTAAATAAAAATTCAAAATGTTGAATAAAA
TATTTTTAATATTTTATCATTTTTAATTAGTAATTTGAG
Found at i:2981729 original size:39 final size:39
Alignment explanation
Indices: 2981610--2981730 Score: 136
Period size: 39 Copynumber: 3.1 Consensus size: 39
2981600 AAGATATAGA
* * *
2981610 TTTTATTGGAATCTAAACGATGGTTACTAATGCATGGATT
1 TTTTATTGGAATCTAAAAGAT-GTGACTAATGCATGAATT
** *
2981650 CCTTATTGGAATTTAAAAGATGTGACTAATGCAT-AGATT
1 TTTTATTGGAATCTAAAAGATGTGACTAATGCATGA-ATT
* * *
2981689 TTTTATTGGAATCCAAATGATGTGACTAATACATGAATT
1 TTTTATTGGAATCTAAAAGATGTGACTAATGCATGAATT
2981728 TTT
1 TTT
2981731 ATAGAAATCC
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
39 49 0.73
40 18 0.27
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (39 bp):
TTTTATTGGAATCTAAAAGATGTGACTAATGCATGAATT
Found at i:2981740 original size:38 final size:39
Alignment explanation
Indices: 2981665--2981754 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 39
2981655 TTGGAATTTA
* * * *
2981665 AAAGATGTGACTAATGCATAGATTTTTTATTGGAATCC-
1 AAAGATGTGACTAATACATAGAATTTTTATAGAAATCCT
2981703 AAATGATGTGACTAATACAT-GAATTTTTATAGAAATCCT
1 AAA-GATGTGACTAATACATAGAATTTTTATAGAAATCCT
*
2981742 AAAGATATGACTA
1 AAAGATGTGACTA
2981755 TTGTATAGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 27 0.60
39 18 0.40
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (39 bp):
AAAGATGTGACTAATACATAGAATTTTTATAGAAATCCT
Found at i:2982652 original size:20 final size:20
Alignment explanation
Indices: 2982627--2982733 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
2982617 TTCTACCCAG
2982627 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* *
2982647 ATGTATCGATACATGTATGC-
1 ATGTATCGATACAT-TTTTCA
*
2982667 ATGTATCAATACATTCTGTTTTCTACCCA
1 ATGTATCGATACA-----TTTT-T---CA
2982696 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
2982717 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
2982734 GTTTTTTTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
20 43 0.62
21 5 0.07
24 3 0.04
25 5 0.07
28 1 0.01
30 12 0.17
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2982690 original size:70 final size:70
Alignment explanation
Indices: 2982596--2982730 Score: 243
Period size: 70 Copynumber: 1.9 Consensus size: 70
2982586 ATGAACAATA
* *
2982596 CATGTATCGATACATTTTATTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1 CATGTATCAATACATTCTATTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
2982661 GTATG
66 GTATG
*
2982666 CATGTATCAATACATTCTGTTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1 CATGTATCAATACATTCTATTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
2982731 TTTGTTTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (70 bp):
CATGTATCAATACATTCTATTTTCTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
GTATG
Found at i:2982760 original size:51 final size:50
Alignment explanation
Indices: 2982647--2982781 Score: 200
Period size: 51 Copynumber: 2.7 Consensus size: 50
2982637 ACATTTTTCA
* * *
2982647 ATGTATCGATACATGTATGC-ATGTATCAATACATTCTGTTTTCTACCCAG
1 ATGTATCGATACAT-TTTTCAATGTATCGATACATTCTGTTTTCTACCCAG
* *
2982697 ATGTATCGATACATTTTTCAATGTATCGATACATTTTGTTTTTTTACCCAG
1 ATGTATCGATACATTTTTCAATGTATCGATACATTCTG-TTTTCTACCCAG
2982748 ATGTATCGATACATTTTTCAATGTATCGATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACAT
2982782 CTAGTTAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
49 3 0.04
50 30 0.38
51 45 0.58
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (50 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATTCTGTTTTCTACCCAG
Found at i:2987951 original size:26 final size:26
Alignment explanation
Indices: 2987915--2987965 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
2987905 ACTAAGATTG
*
2987915 TTAAGATAAAA-TAAACATAAAAAATT
1 TTAAAATAAAAGTAAA-ATAAAAAATT
2987941 TTAAAATAAAATGTAAAATAAAAAA
1 TTAAAATAAAA-GTAAAATAAAAAA
2987966 AATGAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 8 0.36
28 4 0.18
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (26 bp):
TTAAAATAAAAGTAAAATAAAAAATT
Found at i:2989445 original size:13 final size:12
Alignment explanation
Indices: 2989413--2989443 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2989403 ATATTAATGA
2989413 ATTTTTTAAAAT
1 ATTTTTTAAAAT
2989425 ATTTTTTAAAAT
1 ATTTTTTAAAAT
2989437 ATTTTTT
1 ATTTTTT
2989444 TAGATGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTTTAAAAT
Found at i:2992139 original size:18 final size:19
Alignment explanation
Indices: 2992113--2992160 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
2992103 CGGCCTTTGA
* *
2992113 TCATACATTTTTAC-TGTT
1 TCATGCATTTTTACATGCT
2992131 TCATGCATTTTTACTATGCT
1 TCATGCATTTTTAC-ATGCT
2992151 TCATGCATTT
1 TCATGCATTT
2992161 ATAGTAGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.52
Consensus pattern (19 bp):
TCATGCATTTTTACATGCT
Found at i:2996285 original size:53 final size:51
Alignment explanation
Indices: 2996179--2996399 Score: 202
Period size: 53 Copynumber: 4.3 Consensus size: 51
2996169 AGATAAATCG
* * *
2996179 ATTTAGAATTTAATATATAATATTTTTAATTTTTTATTATTTTTAAATAGTA
1 ATTTAAAATTTAATATAAAATATTTTTAATATTTTA-TATTTTTAAATAGTA
* * *
2996231 ATTTAAAATGTT-GTATAAAATATTTTTAAATATTTTATCATTTTTAATTTGTA
1 ATTTAAAAT-TTAATATAAAATATTTTT-AATATTTTAT-ATTTTTAAATAGTA
* * * **
2996284 ATTTGAGATTTAATATAAAATATTTTTTAATCTTTTAT-TTTTTAAATAAAA
1 ATTTAAAATTTAATATAAAATA-TTTTTAATATTTTATATTTTTAAATAGTA
* * *
2996335 ATTCAAGATTTAATAT--AATTTTTTTAAT-TTTTAGTATTTTT-AATAGTA
1 ATTTAAAATTTAATATAAAATATTTTTAATATTTTA-TATTTTTAAATAGTA
* *
2996383 ATTTGAGATTTAATATA
1 ATTTAAAATTTAATATA
2996400 GATTGTTTAA
Statistics
Matches: 140, Mismatches: 21, Indels: 19
0.78 0.12 0.11
Matches are distributed among these distances:
47 5 0.04
48 28 0.20
49 8 0.06
51 23 0.16
52 24 0.17
53 47 0.34
54 5 0.04
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (51 bp):
ATTTAAAATTTAATATAAAATATTTTTAATATTTTATATTTTTAAATAGTA
Found at i:2996391 original size:99 final size:105
Alignment explanation
Indices: 2996186--2996399 Score: 264
Period size: 99 Copynumber: 2.1 Consensus size: 105
2996176 TCGATTTAGA
* * ** * *
2996186 ATTTAATATATAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAAATGTTGTATAAAA
1 ATTTAATATAAAATATTTTTAATCTTTTATTATTTTTAAATAAAAATTCAAAATGTTGAATAAAA
*
2996251 TATTTTTAAATATTTTATCATTTTTAATTTGTAATTTGAG
66 TATTTTTAAATATTTTATCATTTTTAATTAGTAATTTGAG
* *
2996291 ATTTAATATAAAATATTTTTTAATCTTTTA-T-TTTTTAAATAAAAATTCAAGAT-TT-AATATA
1 ATTTAATATAAAATA-TTTTTAATCTTTTATTATTTTTAAATAAAAATTCAAAATGTTGAATAAA
*
2996352 AT-TTTTTTAAT-TTTTAGT-ATTTTTAA-TAGTAATTTGAG
65 ATATTTTTAAATATTTTA-TCATTTTTAATTAGTAATTTGAG
2996390 ATTTAATATA
1 ATTTAATATA
2996400 GATTGTTTAA
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
99 21 0.22
100 13 0.13
101 9 0.09
102 6 0.06
103 2 0.02
104 18 0.19
105 15 0.15
106 13 0.13
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (105 bp):
ATTTAATATAAAATATTTTTAATCTTTTATTATTTTTAAATAAAAATTCAAAATGTTGAATAAAA
TATTTTTAAATATTTTATCATTTTTAATTAGTAATTTGAG
Found at i:2996409 original size:48 final size:47
Alignment explanation
Indices: 2996193--2996409 Score: 159
Period size: 48 Copynumber: 4.3 Consensus size: 47
2996183 AGAATTTAAT
* * * *
2996193 ATATAATATTTTTAATTTTTTATTATTTTTAAATAGTAATTTAAAATGTTGT
1 ATATAAT-TTTTTAATCTTTTA-TATTTTT-AATAGTAATTTGAGAT-TT-A
* * *
2996245 ATAAAATATTTTTAAATATTTTATCATTTTTAATTTGTAATTTGAGATTTA
1 ATATAAT-TTTTT-AATCTTTTAT-ATTTTTAA-TAGTAATTTGAGATTTA
** **
2996296 ATATAAAATATTTTTTAATCTTTTAT-TTTTTAAATAAAAATTCAAGATTTA
1 ATAT---A-ATTTTTTAATCTTTTATATTTTT-AATAGTAATTTGAGATTTA
2996347 ATATAATTTTTTTAAT-TTTTAGTATTTTTAATAGTAATTTGAGATTTA
1 ATATAA-TTTTTTAATCTTTTA-TATTTTTAATAGTAATTTGAGATTTA
*
2996395 ATATAGATTGTTTAA
1 ATATA-ATTTTTTAA
2996410 GATAAATATA
Statistics
Matches: 135, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
47 6 0.04
48 38 0.28
49 6 0.04
51 24 0.18
52 19 0.14
53 34 0.25
54 6 0.04
55 2 0.01
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (47 bp):
ATATAATTTTTTAATCTTTTATATTTTTAATAGTAATTTGAGATTTA
Found at i:2998234 original size:39 final size:39
Alignment explanation
Indices: 2998115--2998235 Score: 136
Period size: 39 Copynumber: 3.1 Consensus size: 39
2998105 AAGATATAGA
* * *
2998115 TTTTATTGGAATCTAAACGATGGTTACTAATGCATGGATT
1 TTTTATTGGAATCTAAAAGAT-GTGACTAATGCATGAATT
** *
2998155 CCTTATTGGAATTTAAAAGATGTGACTAATGCAT-AGATT
1 TTTTATTGGAATCTAAAAGATGTGACTAATGCATGA-ATT
* * *
2998194 TTTTATTGGAATCCAAATGATGTGACTAATACATGAATT
1 TTTTATTGGAATCTAAAAGATGTGACTAATGCATGAATT
2998233 TTT
1 TTT
2998236 ATAGAAATCC
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
39 49 0.73
40 18 0.27
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (39 bp):
TTTTATTGGAATCTAAAAGATGTGACTAATGCATGAATT
Found at i:2998245 original size:38 final size:39
Alignment explanation
Indices: 2998170--2998259 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 39
2998160 TTGGAATTTA
* * * *
2998170 AAAGATGTGACTAATGCATAGATTTTTTATTGGAATCC-
1 AAAGATGTGACTAATACATAGAATTTTTATAGAAATCCT
2998208 AAATGATGTGACTAATACAT-GAATTTTTATAGAAATCCT
1 AAA-GATGTGACTAATACATAGAATTTTTATAGAAATCCT
*
2998247 AAAGATATGACTA
1 AAAGATGTGACTA
2998260 TTGTATAGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 27 0.60
39 18 0.40
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (39 bp):
AAAGATGTGACTAATACATAGAATTTTTATAGAAATCCT
Found at i:3011122 original size:28 final size:28
Alignment explanation
Indices: 3011073--3011142 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
3011063 ATAAGAAATG
* * *
3011073 TCTTGATAAGACAATGCAGATAAACTTA
1 TCTTAATAAGATAAAGCAGATAAACTTA
* ***
3011101 TCTTAATAAGATAAAGCGGATAGGGTTA
1 TCTTAATAAGATAAAGCAGATAAACTTA
*
3011129 TCTTAATACGATAA
1 TCTTAATAAGATAA
3011143 TGTCTAAAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (28 bp):
TCTTAATAAGATAAAGCAGATAAACTTA
Found at i:3011199 original size:28 final size:28
Alignment explanation
Indices: 3011163--3011227 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
3011153 AAACATATGT
*
3011163 TAAGACAATATGGATAA-GCTTGTCTTAA
1 TAAGACAATATAGATAATG-TTGTCTTAA
*
3011191 TAAGACAATATAGATAATGTTGTTTTAA
1 TAAGACAATATAGATAATGTTGTCTTAA
*
3011219 CAAGACAAT
1 TAAGACAAT
3011228 GTTTAAAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (28 bp):
TAAGACAATATAGATAATGTTGTCTTAA
Found at i:3011282 original size:84 final size:84
Alignment explanation
Indices: 3011126--3011335 Score: 224
Period size: 84 Copynumber: 2.5 Consensus size: 84
3011116 GCGGATAGGG
* * * * * * *
3011126 TTATCTTAATACGATAATGTCTAAAGTAAACATATGTTAAGACAATATGGATAAGCTTGTCTTAA
1 TTATCTTAACAAGACAATGTCTAAAGTAGATATGTGTTAAGACAAAATGGATAAGCTTGTCTTAA
* **
3011191 TAAGACAATATAGATAATG
66 CAAGACAATATAGATAAAC
* * * *
3011210 TTGTTTTAACAAGACAATGTTTAAAGTAGATATGTGTTAAGACAAAATGGATAAGCTT-TTTTCA
1 TTATCTTAACAAGACAATGTCTAAAGTAGATATGTGTTAAGACAAAATGGATAAGCTTGTCTT-A
* *
3011274 ACAAGACAATGTGGATAAAC
65 ACAAGACAATATAGATAAAC
** * *
3011294 TTATCTTAACAAGGTAATCTCTAAAGTAGATATGTCTTAAGA
1 TTATCTTAACAAGACAATGTCTAAAGTAGATATGTGTTAAGA
3011336 TATAAGTTAT
Statistics
Matches: 102, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
83 3 0.03
84 99 0.97
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (84 bp):
TTATCTTAACAAGACAATGTCTAAAGTAGATATGTGTTAAGACAAAATGGATAAGCTTGTCTTAA
CAAGACAATATAGATAAAC
Found at i:3011868 original size:25 final size:24
Alignment explanation
Indices: 3011840--3011907 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
3011830 TAATAACATA
*
3011840 AATTAATATCTTAATAAAATATTTT
1 AATTAATAT-TTAATAAAATATTAT
* *
3011865 AATTTAATATTTTATAATATATTAT
1 AA-TTAATATTTAATAAAATATTAT
*
3011890 AACTAATGATTTGAATAA
1 AATTAAT-ATTT-AATAA
3011908 TATTTAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 4 0.11
25 20 0.57
26 11 0.31
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (24 bp):
AATTAATATTTAATAAAATATTAT
Found at i:3011967 original size:21 final size:22
Alignment explanation
Indices: 3011903--3011983 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 22
3011893 TAATGATTTG
* * *
3011903 AATAATATTTAAAAATATATTG
1 AATAATATTTAATAATAAATTA
* *
3011925 CA-AATAGTTTAATAAT--ATTT
1 AATAATA-TTTAATAATAAATTA
3011945 AATAATATTTAATAATAAATTA
1 AATAATATTTAATAATAAATTA
*
3011967 AACAAT-TTTAATAATAA
1 AATAATATTTAATAATAA
3011984 TATTTAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 13 0.27
21 19 0.39
22 17 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AATAATATTTAATAATAAATTA
Found at i:3011991 original size:10 final size:10
Alignment explanation
Indices: 3011866--3011961 Score: 72
Period size: 10 Copynumber: 9.1 Consensus size: 10
3011856 AAATATTTTA
3011866 ATTTAAT-AT
1 ATTTAATAAT
*
3011875 TTTATAAT-AT
1 ATT-TAATAAT
3011885 ATTATAACTAAT
1 ATT-TAA-TAAT
3011897 GATTTGAATAAT
1 -ATTT-AATAAT
*
3011909 ATTTAAAAAT
1 ATTTAATAAT
*
3011919 ATATTGCA-AAT
1 AT-TT-AATAAT
3011930 AGTTTAATAAT
1 A-TTTAATAAT
3011941 ATTTAATAAT
1 ATTTAATAAT
3011951 ATTTAATAAT
1 ATTTAATAAT
3011961 A
1 A
3011962 AATTAAACAA
Statistics
Matches: 73, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
9 2 0.03
10 40 0.55
11 17 0.23
12 9 0.12
13 5 0.07
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (10 bp):
ATTTAATAAT
Found at i:3013000 original size:50 final size:50
Alignment explanation
Indices: 3012917--3013011 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 50
3012907 AAAGTCATAT
***
3012917 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTTTGTC
1 TTTTACCCAGATGTATCGATACATTGAACAATGTATCGATACATTTTGTC
*
3012967 TTTTACCCAGATGTATCGATACATTGAAGAATGTATCGATACATT
1 TTTTACCCAGATGTATCGATACATTGAACAATGTATCGATACATT
3013012 CTTCAATGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (50 bp):
TTTTACCCAGATGTATCGATACATTGAACAATGTATCGATACATTTTGTC
Found at i:3013032 original size:20 final size:20
Alignment explanation
Indices: 3012927--3013033 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
3012917 TTTTACCCAG
*
3012927 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
3012947 ATGTATCGATACATTTTGTCTTTTACCCA
1 ATGTATCGATACA---T-TC--TT---CA
****
3012976 GATGTATCGATACATTGAAGA
1 -ATGTATCGATACATTCTTCA
3012997 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
3013017 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
3013034 GTCTTTTTAC
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
20 46 0.68
21 1 0.01
23 1 0.01
24 1 0.01
26 3 0.04
27 1 0.01
29 2 0.03
30 13 0.19
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:3013040 original size:70 final size:71
Alignment explanation
Indices: 3012927--3013058 Score: 221
Period size: 70 Copynumber: 1.9 Consensus size: 71
3012917 TTTTACCCAG
* *
3012927 ATGTATCGATACATTTTTCAATGTATCGATACATTTTGTC-TTTTACCCAGATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATACAT
3012991 TGAAGA
66 TGAAGA
* *
3012997 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCTAGATGTATTGATA
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATA
3013059 TATTTTTCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
70 38 0.67
71 19 0.33
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.42
Consensus pattern (71 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAGATGTATCGATACAT
TGAAGA
Found at i:3017192 original size:52 final size:52
Alignment explanation
Indices: 3017044--3017172 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
3017034 CGAAATATGA
3017044 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
3017096 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
3017148 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3017173 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:3017199 original size:13 final size:13
Alignment explanation
Indices: 3017181--3017205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3017171 CAAAGATCAG
3017181 TGTATCGATACAA
1 TGTATCGATACAA
3017194 TGTATCGATACA
1 TGTATCGATACA
3017206 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3017284 original size:32 final size:33
Alignment explanation
Indices: 3017243--3017311 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
3017233 GGCAGTAGCT
3017243 TACATTGTATCGATACAAAAC-TTATGTATCGA
1 TACATTGTATCGATACAAAACTTTATGTATCGA
*
3017275 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAACTTTATGTATCGA
3017308 TACA
1 TACA
3017312 AATCGTTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
TACATTGTATCGATACAAAACTTTATGTATCGA
Found at i:3017285 original size:13 final size:13
Alignment explanation
Indices: 3017267--3017291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3017257 ACAAAACTTA
3017267 TGTATCGATACAT
1 TGTATCGATACAT
3017280 TGTATCGATACA
1 TGTATCGATACA
3017292 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3018184 original size:67 final size:68
Alignment explanation
Indices: 3018062--3018188 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
3018052 ATTGGGTTTT
* * *
3018062 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGCACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGCACTTAAAGATGAAGATG
3018127 AGA
66 AGA
* * * **
3018130 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGCACTTAAAGATGA
3018189 GAAAAAAGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGCACTTAAAGATGAAGATG
AGA
Found at i:3018237 original size:55 final size:52
Alignment explanation
Indices: 3018138--3018458 Score: 224
Period size: 43 Copynumber: 6.6 Consensus size: 52
3018128 GAAAAGTGAT
* * * * * **
3018138 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G--A
* *
3018193 AAAGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
3018245 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3018292 ---G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---A
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * **
3018337 GAAGGTGCCAATATGCTGATTCAAGGCCAG-TGATATTGGGC-T-----T--A
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCT-ACATTGAACTTAAAGATGGA
* * *
3018381 AAAG-TGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAT-G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
*
3018430 -AAGGTGCCAATATGCTGATTCAAGGCCAG
1 AAAGATGCCAATATGCTGATTCAAGGCCAG
3018459 TGATATTGGG
Statistics
Matches: 222, Mismatches: 26, Indels: 42
0.77 0.09 0.14
Matches are distributed among these distances:
43 66 0.30
44 9 0.04
45 1 0.00
48 7 0.03
49 55 0.25
50 1 0.00
51 2 0.01
52 39 0.18
54 1 0.00
55 41 0.18
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:3018381 original size:92 final size:92
Alignment explanation
Indices: 3018201--3018477 Score: 448
Period size: 92 Copynumber: 3.0 Consensus size: 92
3018191 AAAAAGATGT
* *
3018201 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAATATGCTGATT
*
3018266 CAAGGCCAGCT-ATATTGGACTTAAAGGTGC
63 CAAGGCCAG-TGATATTGGGCTTAAAGGTGC
3018296 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
*
3018361 GGCCAGTGATATTGGGCTTAAAAGTGC
66 GGCCAGTGATATTGGGCTTAAAGGTGC
* *
3018388 CAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
3018453 GGCCAGTGATATTGGGCTTAGAAGG
66 GGCCAGTGATATTGGGCTTA-AAGG
3018478 GTTGCCACCG
Statistics
Matches: 173, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
91 1 0.01
92 130 0.75
93 3 0.02
95 39 0.23
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
GGCCAGTGATATTGGGCTTAAAGGTGC
Found at i:3018467 original size:49 final size:48
Alignment explanation
Indices: 3018201--3018458 Score: 304
Period size: 43 Copynumber: 5.5 Consensus size: 48
3018191 AAAAAGATGT
* *
3018201 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA--G--AAGGTGC
*
3018253 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAGAAGGTGC
*
3018296 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG-AGAAGGTGC
* *
3018345 CAATATGCTGATTCAAGGCCAG-TGATATTGGGCTT--A-A-AA-GTGC
1 CAATATGCTGATTCAAGGCCAGCT-ACATTGGACTTAAAGAGAAGGTGC
* *
3018388 CAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-GAAGGTGC
3018437 CAATATGCTGATTCAAGGCCAG
1 CAATATGCTGATTCAAGGCCAG
3018459 TGATATTGGG
Statistics
Matches: 178, Mismatches: 14, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
43 73 0.41
44 3 0.02
45 2 0.01
46 1 0.01
47 1 0.01
48 5 0.03
49 61 0.34
52 32 0.18
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAGAAGGTGC
Found at i:3018513 original size:32 final size:33
Alignment explanation
Indices: 3018475--3018881 Score: 557
Period size: 32 Copynumber: 12.6 Consensus size: 33
3018465 TGGGCTTAGA
3018475 AGGGTTGCCACCGACTTGTGTGGGCTTTAG-GG
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
* *
3018507 AGGGTTGCCACCAACTTGTGTGGGCTTT-GAGA
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
3018539 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
* * **
3018572 -GGATTGCCACCAACTTGTGTGGGCTTTAGAAA
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
3018604 AGGGTTGCCACCGACTTGTGTGGGCTTT-GAGG
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
**
3018636 -GGGTTGCCACCGACTTGTGTGGGCTTTAGAAA
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
3018668 AGGGTTGCCACCGACTTGTGTGGGCTTT-G-GG
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
*
3018699 AAGGGTTGCCATCGACTTGTGTGGGCTTTAGAGG
1 -AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
* * *
3018733 -GGATTGCCACCAACTTGTGTGGGCTTTAGAAG
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
* * *
3018765 AAGGTTGCCACCAACTTGTGTGGGCTTT-GAGA
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
**
3018797 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAAA
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
*
3018830 ATGGTTGCCACCGACTTGTGTGGGCTTT-G-GG
1 AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
3018861 AAGGGTTGCCACCGACTTGTG
1 -AGGGTTGCCACCGACTTGTG
3018882 GACTTAGAAG
Statistics
Matches: 332, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
31 28 0.08
32 191 0.58
33 111 0.33
34 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.28
Consensus pattern (33 bp):
AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGG
Found at i:3018678 original size:97 final size:97
Alignment explanation
Indices: 3018474--3018881 Score: 571
Period size: 97 Copynumber: 4.2 Consensus size: 97
3018464 TTGGGCTTAG
* *
3018474 AAGGGTTGCCACCGACTTGTGTGGGCTTT-AGGGAGGGTTGCCACCAACTTGTGTGGGCTTT-GA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGA-GAAGGGTTGCCACCGACTTGTGTGGGCTTTAGA
3018537 GAAGGGTTGCCACCGACTTGTGTGGGCTTTAG--
65 G-AGGGTTGCCACCGACTTGTGTGGGCTTTAGAA
* * *
3018569 AGGGGATTGCCACCAACTTGTGTGGGCTTTAGAAAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AAGGG-TTGCCACCGACTTGTGTGGGCTTT-GAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
3018633 AGGGGGTTGCCACCGACTTGTGTGGGCTTTAGAA
64 AGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAA
* *
3018667 AAGGGTTGCCACCGACTTGTGTGGGCTTTGGGAAGGGTTGCCATCGACTTGTGTGGGCTTTAGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG
*
3018732 -GGGATTGCCACCAACTTGTGTGGGCTTTAGAA
66 AGGG-TTGCCACCGACTTGTGTGGGCTTTAGAA
*
3018764 GAA-GGTTGCCACCAACTTGTGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGA
1 -AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG-
* * **
3018828 AAATGGTTGCCACCGACTTGTGTGGGCTTT-GGG
64 AGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAA
3018861 AAGGGTTGCCACCGACTTGTG
1 AAGGGTTGCCACCGACTTGTG
3018882 GACTTAGAAG
Statistics
Matches: 281, Mismatches: 21, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
95 4 0.01
96 86 0.31
97 158 0.56
98 31 0.11
99 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.28
Consensus pattern (97 bp):
AAGGGTTGCCACCGACTTGTGTGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG
AGGGTTGCCACCGACTTGTGTGGGCTTTAGAA
Found at i:3018771 original size:65 final size:63
Alignment explanation
Indices: 3018465--3018881 Score: 572
Period size: 65 Copynumber: 6.5 Consensus size: 63
3018455 CCAGTGATAT
* *
3018465 TGGGC-TTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGGAGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTG
*
3018527 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG-GGGATTGCCACCAACTTGTG
1 TGGGCTTT-AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG-TTGCCACCAACTTGTG
** *
3018591 TGGGCTTTAGAAAAGGGTTGCCACCGACTTGTGTGGGCTTT-GAGGGGGTTGCCACCGACTTGTG
1 TGGGCTTTAG--AAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTG
* * *
3018655 TGGGCTTTAGAAAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGGAAGGGTTGCCATCGACTTGT
1 TGGGCTTTAG--AAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCAACTTGT
3018719 G
63 G
* *
3018720 TGGGCTTTAGAGGGGATTGCCACCAACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG-AGAAGGTTGCCACCAACTTGTG
* *
3018785 TGGGCTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAATGGTTGCCACCGACTTGTG
1 TGGGCTTT-AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAA-GGTTGCCACCAACTTGTG
*
3018850 TGGGCTTTGGGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTT-AGAAGGGTTGCCACCGACTTGTG
3018882 GACTTAGAAG
Statistics
Matches: 327, Mismatches: 16, Indels: 21
0.90 0.04 0.06
Matches are distributed among these distances:
62 5 0.02
63 11 0.03
64 145 0.44
65 157 0.48
66 9 0.03
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.28
Consensus pattern (63 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGTTGCCACCAACTTGTG
Found at i:3019028 original size:35 final size:34
Alignment explanation
Indices: 3018982--3019160 Score: 183
Period size: 35 Copynumber: 5.7 Consensus size: 34
3018972 TTGTGGGCTT
*
3018982 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGG-A
* *
3019017 AAAAGAGTGCCACGGAGTTGTGGGCTTA-AACG-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGA
3019049 ----G-GTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGG-A
* *
3019079 AAAAGAGTGCCACGGAGTTGTGGGCTT--AACG-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGA
3019110 ----G-GTGCCACGGAGTTGTGGACTTAGAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGA
3019139 AAAA-AGTGCCACGGAGTTGTGG
1 AAAAGAGTGCCACGGAGTTGTGG
3019161 GCTTTGCAGA
Statistics
Matches: 119, Mismatches: 9, Indels: 34
0.73 0.06 0.21
Matches are distributed among these distances:
26 20 0.17
27 22 0.18
28 7 0.06
33 20 0.17
34 4 0.03
35 46 0.39
ACGTcount: A:0.30, C:0.14, G:0.37, T:0.19
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGA
Found at i:3019052 original size:62 final size:61
Alignment explanation
Indices: 3018861--3019164 Score: 522
Period size: 61 Copynumber: 5.0 Consensus size: 61
3018851 GGGCTTTGGG
* *
3018861 AAGGGTTGCCACCGACTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
1 AAGGG-TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
*
3018923 AAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
3018984 AAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
1 AAGGGTGCCACGGAGTTGTGGACTTAGAAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTAA
*
3019046 ACGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTT-A
1 AAGGGTGCCACGGAGTTGTGGACTTAGAAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTAA
*
3019107 ACGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAA-AGTGCCACGGAGTTGTGGGCTT
1 AAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
3019165 TGCAGAAAAG
Statistics
Matches: 236, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
59 22 0.09
60 5 0.02
61 116 0.49
62 93 0.39
ACGTcount: A:0.29, C:0.14, G:0.37, T:0.20
Consensus pattern (61 bp):
AAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
Found at i:3019214 original size:123 final size:122
Alignment explanation
Indices: 3018861--3019164 Score: 522
Period size: 123 Copynumber: 2.5 Consensus size: 122
3018851 GGGCTTTGGG
* *
3018861 AAGGGTTGCCACCGACTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAG
1 AAGGG-TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAG
*
3018926 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAA
65 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
*
3018984 AAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACG
1 AAGGGTGCCACGGAGTTGTGGACTTAGAAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAG
3019049 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTT-A
65 GGTGCCACGGAGTTGTGGACTTAGAAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTAA
*
3019107 ACGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAA-AGTGCCACGGAGTTGTGGGCTT
1 AAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
3019165 TGCAGAAAAG
Statistics
Matches: 174, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
121 22 0.13
122 29 0.17
123 96 0.55
124 27 0.16
ACGTcount: A:0.29, C:0.14, G:0.37, T:0.20
Consensus pattern (122 bp):
AAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG
GTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAA
Found at i:3019236 original size:64 final size:63
Alignment explanation
Indices: 3019140--3019320 Score: 253
Period size: 64 Copynumber: 2.9 Consensus size: 63
3019130 TTAGAAGGAA
* * *
3019140 AAAAG-TGCCACGGAGTTGTGGGCTTTGCAGAAAAGGATGCCACTAAGTCATGGACTTTGAGAC
1 AAAAGATGCCACTGAGTCGTGGGCTTTG-AGAAAAGGATGCCACTGAGTCATGGACTTTGAGAC
*
3019203 AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCATGGACTTTGAGAC
1 AAAAGATGCCACTGAGTCGTGGGCTTTG-AGAAAAGGATGCCACTGAGTCATGGACTTTGAGAC
* *
3019267 --AAGATGCCACTGAGTCGTGGGCTTTGAGAAGA-GATTGCCACTGAGTCGTGGACT
1 AAAAGATGCCACTGAGTCGTGGGCTTTGAGAAAAGGA-TGCCACTGAGTCATGGACT
3019321 ATAAAAAGGT
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
60 2 0.02
61 23 0.21
62 25 0.23
63 5 0.05
64 53 0.49
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (63 bp):
AAAAGATGCCACTGAGTCGTGGGCTTTGAGAAAAGGATGCCACTGAGTCATGGACTTTGAGAC
Found at i:3019309 original size:31 final size:30
Alignment explanation
Indices: 3019112--3019320 Score: 211
Period size: 32 Copynumber: 6.6 Consensus size: 30
3019102 GCTTAACGGG
* * * *
3019112 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAA
1 TGCCACTGAGTCGTGGACTTTG-A-GAAAAGA
* * *
3019144 GTGCCACGGAGTTGTGGGCTTTGCAGAAAAGGA
1 -TGCCACTGAGTCGTGGACTTTG-AGAAAA-GA
* *
3019177 TGCCACTAAGTCATGGACTTTGAGACAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAG--AAAAGA
3019209 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTTG-AGAAAA-GA
* *
3019241 TGCCACTGAGTCATGGACTTTGAGACAAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAAAGA
* *
3019271 TGCCACTGAGTCGTGGGCTTTGAGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAGAAAAGA
3019301 TTGCCACTGAGTCGTGGACT
1 -TGCCACTGAGTCGTGGACT
3019321 ATAAAAAGGT
Statistics
Matches: 152, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
30 28 0.18
31 29 0.19
32 67 0.44
33 28 0.18
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAGAAAAGA
Found at i:3021257 original size:98 final size:98
Alignment explanation
Indices: 3021141--3021380 Score: 363
Period size: 98 Copynumber: 2.4 Consensus size: 98
3021131 CATCAAGGAT
* * * * ***
3021141 ACTCCAGCCTCATTCCTCCAAGGGGATACTTCAATCTTGTTTTTAAAACTTGTCAAGATTTGAAA
1 ACTCCAACCTCATTCCTCCGAGGGGATACTCCAACCCCATTTTTAAAACTTGTCAAGATTTGAAA
3021206 CTTATTCTTGCCTAAATTATCATTGTCGGGGAC
66 CTTATTCTTGCCTAAATTATCATTGTCGGGGAC
* *
3021239 ACTCCAACCTCATTCCTCCGAGAGGATACTCCACCCCCATTTTTAAAACTTGTCAAGATTTGAAA
1 ACTCCAACCTCATTCCTCCGAGGGGATACTCCAACCCCATTTTTAAAACTTGTCAAGATTTGAAA
3021304 CTTATTCTTGCCTAAATTATCATTGTCGGGGAC
66 CTTATTCTTGCCTAAATTATCATTGTCGGGGAC
* * * *
3021337 ACTCCAACCCCATTCCTCCGAGGAGATACTCTAATCCCATTTTT
1 ACTCCAACCTCATTCCTCCGAGGGGATACTCCAACCCCATTTTT
3021381 CAATAAAAAA
Statistics
Matches: 127, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 127 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (98 bp):
ACTCCAACCTCATTCCTCCGAGGGGATACTCCAACCCCATTTTTAAAACTTGTCAAGATTTGAAA
CTTATTCTTGCCTAAATTATCATTGTCGGGGAC
Found at i:3028064 original size:12 final size:13
Alignment explanation
Indices: 3028043--3028074 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3028033 GTCAAAAGCC
3028043 AAAT-TGAGTG-A
1 AAATATGAGTGCA
3028054 AAATATGAGTGCA
1 AAATATGAGTGCA
3028067 AAATATGA
1 AAATATGA
3028075 ATTAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.21
12 6 0.32
13 9 0.47
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (13 bp):
AAATATGAGTGCA
Found at i:3033942 original size:32 final size:32
Alignment explanation
Indices: 3033901--3033976 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
3033891 GATACATTGA
*
3033901 AGAATGTATCGATATATTTGGGTCAGAAACCT
1 AGAATGTATCGATATATTTGGGTCAAAAACCT
3033933 AGAATGTATCGATATATTTGGGTCAAAAACCT
1 AGAATGTATCGATATATTTGGGTCAAAAACCT
3033965 AGAATGTATCGA
1 AGAATGTATCGA
3033977 CACAATGAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (32 bp):
AGAATGTATCGATATATTTGGGTCAAAAACCT
Found at i:3038712 original size:50 final size:51
Alignment explanation
Indices: 3038630--3038762 Score: 189
Period size: 50 Copynumber: 2.6 Consensus size: 51
3038620 ATTTGCCTGC
* * *
3038630 ATGTATCGATACATTGAATAATGTATCGATACATCTGGGT-AAAATCTAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGAGTAAAAACCTAGA
* * *
3038680 ATGTATCGATACAATGAAGAATGCATCAATACATCTGAGTAAAAACCTAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGAGTAAAAACCTAGA
*
3038731 ATGTATTGATACAAT-AATAATGTATCGATACA
1 ATGTATCGATACAATGAATAATGTATCGATACA
3038763 AATAGTAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
50 49 0.68
51 23 0.32
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACAATGAATAATGTATCGATACATCTGAGTAAAAACCTAGA
Found at i:3039701 original size:49 final size:50
Alignment explanation
Indices: 3039648--3039755 Score: 137
Period size: 52 Copynumber: 2.1 Consensus size: 50
3039638 GCGATATCGA
* * * * *
3039648 ACTTAGA-GATAAAGGTGCCAATGTGTTGATTCAAGCCCTACGACGTTGG
1 ACTTAGATGACAAAGGTGCCAATATGCTGATTCAAGCCCAACGACATTGG
*
3039697 ACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCCAACGACATTGG
1 ACTT--AGATGACAAAGGTGCCAATATGCTGATTCAAGCCCAACGACATTGG
3039749 ACTTAGA
1 ACTTAGA
3039756 AAGAGATGGT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 4 0.08
50 3 0.06
51 3 0.06
52 40 0.80
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (50 bp):
ACTTAGATGACAAAGGTGCCAATATGCTGATTCAAGCCCAACGACATTGG
Found at i:3039919 original size:31 final size:31
Alignment explanation
Indices: 3039821--3040198 Score: 420
Period size: 32 Copynumber: 11.9 Consensus size: 31
3039811 TAGAAAGAGA
* * *
3039821 TGCCACCAACTTGTGTGGACTTTTGAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AAGGGT
*
3039853 TGCCACCGACTTGTGTGGACTTTTA-AAGGGGT
1 TGCCACCGACTTGTGTGGGC-TTTAGAA-GGGT
*
3039885 TGCCACTGACTTGTGTGGGCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
3039916 TGCCACTGACTTATGTGGGCTTTGGAGAAAGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
* *
3039949 TGCCACCGACTTATGTGGG-TTTTGAAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AA-GGGT
* *
3039981 AGCCATCGACTTGTGTGGGCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
3040012 TGCCAACGACTTGTGTGGGCTTTGGAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AAGGGT
* *
3040044 TGCCACCGACTTGTATGGGCTTTTGAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAA-GGGT
3040076 TGCCACCGACTTGTGT-GGCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
*
3040106 TGCCACCGACTTGTGTGGGCTTTGGAGAAAGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
* *** * *
3040139 TGTCATTAACTTGTGTGGGCTTTGGAAGGGG
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
3040170 TGCCACCGACTTGTGTGGGCTTTAGAAGG
1 TGCCACCGACTTGTGTGGGCTTTAGAAGG
3040199 TTTCTCCACT
Statistics
Matches: 297, Mismatches: 36, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
30 21 0.07
31 106 0.36
32 112 0.38
33 58 0.20
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.30
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
Found at i:3040137 original size:95 final size:95
Alignment explanation
Indices: 3039821--3040198 Score: 537
Period size: 95 Copynumber: 4.0 Consensus size: 95
3039811 TAGAAAGAGA
* * * * * *
3039821 TGCCACCAACTTGTGTGGACTTTTGAAAGGGTTGCCACCGACTTGTGTGGACTTTTAAAGGGGTT
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAGGTTGCCACCGACTTGTGTGGGCTTTTGAAGGGGTT
*
3039886 GCCACTGACTTGTGTGGGCTTTAGAAGGGT
66 GCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
3039916 TGCCACTGACTTATGTGGGCTTTGGAGAAAGGTTGCCACCGACTTATGTGGG-TTTTGAAAGGGG
1 TGCCACCGACTTGTGTGGGCTTTGGA-AAAGGTTGCCACCGACTTGTGTGGGCTTTTG-AAGGGG
* *
3039980 TAGCCATCGACTTGTGTGGGCTTTAGAAGGGT
64 TTGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* *
3040012 TGCCAACGACTTGTGTGGGCTTTGGAAAAGGTTGCCACCGACTTGTATGGGCTTTTGAAGGGGTT
1 TGCCACCGACTTGTGTGGGCTTTGGAAAAGGTTGCCACCGACTTGTGTGGGCTTTTGAAGGGGTT
3040077 GCCACCGACTTGTGT-GGCTTTAGAAGGGT
66 GCCACCGACTTGTGTGGGCTTTAGAAGGGT
* *** *
3040106 TGCCACCGACTTGTGTGGGCTTTGGAGAAAGGTTGTCATTAACTTGTGTGGGCTTTGGAAGGGG-
1 TGCCACCGACTTGTGTGGGCTTTGGA-AAAGGTTGCCACCGACTTGTGTGGGCTTTTGAAGGGGT
3040170 TGCCACCGACTTGTGTGGGCTTTAGAAGG
65 TGCCACCGACTTGTGTGGGCTTTAGAAGG
3040199 TTTCTCCACT
Statistics
Matches: 252, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
94 55 0.22
95 112 0.44
96 85 0.34
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.30
Consensus pattern (95 bp):
TGCCACCGACTTGTGTGGGCTTTGGAAAAGGTTGCCACCGACTTGTGTGGGCTTTTGAAGGGGTT
GCCACCGACTTGTGTGGGCTTTAGAAGGGT
Found at i:3040431 original size:28 final size:28
Alignment explanation
Indices: 3040372--3040443 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
3040362 TATATAGCAA
*
3040372 GTGCCACTGA-TTATGGACTTCGAAAAG
1 GTGCCACTGACTTGTGGACTTCGAAAAG
*
3040399 ATGCCACTGACTTGTGGACTTC-AAAGAG
1 GTGCCACTGACTTGTGGACTTCGAAA-AG
* *
3040427 GTGCCACTAACTAGTGG
1 GTGCCACTGACTTGTGG
3040444 GCTTTGAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 12 0.32
28 26 0.68
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGACTTCGAAAAG
Found at i:3041792 original size:20 final size:20
Alignment explanation
Indices: 3041769--3041812 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3041759 CCCCTTTTCT
3041769 TGTTTATTAT-TATTTTTTTG
1 TGTTT-TTATGTATTTTTTTG
* *
3041789 TGTTTTTTTGTGTTTTTTTG
1 TGTTTTTATGTATTTTTTTG
3041809 TGTT
1 TGTT
3041813 GTTTTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.07, C:0.00, G:0.16, T:0.77
Consensus pattern (20 bp):
TGTTTTTATGTATTTTTTTG
Found at i:3041796 original size:9 final size:9
Alignment explanation
Indices: 3041782--3041838 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
3041772 TTATTATTAT
3041782 TTTTTTGTG
1 TTTTTTGTG
3041791 TTTTTTTGTG
1 -TTTTTTGTG
3041801 TTTTTT-TG
1 TTTTTTGTG
*
3041809 --TGTTGT-
1 TTTTTTGTG
3041815 TTTTTT-TG
1 TTTTTTGTG
*
3041823 TTTTTTGTC
1 TTTTTTGTG
3041832 TTTTTTG
1 TTTTTTG
3041839 GCGAAAGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
6 3 0.08
7 2 0.05
8 11 0.28
9 14 0.36
10 9 0.23
ACGTcount: A:0.00, C:0.02, G:0.18, T:0.81
Consensus pattern (9 bp):
TTTTTTGTG
Found at i:3041806 original size:12 final size:10
Alignment explanation
Indices: 3041781--3041837 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
3041771 TTTATTATTA
3041781 TTTTTTTGTG
1 TTTTTTTGTG
3041791 TTTTTTTGTG
1 TTTTTTTGTG
3041801 TTTTTTTGTG
1 TTTTTTTGTG
*
3041811 TTGTTTTT-TT
1 TT-TTTTTGTG
*
3041821 TGTTTTTTGTC
1 T-TTTTTTGTG
3041832 TTTTTT
1 TTTTTT
3041838 GGCGAAAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 34 0.81
11 8 0.19
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (10 bp):
TTTTTTTGTG
Found at i:3045631 original size:313 final size:313
Alignment explanation
Indices: 3045050--3045679 Score: 1190
Period size: 313 Copynumber: 2.0 Consensus size: 313
3045040 AAGTGCAAGG
*
3045050 GCTTCCGTCATGCTCCTGTCGTCAAAGACAGGTCATAATAGAGGGGCACGAGTTTCATGGCTCAG
1 GCTTCCATCATGCTCCTGTCGTCAAAGACAGGTCATAATAGAGGGGCACGAGTTTCATGGCTCAG
*
3045115 TGTCTAGGAGATAGAGGTTGTGGAGTGCCCTATTTAAGATAACCAAGACGTCTTTAGTCTTCTGT
66 TGTCTAGGAGATAGAGGTTGTGGAGTGCCCTATTTAAGATAACCAAGACGTCTTTAGCCTTCTGT
3045180 TCTTCGGGTCGATTTGAATCGATTCGTCCCCCCGAGCAAAATATCTCATAGAGTGGTGGGAACAT
131 TCTTCGGGTCGATTTGAATCGATTCGTCCCCCCGAGCAAAATATCTCATAGAGTGGTGGGAACAT
3045245 CATTGATTTTAATTCCCTCTCTTGACCCGATGATCGAGTCACTCTCTGGCTGTGGGTCATTTTTG
196 CATTGATTTTAATTCCCTCTCTTGACCCGATGATCGAGTCACTCTCTGGCTGTGGGTCATTTTTG
*
3045310 CTTGCTGCTTCTTTGACCACACATTGGCCTTAAATCCTAGGCCTCTTTTATCA
261 CCTGCTGCTTCTTTGACCACACATTGGCCTTAAATCCTAGGCCTCTTTTATCA
3045363 GCTTCCATCATGCT-CTCGTCGTCAAAGACAGGTCATAATAGAGGGGCACGAGTTTCATGGCTCA
1 GCTTCCATCATGCTCCT-GTCGTCAAAGACAGGTCATAATAGAGGGGCACGAGTTTCATGGCTCA
* * *
3045427 GTGTCTGGGAGATGGAGGTTGTGGAGTGCCCTATTTAAGATAACCAAGATGTCTTTAGCCTTCTG
65 GTGTCTAGGAGATAGAGGTTGTGGAGTGCCCTATTTAAGATAACCAAGACGTCTTTAGCCTTCTG
3045492 TTCTTCGGGTCGATTTGAATCGATTCGTCCCCCCGAGCAAAATATCTCATAGAGTGGTGGGAACA
130 TTCTTCGGGTCGATTTGAATCGATTCGTCCCCCCGAGCAAAATATCTCATAGAGTGGTGGGAACA
3045557 TCATTGATTTTAATTCCCTCTCTTGACCCGATGATCGAGTCACTCTCTGGCTGTGGGTCATTTTT
195 TCATTGATTTTAATTCCCTCTCTTGACCCGATGATCGAGTCACTCTCTGGCTGTGGGTCATTTTT
3045622 GCCTGCTGCTTCTTTGACCACACATTGGCCTTAAATCCTAGGCCTCTTTTATCA
260 GCCTGCTGCTTCTTTGACCACACATTGGCCTTAAATCCTAGGCCTCTTTTATCA
3045676 GCTT
1 GCTT
3045680 GAGTGGTGGC
Statistics
Matches: 310, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
312 2 0.01
313 308 0.99
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (313 bp):
GCTTCCATCATGCTCCTGTCGTCAAAGACAGGTCATAATAGAGGGGCACGAGTTTCATGGCTCAG
TGTCTAGGAGATAGAGGTTGTGGAGTGCCCTATTTAAGATAACCAAGACGTCTTTAGCCTTCTGT
TCTTCGGGTCGATTTGAATCGATTCGTCCCCCCGAGCAAAATATCTCATAGAGTGGTGGGAACAT
CATTGATTTTAATTCCCTCTCTTGACCCGATGATCGAGTCACTCTCTGGCTGTGGGTCATTTTTG
CCTGCTGCTTCTTTGACCACACATTGGCCTTAAATCCTAGGCCTCTTTTATCA
Found at i:3050434 original size:41 final size:41
Alignment explanation
Indices: 3050389--3050470 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
3050379 AGAAGAAACT
3050389 TTGTTTGGCTTTCCCCTTTCTAACATGAAGATGACCTGATA
1 TTGTTTGGCTTTCCCCTTTCTAACATGAAGATGACCTGATA
3050430 TTGTTTGGCTTTCCCCTTTCTAACATGAAGATGACCTGATA
1 TTGTTTGGCTTTCCCCTTTCTAACATGAAGATGACCTGATA
3050471 GCCATATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (41 bp):
TTGTTTGGCTTTCCCCTTTCTAACATGAAGATGACCTGATA
Found at i:3055699 original size:51 final size:51
Alignment explanation
Indices: 3055631--3055757 Score: 209
Period size: 51 Copynumber: 2.5 Consensus size: 51
3055621 GCATGTATTA
*
3055631 ATACATTGAAGAATGTATCGATACATCCGAGTAAAAACCCAGAATGTATCG
1 ATACAATGAAGAATGTATCGATACATCCGAGTAAAAACCCAGAATGTATCG
* * *
3055682 ATACAATGAAGAATGTATCGATACATCCGGGTAAAAATCCAGAATGTATGG
1 ATACAATGAAGAATGTATCGATACATCCGAGTAAAAACCCAGAATGTATCG
*
3055733 ATACAATGAATAATGTATCGATACA
1 ATACAATGAAGAATGTATCGATACA
3055758 AAGAGTAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (51 bp):
ATACAATGAAGAATGTATCGATACATCCGAGTAAAAACCCAGAATGTATCG
Found at i:3064980 original size:26 final size:26
Alignment explanation
Indices: 3064899--3064980 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 26
3064889 TAGCCTCTAT
* * *
3064899 TAGTTGGCACATGAATGGAAGCCCACAT
1 TAGTTGGCACCT-AA-GTAAGCCCACAC
* *
3064927 TACTTGGCATCTAAGTCTAAGCCCACAC
1 TAGTTGGCACCTAAG--TAAGCCCACAC
3064955 TAGTTGGCACCTAAGTAAGCCCACAC
1 TAGTTGGCACCTAAGTAAGCCCACAC
3064981 AACCGGGCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
26 12 0.27
27 2 0.04
28 31 0.69
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (26 bp):
TAGTTGGCACCTAAGTAAGCCCACAC
Done.