Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167971.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_23, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19268551
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 68000 characters in sequence are not A, C, G, or T
File 93 of 120
Found at i:12441590 original size:12 final size:13
Alignment explanation
Indices: 12441503--12441615 Score: 58
Period size: 12 Copynumber: 8.5 Consensus size: 13
12441493 TGGATTATAT
*
12441503 TATAATTATGATAA
1 TATAATTA-AATAA
12441517 T-TATATTAAATTAA
1 TATA-ATTAAA-TAA
*
12441531 GAT-ATTAAATAA
1 TATAATTAAATAA
*
12441543 TATCTTATTAATATAA
1 TA--TAATTAA-ATAA
*
12441559 TACATATATAAAT-A
1 TATA-AT-TAAATAA
12441573 TA-AATTAAATAA
1 TATAATTAAATAA
12441585 -ATAATTAAA-AA
1 TATAATTAAATAA
*
12441596 TATAATTTAATATA
1 TATAATTAAATA-A
12441610 TATAAT
1 TATAAT
12441616 CAAGACAAGA
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
11 8 0.10
12 22 0.28
13 11 0.14
14 19 0.24
15 10 0.13
16 9 0.11
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (13 bp):
TATAATTAAATAA
Found at i:12442485 original size:24 final size:22
Alignment explanation
Indices: 12442464--12442507 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12442454 ATATAAAAGT
12442464 GACCAAAAAATTAAAAACAAAA
1 GACCAAAAAATTAAAAACAAAA
* * *
12442486 GACTAAAAAACTAAAAAGAAAA
1 GACCAAAAAATTAAAAACAAAA
12442508 AAAAGGCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.73, C:0.11, G:0.07, T:0.09
Consensus pattern (22 bp):
GACCAAAAAATTAAAAACAAAA
Found at i:12449422 original size:11 final size:11
Alignment explanation
Indices: 12449406--12449442 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
12449396 AAATTTTAAA
12449406 TTATATTATAT
1 TTATATTATAT
12449417 TTATATT-T-T
1 TTATATTATAT
12449426 TTATATTATAT
1 TTATATTATAT
12449437 TTATAT
1 TTATAT
12449443 CAAATTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.33
10 2 0.08
11 14 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATTATAT
Found at i:12450026 original size:13 final size:12
Alignment explanation
Indices: 12450004--12450038 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12449994 TTTCTAAAGC
12450004 TTTTGTTTTTTT
1 TTTTGTTTTTTT
*
12450016 TTTTGGTTTTTT
1 TTTTGTTTTTTT
*
12450028 TTTTATTTTTT
1 TTTTGTTTTTT
12450039 GTTGTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.89
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:12450378 original size:19 final size:20
Alignment explanation
Indices: 12450346--12450386 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12450336 ATTCGGCTTT
* *
12450346 TTTTTTAATCATTTTTTTTA
1 TTTTTTAATAATTTTATTTA
12450366 TTTTTTAA-AATTTTATTTA
1 TTTTTTAATAATTTTATTTA
12450385 TT
1 TT
12450387 AGATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTAATAATTTTATTTA
Found at i:12450690 original size:23 final size:22
Alignment explanation
Indices: 12450663--12450726 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
12450653 ATATTTTAAT
12450663 TTAATAAAAAAATATATTTATA
1 TTAATAAAAAAATATATTTATA
* **
12450685 TATAATTAAATTATA-ATTTATA
1 T-TAATAAAAAAATATATTTATA
12450707 TTAA-AAAATAAATATATTTA
1 TTAATAAAA-AAATATATTTA
12450727 GATTTGTCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 3 0.09
21 6 0.18
22 14 0.42
23 10 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAATAAAAAAATATATTTATA
Found at i:12460674 original size:23 final size:23
Alignment explanation
Indices: 12460648--12460701 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
12460638 TATAGTTATC
*
12460648 TATTATATTTATT-TATTTAAAAA
1 TATTATATTTATTATATAT-AAAA
* *
12460671 TATTATTTTTATTATATATAATA
1 TATTATATTTATTATATATAAAA
12460694 TATTATAT
1 TATTATAT
12460702 ATCCAATCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTATATTTATTATATATAAAA
Found at i:12463305 original size:15 final size:15
Alignment explanation
Indices: 12463276--12463314 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
12463266 TTTTAAAAAA
*
12463276 TATAAGTTTAAATTT
1 TATAATTTTAAATTT
12463291 TA-AATTTTAATATTT
1 TATAATTTTAA-ATTT
12463306 TATAATTTT
1 TATAATTTT
12463315 TTTTATCCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TATAATTTTAAATTT
Found at i:12464149 original size:2 final size:2
Alignment explanation
Indices: 12464142--12464167 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12464132 GACGGCGGGG
12464142 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12464168 GAACTGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12468077 original size:37 final size:38
Alignment explanation
Indices: 12468012--12468090 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
12468002 GTAAGCTATT
*
12468012 AAAAGAGTGTAATTAAGTTTTTTATTAAGTTTTGAATA
1 AAAAGAGTGTAATTAAGTTATTTATTAAGTTTTGAATA
* *
12468050 AAAAGTGTGTAATTGAGTTATTT-TTAAGTTTTGAATA
1 AAAAGAGTGTAATTAAGTTATTTATTAAGTTTTGAATA
12468087 AAAA
1 AAAA
12468091 TTTTTGATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 18 0.47
38 20 0.53
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (38 bp):
AAAAGAGTGTAATTAAGTTATTTATTAAGTTTTGAATA
Found at i:12475207 original size:19 final size:18
Alignment explanation
Indices: 12475178--12475213 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12475168 CAAAGTCTTA
12475178 AATAAAAAAATAAATAAT
1 AATAAAAAAATAAATAAT
*
12475196 AATAATAAAAATATATAA
1 AATAA-AAAAATAAATAA
12475214 AATGATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AATAAAAAAATAAATAAT
Found at i:12475530 original size:29 final size:27
Alignment explanation
Indices: 12475486--12475602 Score: 108
Period size: 30 Copynumber: 4.1 Consensus size: 27
12475476 TTAAAAAAAA
* *
12475486 AAAACTAAACCCTAAACTTTCCAAACCCT
1 AAAACTAAACCCTAAA--ATCAAAACCCT
*
12475515 AAAACTAAACCTTAAAATCAAAACCCT
1 AAAACTAAACCCTAAAATCAAAACCCT
* *
12475542 AAAACTTTCAAACCTTAAAATCAAAACCAT
1 AAAAC--T-AAACCCTAAAATCAAAACCCT
* **
12475572 AAACCTTAAACCCTAAAATTGAAACCCT
1 AAAAC-TAAACCCTAAAATCAAAACCCT
12475600 AAA
1 AAA
12475603 CCTTCTAAAC
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
27 14 0.18
28 20 0.26
29 18 0.24
30 24 0.32
ACGTcount: A:0.51, C:0.27, G:0.01, T:0.21
Consensus pattern (27 bp):
AAAACTAAACCCTAAAATCAAAACCCT
Found at i:12475544 original size:14 final size:14
Alignment explanation
Indices: 12475508--12475602 Score: 61
Period size: 14 Copynumber: 6.7 Consensus size: 14
12475498 TAAACTTTCC
*
12475508 AAACCCTAAAA-CT
1 AAACCCTAAAATCA
*
12475521 AAACCTTAAAATCA
1 AAACCCTAAAATCA
12475535 AAACCCTAAAACTTTC-
1 AAACCCTAAAA---TCA
*
12475551 AAACCTTAAAATCA
1 AAACCCTAAAATCA
* * *
12475565 AAACCAT-AAACCTT
1 AAACCCTAAAATC-A
**
12475579 AAACCCTAAAATTG
1 AAACCCTAAAATCA
12475593 AAACCCTAAA
1 AAACCCTAAA
12475603 CCTTCTAAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
13 16 0.25
14 33 0.52
15 3 0.05
16 10 0.16
17 2 0.03
ACGTcount: A:0.53, C:0.26, G:0.01, T:0.20
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:12475557 original size:30 final size:29
Alignment explanation
Indices: 12475508--12475640 Score: 141
Period size: 30 Copynumber: 4.7 Consensus size: 29
12475498 TAAACTTTCC
12475508 AAACCCTAAAA-C-TAAACCTTAAAATCA
1 AAACCCTAAAACCTTAAACCTTAAAATCA
*
12475535 AAACCCTAAAACTTTCAAACCTTAAAATCA
1 AAACCCTAAAACCTT-AAACCTTAAAATCA
* * **
12475565 AAACCAT-AAACCTTAAACCCTAAAATTG
1 AAACCCTAAAACCTTAAACCTTAAAATCA
* *
12475593 AAACCCT-AAACCTTCTAAACTTTAAAACCA
1 AAACCCTAAAACC-T-TAAACCTTAAAATCA
12475623 AAACCCT-AAACCTTAAAC
1 AAACCCTAAAACCTTAAAC
12475641 TTTTCAAACC
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
27 11 0.12
28 27 0.30
29 9 0.10
30 42 0.47
ACGTcount: A:0.50, C:0.28, G:0.01, T:0.21
Consensus pattern (29 bp):
AAACCCTAAAACCTTAAACCTTAAAATCA
Found at i:12475583 original size:44 final size:44
Alignment explanation
Indices: 12475485--12475589 Score: 117
Period size: 43 Copynumber: 2.4 Consensus size: 44
12475475 TTTAAAAAAA
* * *
12475485 AAAAACTAAACCCT-AAACTTTCCAAACCCTAAAACTAAACCTT
1 AAAATCTAAACCCTAAAACTTTCCAAACCCTAAAACAAAACCAT
* *
12475528 AAAATCAAAACCCTAAAACTTT-CAAACCTTAAAATCAAAACCAT
1 AAAATCTAAACCCTAAAACTTTCCAAACCCTAAAA-CAAAACCAT
*
12475572 -AAACCTTAAACCCTAAAA
1 AAAATC-TAAACCCTAAAA
12475590 TTGAAACCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
43 27 0.52
44 25 0.48
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (44 bp):
AAAATCTAAACCCTAAAACTTTCCAAACCCTAAAACAAAACCAT
Found at i:12475583 original size:58 final size:58
Alignment explanation
Indices: 12475520--12475640 Score: 163
Period size: 58 Copynumber: 2.1 Consensus size: 58
12475510 ACCCTAAAAC
* * *
12475520 TAAACCTTAAAATCAAAACCCTAAAACTT-TCAAACCTTAAAATCAAAACCATAAACCT
1 TAAACCCTAAAATCAAAACCCTAAACCTTCT-AAACCTTAAAACCAAAACCATAAACCT
** * *
12475578 TAAACCCTAAAATTGAAACCCTAAACCTTCTAAACTTTAAAACCAAAACCCTAAACCT
1 TAAACCCTAAAATCAAAACCCTAAACCTTCTAAACCTTAAAACCAAAACCATAAACCT
12475636 TAAAC
1 TAAAC
12475641 TTTTCAAACC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 54 0.98
59 1 0.02
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (58 bp):
TAAACCCTAAAATCAAAACCCTAAACCTTCTAAACCTTAAAACCAAAACCATAAACCT
Found at i:12475640 original size:14 final size:14
Alignment explanation
Indices: 12475565--12475640 Score: 57
Period size: 14 Copynumber: 5.3 Consensus size: 14
12475555 CTTAAAATCA
*
12475565 AAACCATAAACCTT
1 AAACCCTAAACCTT
*
12475579 AAACCCTAAA-ATT
1 AAACCCTAAACCTT
12475592 GAAACCCTAAACCTTCT
1 -AAACCCTAAACC-T-T
** *
12475609 AAACTTTAAAACC-A
1 AAACCCT-AAACCTT
12475623 AAACCCTAAACCTT
1 AAACCCTAAACCTT
12475637 AAAC
1 AAAC
12475641 TTTTCAAACC
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
13 7 0.15
14 28 0.60
16 6 0.13
17 6 0.13
ACGTcount: A:0.49, C:0.29, G:0.01, T:0.21
Consensus pattern (14 bp):
AAACCCTAAACCTT
Found at i:12475669 original size:30 final size:29
Alignment explanation
Indices: 12475633--12475690 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
12475623 AAACCCTAAA
*
12475633 CCTT-AAACTTTTCAAACCCTAAAACTCAAG
1 CCTTAAAACCTTT-AAACCCTAAAA-TCAAG
12475663 CCTTAAAACCTTTAAACCCTAAAATCAA
1 CCTTAAAACCTTTAAACCCTAAAATCAA
12475691 AACTCTAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 4 0.15
30 15 0.58
31 7 0.27
ACGTcount: A:0.43, C:0.29, G:0.02, T:0.26
Consensus pattern (29 bp):
CCTTAAAACCTTTAAACCCTAAAATCAAG
Found at i:12475725 original size:16 final size:16
Alignment explanation
Indices: 12475704--12475737 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12475694 TCTAAACTCC
12475704 AAACCTTAAAATCCAA
1 AAACCTTAAAATCCAA
* *
12475720 AAACCTTTAAATCTAA
1 AAACCTTAAAATCCAA
12475736 AA
1 AA
12475738 TCTCAAACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.24
Consensus pattern (16 bp):
AAACCTTAAAATCCAA
Found at i:12475746 original size:52 final size:53
Alignment explanation
Indices: 12475667--12475766 Score: 150
Period size: 52 Copynumber: 1.9 Consensus size: 53
12475657 CTCAAGCCTT
*
12475667 AAAACCTTTAAACCCTAAAATCAAAACTCTAAACTCC-AAACCTTAAAATCCA
1 AAAACCTTTAAACCCTAAAATCAAAACTCTAAAATCCTAAACCTTAAAATCCA
* *
12475719 AAAACCTTTAAA-TCTAAAATCTCAAACTCTAAAATCCTAAACCTTAAA
1 AAAACCTTTAAACCCTAAAATC-AAAACTCTAAAATCCTAAACCTTAAA
12475767 TTCAGCACAC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 8 0.19
52 25 0.58
53 10 0.23
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (53 bp):
AAAACCTTTAAACCCTAAAATCAAAACTCTAAAATCCTAAACCTTAAAATCCA
Found at i:12479000 original size:35 final size:35
Alignment explanation
Indices: 12478953--12479070 Score: 89
Period size: 35 Copynumber: 3.4 Consensus size: 35
12478943 CCCGATCTCG
12478953 TTATTCTT-TGACTCATGGTTTAATCTCAGTCATCT
1 TTATT-TTCTGACTCATGGTTTAATCTCAGTCATCT
* *** ** * *
12478988 TTATTTTATGACTTGCGGTCCAATCCCAGTC-TCA
1 TTATTTTCTGACTCATGGTTTAATCTCAGTCATCT
* * **
12479022 TTATTCTCTGACCCATAATTTAATCTCAGTCA-CTT
1 TTATTTTCTGACTCATGGTTTAATCTCAGTCATC-T
12479057 TTATTTTCTGACTC
1 TTATTTTCTGACTC
12479071 GCGATTCAAT
Statistics
Matches: 59, Mismatches: 21, Indels: 6
0.69 0.24 0.07
Matches are distributed among these distances:
34 25 0.42
35 34 0.58
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (35 bp):
TTATTTTCTGACTCATGGTTTAATCTCAGTCATCT
Found at i:12479044 original size:69 final size:69
Alignment explanation
Indices: 12478929--12479241 Score: 276
Period size: 69 Copynumber: 4.5 Consensus size: 69
12478919 CCAGTCATTA
* * * * * *
12478929 ACTTGCTGATCAATCCCGATCTCGTTATTCTTTGACTCATGGTTTAATCTCAGTCATCTTTATTT
1 ACTTGCGGTTCAATCCCGATCTCTTTATTCTCTGACTCACGATTTAATCTCAGTCATCTTTATTT
12478994 TATG
66 TATG
* * * **
12478998 ACTTGCGGTCCAATCCC-AGTCTCATTATTCTCTGACCCATAATTTAATCTCAGTCA-CTTTTAT
1 ACTTGCGGTTCAATCCCGA-TCTCTTTATTCTCTGACTCACGATTTAATCTCAGTCATC-TTTAT
*
12479061 TTTCTG
64 TTTATG
* * * * * *
12479067 ACTCGCGATTCAAT-CCTAGTCTCTTTATTCTCAT-ACTCACGATTTAATCTCAATTATTTTTAT
1 ACTTGCGGTTCAATCCCGA-TCTCTTTATTCTC-TGACTCACGATTTAATCTCAGTCATCTTTAT
*
12479130 TTTTTG
64 TTTATG
* * *
12479136 ACTAGCGGTTCAATCCCGATCTCTTTATTCTCTGACTCGCGATTTAAATCT-AGTCATTTTTATT
1 ACTTGCGGTTCAATCCCGATCTCTTTATTCTCTGACTCACGATTT-AATCTCAGTCATCTTTATT
*
12479200 TTATT
65 TTATG
* * * ** * *
12479205 ACTTACGATTTAATCTTGATTTCTTTATTTTCTGACT
1 ACTTGCGGTTCAATCCCGATCTCTTTATTCTCTGACT
12479242 TGTAGTTCAA
Statistics
Matches: 200, Mismatches: 36, Indels: 16
0.79 0.14 0.06
Matches are distributed among these distances:
68 5 0.03
69 186 0.93
70 9 0.05
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (69 bp):
ACTTGCGGTTCAATCCCGATCTCTTTATTCTCTGACTCACGATTTAATCTCAGTCATCTTTATTT
TATG
Found at i:12479198 original size:35 final size:34
Alignment explanation
Indices: 12479039--12479199 Score: 112
Period size: 34 Copynumber: 4.6 Consensus size: 34
12479029 CTGACCCATA
* *
12479039 ATTTAATCTCAGTCACTTTTATTTTCTGACTCGCG
1 ATTTAATCT-AGTCATTTTTATTCTCTGACTCGCG
* * *
12479074 ATTCAATCCTAGTC-TCTTTATTCTCAT-ACTCACG
1 ATTTAAT-CTAGTCATTTTTATTCTC-TGACTCGCG
* * * * *
12479108 ATTTAATCTCAATTATTTTTATTTTTTGACTAGCG
1 ATTTAATCT-AGTCATTTTTATTCTCTGACTCGCG
* * ** *
12479143 GTTCAATCCCGATC-TCTTTATTCTCTGACTCGCG
1 ATTTAATCTAG-TCATTTTTATTCTCTGACTCGCG
12479177 ATTTAAATCTAGTCATTTTTATT
1 ATTT-AATCTAGTCATTTTTATT
12479200 TTATTACTTA
Statistics
Matches: 90, Mismatches: 28, Indels: 16
0.67 0.21 0.12
Matches are distributed among these distances:
33 2 0.02
34 43 0.48
35 43 0.48
36 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (34 bp):
ATTTAATCTAGTCATTTTTATTCTCTGACTCGCG
Found at i:12479232 original size:103 final size:104
Alignment explanation
Indices: 12479056--12479287 Score: 247
Period size: 103 Copynumber: 2.2 Consensus size: 104
12479046 CTCAGTCACT
* *
12479056 TTTATTTTCTGACTCGCGA-TTCAATCCTAGTCTCTTTATTCTCATACTCACGATTTAATCTCAA
1 TTTATTCTCTGACTCGCGATTTAAATCCTAGTCTCTTTATTCTCATACTCACGATTTAATCTCAA
* * *
12479120 TTATTTTTATTTTTTGACTAGCGGTTCAATCCCGATCTC
66 TTATCTTTATTTTCTGACTAGCAGTTCAATCCCGATCTC
* * * *
12479159 TTTATTCTCTGACTCGCGATTTAAAT-CTAGTCATTTTTATT-TTATTACTTACGATTTAATCTT
1 TTTATTCTCTGACTCGCGATTTAAATCCTAGTC-TCTTTATTCTCA-TACTCACGATTTAATCTC
* * * ** * *
12479222 GATT-TCTTTATTTTCTGACTTGTAGTTCAATCTTGATTTT
64 AATTATCTTTATTTTCTGACTAGCAGTTCAATCCCGATCTC
*
12479262 TTTAGTTTCTCTGACTCGCAATTTAA
1 TTTA--TTCTCTGACTCGCGATTTAA
12479288 TACCAATCAT
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
103 57 0.53
104 31 0.29
105 19 0.18
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.50
Consensus pattern (104 bp):
TTTATTCTCTGACTCGCGATTTAAATCCTAGTCTCTTTATTCTCATACTCACGATTTAATCTCAA
TTATCTTTATTTTCTGACTAGCAGTTCAATCCCGATCTC
Found at i:12479233 original size:138 final size:138
Alignment explanation
Indices: 12478971--12479219 Score: 313
Period size: 138 Copynumber: 1.8 Consensus size: 138
12478961 TGACTCATGG
* *
12478971 TTTAATCTCAGTCATCTTTATTTTATGACTTGCGGTCCAATCCCAGTCTCATTATTCTCTGACCC
1 TTTAATCTCAATCATCTTTATTTTATGACTAGCGGTCCAATCCCAGTCTCATTATTCTCTGACCC
* * *
12479036 ATAATTTAATCTCAGTCACTTTTATTTTCTGACTCGCGATTCAATCCTAGTCTCTTTATTCTCAT
66 ACAATTTAATCTCAGTCACTTTTATTTTATGACTCACGATTCAATCCTAGTCTCTTTATTCTCAT
12479101 ACTCACGA
131 ACTCACGA
* * * * * *
12479109 TTTAATCTCAATTATTTTTATTTTTTGACTAGCGGTTCAATCCC-GATCTCTTTATTCTCTGACT
1 TTTAATCTCAATCATCTTTATTTTATGACTAGCGGTCCAATCCCAG-TCTCATTATTCTCTGACC
* * * * * *
12479173 CGCGATTTAAATCT-AGTCATTTTTATTTTATTACTTACGATTTAATC
65 CACAATTT-AATCTCAGTCACTTTTATTTTATGACTCACGATTCAATC
12479220 TTGATTTCTT
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
137 1 0.01
138 86 0.93
139 5 0.05
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.45
Consensus pattern (138 bp):
TTTAATCTCAATCATCTTTATTTTATGACTAGCGGTCCAATCCCAGTCTCATTATTCTCTGACCC
ACAATTTAATCTCAGTCACTTTTATTTTATGACTCACGATTCAATCCTAGTCTCTTTATTCTCAT
ACTCACGA
Found at i:12479323 original size:70 final size:68
Alignment explanation
Indices: 12479249--12479443 Score: 169
Period size: 70 Copynumber: 2.8 Consensus size: 68
12479239 ACTTGTAGTT
* **
12479249 CAATCTTGATTTTTTTAGTTTCTCTGACTCGCAATTTAATACCAATCATCTTTATTTATGACTTG
1 CAATCTTGATTTTTTTA--TTCTCTGACTCGTAATTTAATACCAATCATCTTTATTTATGACTCA
12479314 CGATC
64 CGATC
* * * * * * * *
12479319 CAATCCT-AGTCTTGTTATTATCTGA-TCTGTGATTTAATTCCAATCATTTTTTATTTTTTGACT
1 CAATCTTGA-TTTTTTTATTCTCTGACTC-GTAATTTAATACCAATCA-TCTTTA-TTTATGACT
* *
12479382 CACGGTT
62 CACGATC
* * * *
12479389 TAATCTCGATTTTTTTATTCTCTGACTCGTAGTTTAATCCCAATCATCTTTATTT
1 CAATCTTGATTTTTTTATTCTCTGACTCGTAATTTAATACCAATCATCTTTATTT
12479444 TTTTACTCAT
Statistics
Matches: 96, Mismatches: 23, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
67 2 0.02
68 25 0.26
69 11 0.11
70 55 0.57
71 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.49
Consensus pattern (68 bp):
CAATCTTGATTTTTTTATTCTCTGACTCGTAATTTAATACCAATCATCTTTATTTATGACTCACG
ATC
Found at i:12479415 original size:34 final size:34
Alignment explanation
Indices: 12479364--12479513 Score: 140
Period size: 34 Copynumber: 4.4 Consensus size: 34
12479354 AATTCCAATC
*
12479364 ATTT-TTTATTTTTTGACTCACGGTTTAATCTCG
1 ATTTCTTTATTTTTTGACTCATGGTTTAATCTCG
* * * * * * *
12479397 ATTTTTTTATTCTCTGACTCGTAGTTTAATCCCA
1 ATTTCTTTATTTTTTGACTCATGGTTTAATCTCG
* *
12479431 ATCATCTTTATTTTTTTACTCATGGTTTAATCTCG
1 AT-TTCTTTATTTTTTGACTCATGGTTTAATCTCG
** * *
12479466 ATTTCTTTATTTTTTGACTTGTGGTTCAATCTCA
1 ATTTCTTTATTTTTTGACTCATGGTTTAATCTCG
*
12479500 ATCGTCTTTATTTT
1 AT-TTCTTTATTTT
12479514 CTAACTCGCG
Statistics
Matches: 91, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
33 4 0.04
34 52 0.57
35 35 0.38
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.55
Consensus pattern (34 bp):
ATTTCTTTATTTTTTGACTCATGGTTTAATCTCG
Found at i:12479468 original size:69 final size:69
Alignment explanation
Indices: 12479351--12479532 Score: 211
Period size: 69 Copynumber: 2.6 Consensus size: 69
12479341 TGATCTGTGA
* * *
12479351 TTTAATTCCAATCATTTTTTATTTTTTGACTCACGGTTTAATCTCGATTTTTTTATTCTCTGACT
1 TTTAATCCCAATCA-TCTTTATTTTTTGACTCACGGTTTAATCTCGATTTCTTTATTCTCTGACT
12479416 CGTAG
65 CGTAG
* * * * *
12479421 TTTAATCCCAATCATCTTTATTTTTTTACTCATGGTTTAATCTCGATTTCTTTATTTTTTGACTT
1 TTTAATCCCAATCATCTTTATTTTTTGACTCACGGTTTAATCTCGATTTCTTTATTCTCTGACTC
*
12479486 GTGG
66 GTAG
* * * * * * *
12479490 TTCAATCTCAATCGTCTTTATTTTCTAACTCGCGATTTAATCT
1 TTTAATCCCAATCATCTTTATTTTTTGACTCACGGTTTAATCT
12479533 TGATATCGTT
Statistics
Matches: 95, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
69 82 0.86
70 13 0.14
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.52
Consensus pattern (69 bp):
TTTAATCCCAATCATCTTTATTTTTTGACTCACGGTTTAATCTCGATTTCTTTATTCTCTGACTC
GTAG
Found at i:12479532 original size:35 final size:35
Alignment explanation
Indices: 12479351--12479532 Score: 118
Period size: 34 Copynumber: 5.2 Consensus size: 35
12479341 TGATCTGTGA
* * **
12479351 TTTAAT-TCCAATCATTTTTTATTTTTTGACTCACGG
1 TTTAATCT-CAATCA-TCTTTATTTTTTAACTCGTGG
* * * * * * *
12479387 TTTAATCTCGAT-TTTTTTATTCTCTGACTCGTAG
1 TTTAATCTCAATCATCTTTATTTTTTAACTCGTGG
* * *
12479421 TTTAATCCCAATCATCTTTATTTTTTTACTCATGG
1 TTTAATCTCAATCATCTTTATTTTTTAACTCGTGG
* * * *
12479456 TTTAATCTCGAT-TTCTTTATTTTTTGACTTGTGG
1 TTTAATCTCAATCATCTTTATTTTTTAACTCGTGG
* * * * *
12479490 TTCAATCTCAATCGTCTTTATTTTCTAACTCGCGA
1 TTTAATCTCAATCATCTTTATTTTTTAACTCGTGG
12479525 TTTAATCT
1 TTTAATCT
12479533 TGATATCGTT
Statistics
Matches: 112, Mismatches: 31, Indels: 7
0.75 0.21 0.05
Matches are distributed among these distances:
34 54 0.48
35 48 0.43
36 9 0.08
37 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.52
Consensus pattern (35 bp):
TTTAATCTCAATCATCTTTATTTTTTAACTCGTGG
Found at i:12479682 original size:14 final size:12
Alignment explanation
Indices: 12479663--12479712 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
12479653 TGACTCATGG
12479663 TAACAAAAAATATA
1 TAACAAAAAA-A-A
12479677 TAACAAAAAAAA
1 TAACAAAAAAAA
*
12479689 CAACAAAAAACAA
1 TAACAAAAAA-AA
*
12479702 AAACAAAAAAA
1 TAACAAAAAAA
12479713 TTTTTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 11 0.33
13 12 0.36
14 10 0.30
ACGTcount: A:0.80, C:0.12, G:0.00, T:0.08
Consensus pattern (12 bp):
TAACAAAAAAAA
Found at i:12479972 original size:14 final size:15
Alignment explanation
Indices: 12479953--12479982 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12479943 AGTATTGCTT
12479953 AAATAAT-AAAATAA
1 AAATAATAAAAATAA
12479967 AAATAATAAAAATAA
1 AAATAATAAAAATAA
12479982 A
1 A
12479983 TATATATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAATAAAAATAA
Found at i:12481133 original size:12 final size:11
Alignment explanation
Indices: 12481095--12481134 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
12481085 GTAAAAAAAA
*
12481095 ATTTTTTATTTT
1 ATTTTTTA-TAT
12481107 ATTTTTTATAT
1 ATTTTTTATAT
12481118 ATTTTTTATAT
1 ATTTTTTATAT
12481129 CATTTT
1 -ATTTT
12481135 AAACATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 13 0.50
12 13 0.50
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (11 bp):
ATTTTTTATAT
Found at i:12481215 original size:3 final size:3
Alignment explanation
Indices: 12481209--12481264 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
12481199 TTGTTGTTTC
* * *
12481209 ATA ATA ATA ATTA TTA ATA ATA ACA ATA ATA ATA ATA ATA ATA ACA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
12481255 ACA ATA ATA A
1 ATA ATA ATA A
12481265 AAATGATTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:12481525 original size:36 final size:37
Alignment explanation
Indices: 12481480--12481562 Score: 118
Period size: 36 Copynumber: 2.3 Consensus size: 37
12481470 AAAAACACAC
12481480 TAAATAAATTAGT-AATA-TTATTAATAACATATTTTCA
1 TAAA-AAATTAGTAAATAGTT-TTAATAACATATTTTCA
*
12481517 TAAAAAATT-TTAAATAGTTTTAATAACATATTTTCA
1 TAAAAAATTAGTAAATAGTTTTAATAACATATTTTCA
12481553 TAAAAAATTA
1 TAAAAAATTA
12481563 ATAACATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
35 1 0.02
36 35 0.83
37 6 0.14
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (37 bp):
TAAAAAATTAGTAAATAGTTTTAATAACATATTTTCA
Found at i:12481688 original size:14 final size:14
Alignment explanation
Indices: 12481666--12481726 Score: 68
Period size: 14 Copynumber: 4.2 Consensus size: 14
12481656 TTTTTATTAA
*
12481666 AAAAACTAAACCTT
1 AAAATCTAAACCTT
*
12481680 AAAATCTAAACCCT
1 AAAATCTAAACCTT
*
12481694 AAACTCTTCAAACCTT
1 AAAATC-T-AAACCTT
*
12481710 AAAATCAAAACCTT
1 AAAATCTAAACCTT
12481724 AAA
1 AAA
12481727 CCCTTTAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 27 0.69
15 1 0.03
16 11 0.28
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATCTAAACCTT
Found at i:12481709 original size:30 final size:30
Alignment explanation
Indices: 12481673--12481814 Score: 150
Period size: 30 Copynumber: 4.8 Consensus size: 30
12481663 TAAAAAAACT
*
12481673 AAACCTTAAAATCTAAACCCTAAACTCTTC
1 AAACCTTAAAATCAAAACCCTAAACTCTTC
* * *
12481703 AAACCTTAAAATCAAAACCTTAAACCCTTT
1 AAACCTTAAAATCAAAACCCTAAACTCTTC
* * *
12481733 AAACCCTAAAATCAAAGCCCCAAAC-C-TC
1 AAACCTTAAAATCAAAACCCTAAACTCTTC
12481761 AAA-CTCTAAAATCAAAACCCTAAAACT-TTC
1 AAACCT-TAAAATCAAAACCCT-AAACTCTTC
*
12481791 AAATCC-TAAAATCGAAACCCTAAA
1 AAA-CCTTAAAATCAAAACCCTAAA
12481815 ATCAAAACCC
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.01
28 17 0.18
29 8 0.09
30 66 0.71
32 1 0.01
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.21
Consensus pattern (30 bp):
AAACCTTAAAATCAAAACCCTAAACTCTTC
Found at i:12481778 original size:58 final size:59
Alignment explanation
Indices: 12481672--12481810 Score: 160
Period size: 58 Copynumber: 2.4 Consensus size: 59
12481662 TTAAAAAAAC
* * * *
12481672 TAAACCTTAAAATCTAAACCCTAAACTCTTCAAACCTTAAAATCAAAACCTTAAACCCTT
1 TAAACCCTAAAATCTAAACCCCAAACTCTTCAAACCTTAAAATCAAAACCCTAAA-ACTT
12481732 TAAACCCTAAAATC-AAAGCCCCAAAC-C-TCAAA-CTCTAAAATCAAAACCCTAAAACTT
1 TAAACCCTAAAATCTAAA-CCCCAAACTCTTCAAACCT-TAAAATCAAAACCCTAAAACTT
* *
12481789 TCAAATCCTAAAATCGAAACCC
1 T-AAACCCTAAAATCTAAACCC
12481811 TAAAATCAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
57 6 0.09
58 37 0.53
59 7 0.10
60 20 0.29
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (59 bp):
TAAACCCTAAAATCTAAACCCCAAACTCTTCAAACCTTAAAATCAAAACCCTAAAACTT
Found at i:12481783 original size:14 final size:14
Alignment explanation
Indices: 12481673--12481858 Score: 97
Period size: 14 Copynumber: 12.7 Consensus size: 14
12481663 TAAAAAAACT
* *
12481673 AAACCTTAAAATCT
1 AAACCCTAAAATCA
* *
12481687 AAACCCTAAACTCTTC
1 AAACCCTAAAATC--A
*
12481703 AAACCTTAAAATCA
1 AAACCCTAAAATCA
* * **
12481717 AAACCTTAAACCCTTT
1 AAACCCTAAA--ATCA
12481733 AAACCCTAAAATCA
1 AAACCCTAAAATCA
* * *
12481747 AAGCCCCAAACCTC-
1 AAACCCTAAA-ATCA
*
12481761 AAACTCTAAAATCA
1 AAACCCTAAAATCA
12481775 AAACCCTAAAACTTTC-
1 AAACCCTAAAA---TCA
* *
12481791 AAATCCTAAAATCG
1 AAACCCTAAAATCA
12481805 AAACCCTAAAATCA
1 AAACCCTAAAATCA
* *
12481819 AAACCCTAAACCCTCT
1 AAACCCTAAA--ATCA
* *
12481835 AAACTCTAAAACCA
1 AAACCCTAAAATCA
12481849 AAACCCTAAA
1 AAACCCTAAA
12481859 TCTCAAACAT
Statistics
Matches: 129, Mismatches: 31, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
13 4 0.03
14 79 0.61
15 2 0.02
16 42 0.33
17 2 0.02
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:12481828 original size:58 final size:56
Alignment explanation
Indices: 12481672--12481828 Score: 154
Period size: 58 Copynumber: 2.7 Consensus size: 56
12481662 TTAAAAAAAC
* * * *
12481672 TAAACCTTAAAATCTAAACCCTAAACTCTTCAAACCTTAAAATCAAAACCTTAAACCCTT
1 TAAACCCTAAAATC-AAACCCTAAA--C-TCAAACCCTAAAATCAAAACCCTAAACACTT
* *
12481732 TAAACCCTAAAATCAAAGCCCCAAACCTCAAACTCTAAAATCAAAACCCTAAA-ACTT
1 TAAACCCTAAAATCAAA-CCCTAAA-CTCAAACCCTAAAATCAAAACCCTAAACACTT
* *
12481789 TCAAATCCTAAAATCGAAACCCTAAAATCAAAACCCTAAA
1 T-AAACCCTAAAATC-AAACCCTAAACTC-AAACCCTAAA
12481829 CCCTCTAAAC
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
57 6 0.07
58 50 0.61
59 7 0.09
60 19 0.23
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.21
Consensus pattern (56 bp):
TAAACCCTAAAATCAAACCCTAAACTCAAACCCTAAAATCAAAACCCTAAACACTT
Found at i:12481844 original size:44 final size:44
Alignment explanation
Indices: 12481761--12481858 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
12481751 CCCAAACCTC
* * * *
12481761 AAACTCTAAAATCAAAACCCTAAAACTTTCAAATCCTAAAATCG
1 AAACCCTAAAATCAAAACCCTAAAACTCTCAAATCCTAAAACCA
*
12481805 AAACCCTAAAATCAAAACCCT-AAACCCTCTAAA-CTCTAAAACCA
1 AAACCCTAAAATCAAAACCCTAAAACTCTC-AAATC-CTAAAACCA
12481849 AAACCCTAAA
1 AAACCCTAAA
12481859 TCTCAAACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 7 0.15
44 40 0.85
ACGTcount: A:0.51, C:0.30, G:0.01, T:0.18
Consensus pattern (44 bp):
AAACCCTAAAATCAAAACCCTAAAACTCTCAAATCCTAAAACCA
Found at i:12481936 original size:8 final size:8
Alignment explanation
Indices: 12481923--12481992 Score: 53
Period size: 8 Copynumber: 9.2 Consensus size: 8
12481913 TTGATACCAT
12481923 AAATCCTA
1 AAATCCTA
12481931 AAATCC--
1 AAATCCTA
*
12481937 AAACCCTA
1 AAATCCTA
12481945 AAATCC-A
1 AAATCCTA
*
12481952 AAAACCTTA
1 AAATCC-TA
12481961 AAATCC-A
1 AAATCCTA
*
12481968 AAAT-CTC
1 AAATCCTA
12481975 AAA-CTCTA
1 AAATC-CTA
12481983 AAATCCTA
1 AAATCCTA
12481991 AA
1 AA
12481993 TCTTAAATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
6 6 0.12
7 14 0.29
8 21 0.44
9 7 0.15
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (8 bp):
AAATCCTA
Found at i:12481944 original size:14 final size:14
Alignment explanation
Indices: 12481927--12481969 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
12481917 TACCATAAAT
12481927 CCTAAAATCCAAAC
1 CCTAAAATCCAAAC
12481941 CCTAAAATCCAAAAAC
1 CCTAAAATCC--AAAC
*
12481957 CTTAAAATCCAAA
1 CCTAAAATCCAAA
12481970 ATCTCAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.16
Consensus pattern (14 bp):
CCTAAAATCCAAAC
Found at i:12481962 original size:16 final size:16
Alignment explanation
Indices: 12481927--12481970 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
12481917 TACCATAAAT
12481927 CCTAAAATCC--AAAC
1 CCTAAAATCCAAAAAC
12481941 CCTAAAATCCAAAAAC
1 CCTAAAATCCAAAAAC
*
12481957 CTTAAAATCCAAAA
1 CCTAAAATCCAAAA
12481971 TCTCAAACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 10 0.37
16 17 0.63
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.16
Consensus pattern (16 bp):
CCTAAAATCCAAAAAC
Found at i:12491526 original size:11 final size:10
Alignment explanation
Indices: 12491499--12491534 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
12491489 TTATTTTTTC
12491499 TTAAAATATA
1 TTAAAATATA
12491509 -TAAAATATA
1 TTAAAATATA
12491518 TTAATAATATA
1 TTAA-AATATA
12491529 TTAAAA
1 TTAAAA
12491535 AAAATTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.38
10 5 0.21
11 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TTAAAATATA
Found at i:12496531 original size:6 final size:6
Alignment explanation
Indices: 12496516--12496548 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
12496506 AGCTGCTGAC
12496516 TTTT-T TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
12496549 TTTCAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:12500418 original size:10 final size:10
Alignment explanation
Indices: 12500392--12500425 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12500382 TTGTTTTTTT
* *
12500392 AATTTTAATT
1 AATTTTGATG
12500402 AATTTTGATG
1 AATTTTGATG
12500412 AATTTTGATG
1 AATTTTGATG
12500422 AATT
1 AATT
12500426 ATCATATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (10 bp):
AATTTTGATG
Found at i:12500627 original size:35 final size:34
Alignment explanation
Indices: 12500581--12500648 Score: 118
Period size: 35 Copynumber: 2.0 Consensus size: 34
12500571 TTATTTTCTC
12500581 TTATATTTTATTTTTTCGAACCAAAATTTATAAT
1 TTATATTTTATTTTTTCGAACCAAAATTTATAAT
*
12500615 TTATACTTTTATTTTTTTGAACCAAAATTTATAA
1 TTATA-TTTTATTTTTTCGAACCAAAATTTATAA
12500649 ATATTTCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 5 0.16
35 27 0.84
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (34 bp):
TTATATTTTATTTTTTCGAACCAAAATTTATAAT
Found at i:12504816 original size:29 final size:29
Alignment explanation
Indices: 12504784--12504853 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
12504774 TTAGAATTAC
*
12504784 AATGATAAATTTACT-CTAATTAAAAATAT-
1 AATGATAAATTTA-TACGAATT-AAAATATG
*
12504813 AATGATAAAATTATACGAATTAAAATATG
1 AATGATAAATTTATACGAATTAAAATATG
12504842 AATGATAAATTT
1 AATGATAAATTT
12504854 GGACCTTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 8 0.22
29 28 0.78
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (29 bp):
AATGATAAATTTATACGAATTAAAATATG
Found at i:12507847 original size:2 final size:2
Alignment explanation
Indices: 12507840--12507865 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12507830 CAGACGGGTA
12507840 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12507866 GTGCTAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12510829 original size:25 final size:28
Alignment explanation
Indices: 12510791--12510845 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
12510781 AGATACTATA
*
12510791 ATTATAAATATAATATAAA-TAAAAAAT
1 ATTATAAATATAATAAAAATTAAAAAAT
*
12510818 ATTA-AAAT-TAATAAAAATTTAAAAAT
1 ATTATAAATATAATAAAAATTAAAAAAT
12510844 AT
1 AT
12510846 ACTTTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.32
26 13 0.52
27 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
ATTATAAATATAATAAAAATTAAAAAAT
Found at i:12519310 original size:2 final size:2
Alignment explanation
Indices: 12519299--12519328 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12519289 ATTGTTCATT
12519299 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12519329 TATTGATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12521076 original size:49 final size:47
Alignment explanation
Indices: 12520989--12521080 Score: 141
Period size: 47 Copynumber: 1.9 Consensus size: 47
12520979 TTATTTTATT
*
12520989 TATTTAAATATATATATAAATATAATTAAAATATTTAATCACTTAAA
1 TATTTAAAAATATATATAAATATAATTAAAATATTTAATCACTTAAA
12521036 TATTTAAAAATATATATAAATATAAAAATTAAAATA-TTAATCACT
1 TATTTAAAAATATATATAAATAT---AATTAAAATATTTAATCACT
12521081 CAATTAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
47 22 0.54
49 9 0.22
50 10 0.24
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (47 bp):
TATTTAAAAATATATATAAATATAATTAAAATATTTAATCACTTAAA
Found at i:12522409 original size:102 final size:103
Alignment explanation
Indices: 12522243--12522481 Score: 268
Period size: 102 Copynumber: 2.3 Consensus size: 103
12522233 AATTTATAAT
* * * *
12522243 AACGATATTTAATCGTTACAAAGTATGTTATATATCAAAAATAATATTGGTACTTAAGACTTTTT
1 AACGATATTTAATCGTAACAAAATATGTTATGTAACAAAAATAATATTGGTACTTAAGACTTTTT
12522308 GTAACCAACT-TAT-ATGATTGCTAAAAATAATTTAACA
66 GTAACCAA-TATATAATGATTGCTAAAAATAATTTAACA
* * * *
12522345 AACGACATTTAATCGTAACAAAATATGTTATGTAACTACAATAATA-TGGTTACTTAAGAGTTTT
1 AACGATATTTAATCGTAACAAAATATGTTATGTAACAAAAATAATATTGG-TACTTAAGACTTTT
* * * * * * *
12522409 TGTGATCAATATTTAATGATTGTTGACAATATTTTAACA
65 TGTAACCAATATATAATGATTGCTAAAAATAATTTAACA
* * * *
12522448 AATGATATTTAATTGTAACGAAACATGTTATGTA
1 AACGATATTTAATCGTAACAAAATATGTTATGTA
12522482 TGGCAAGAAC
Statistics
Matches: 114, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
101 4 0.04
102 61 0.54
103 49 0.43
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (103 bp):
AACGATATTTAATCGTAACAAAATATGTTATGTAACAAAAATAATATTGGTACTTAAGACTTTTT
GTAACCAATATATAATGATTGCTAAAAATAATTTAACA
Found at i:12522513 original size:103 final size:103
Alignment explanation
Indices: 12522290--12522525 Score: 241
Period size: 103 Copynumber: 2.3 Consensus size: 103
12522280 AAAATAATAT
* * * * * *
12522290 TGGT-ACTTAAGACTTTTTGTAACC-A-ACTTATATGATTGCTAAAAATAATTTAACAAACGACA
1 TGGTCACTTAAGAGTTTTTGTGACCAATATTTA-ATGATTGTTGACAATAATTTAACAAACGACA
* * *
12522352 TTTAATCGTAACAAAATATGTTATGTAACTACAATAATA
65 TTTAATCGTAACAAAACATGTTATGTAACTACAAGAACA
* * * * *
12522391 TGGTTACTTAAGAGTTTTTGTGATCAATATTTAATGATTGTTGACAATATTTTAACAAATGATAT
1 TGGTCACTTAAGAGTTTTTGTGACCAATATTTAATGATTGTTGACAATAATTTAACAAACGACAT
* * *
12522456 TTAATTGTAACGAAACATGTTATGT-A-TGGCAAGAACA
66 TTAATCGTAACAAAACATGTTATGTAACT-ACAAGAACA
12522493 TGGTCACTTTTAAGAG-TTTTGTGACCAATATTT
1 TGGTCAC--TTAAGAGTTTTTGTGACCAATATTT
12522526 TATGGTTGCA
Statistics
Matches: 111, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
101 5 0.05
102 30 0.27
103 65 0.59
104 11 0.10
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (103 bp):
TGGTCACTTAAGAGTTTTTGTGACCAATATTTAATGATTGTTGACAATAATTTAACAAACGACAT
TTAATCGTAACAAAACATGTTATGTAACTACAAGAACA
Found at i:12523170 original size:2 final size:2
Alignment explanation
Indices: 12523163--12523187 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12523153 ATATTTGGTT
12523163 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12523188 TAGTTCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12528185 original size:32 final size:33
Alignment explanation
Indices: 12528120--12528191 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
12528110 GAAGGGCGGG
* *
12528120 ATGTCATGTCCCACCGGGCCCAGAAGTACATAT
1 ATGTCATGTCCCACCGGCCCCACAAGTACATAT
* **
12528153 ATGTCATGTCTCAGTGGCCCCACAAGTA-ATAT
1 ATGTCATGTCCCACCGGCCCCACAAGTACATAT
*
12528185 ATATCAT
1 ATGTCAT
12528192 TTCATTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (33 bp):
ATGTCATGTCCCACCGGCCCCACAAGTACATAT
Found at i:12534771 original size:2 final size:2
Alignment explanation
Indices: 12534764--12534792 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12534754 CAATATTAAA
12534764 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12534793 AACAAGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12541741 original size:8 final size:7
Alignment explanation
Indices: 12541692--12541757 Score: 51
Period size: 7 Copynumber: 8.7 Consensus size: 7
12541682 AAATTATATA
12541692 TTTTTAT
1 TTTTTAT
*
12541699 CTTTTAT
1 TTTTTAT
12541706 TTATTTAT
1 TT-TTTAT
12541714 TTATTTAGAT
1 TT-TTT--AT
12541724 TTATTTAT
1 TT-TTTAT
*
12541732 TTTTTAA
1 TTTTTAT
*
12541739 TTTCTAT
1 TTTTTAT
*
12541746 TTTTAAT
1 TTTTTAT
12541753 TTTTT
1 TTTTT
12541758 TGAAATATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
7 25 0.52
8 15 0.31
10 8 0.17
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (7 bp):
TTTTTAT
Found at i:12541747 original size:18 final size:18
Alignment explanation
Indices: 12541704--12541741 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12541694 TTTATCTTTT
12541704 ATTTATTTATTTATTTAG
1 ATTTATTTATTTATTTAG
12541722 ATTTATTTATTT-TTTA-
1 ATTTATTTATTTATTTAG
12541738 ATTT
1 ATTT
12541742 CTATTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 4 0.20
18 12 0.60
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
ATTTATTTATTTATTTAG
Found at i:12543619 original size:34 final size:33
Alignment explanation
Indices: 12543544--12543619 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 33
12543534 ATATAATATT
12543544 TATAATAATTTTTATATTAAATAGAATAATTAA
1 TATAATAATTTTTATATTAAATAGAATAATTAA
* * * *
12543577 TTTGATAATTTTTAATATTGAAT-GATATTATTAA
1 TATAATAATTTTT-ATATTAAATAGA-ATAATTAA
12543611 TATAATAAT
1 TATAATAAT
12543620 CTTAGAGGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
33 13 0.37
34 22 0.63
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (33 bp):
TATAATAATTTTTATATTAAATAGAATAATTAA
Found at i:12544772 original size:2 final size:2
Alignment explanation
Indices: 12544765--12544792 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12544755 AGTAGGACAA
12544765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12544793 GAGATGTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12545662 original size:31 final size:31
Alignment explanation
Indices: 12545625--12545716 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
12545615 ATTTTTAAAG
12545625 TATTATATTAATTAATATATTTATAATTTAA
1 TATTATATTAATTAATATATTTATAATTTAA
* * * *
12545656 TATTATA-TAATTAAAATTTTTAAAATTAAAA
1 TATTATATTAATTAATATATTTATAATT-TAA
* * *
12545687 TATTATATTAAATATTTTA-TTATAATTTAA
1 TATTATATTAATTAATATATTTATAATTTAA
12545717 AAATCATTCA
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
30 19 0.40
31 23 0.48
32 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TATTATATTAATTAATATATTTATAATTTAA
Found at i:12545664 original size:15 final size:15
Alignment explanation
Indices: 12545625--12545667 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
12545615 ATTTTTAAAG
12545625 TATTATATTAA-TTAA
1 TATTATA-TAATTTAA
*
12545640 TATATTTATAATTTAA
1 TAT-TATATAATTTAA
12545656 TATTATATAATT
1 TATTATATAATT
12545668 AAAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATATAATTTAA
Found at i:12547395 original size:19 final size:19
Alignment explanation
Indices: 12547352--12547395 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12547342 TATTTTTATG
*
12547352 ATTTTTTAGATTTTTTTAA
1 ATTTTTTAGATTTTGTTAA
* *
12547371 AATTTTTAGATTTTGTTGA
1 ATTTTTTAGATTTTGTTAA
12547390 ATTTTT
1 ATTTTT
12547396 CAATGAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (19 bp):
ATTTTTTAGATTTTGTTAA
Found at i:12552316 original size:1 final size:1
Alignment explanation
Indices: 12552312--12552355 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
12552302 AAAAATGAAT
* * * *
12552312 AAAAAAGAAAAAAAAAAAAAGAAACAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12552356 GAAGAATTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.02, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:12552325 original size:10 final size:10
Alignment explanation
Indices: 12552302--12552355 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
12552292 ATTTTTCTTG
* *
12552302 AAAAATGAAT
1 AAAAAAGAAA
12552312 AAAAAAGAAA
1 AAAAAAGAAA
12552322 AAAAAA-AAA
1 AAAAAAGAAA
*
12552331 AGAAACA-AAA
1 A-AAAAAGAAA
12552341 AAAAAAGAAA
1 AAAAAAGAAA
12552351 AAAAA
1 AAAAA
12552356 GAAGAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 8 0.21
10 30 0.79
ACGTcount: A:0.87, C:0.02, G:0.07, T:0.04
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:12552331 original size:14 final size:14
Alignment explanation
Indices: 12552312--12552355 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
12552302 AAAAATGAAT
12552312 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
12552326 AAAAAAGAAACAAAA
1 AAAAAAGAAA-AAAA
12552341 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
12552355 A
1 A
12552356 GAAGAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 15 0.52
15 14 0.48
ACGTcount: A:0.91, C:0.02, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAA
Found at i:12552340 original size:24 final size:24
Alignment explanation
Indices: 12552312--12552358 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
12552302 AAAAATGAAT
*
12552312 AAAAAAGAAAAAAAAAAAAAGAAAC
1 AAAAAA-AAAAGAAAAAAAAGAAAC
12552337 AAAAAAAAAAGAAAAAAAAGAA
1 AAAAAAAAAAGAAAAAAAAGAA
12552359 GAATTTATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.89, C:0.02, G:0.09, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAGAAAAAAAAGAAAC
Found at i:12552360 original size:12 final size:12
Alignment explanation
Indices: 12552302--12552361 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
12552292 ATTTTTCTTG
* *
12552302 AAAAATGAATAA
1 AAAAAAGAAGAA
*
12552314 AAAAGAA-AAAAA
1 AAAA-AAGAAGAA
12552326 AAAAAAGAA-ACA
1 AAAAAAGAAGA-A
*
12552338 AAAAAAAAAGAA
1 AAAAAAGAAGAA
12552350 AAAAAAGAAGAA
1 AAAAAAGAAGAA
12552362 TTTATGGGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 3 0.08
12 35 0.88
13 2 0.05
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAGAA
Found at i:12553501 original size:20 final size:20
Alignment explanation
Indices: 12553476--12553543 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
12553466 ATAGGTTGTA
12553476 GCATTTGCATCATTTACAAG
1 GCATTTGCATCATTTACAAG
12553496 GCATTTGCATCATTTACAAG
1 GCATTTGCATCATTTACAAG
* * *
12553516 GCATTTGCATTATTAACATG
1 GCATTTGCATCATTTACAAG
12553536 GCATTTGC
1 GCATTTGC
12553544 CTTTGTTGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (20 bp):
GCATTTGCATCATTTACAAG
Found at i:12553874 original size:22 final size:22
Alignment explanation
Indices: 12553809--12553874 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
12553799 TTTGAATCAA
* * **
12553809 AATCTTTAAAATTTTGGATAAG
1 AATCTTTTAATTTTTGGATGTG
* *
12553831 AAT-TTTTAAAATTTTCGAATGTG
1 AATCTTTT--AATTTTTGGATGTG
12553854 AATCTTTTAATTTTTGGATGT
1 AATCTTTTAATTTTTGGATGT
12553875 AAAACCTTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 3 0.09
22 14 0.42
23 12 0.36
24 4 0.12
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (22 bp):
AATCTTTTAATTTTTGGATGTG
Found at i:12554122 original size:17 final size:17
Alignment explanation
Indices: 12554083--12554217 Score: 94
Period size: 17 Copynumber: 8.0 Consensus size: 17
12554073 GTGAATCTAA
*
12554083 AAATTCTTGCAAACATT
1 AAATTCTTGCAAACCTT
* *
12554100 AGATTCTTGCAAACTTT
1 AAATTCTTGCAAACCTT
* **
12554117 AAATTCATGTGAACCTT
1 AAATTCTTGCAAACCTT
* * *
12554134 AAATTTTTGTAGACCTT
1 AAATTCTTGCAAACCTT
* *
12554151 AAGTTCTTACAAA-CTT
1 AAATTCTTGCAAACCTT
* *
12554167 GAAATTCTTGAAAACCTG
1 -AAATTCTTGCAAACCTT
* ** *
12554185 AAGTTCTTGTGAACCTA
1 AAATTCTTGCAAACCTT
12554202 AAATTCTTG-AAACCTT
1 AAATTCTTGCAAACCTT
12554218 GAAGCTCTTG
Statistics
Matches: 89, Mismatches: 27, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
16 8 0.09
17 79 0.89
18 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (17 bp):
AAATTCTTGCAAACCTT
Found at i:12554206 original size:34 final size:34
Alignment explanation
Indices: 12554168--12554244 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
12554158 TACAAACTTG
*
12554168 AAATTCTTGAAAACC-TGAAGTTCTTGTGAACCTA
1 AAATTCTTG-AAACCTTGAAGCTCTTGTGAACCTA
12554202 AAATTCTTGAAACCTTGAAGCTCTTGTGAACCTA
1 AAATTCTTGAAACCTTGAAGCTCTTGTGAACCTA
*
12554236 AAGTTCTTG
1 AAATTCTTG
12554245 CGAAACTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 5 0.12
34 35 0.88
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (34 bp):
AAATTCTTGAAACCTTGAAGCTCTTGTGAACCTA
Found at i:12554243 original size:17 final size:17
Alignment explanation
Indices: 12554179--12554244 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
12554169 AATTCTTGAA
*
12554179 AACCTGAAGTTCTTGTG
1 AACCTAAAGTTCTTGTG
* *
12554196 AACCTAAAATTCTTG-A
1 AACCTAAAGTTCTTGTG
* *
12554212 AACCTTGAAGCTCTTGTG
1 AACC-TAAAGTTCTTGTG
12554230 AACCTAAAGTTCTTG
1 AACCTAAAGTTCTTG
12554245 CGAAACTTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
16 4 0.11
17 30 0.79
18 4 0.11
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (17 bp):
AACCTAAAGTTCTTGTG
Found at i:12554380 original size:17 final size:17
Alignment explanation
Indices: 12554358--12554405 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
12554348 AAATCTTTGG
12554358 ATTCTTATGAAACTAAA
1 ATTCTTATGAAACTAAA
* * *
12554375 ATTCTTGTGAATCTGAA
1 ATTCTTATGAAACTAAA
12554392 A-TCTCTATGAAACT
1 ATTCT-TATGAAACT
12554406 TTAAACCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (17 bp):
ATTCTTATGAAACTAAA
Found at i:12554604 original size:18 final size:18
Alignment explanation
Indices: 12554581--12554618 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12554571 TTATAAACTT
*
12554581 TTGAAA-TCTTCGTAAAAC
1 TTGAAATTCTT-GCAAAAC
12554599 TTGAAATTCTTGCAAAAC
1 TTGAAATTCTTGCAAAAC
12554617 TT
1 TT
12554619 TACAAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (18 bp):
TTGAAATTCTTGCAAAAC
Found at i:12554937 original size:85 final size:85
Alignment explanation
Indices: 12554822--12555118 Score: 273
Period size: 85 Copynumber: 3.5 Consensus size: 85
12554812 CATTTCCCAT
* *
12554822 TTCTTATTTTAAAGTTGTTTAGTCTCTATTTAGAAGAGCACATTCTTATTCTAAAGTTGTTTAGT
1 TTCTTATTTTAAAGTTGTTTAGCCTCTATTTAGAAGAGCACATTCTTATTCTAAAGTTGTTTAGC
12554887 CTCTGTTTAAAGAAGCCAAC
66 CTCTGTTTAAAGAAGCCAAC
* * * *
12554907 TTCTTATTTTAAAATTATTTAGCCTCTATTTA-AAGGAGGCA-ATTTCTTATTTTAAATTTGTTT
1 TTCTTATTTTAAAGTTGTTTAGCCTCTATTTAGAA-GA-GCACA-TTCTTATTCTAAAGTTGTTT
* * * * *
12554970 AGCCTCTGTTTAGAGAGGTCTAT
63 AGCCTCTGTTTAAAGAAGCCAAC
* * * * * *
12554993 TTCTTATTCT-AAGTTGTTTAACCTCTGTTTAGAGGAGCCCTATTCTTATTCTGAAGTTGTTTAG
1 TTCTTATTTTAAAGTTGTTTAGCCTCTATTTAGAAGAGCAC-ATTCTTATTCTAAAGTTGTTTAG
* * *
12555057 CCTC---TTAATGGATGAGCCCAT
65 CCTCTGTTTAA-AGA--AGCCAAC
* *
12555078 TTCTTATTTTTTAAAGTTGTTTAGCCTCTATATAGAGGAGC
1 TTCTTA--TTTTAAAGTTGTTTAGCCTCTATTTAGAAGAGC
12555119 TTATTTCTTA
Statistics
Matches: 170, Mismatches: 30, Indels: 21
0.77 0.14 0.10
Matches are distributed among these distances:
82 3 0.02
83 2 0.01
84 4 0.02
85 84 0.49
86 49 0.29
87 3 0.02
88 25 0.15
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.45
Consensus pattern (85 bp):
TTCTTATTTTAAAGTTGTTTAGCCTCTATTTAGAAGAGCACATTCTTATTCTAAAGTTGTTTAGC
CTCTGTTTAAAGAAGCCAAC
Found at i:12555056 original size:128 final size:128
Alignment explanation
Indices: 12554820--12555118 Score: 322
Period size: 128 Copynumber: 2.3 Consensus size: 128
12554810 GACATTTCCC
*
12554820 ATTTCTTATTTTAAAGTTGTTTAGTCTCTATTTAGAAGAGCACATTCTTATTCTAAAGTTGTTTA
1 ATTTCTTATTTTAAAGTTGTTTAGCCTCTATTTAGAAGAGCACATTCTTATTCTAAAGTTGTTTA
** *
12554885 GTCTCTGTTTAAAGAAGCCAACTTCTTATTTTAAAATTATTTAGCCTCTATTTAAAGGAGGCA
66 ACCTCTGTTTAAAGAAGCCAACTTCTTATTCTAAAATTATTTAGCCTCTATTTAAAGGAGGCA
* * **
12554948 ATTTCTTATTTTAAATTTGTTTAGCCTCTGTTTAG-AGAGGTCTATTTCTTATTCT-AAGTTGTT
1 ATTTCTTATTTTAAAGTTGTTTAGCCTCTATTTAGAAGAGCAC-A-TTCTTATTCTAAAGTTGTT
* * * * * * *
12555011 TAACCTCTGTTTAGAGGAGCCCTA-TTCTTATTCTGAAGTTGTTTAGCCTC---TTAATGGATGA
64 TAACCTCTGTTTAAAGAAG-CCAACTTCTTATTCTAAAATTATTTAGCCTCTATTTAAAGGA-G-
*
12555072 GCCC
126 G-CA
* *
12555076 ATTTCTTATTTTTTAAAGTTGTTTAGCCTCTATATAGAGGAGC
1 ATTTCTTA--TTTTAAAGTTGTTTAGCCTCTATTTAGAAGAGC
12555119 TTATTTCTTA
Statistics
Matches: 141, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
125 7 0.05
126 1 0.01
127 6 0.04
128 87 0.62
129 13 0.09
130 24 0.17
131 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.45
Consensus pattern (128 bp):
ATTTCTTATTTTAAAGTTGTTTAGCCTCTATTTAGAAGAGCACATTCTTATTCTAAAGTTGTTTA
ACCTCTGTTTAAAGAAGCCAACTTCTTATTCTAAAATTATTTAGCCTCTATTTAAAGGAGGCA
Found at i:12555173 original size:43 final size:43
Alignment explanation
Indices: 12554820--12555173 Score: 197
Period size: 43 Copynumber: 8.2 Consensus size: 43
12554810 GACATTTCCC
* * * * **
12554820 ATTTCTTATTTTAAAGTTGTTTAGTCTCTATTTAGAAGAGCAC
1 ATTTCTTAATTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTT
* * * * * **
12554863 A-TTCTT-ATTCTAAAGTTGTTTAGTCTCTGTTTAAAGAAGCCA
1 ATTTCTTAATT-TAAAGTTGTTTAGCCTCTATATAGAGGAGCTT
* * * * * * *
12554905 ACTTCTTATTTTAAAATTATTTAGCCTCTATTTAAAGGAGGC-A
1 ATTTCTTAATTTAAAGTTGTTTAGCCTCTATATAGAGGA-GCTT
* * * * *
12554948 ATTTCTTATTTTAAATTTGTTTAGCCTCTGTTTAGA-GAGGTCT
1 ATTTCTTAATTTAAAGTTGTTTAGCCTCTATATAGAGGAGCT-T
* * * *
12554991 ATTTCTT-ATTCT-AAGTTGTTTAACCTCTGTTTAGAGGAGCCCT
1 ATTTCTTAATT-TAAAGTTGTTTAGCCTCTATATAGAGGAG-CTT
* * * **
12555034 A-TTCTT-ATTCTGAAGTTGTTTAGCCTCT-TAATGGATGAGCCC
1 ATTTCTTAATT-TAAAGTTGTTTAGCCTCTAT-ATAGAGGAGCTT
*
12555076 ATTTCTTATTTTTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTT
1 ATTTCTTA--ATTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTT
* * *
12555121 ATTTCTTAATTTAAATTTGTTT-GCCTTTATATAGAGGAGTTT
1 ATTTCTTAATTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTT
*
12555163 AGTTTGTTAAT
1 A-TTTCTTAAT
12555174 CCTCTGTTTA
Statistics
Matches: 253, Mismatches: 41, Indels: 34
0.77 0.12 0.10
Matches are distributed among these distances:
41 3 0.01
42 90 0.36
43 120 0.47
44 4 0.02
45 33 0.13
46 3 0.01
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (43 bp):
ATTTCTTAATTTAAAGTTGTTTAGCCTCTATATAGAGGAGCTT
Found at i:12561586 original size:23 final size:23
Alignment explanation
Indices: 12561552--12561604 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
12561542 GAGATTTAAG
*
12561552 TTTTTTATTGTTATTGTTATTT-T
1 TTTTTTA-TGTTATTATTATTTAT
*
12561575 TTTTGTTATGTTGTTATTATTTAT
1 TTTT-TTATGTTATTATTATTTAT
12561599 TTTTTT
1 TTTTTT
12561605 TATTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.77
Consensus pattern (23 bp):
TTTTTTATGTTATTATTATTTAT
Found at i:12561588 original size:20 final size:19
Alignment explanation
Indices: 12561552--12561599 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
12561542 GAGATTTAAG
12561552 TTTTTTATTGTTATTGTTA
1 TTTTTTATTGTTATTGTTA
12561571 TTTTTT-TTGTTATGTTGTTA
1 TTTTTTATTGTTA--TTGTTA
*
12561591 TTATTTATT
1 TTTTTTATT
12561600 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 6 0.24
20 11 0.44
21 2 0.08
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.75
Consensus pattern (19 bp):
TTTTTTATTGTTATTGTTA
Found at i:12561960 original size:3 final size:3
Alignment explanation
Indices: 12561952--12561992 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
12561942 TTTAATTCCT
* *
12561952 TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12561993 TTAAAAGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12562950 original size:3 final size:3
Alignment explanation
Indices: 12562944--12563000 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
12562934 TTGTTGTGAA
12562944 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12562992 ATT ATT ATT
1 ATT ATT ATT
12563001 TTAGCATTCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12563453 original size:3 final size:3
Alignment explanation
Indices: 12563378--12563436 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
12563368 ACAGTTAGCT
12563378 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12563426 TTA TTA TTA TT
1 TTA TTA TTA TT
12563437 TGTTCTTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12564085 original size:3 final size:3
Alignment explanation
Indices: 12564079--12564113 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
12564069 TATGATATTA
*
12564079 TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
12564114 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.29, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:12564090 original size:9 final size:9
Alignment explanation
Indices: 12564076--12564116 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
12564066 TTTTATGATA
12564076 TTATTGTTG
1 TTATTGTTG
12564085 TTATTGTTG
1 TTATTGTTG
*
12564094 TTGTTGTTG
1 TTATTGTTG
*
12564103 TTGTTGTTG
1 TTATTGTTG
12564112 TTATT
1 TTATT
12564117 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.07, C:0.00, G:0.24, T:0.68
Consensus pattern (9 bp):
TTATTGTTG
Found at i:12564118 original size:3 final size:3
Alignment explanation
Indices: 12564112--12564155 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
12564102 GTTGTTGTTG
12564112 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12564156 CATCCTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12571148 original size:19 final size:19
Alignment explanation
Indices: 12571124--12571177 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
12571114 TGATAGTTTT
12571124 AATGCATGAATATTTGGTC
1 AATGCATGAATATTTGGTC
12571143 AATGCATGAATATTTGGTC
1 AATGCATGAATATTTGGTC
* *
12571162 AATGTATGAATCTTTG
1 AATGCATGAATATTTG
12571178 AACATAGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (19 bp):
AATGCATGAATATTTGGTC
Found at i:12573530 original size:19 final size:19
Alignment explanation
Indices: 12573503--12573540 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12573493 TCAAGTAAGG
*
12573503 CAAAGAATCGATCCCCTAT
1 CAAACAATCGATCCCCTAT
12573522 CAAACAATCGATCCCCTAT
1 CAAACAATCGATCCCCTAT
12573541 GCCCAGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.34, G:0.08, T:0.21
Consensus pattern (19 bp):
CAAACAATCGATCCCCTAT
Found at i:12574104 original size:23 final size:24
Alignment explanation
Indices: 12574074--12574127 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
12574064 TCCGTATCTT
12574074 TTTATTTTAATT-AT-AATTTATA
1 TTTATTTTAATTCATCAATTTATA
12574096 TTTACTTTTAATTCATCAATTTAT-
1 TTTA-TTTTAATTCATCAATTTATA
12574120 TATTATTT
1 T-TTATTT
12574128 GTTTCATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.14
23 8 0.29
24 6 0.21
25 10 0.36
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTATTTTAATTCATCAATTTATA
Found at i:12574841 original size:15 final size:15
Alignment explanation
Indices: 12574821--12574852 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12574811 AACTAAACAT
12574821 TTAATACTTAATTTG
1 TTAATACTTAATTTG
*
12574836 TTAATATTTAATTTG
1 TTAATACTTAATTTG
12574851 TT
1 TT
12574853 CAATTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (15 bp):
TTAATACTTAATTTG
Found at i:12577549 original size:16 final size:17
Alignment explanation
Indices: 12577522--12577566 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 17
12577512 AAAAATTCAA
12577522 ATATATATTTTTATAATT
1 ATATATA-TTTTATAATT
12577540 ATA-ATA-TTT-TAATT
1 ATATATATTTTATAATT
12577554 ATATATATTTTAT
1 ATATATATTTTAT
12577567 TCGAATTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
16 3 0.12
17 4 0.17
18 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATATATTTTATAATT
Found at i:12577552 original size:14 final size:15
Alignment explanation
Indices: 12577523--12577565 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
12577513 AAAATTCAAA
*
12577523 TATATATTTTTATAAT
1 TATATATATTT-TAAT
12577539 TATA-ATATTTTAAT
1 TATATATATTTTAAT
12577553 TATATATATTTTA
1 TATATATATTTTA
12577566 TTCGAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 13 0.52
16 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATATATTTTAAT
Found at i:12578443 original size:3 final size:3
Alignment explanation
Indices: 12578437--12578471 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12578427 AGTTCTTTTT
12578437 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12578472 TATAGAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12580401 original size:25 final size:25
Alignment explanation
Indices: 12580350--12580412 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
12580340 AAATAATAAT
* * *
12580350 AAAATTTATTATAATAATGGTTGAA
1 AAAAATTATTATAATAATGATTAAA
* *
12580375 AAAAATTATTATAATTATTATTAAA
1 AAAAATTATTATAATAATGATTAAA
*
12580400 AAATATT-TTATAA
1 AAAAATTATTATAA
12580413 AAAAATTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 6 0.19
25 26 0.81
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (25 bp):
AAAAATTATTATAATAATGATTAAA
Found at i:12581679 original size:13 final size:13
Alignment explanation
Indices: 12581661--12581690 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12581651 TAAAAAAAGA
12581661 TTTAGGGTTCAAG
1 TTTAGGGTTCAAG
*
12581674 TTTAGGGTTTAAG
1 TTTAGGGTTCAAG
12581687 TTTA
1 TTTA
12581691 ATTAAAACGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (13 bp):
TTTAGGGTTCAAG
Found at i:12583689 original size:34 final size:34
Alignment explanation
Indices: 12583548--12583694 Score: 95
Period size: 34 Copynumber: 4.3 Consensus size: 34
12583538 TAAAGAAATT
* *
12583548 GGGATTGAACCGTGAATCAGAAAATAAAAAGATC
1 GGGATTAAACCGTGAATCAGAGAATAAAAAGATC
* * * *
12583582 GGGATTAAACTGTGAGTCAAAGGATAATAACA-ATC
1 GGGATTAAACCGTGAATCAGAGAATAA-AA-AGATC
** * ** * *
12583617 AAGATTAAA-C-TACAACTTTGA-ATTAAAGAGATC
1 GGGATTAAACCGT-GAA-TCAGAGAATAAAAAGATC
* *
12583650 AGGATTGAACCGTGAATCAGAGAATAAAAAGATC
1 GGGATTAAACCGTGAATCAGAGAATAAAAAGATC
12583684 GGGATTAAACC
1 GGGATTAAACC
12583695 TCAAGTCAGA
Statistics
Matches: 79, Mismatches: 26, Indels: 16
0.65 0.21 0.13
Matches are distributed among these distances:
32 1 0.01
33 15 0.19
34 47 0.59
35 15 0.19
36 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (34 bp):
GGGATTAAACCGTGAATCAGAGAATAAAAAGATC
Found at i:12583829 original size:202 final size:202
Alignment explanation
Indices: 12583503--12584171 Score: 850
Period size: 202 Copynumber: 3.3 Consensus size: 202
12583493 GAGTCAAAAA
*** * * *
12583503 ATAACAACAATCGAGATTAAACTACGA-TTATAAATTAAAGAAATTGGGATTGAAC-CGTGAATC
1 ATAACAACAATCGAGATTAAACTGTAACTT-TGAATTAAAGAGATCGGGATTGAACAC--GAATC
* * * * *
12583566 AGAA-AATAAAAAGATCGGGATTAAACTGTGAGTCAAAGGATAATAACAATCAAGATTAAACTAC
63 -GAAGAATAAAAAGATCGGGATTAAACCGCGAGTCAAAGGATAACAACAATCGAGATTAAACTGC
* * * * *
12583630 AACTTTGAATTAAAGAGATCAGGATTGAACCGTGAATCAGAGAATAAAAAGATCGGGATTAAACC
127 GACTTTGAATTAAAGAGATC-GGATTGAACCATAAATCAGAGAATAAAAAGATCGAGATTAAATC
*
12583695 TCAAGTCAGAGG
191 ACAAGTCAGAGG
* * *
12583707 ATAACAACAATCAAAATTAATCTGTAACTTTGAATT-AA-AGATCGGGATTGAATCACGAATCGA
1 ATAACAACAATCGAGATTAAACTGTAACTTTGAATTAAAGAGATCGGGATTGAA-CACGAATCGA
* *
12583770 AGAATAAAAAGATTGGGATTAAACCCCGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGAC
65 AGAATAAAAAGATCGGGATTAAACCGCGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGAC
* * *
12583835 TTTGAATTTAAGAGATCGAGATTGAACCATAAATCAAAGAATAAAAAGATCGAGATTAAATCACG
130 TTTGAATTAAAGAGATCG-GATTGAACCATAAATCAGAGAATAAAAAGATCGAGATTAAATCACA
12583900 AGTCAGAGG
194 AGTCAGAGG
* * * *
12583909 ATAACAACAATTGAGATTAAACTGTGACTTTGAATTAAAGAGATCGAGATTGAAC-CGTAAAT-T
1 ATAACAACAATCGAGATTAAACTGTAACTTTGAATTAAAGAGATCGGGATTGAACACG--AATCG
* * *
12583972 AGAGAATAAAAAGATCGAGATTAAACCGCGAGCCAAAGGAT-ACAACAATTGAGATTAAACTGCG
64 A-AGAATAAAAAGATCGGGATTAAACCGCGAGTCAAAGGATAACAACAATCGAGATTAAACTGCG
* *
12584036 ACTTTGAATTAAAGAGATCGGGATTGAACCACAAATCAGAGAATAAAAAGATCGAGATTGAATCA
128 ACTTTGAATTAAAGAGATC-GGATTGAACCATAAATCAGAGAATAAAAAGATCGAGATTAAATCA
12584101 CAAGTCAGAGG
192 CAAGTCAGAGG
* *
12584112 ATAATAACAATCGAGATTAAACTGCAACTTTGAATTAAAGAGATCGGGATTGAACCACGA
1 ATAACAACAATCGAGATTAAACTGTAACTTTGAATTAAAGAGATCGGGATTGAA-CACGA
12584172 GTGAGAAAAA
Statistics
Matches: 405, Mismatches: 47, Indels: 27
0.85 0.10 0.06
Matches are distributed among these distances:
201 4 0.01
202 169 0.42
203 148 0.37
204 80 0.20
205 4 0.01
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.22
Consensus pattern (202 bp):
ATAACAACAATCGAGATTAAACTGTAACTTTGAATTAAAGAGATCGGGATTGAACACGAATCGAA
GAATAAAAAGATCGGGATTAAACCGCGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACT
TTGAATTAAAGAGATCGGATTGAACCATAAATCAGAGAATAAAAAGATCGAGATTAAATCACAAG
TCAGAGG
Found at i:12583988 original size:34 final size:34
Alignment explanation
Indices: 12583847--12583999 Score: 107
Period size: 34 Copynumber: 4.5 Consensus size: 34
12583837 TGAATTTAAG
* * *
12583847 AGATCGAGATTGAACCATAAATCAAAGAATAAAA
1 AGATCGAGATTAAACCGTAAATCAGAGAATAAAA
* *
12583881 AGATCGAGATTAAATCACG--AGTCAGAGGATAACAA
1 AGATCGAGATTAAA-C-CGTAAATCAGAGAATAA-AA
* * * * ** * *
12583916 CA-ATTGAGATTAAACTGTGACTTTGA-ATTAAAG
1 -AGATCGAGATTAAACCGTAAATCAGAGAATAAAA
* *
12583949 AGATCGAGATTGAACCGTAAATTAGAGAATAAAA
1 AGATCGAGATTAAACCGTAAATCAGAGAATAAAA
12583983 AGATCGAGATTAAACCG
1 AGATCGAGATTAAACCG
12584000 CGAGCCAAAG
Statistics
Matches: 89, Mismatches: 22, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
32 1 0.01
33 20 0.22
34 48 0.54
35 18 0.20
36 2 0.02
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.22
Consensus pattern (34 bp):
AGATCGAGATTAAACCGTAAATCAGAGAATAAAA
Found at i:12584095 original size:34 final size:34
Alignment explanation
Indices: 12584045--12584129 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
12584035 GACTTTGAAT
* *
12584045 TAAAGAGATCGGGATTGAACCACAAATCAGAGAA
1 TAAAAAGATCGAGATTGAACCACAAATCAGAGAA
* * *
12584079 TAAAAAGATCGAGATTGAATCACAAGTCAGAGGA
1 TAAAAAGATCGAGATTGAACCACAAATCAGAGAA
12584113 TAATAACA-ATCGAGATT
1 TAA-AA-AGATCGAGATT
12584130 AAACTGCAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
34 32 0.73
35 11 0.25
36 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (34 bp):
TAAAAAGATCGAGATTGAACCACAAATCAGAGAA
Found at i:12584169 original size:102 final size:102
Alignment explanation
Indices: 12583482--12584168 Score: 817
Period size: 102 Copynumber: 6.8 Consensus size: 102
12583472 TAAAGATTAG
* ** * * *
12583482 GATTAAACCATGAGTCAAAAAATAACAACAATCGAGATTAAACTACGA-TTATAAATTAAAGAAA
1 GATTAAACCACGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACTT-TGAATTAAAGAGA
* * * * *
12583546 TTGGGATTGAACCGTGAATCAGAAAATAAAAAGATCGG
65 TCGGGATTGAACCATAAATCAGAGAATAAAAAGATCGA
*** * * * *
12583584 GATTAAACTGTGAGTCAAAGGATAATAACAATCAAGATTAAACTACAACTTTGAATTAAAGAGAT
1 GATTAAACCACGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACTTTGAATTAAAGAGAT
* * * *
12583649 CAGGATTGAACCGTGAATCAGAGAATAAAAAGATCGG
66 CGGGATTGAACCATAAATCAGAGAATAAAAAGATCGA
* * * * * * **
12583686 GATTAAACCTCAAGTCAGAGGATAACAACAATCAAAATTAATCTGTAACTTTGAATT-AA-AGAT
1 GATTAAACCACGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACTTTGAATTAAAGAGAT
* ** * *
12583749 CGGGATTGAATCACGAATC-GAAGAATAAAAAGATTGG
66 CGGGATTGAACCATAAATCAG-AGAATAAAAAGATCGA
* *
12583786 GATTAAACCCCGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACTTTGAATTTAAGAGAT
1 GATTAAACCACGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACTTTGAATTAAAGAGAT
* *
12583851 CGAGATTGAACCATAAATCAAAGAATAAAAAGATCGA
66 CGGGATTGAACCATAAATCAGAGAATAAAAAGATCGA
* * * *
12583888 GATTAAATCACGAGTCAGAGGATAACAACAATTGAGATTAAACTGTGACTTTGAATTAAAGAGAT
1 GATTAAACCACGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACTTTGAATTAAAGAGAT
* * *
12583953 CGAGATTGAACCGTAAATTAGAGAATAAAAAGATCGA
66 CGGGATTGAACCATAAATCAGAGAATAAAAAGATCGA
* * *
12583990 GATTAAACCGCGAGCCAAAGGAT-ACAACAATTGAGATTAAACTGCGACTTTGAATTAAAGAGAT
1 GATTAAACCACGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACTTTGAATTAAAGAGAT
*
12584054 CGGGATTGAACCACAAATCAGAGAATAAAAAGATCGA
66 CGGGATTGAACCATAAATCAGAGAATAAAAAGATCGA
* * * * * *
12584091 GATTGAATCACAAGTCAGAGGATAATAACAATCGAGATTAAACTGCAACTTTGAATTAAAGAGAT
1 GATTAAACCACGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACTTTGAATTAAAGAGAT
12584156 CGGGATTGAACCA
66 CGGGATTGAACCA
12584169 CGAGTGAGAA
Statistics
Matches: 510, Mismatches: 69, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
99 1 0.00
100 83 0.16
101 94 0.18
102 330 0.65
103 2 0.00
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (102 bp):
GATTAAACCACGAGTCAAAGGATAACAACAATCGAGATTAAACTGCGACTTTGAATTAAAGAGAT
CGGGATTGAACCATAAATCAGAGAATAAAAAGATCGA
Found at i:12584286 original size:35 final size:35
Alignment explanation
Indices: 12584238--12584438 Score: 118
Period size: 35 Copynumber: 5.6 Consensus size: 35
12584228 TGATCAGGAT
* *
12584238 TAAACCACGAGTCAAAAAATAAAGATGACTGGGAC
1 TAAACCGCAAGTCAAAAAATAAAGATGACTGGGAC
* * * *
12584273 TAAACCGTAAGTCAAGGAATTAATGAA-ATGACTGAGAT
1 TAAACCGCAAGTCAA--AA--AATAAAGATGACTGGGAC
* * * * *
12584311 TAAACCACGAGCCAAATATTAAAGATGACTGGGAC
1 TAAACCGCAAGTCAAAAAATAAAGATGACTGGGAC
* * * * ** *
12584346 TAAATCGTAAGTCAGAAAATTAATGAAATGA-TCGAAAT
1 TAAACCGCAAGTCA-AAAAATAA--AGATGACT-GGGAC
* * * *
12584384 TAAACCACGAGTCAAAGATTAAAGATGACTGGGAC
1 TAAACCGCAAGTCAAAAAATAAAGATGACTGGGAC
12584419 TAAACCGCAAGTCAAAAAAT
1 TAAACCGCAAGTCAAAAAAT
12584439 TATATAAGAC
Statistics
Matches: 118, Mismatches: 38, Indels: 20
0.67 0.22 0.11
Matches are distributed among these distances:
34 4 0.03
35 53 0.45
36 9 0.08
37 10 0.08
38 37 0.31
39 5 0.04
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (35 bp):
TAAACCGCAAGTCAAAAAATAAAGATGACTGGGAC
Found at i:12584312 original size:73 final size:74
Alignment explanation
Indices: 12584215--12584440 Score: 311
Period size: 73 Copynumber: 3.1 Consensus size: 74
12584205 ACGAGTAAGA
*
12584215 AAAATT-ATAGAAATGATC-AGGATTAAACCACGAGTCAAAAAATAAAGATGACTGGGACTAAAC
1 AAAATTAAT-GAAATGATCGA-GATTAAACCACGAGTCAAAAATTAAAGATGACTGGGACTAAAC
12584278 CGTAAGTCAAG
64 CGTAAGTCAAG
* * * *
12584289 -GAATTAATGAAATGA-CTGAGATTAAACCACGAGCCAAATATTAAAGATGACTGGGACTAAATC
1 AAAATTAATGAAATGATC-GAGATTAAACCACGAGTCAAAAATTAAAGATGACTGGGACTAAACC
12584352 GTAAGTC-AG
65 GTAAGTCAAG
* *
12584361 AAAATTAATGAAATGATCGAAATTAAACCACGAGTCAAAGATTAAAGATGACTGGGACTAAACCG
1 AAAATTAATGAAATGATCGAGATTAAACCACGAGTCAAAAATTAAAGATGACTGGGACTAAACCG
*
12584426 CAAGTCAA-
66 TAAGTCAAG
12584434 AAAATTA
1 AAAATTA
12584441 TATAAGACTG
Statistics
Matches: 135, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
72 3 0.02
73 127 0.94
74 5 0.04
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (74 bp):
AAAATTAATGAAATGATCGAGATTAAACCACGAGTCAAAAATTAAAGATGACTGGGACTAAACCG
TAAGTCAAG
Found at i:12585450 original size:9 final size:9
Alignment explanation
Indices: 12585425--12585488 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 9
12585415 ATCACTTCCA
12585425 TTTTCA-TT
1 TTTTCATTT
12585433 TTTTC--TT
1 TTTTCATTT
12585440 TTTTCATTT
1 TTTTCATTT
12585449 TTTT-ATTT
1 TTTTCATTT
**
12585457 TTTGGATTT
1 TTTTCATTT
12585466 TTTTCTATATT
1 TTTTC-AT-TT
12585477 TTTTC-TTT
1 TTTTCATTT
12585485 TTTT
1 TTTT
12585489 TTAAGCAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
7 7 0.15
8 18 0.38
9 14 0.29
10 2 0.04
11 7 0.15
ACGTcount: A:0.09, C:0.08, G:0.03, T:0.80
Consensus pattern (9 bp):
TTTTCATTT
Found at i:12592206 original size:266 final size:266
Alignment explanation
Indices: 12591709--12592237 Score: 799
Period size: 266 Copynumber: 2.0 Consensus size: 266
12591699 AGTTTATCAA
* *
12591709 GGGCTGTATCCAAATGTACTTATACTGAGCAAGAAAAACTTTGGCCAAGTCTTTTCATGAACGAA
1 GGGCTGTATCCAAACGTACTTATACTAAGCAAGAAAAACTTTGGCCAAGTCTTTTCATGAACGAA
* ** *
12591774 TCTTACTCCGATCTAACTGCACGTATCATTTAGTTGCTGAACCAGTCAAACTATCTTGAAAATAG
66 TCTTACTCCGATCTAACTGCACGTACCATTTAACTGCTGAACCAGTCAAACTATCTTGAAAACAG
12591839 TGTATCAATAGTTTATCGTTATGGGTATGACCCATCATCTTTCTATAAAATATGGTGATATAAGC
131 TGTATCAATAGTTTATCGTTATGGGTATGACCCATCATCTTTCTATAAAATATGGTGATATAAGC
* * * *
12591904 AGAATGACACTTTGTCTCATCGTATTTCTCGAAATCTGAGGTCTTAAATTTTGGT-GAGATAACC
196 AAAATGACACTTTATCCCATCATATTTCTCGAAATCTGAGGTCTTAAATTTTGGTAG-GATAACC
12591968 AAGTCAG
260 AAGTCAG
* *
12591975 GGGCTGTATCCAAACGTGCTTATACTAAGTAAGAAAAACTTTGGCCAAGTCTTTTCATGAACGAA
1 GGGCTGTATCCAAACGTACTTATACTAAGCAAGAAAAACTTTGGCCAAGTCTTTTCATGAACGAA
* * * * * *
12592040 TCTTGCTCTGATCTAACTGTATGTACCATTTAACTGTTGAACCAGTCAAATTATCTTGAAAACAG
66 TCTTACTCCGATCTAACTGCACGTACCATTTAACTGCTGAACCAGTCAAACTATCTTGAAAACAG
* * * *
12592105 TGTATCAATAGTTTATTGTTATGGGTATGACCCGTCATCTTTTTATAAAATATGGTGATATGAGC
131 TGTATCAATAGTTTATCGTTATGGGTATGACCCATCATCTTTCTATAAAATATGGTGATATAAGC
* * * * *
12592170 AAAATGACATTTTATCCCATCATATTTTTTGAAATCTGGGGTCTTGAATTTTGGTAGGATAACCA
196 AAAATGACACTTTATCCCATCATATTTCTCGAAATCTGAGGTCTTAAATTTTGGTAGGATAACCA
12592235 AGT
261 AGT
12592238 TAGGCACTAG
Statistics
Matches: 235, Mismatches: 27, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
266 234 1.00
267 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (266 bp):
GGGCTGTATCCAAACGTACTTATACTAAGCAAGAAAAACTTTGGCCAAGTCTTTTCATGAACGAA
TCTTACTCCGATCTAACTGCACGTACCATTTAACTGCTGAACCAGTCAAACTATCTTGAAAACAG
TGTATCAATAGTTTATCGTTATGGGTATGACCCATCATCTTTCTATAAAATATGGTGATATAAGC
AAAATGACACTTTATCCCATCATATTTCTCGAAATCTGAGGTCTTAAATTTTGGTAGGATAACCA
AGTCAG
Found at i:12597154 original size:3 final size:3
Alignment explanation
Indices: 12597146--12597196 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
12597136 AGCTTATTCC
12597146 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12597194 ATT
1 ATT
12597197 TAAACATTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12598591 original size:18 final size:17
Alignment explanation
Indices: 12598569--12598608 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
12598559 AATTTCTCCA
12598569 CCAAACAAAACAAAAATT
1 CCAAAC-AAACAAAAATT
* *
12598587 TCAAACAACCAAAAATT
1 CCAAACAAACAAAAATT
12598604 CCAAA
1 CCAAA
12598609 ACTATCTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.62, C:0.25, G:0.00, T:0.12
Consensus pattern (17 bp):
CCAAACAAACAAAAATT
Found at i:12600039 original size:24 final size:21
Alignment explanation
Indices: 12599993--12600035 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12599983 TAATCACATC
*
12599993 ATTATAATACTTAATTTTACT
1 ATTATAATAATTAATTTTACT
*
12600014 ATTATAATAATTAATCTTACT
1 ATTATAATAATTAATTTTACT
12600035 A
1 A
12600036 CTATCATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATAATAATTAATTTTACT
Found at i:12605309 original size:2 final size:2
Alignment explanation
Indices: 12605302--12605335 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12605292 ATATGAATTT
*
12605302 TG TG TG TG TG TG TG TG TG TG TG TG TG GG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
12605336 GATAAACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (2 bp):
TG
Found at i:12608035 original size:24 final size:24
Alignment explanation
Indices: 12607982--12608027 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
12607972 GACAAAAGTA
*
12607982 AGGGAATTAGATTCGATGTCATAC
1 AGGGAATTAGATTCGATCTCATAC
12608006 AGGGAATTAGATTCGATCTCAT
1 AGGGAATTAGATTCGATCTCAT
12608028 CTTAGGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (24 bp):
AGGGAATTAGATTCGATCTCATAC
Found at i:12608994 original size:2 final size:2
Alignment explanation
Indices: 12608987--12609019 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12608977 TGTTTTTACA
*
12608987 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12609020 GCATGACTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12610531 original size:6 final size:6
Alignment explanation
Indices: 12610495--12610529 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
12610485 GTTGGCCCAT
* *
12610495 CCACTC CCACTC CCACTC CCACCC CCACTG CCACT
1 CCACTC CCACTC CCACTC CCACTC CCACTC CCACT
12610530 GCTACTGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.17, C:0.66, G:0.03, T:0.14
Consensus pattern (6 bp):
CCACTC
Found at i:12613690 original size:19 final size:19
Alignment explanation
Indices: 12613650--12613691 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12613640 TAATTCAATG
* *
12613650 TAATAATTAAATTTTGTTA
1 TAATAATTAAATTCTGTCA
12613669 TAATAATTAAATATCT-TCA
1 TAATAATTAAAT-TCTGTCA
12613688 TAAT
1 TAAT
12613692 TAAATAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATAATTAAATTCTGTCA
Found at i:12613789 original size:21 final size:22
Alignment explanation
Indices: 12613763--12613817 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 22
12613753 ATAAATTTAA
12613763 TTTAAA-TTATTATATTCAAAC
1 TTTAAATTTATTATATTCAAAC
12613784 TTTAAATAATTTATTATATTCAAA-
1 TTT--A-AATTTATTATATTCAAAC
*
12613808 TTTTAATTTA
1 TTTAAATTTA
12613818 ACGGTTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
21 9 0.31
23 1 0.03
24 5 0.17
25 14 0.48
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAAATTTATTATATTCAAAC
Found at i:12613911 original size:6 final size:6
Alignment explanation
Indices: 12613900--12613968 Score: 66
Period size: 6 Copynumber: 11.0 Consensus size: 6
12613890 TTAATAAGTA
* *
12613900 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT AATAATTAA TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT --T-TTTAT TTTTAT TTTTAT
** *
12613951 CATTAT TTTTAA TTTTAT
1 TTTTAT TTTTAT TTTTAT
12613969 CGAAATTAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
6 45 0.90
7 1 0.02
8 1 0.02
9 3 0.06
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTAT
Found at i:12613980 original size:39 final size:39
Alignment explanation
Indices: 12613891--12613968 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
12613881 TTTTGCATTT
* ** *
12613891 TAATAAGT-ATTTTATTTTTATTTTTATTTTTATTTTTA
1 TAATAATTAATTTTATTTTTATCATTATTTTTAATTTTA
12613929 TAATAATTAATTTTATTTTTATCATTATTTTTAATTTTA
1 TAATAATTAATTTTATTTTTATCATTATTTTTAATTTTA
12613968 T
1 T
12613969 CGAAATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 7 0.20
39 28 0.80
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (39 bp):
TAATAATTAATTTTATTTTTATCATTATTTTTAATTTTA
Found at i:12614693 original size:21 final size:21
Alignment explanation
Indices: 12614652--12614713 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
12614642 AAATAATAAT
12614652 AATAAATAAAAGAAACTAAAA
1 AATAAATAAAAGAAACTAAAA
* *
12614673 AATATATAAAAGAGA-TGAAAA
1 AATAAATAAAAGAAACT-AAAA
12614694 AA-AAATAAAAGGAAA-TAAAA
1 AATAAATAAAA-GAAACTAAAA
12614714 TCAAGAACAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 12 0.34
21 23 0.66
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.15
Consensus pattern (21 bp):
AATAAATAAAAGAAACTAAAA
Found at i:12614901 original size:22 final size:21
Alignment explanation
Indices: 12614874--12614923 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 21
12614864 TTTACATAAA
12614874 TAATATTTTAATTATATAAATT
1 TAATATTTTAATTAT-TAAATT
12614896 TAATA-TTT--TTATTAAATT
1 TAATATTTTAATTATTAAATT
12614914 T-ATATTTTAA
1 TAATATTTTAA
12614924 ATAATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 3 0.12
18 10 0.40
19 4 0.16
21 3 0.12
22 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TAATATTTTAATTATTAAATT
Found at i:12614920 original size:17 final size:19
Alignment explanation
Indices: 12614885--12614921 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
12614875 AATATTTTAA
12614885 TTATATAAATTTAATATTT
1 TTATATAAATTTAATATTT
12614904 TTAT-TAAATTT-ATATTT
1 TTATATAAATTTAATATTT
12614921 T
1 T
12614922 AAATAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATAAATTTAATATTT
Found at i:12615361 original size:24 final size:24
Alignment explanation
Indices: 12615334--12615381 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12615324 AATTTTTTTT
12615334 AAAAGAAAAAACTTTTA-AAAAATA
1 AAAAGAAAAAA-TTTTATAAAAATA
* *
12615358 AAAAGTATAAATTTTATAAAAATA
1 AAAAGAAAAAATTTTATAAAAATA
12615382 CTTTTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (24 bp):
AAAAGAAAAAATTTTATAAAAATA
Done.