Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 47 of 135
Found at i:12176228 original size:34 final size:35
Alignment explanation
Indices: 12176177--12176244 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
12176167 TTTTTCTGTT
* * *
12176177 ATGTTATGCTTGCAAGTTTTGTTAAGGGATTACTA
1 ATGTTATGCTTGAAAGTTTTGTTAAAGGACTACTA
12176212 ATGTT-TGCTTGAAAGTTTTGTTAAAGGACTACT
1 ATGTTATGCTTGAAAGTTTTGTTAAAGGACTACT
12176245 TATATTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 25 0.83
35 5 0.17
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (35 bp):
ATGTTATGCTTGAAAGTTTTGTTAAAGGACTACTA
Found at i:12181145 original size:17 final size:17
Alignment explanation
Indices: 12181123--12181181 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
12181113 CCCTTGACTT
12181123 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
*
12181140 TTAACC-TCCAT-TGACC
1 TTAACCTTCCATCT-TCC
12181156 TTTAACCTTCCATCTTCC
1 -TTAACCTTCCATCTTCC
12181174 TTAACCTT
1 TTAACCTT
12181182 TCATATTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 1 0.03
16 7 0.19
17 20 0.56
18 7 0.19
19 1 0.03
ACGTcount: A:0.20, C:0.37, G:0.02, T:0.41
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:12181160 original size:34 final size:34
Alignment explanation
Indices: 12181111--12181180 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
12181101 AACCTTTCAT
* *
12181111 CTCCCTTGACTTTTAACCTTCCATCTTCCTTAAC
1 CTCCATTGACCTTTAACCTTCCATCTTCCTTAAC
12181145 CTCCATTGACCTTTAACCTTCCATCTTCCTTAAC
1 CTCCATTGACCTTTAACCTTCCATCTTCCTTAAC
12181179 CT
1 CT
12181181 TTCATATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.19, C:0.39, G:0.03, T:0.40
Consensus pattern (34 bp):
CTCCATTGACCTTTAACCTTCCATCTTCCTTAAC
Found at i:12185741 original size:20 final size:21
Alignment explanation
Indices: 12185705--12185754 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
12185695 ATTGGTATGG
*
12185705 TTTATATTAAGTATAAATA-GA
1 TTTA-ATTAAGTATAAAAATGA
12185726 TTTAATTAAG-ATTAAAAATGA
1 TTTAATTAAGTA-TAAAAATGA
12185747 -TTAATTAA
1 TTTAATTAA
12185755 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 19 0.73
21 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (21 bp):
TTTAATTAAGTATAAAAATGA
Found at i:12189142 original size:20 final size:20
Alignment explanation
Indices: 12189105--12189158 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
12189095 CTCCAGTGAG
* * * *
12189105 ACTTCTACTGGTAGAACTCC
1 ACTTCTACCGATACAACTAC
12189125 ACTTCTACCGATACAACTAC
1 ACTTCTACCGATACAACTAC
*
12189145 AGTTCTACCGATAC
1 ACTTCTACCGATAC
12189159 CTTGAAGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.31, G:0.11, T:0.28
Consensus pattern (20 bp):
ACTTCTACCGATACAACTAC
Found at i:12206034 original size:5 final size:5
Alignment explanation
Indices: 12206024--12206049 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12206014 AAAAGACTTG
12206024 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
12206050 AAATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:12209673 original size:16 final size:16
Alignment explanation
Indices: 12209649--12209688 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12209639 TTTTTTTCTT
*
12209649 TTTACTTTTATATTTA
1 TTTATTTTTATATTTA
*
12209665 TTTATTTTTATTTTTA
1 TTTATTTTTATATTTA
12209681 TATTATTT
1 T-TTATTT
12209689 ATTTGTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTTTTATATTTA
Found at i:12209703 original size:22 final size:22
Alignment explanation
Indices: 12209638--12209692 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
12209628 GGTAACCCAA
* *
12209638 ATTTTTTTCTTTTTACTTTTAT
1 ATTTATTTATTTTTACTTTTAT
*
12209660 ATTTATTTATTTTTATTTTTAT
1 ATTTATTTATTTTTACTTTTAT
12209682 A-TTATTTATTT
1 ATTTATTTATTT
12209693 GTTTATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (22 bp):
ATTTATTTATTTTTACTTTTAT
Found at i:12211279 original size:60 final size:60
Alignment explanation
Indices: 12211177--12211292 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
12211167 TAGGATATTA
* * * * *
12211177 TTTATATTTAATTTCTATTTATCTTTTAGAGTTTAAAGTGGATCCAATTAGAGAATTAATG
1 TTTAGATTTAATTTCTAATTATCTTTTAAAATTTAAAGTGGATCCAACTAG-GAATTAATG
* * *
12211238 TTTAGATTTAA-TTCTAATTATCTTTTAAAATTTAGATTGGATTCAACTAGGAATT
1 TTTAGATTTAATTTCTAATTATCTTTTAAAATTTAAAGTGGATCCAACTAGGAATT
12211293 TATATATACT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 5 0.11
60 32 0.68
61 10 0.21
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (60 bp):
TTTAGATTTAATTTCTAATTATCTTTTAAAATTTAAAGTGGATCCAACTAGGAATTAATG
Found at i:12229068 original size:18 final size:18
Alignment explanation
Indices: 12229045--12229083 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12229035 GTTGTAAAAG
12229045 TATATAGATTATACAAAT
1 TATATAGATTATACAAAT
*
12229063 TATATAGATTGTACAAAT
1 TATATAGATTATACAAAT
12229081 TAT
1 TAT
12229084 TTTGCCCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (18 bp):
TATATAGATTATACAAAT
Found at i:12230912 original size:24 final size:24
Alignment explanation
Indices: 12230850--12231008 Score: 151
Period size: 24 Copynumber: 6.6 Consensus size: 24
12230840 AAACATATGC
*
12230850 AATTCAGATACAGATACAGTTGCA
1 AATTCAGATACAGATACAATTGCA
* * *
12230874 GACA-T-AAATATAGATACAATTTCA
1 -A-ATTCAGATACAGATACAATTGCA
*
12230898 AATTCAGATACAGATACAGTTGCA
1 AATTCAGATACAGATACAATTGCA
** * *
12230922 AACACAGATACAAATACAATTTCA
1 AATTCAGATACAGATACAATTGCA
*
12230946 AATTCAGATACAGATACAGTTGCA
1 AATTCAGATACAGATACAATTGCA
** * *
12230970 AACACAGATACAAATACAATTTCA
1 AATTCAGATACAGATACAATTGCA
*
12230994 AATTCATATACAGAT
1 AATTCAGATACAGAT
12231009 GCATATTCAG
Statistics
Matches: 104, Mismatches: 27, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
22 1 0.01
23 2 0.02
24 98 0.94
25 2 0.02
26 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.25
Consensus pattern (24 bp):
AATTCAGATACAGATACAATTGCA
Found at i:12230935 original size:12 final size:12
Alignment explanation
Indices: 12230896--12230987 Score: 69
Period size: 12 Copynumber: 7.7 Consensus size: 12
12230886 GATACAATTT
*
12230896 CAAATTCAGATA
1 CAAATACAGATA
* * *
12230908 CAGATACAGTTG
1 CAAATACAGATA
*
12230920 CAAACACAGATA
1 CAAATACAGATA
*
12230932 CAAATACA-ATTT
1 CAAATACAGA-TA
*
12230944 CAAATTCAGATA
1 CAAATACAGATA
* * *
12230956 CAGATACAGTTG
1 CAAATACAGATA
*
12230968 CAAACACAGATA
1 CAAATACAGATA
12230980 CAAATACA
1 CAAATACA
12230988 ATTTCAAATT
Statistics
Matches: 57, Mismatches: 21, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
11 1 0.02
12 55 0.96
13 1 0.02
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.21
Consensus pattern (12 bp):
CAAATACAGATA
Found at i:12231027 original size:48 final size:48
Alignment explanation
Indices: 12230826--12231008 Score: 264
Period size: 48 Copynumber: 3.9 Consensus size: 48
12230816 CCCATACGAA
* *
12230826 CAAA-ACAGATACAAAAAC-ATATGC-AATTCAGATACAGATACAGTTG
1 CAAACACAGATACAAATACAAT-TTCAAATTCAGATACAGATACAGTTG
* * * * *
12230872 CAGACATAAATATAGATACAATTTCAAATTCAGATACAGATACAGTTG
1 CAAACACAGATACAAATACAATTTCAAATTCAGATACAGATACAGTTG
12230920 CAAACACAGATACAAATACAATTTCAAATTCAGATACAGATACAGTTG
1 CAAACACAGATACAAATACAATTTCAAATTCAGATACAGATACAGTTG
*
12230968 CAAACACAGATACAAATACAATTTCAAATTCATATACAGAT
1 CAAACACAGATACAAATACAATTTCAAATTCAGATACAGAT
12231009 GCATATTCAG
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
46 3 0.02
47 11 0.09
48 107 0.88
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.23
Consensus pattern (48 bp):
CAAACACAGATACAAATACAATTTCAAATTCAGATACAGATACAGTTG
Found at i:12238095 original size:19 final size:17
Alignment explanation
Indices: 12238068--12238107 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
12238058 TATCTTTTTA
*
12238068 TAAATTTATAAAACATTAT
1 TAAAATTATAAAA-A-TAT
12238087 TAAAATTATAAAAATAT
1 TAAAATTATAAAAATAT
12238104 TAAA
1 TAAA
12238108 TAAAGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATTATAAAAATAT
Found at i:12241162 original size:16 final size:16
Alignment explanation
Indices: 12241119--12241162 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
12241109 TTAGTTTGTG
* *
12241119 GTAATAGAATAAAGCT
1 GTAATGGAATAGAGCT
12241135 GTAATGGAATAGAGCT
1 GTAATGGAATAGAGCT
12241151 GTAATGGAATAG
1 GTAATGGAATAG
12241163 GACTATAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.27, T:0.25
Consensus pattern (16 bp):
GTAATGGAATAGAGCT
Found at i:12241171 original size:16 final size:16
Alignment explanation
Indices: 12241120--12241171 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
12241110 TAGTTTGTGG
* * *
12241120 TAATAGAATAAAGCTG
1 TAATGGAATAGAGCTA
*
12241136 TAATGGAATAGAGCTG
1 TAATGGAATAGAGCTA
12241152 TAATGGAATAG-GACTA
1 TAATGGAATAGAG-CTA
12241168 TAAT
1 TAAT
12241172 CAGTATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 1 0.03
16 31 0.97
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (16 bp):
TAATGGAATAGAGCTA
Found at i:12241413 original size:56 final size:56
Alignment explanation
Indices: 12241323--12241489 Score: 194
Period size: 56 Copynumber: 2.9 Consensus size: 56
12241313 ATAATTATTG
* *
12241323 TAATTGTAATTAA-ATTTTAATAAGATTATCATTAAATATAATTTAATAAAAAATAAA
1 TAATT-TAA-TAACATTTTAATATGATTATTATTAAATATAATTTAATAAAAAATAAA
* * * * *
12241380 TAATTTAATCATATTTTAACATGATTATTATTAAATATAATTTAATAAAATATTATA
1 TAATTTAATAACATTTTAATATGATTATTATTAAATATAATTTAATAAAA-AATAAA
*
12241437 TAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAA-TTAATAAAAA
1 TAATTTAATAACATT-TTAATATGATTATTATT-AAATAT-AATTTAATAAAAA
12241490 TCATAATATA
Statistics
Matches: 95, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
55 2 0.02
56 38 0.40
57 22 0.23
58 16 0.17
59 15 0.16
60 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (56 bp):
TAATTTAATAACATTTTAATATGATTATTATTAAATATAATTTAATAAAAAATAAA
Found at i:12241685 original size:14 final size:14
Alignment explanation
Indices: 12241666--12241703 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
12241656 TACATTCAAA
12241666 CATAATTTATATGT
1 CATAATTTATATGT
*
12241680 CATAATCTATATGT
1 CATAATTTATATGT
*
12241694 TA-AATTTATA
1 CATAATTTATA
12241704 ACATCAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (14 bp):
CATAATTTATATGT
Found at i:12244021 original size:280 final size:269
Alignment explanation
Indices: 12243675--12244185 Score: 684
Period size: 280 Copynumber: 1.9 Consensus size: 269
12243665 TTAGTAAGTC
*
12243675 TAACCTAAAAATCCCATAGATTTAAAACCAAAAAAAAACTTCAAACTGAAAAGGCTAATAACATC
1 TAACCTAAAAATCCCATAGATTTAAAACCAAAAAAAAACTTCAAACTGAAAAGGCTAAGAACATC
** *
12243740 TATAATAAAAACAACACTAAA-CTTAAAAAATAATCCATAAATTCTCATTAAAAGATACAAAAAA
66 TATAATAAAAACAACACTAAACCCCAAAAAATAACCCATAAATTCTCATTAAAAGATAC------
* * *
12243804 AAGAAAAAAAAGAGAGCACAAAACTCATTTACTCATAGAGGAGAAGGAAGCAAAAGGGTATGTCG
125 -A-AAAAAAAA-A-AGCACAAAACGCATCTACTCATAGAAGAGAAGGAAGCAAAAGGGTATGTCG
* *
12243869 TTTAGTTTCATTAAGAGCAAAATGAATGAAGTTTTGGTAAGAAATTGCAAAGACTTGAAGCAAAC
186 TTTAATTTCA--AAGAGCAAAAAGAATGAAG-TTTGGTAAGAAATTGCAAAGACTTGAAGCAAAC
12243934 AATGCCTTTTCTTCAGTAACTT
248 AATGCCTTTTCTTCAGTAACTT
* * *
12243956 TAACCTAAAAATCCCATAGATTT-AAACCAAAAAAAACCTTGAAATTGAAAAGGCTAAGAACATC
1 TAACCTAAAAATCCCATAGATTTAAAACCAAAAAAAAACTTCAAACTGAAAAGGCTAAGAACATC
* * * *
12244020 TATAGTAAAAACAACAGTAAACCCCCAAAAAATAACCCATAAATTCTCATTAAAAGGTTCAAAAA
66 TATAATAAAAACAACACTAAA-CCCCAAAAAATAACCCATAAATTCTCATTAAAAGATACAAAAA
* ** *
12244085 AAAAAAGCACAGAACGCATCTACTTGTAGAAGAGAATGAAGCAAAAGGGTATGTCGTTTAATTTC
130 AAAAAAGCACAAAACGCATCTACTCATAGAAGAGAAGGAAGCAAAAGGGTATGTCGTTTAATTTC
* *
12244150 AAAGAGTAAAAAGAATGAAGTTTGGTAAGATATTGC
195 AAAGAGCAAAAAGAATGAAGTTTGGTAAGAAATTGC
12244186 CAGGATATTT
Statistics
Matches: 206, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
269 15 0.07
270 17 0.08
272 53 0.26
273 1 0.00
274 8 0.04
275 1 0.00
280 56 0.27
281 23 0.11
282 32 0.16
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (269 bp):
TAACCTAAAAATCCCATAGATTTAAAACCAAAAAAAAACTTCAAACTGAAAAGGCTAAGAACATC
TATAATAAAAACAACACTAAACCCCAAAAAATAACCCATAAATTCTCATTAAAAGATACAAAAAA
AAAAAGCACAAAACGCATCTACTCATAGAAGAGAAGGAAGCAAAAGGGTATGTCGTTTAATTTCA
AAGAGCAAAAAGAATGAAGTTTGGTAAGAAATTGCAAAGACTTGAAGCAAACAATGCCTTTTCTT
CAGTAACTT
Found at i:12244416 original size:62 final size:62
Alignment explanation
Indices: 12244319--12244463 Score: 272
Period size: 62 Copynumber: 2.3 Consensus size: 62
12244309 CCTATAATAG
12244319 GCTATTACAACAAACCAAACAATTGTTTATGGTGGCCCATTGAATAGAGCTAGAATGCATGA
1 GCTATTACAACAAACCAAACAATTGTTTATGGTGGCCCATTGAATAGAGCTAGAATGCATGA
12244381 GCTATTACAACAAACCAAACAATTGTTTATGGTGGCCCATTGAATAGAGCTAGAATGCATGA
1 GCTATTACAACAAACCAAACAATTGTTTATGGTGGCCCATTGAATAGAGCTAGAATGCATGA
* *
12244443 GCTATTACATCCAACCAAACA
1 GCTATTACAACAAACCAAACA
12244464 TGCTGTTAGT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 81 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (62 bp):
GCTATTACAACAAACCAAACAATTGTTTATGGTGGCCCATTGAATAGAGCTAGAATGCATGA
Found at i:12244664 original size:34 final size:34
Alignment explanation
Indices: 12244621--12244688 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
12244611 AACCTGGTGA
12244621 TCGGGTCAAGTATAAGGGTGTTACATAATTTGTT
1 TCGGGTCAAGTATAAGGGTGTTACATAATTTGTT
12244655 TCGGGTCAAGTATAAGGGTGTTACATAATTTGTT
1 TCGGGTCAAGTATAAGGGTGTTACATAATTTGTT
12244689 CGTCCAGACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (34 bp):
TCGGGTCAAGTATAAGGGTGTTACATAATTTGTT
Found at i:12259587 original size:27 final size:27
Alignment explanation
Indices: 12259545--12259598 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
12259535 CCGATATAGG
12259545 TATAAGTTCTACCGAAACAAGTATCCA
1 TATAAGTTCTACCGAAACAAGTATCCA
*
12259572 TATAAGTTCTATCGAAACAAGTATCCA
1 TATAAGTTCTACCGAAACAAGTATCCA
12259599 GAATCTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (27 bp):
TATAAGTTCTACCGAAACAAGTATCCA
Found at i:12260098 original size:35 final size:35
Alignment explanation
Indices: 12260056--12260127 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
12260046 ATTCGTTTTA
12260056 CTCTTTGTTGACACAAAGGTCATGTTGCTCATTTG
1 CTCTTTGTTGACACAAAGGTCATGTTGCTCATTTG
12260091 CTCTTTGTTGACACAAAGGTCATGTTGCTCATTTG
1 CTCTTTGTTGACACAAAGGTCATGTTGCTCATTTG
12260126 CT
1 CT
12260128 TCCTATTGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (35 bp):
CTCTTTGTTGACACAAAGGTCATGTTGCTCATTTG
Found at i:12260149 original size:35 final size:35
Alignment explanation
Indices: 12260063--12260137 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 35
12260053 TTACTCTTTG
* *
12260063 TTGACACAAAGGTCATGTTGCTCATTTGCTCTTTG
1 TTGACACAAAGGTCATGTTGCTCATTTGCTCTCTA
12260098 TTGACACAAAGGTCATGTTGCTCATTTGCT-TCCTA
1 TTGACACAAAGGTCATGTTGCTCATTTGCTCT-CTA
12260133 TTGAC
1 TTGAC
12260138 TCGGGGGTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 1 0.03
35 36 0.97
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (35 bp):
TTGACACAAAGGTCATGTTGCTCATTTGCTCTCTA
Found at i:12262412 original size:21 final size:21
Alignment explanation
Indices: 12262393--12262491 Score: 135
Period size: 21 Copynumber: 4.7 Consensus size: 21
12262383 AAACATCGAG
* *
12262393 GTGCATTATAGGGGCATCGAA
1 GTGCAATATAGGGGCATCGGA
*
12262414 GTGCGATATAGGGGCATCGGA
1 GTGCAATATAGGGGCATCGGA
* *
12262435 GTGTAATATAGGGGCACCGGA
1 GTGCAATATAGGGGCATCGGA
* *
12262456 GTGCAATACAGGGGCACCGGA
1 GTGCAATATAGGGGCATCGGA
12262477 GTGCAATATAGGGGC
1 GTGCAATATAGGGGC
12262492 TTTACATAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.27, C:0.16, G:0.38, T:0.18
Consensus pattern (21 bp):
GTGCAATATAGGGGCATCGGA
Found at i:12290081 original size:21 final size:22
Alignment explanation
Indices: 12290057--12290098 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12290047 CAAAGAATAA
*
12290057 AATT-AACCCAATTTAATAATT
1 AATTAAACCCAAATTAATAATT
*
12290078 AATTAAACCCAAATTATTAAT
1 AATTAAACCCAAATTAATAAT
12290099 AAACTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTAAACCCAAATTAATAATT
Found at i:12294008 original size:29 final size:28
Alignment explanation
Indices: 12293945--12294010 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
12293935 AATTATTAAC
*
12293945 ACAATAAAAATATAATTATAGTATGAAAT
1 ACAATAAAAATATAATCATAGTAT-AAAT
* *
12293974 AAAATAACAATATAATCATAGTA-ATAAT
1 ACAATAAAAATATAATCATAGTATA-AAT
12294002 GACAATAAA
1 -ACAATAAA
12294011 TATTAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
27 1 0.03
28 3 0.10
29 26 0.87
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (28 bp):
ACAATAAAAATATAATCATAGTATAAAT
Found at i:12294477 original size:15 final size:16
Alignment explanation
Indices: 12294444--12294511 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
12294434 TTAGGCATGC
*
12294444 AAATAAAT-GACAAAT
1 AAATAAATAAACAAAT
12294459 AAATAAATAAACAAA-
1 AAATAAATAAACAAAT
*
12294474 AAATCAATAAATCAAAT
1 AAATAAATAAA-CAAAT
* *
12294491 ATCA-AAATAAACAACT
1 A-AATAAATAAACAAAT
12294507 AAATA
1 AAATA
12294512 TAAATAATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
15 19 0.45
16 15 0.36
17 7 0.17
18 1 0.02
ACGTcount: A:0.69, C:0.10, G:0.01, T:0.19
Consensus pattern (16 bp):
AAATAAATAAACAAAT
Found at i:12294498 original size:100 final size:99
Alignment explanation
Indices: 12294337--12294521 Score: 234
Period size: 100 Copynumber: 1.8 Consensus size: 99
12294327 ACAATAAAAT
* *
12294337 GGCATGAAAATAAATAACAACAAGATAAATAAACAAAAAAAATAAAAATTAAATGCTAAAATAAA
1 GGCATGAAAATAAATAACAACAAAATAAATAAACAAAAAAAAT-AAAATCAAATGCTAAAATAAA
12294402 CAAAC-AAATATAAACAATAAAAATAATTGAGATTA
65 C-AACTAAATATAAACAATAAAAATAATTGAGATTA
* * *
12294437 GGCATGCAAATAAATGACAA-ATAAATAAATAAACAAAAAATCAAT-AAATCAAAT-ATCAAAAT
1 GGCATGAAAATAAATAACAACA-AAATAAATAAACAAAAAA--AATAAAATCAAATGCT-AAAAT
*
12294499 AAACAACTAAATATAAATAATAA
62 AAACAACTAAATATAAACAATAA
12294522 TAAAATGGAA
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
99 5 0.07
100 66 0.89
102 3 0.04
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.19
Consensus pattern (99 bp):
GGCATGAAAATAAATAACAACAAAATAAATAAACAAAAAAAATAAAATCAAATGCTAAAATAAAC
AACTAAATATAAACAATAAAAATAATTGAGATTA
Found at i:12295540 original size:49 final size:49
Alignment explanation
Indices: 12295438--12296139 Score: 458
Period size: 49 Copynumber: 14.4 Consensus size: 49
12295428 GCTATTGTGG
* * ** * * * * *
12295438 CTTCAATCTATCCCTCTTTGGTTTTAGGGCATTGGGTCTGTCGTCACGG
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * ** **
12295487 CTTCAACCTATCCCTCTTCGATTTTAAGATGTAAGATTTGTCGTTGTGA
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * *** * *
12295536 CTTCAATCTTTCCCTCTTTGGTTTTAGGGTGTTAGGTCTACCGTTATGG
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * * * * * ** *
12295585 CTTTAACCTTTTCTTTTTTGATTTTAGGGTGTTAGATCTGTTATTACAA
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * *
12295634 CTTCAATCTATCCCTCTTCGATTTTAGAGTGTTAGTTCCGTCATTACGA
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * *
12295683 CTTCAACCTATCCCTCTTTGATTTTAAGGTGTAAGATCCGTCGTTATGA
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * **
12295732 CTTCAATCTTTCCCTCTTC-AGTTTTTGGGTGTTAGGTTCACCGTTACGA
1 CTTCAATCTATCCCTCTTCGA-TTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * * * ** * *
12295781 CTTTAACCTATCCCTCTT-TAGTTTTAAGGTGTAAAATCTATCGTTGCGG
1 CTTCAATCTATCCCTCTTCGA-TTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * * * *
12295830 CTTTAATTTTTCCCTCTTCGATTTTAGGGTATTAGATCCGCCATTACGG
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * * ** *
12295879 TTTCAATCTATCCCTTTTCGATTTTAGGATGTTAGGTCCGCCGTTGTGG
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* ** * * ** *
12295928 CTTCAATCTATCCCTCTTCAATTTTAATGTGTAAGATCTG-CGTTGTGG
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * *
12295976 C-TCAATCTTTCCCTCTTCGATTTTAGGGTGTTAGATCCGCCATTACGA
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * * *
12296024 CTTCAATCTATCCCTCTTCGATTTTAAGATGTTAGGTCCATTGTTATGA
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* * * * *
12296073 CTTCAACCTATCCCTCTTCGGTTTTAGGATGTTAGGTCCGTCGTTACGG
1 CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
* *
12296122 CTTCAACCTATTCCTCTT
1 CTTCAATCTATCCCTCTT
12296140 TAAACTCTAT
Statistics
Matches: 502, Mismatches: 146, Indels: 10
0.76 0.22 0.02
Matches are distributed among these distances:
47 32 0.06
48 15 0.03
49 454 0.90
50 1 0.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (49 bp):
CTTCAATCTATCCCTCTTCGATTTTAGGGTGTTAGATCCGTCGTTACGA
Found at i:12298823 original size:11 final size:11
Alignment explanation
Indices: 12298807--12298868 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
12298797 TGTCTTTTTC
12298807 TTTTTCTTCTT
1 TTTTTCTTCTT
*
12298818 TTTTTCTTTTT
1 TTTTTCTTCTT
12298829 TTTTTCTTTCTT
1 TTTTTC-TTCTT
12298841 CTCTCTTT-TTCTT
1 -T-T-TTTCTTCTT
*
12298854 TTCTT-TTCTT
1 TTTTTCTTCTT
12298864 TTTTT
1 TTTTT
12298869 TTGCTAGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 11 0.26
11 17 0.40
12 5 0.12
13 6 0.14
14 1 0.02
15 3 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:12298828 original size:18 final size:18
Alignment explanation
Indices: 12298801--12298867 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
12298791 CGGCCTTGTC
12298801 TTTTTC-TTTTTCTTCTT
1 TTTTTCTTTTTTCTTCTT
*
12298818 TTTTTCTTTTTTTTTTCTT
1 TTTTTC-TTTTTTCTTCTT
*
12298837 TCTTCTCTCTTTTTCTT-TT
1 T-TTTTCT-TTTTTCTTCTT
*
12298856 CTTTTCTTTTTT
1 TTTTTCTTTTTT
12298868 TTTGCTAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 11 0.27
18 5 0.12
19 14 0.34
20 11 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTTCTTCTT
Found at i:12298849 original size:28 final size:27
Alignment explanation
Indices: 12298801--12298866 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
12298791 CGGCCTTGTC
*
12298801 TTTTTCTTTTTCTTCTTTTTTTCTTTTT
1 TTTTTCTTTTTCTTCTCTTTTTC-TTTT
12298829 TTTTTCTTTCTTC-TCTCTTTTTCTTTT
1 TTTTTCTTT-TTCTTCTCTTTTTCTTTT
*
12298856 CTTTTCTTTTT
1 TTTTTCTTTTT
12298867 TTTTGCTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 2 0.06
27 12 0.34
28 18 0.51
29 3 0.09
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTTTCTTTTTCTTCTCTTTTTCTTTT
Found at i:12298868 original size:18 final size:18
Alignment explanation
Indices: 12298802--12298868 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
12298792 GGCCTTGTCT
*
12298802 TTTTCTTTTTCTTCTTTTT
1 TTTTCTTTTT-TTCTTTTC
*
12298821 TTCTTTTTTTTTTC-TTTC
1 TT-TTCTTTTTTTCTTTTC
* *
12298839 TTCTCTCTTTTTCTTTTC
1 TTTTCTTTTTTTCTTTTC
12298857 TTTTCTTTTTTT
1 TTTTCTTTTTTT
12298869 TTGCTAGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 8 0.21
18 19 0.49
19 5 0.13
20 7 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTTTCTTTTC
Found at i:12308107 original size:18 final size:18
Alignment explanation
Indices: 12308071--12308108 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
12308061 ACCAAATAAT
*
12308071 ATGCGATCACAAGACCAG
1 ATGCGATCACAAAACCAG
*
12308089 ATGCGATCACAAAATCAG
1 ATGCGATCACAAAACCAG
12308107 AT
1 AT
12308109 CAGTCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (18 bp):
ATGCGATCACAAAACCAG
Found at i:12312549 original size:25 final size:25
Alignment explanation
Indices: 12312511--12312570 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
12312501 CTCCTTTTTG
*
12312511 TCGATGCATCTGATAGCACGACTTA
1 TCGATGCATTTGATAGCACGACTTA
*
12312536 TTGATGCATTTGATAGCACGACTTA
1 TCGATGCATTTGATAGCACGACTTA
12312561 TCGATGCATT
1 TCGATGCATT
12312571 CTGTGATGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (25 bp):
TCGATGCATTTGATAGCACGACTTA
Found at i:12317477 original size:15 final size:16
Alignment explanation
Indices: 12317459--12317500 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
12317449 AATTAAATAA
* *
12317459 ATAATAATAAAA-GAG
1 ATAAAAATAAAATGAC
*
12317474 ATAACAATAAAATGAC
1 ATAAAAATAAAATGAC
12317490 ATAAAAATAAA
1 ATAAAAATAAA
12317501 TAACAACAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (16 bp):
ATAAAAATAAAATGAC
Found at i:12317530 original size:16 final size:15
Alignment explanation
Indices: 12317492--12317531 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
12317482 AAAATGACAT
12317492 AAAAATAAATAACAA
1 AAAAATAAATAACAA
* *
12317507 CAAGATAAATAAACAA
1 AAAAATAAAT-AACAA
12317523 AAAAATAAA
1 AAAAATAAA
12317532 ATTAAAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.78, C:0.07, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAAATAAATAACAA
Found at i:12319833 original size:21 final size:21
Alignment explanation
Indices: 12319803--12319880 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
12319793 AAGCATCGAG
*
12319803 GTGCATTACAGGGGCACCGAA
1 GTGCAGTACAGGGGCACCGAA
*
12319824 GTGCAGTACAGGGGCACCAAA
1 GTGCAGTACAGGGGCACCGAA
* *
12319845 GTGC-GATACAGGGGCATCGGA
1 GTGCAG-TACAGGGGCACCGAA
*
12319866 GTGCAATACAGGGGC
1 GTGCAGTACAGGGGC
12319881 TTTACATAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.02
21 48 0.98
ACGTcount: A:0.28, C:0.22, G:0.37, T:0.13
Consensus pattern (21 bp):
GTGCAGTACAGGGGCACCGAA
Found at i:12328505 original size:13 final size:12
Alignment explanation
Indices: 12328453--12328520 Score: 63
Period size: 11 Copynumber: 5.8 Consensus size: 12
12328443 ATTTACGTGT
*
12328453 TTAATTTTTTAA
1 TTAATTATTTAA
12328465 TTAATT-TTTAA
1 TTAATTATTTAA
*
12328476 ATAATATATTT--
1 TTAAT-TATTTAA
12328487 TTAATTATTATAA
1 TTAATTATT-TAA
12328500 TTAATT-TTTAA
1 TTAATTATTTAA
*
12328511 TTTATTATTT
1 TTAATTATTT
12328521 CAATCATTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
10 4 0.09
11 22 0.47
12 12 0.26
13 9 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTAATTATTTAA
Found at i:12328506 original size:20 final size:20
Alignment explanation
Indices: 12328452--12328518 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 20
12328442 AATTTACGTG
*
12328452 TTTAATT-TTTTAATTAATT
1 TTTAATTATTATAATTAATT
*
12328471 TTTAA--ATAAT-A-T-ATT
1 TTTAATTATTATAATTAATT
12328486 TTTAATTATTATAATTAATT
1 TTTAATTATTATAATTAATT
12328506 TTTAATTTATTAT
1 TTTAA-TTATTAT
12328519 TTCAATCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
15 8 0.21
16 1 0.03
17 5 0.13
18 3 0.08
19 6 0.16
20 8 0.21
21 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAATTATTATAATTAATT
Found at i:12342100 original size:17 final size:17
Alignment explanation
Indices: 12342069--12342126 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
12342059 ATAATTGTCC
* *
12342069 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
12342086 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
12342103 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
12342120 TGCATTT
1 TGCATTT
12342127 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:12342107 original size:34 final size:33
Alignment explanation
Indices: 12342062--12342126 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
12342052 CTGTAGTATA
*
12342062 ATTGTCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCTGCATCTA-CAATGTCATTGCATTTTT
*
12342095 ATTGTCGCTGCATCTACATTGTCATTGCATTT
1 ATTGTC-CTGCATCTACAATGTCATTGCATTT
12342127 CCATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 20 0.71
35 2 0.07
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (33 bp):
ATTGTCCTGCATCTACAATGTCATTGCATTTTT
Found at i:12342693 original size:34 final size:34
Alignment explanation
Indices: 12342650--12342716 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
12342640 GGAACCAAGA
** *
12342650 TAACTTCACTAAGTTGCAACGCTGGATGCGTCGC
1 TAACTTCACTAAGTCACAACGCTGGATACGTCGC
12342684 TAACTTCACTAAGTCACAACGCTGGATACGTCG
1 TAACTTCACTAAGTCACAACGCTGGATACGTCG
12342717 ACAAGGTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (34 bp):
TAACTTCACTAAGTCACAACGCTGGATACGTCGC
Found at i:12344867 original size:34 final size:34
Alignment explanation
Indices: 12344810--12344875 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
12344800 TTATATACGG
*
12344810 AAATGCAATGACAATGTAGATGCAGCGACAATAA
1 AAATGCAATGACAATATAGATGCAGCGACAATAA
* *
12344844 AAATGCAATGACATTAATA-ATGCAGGGACAAT
1 AAATGCAATGACAAT-ATAGATGCAGCGACAAT
12344876 TATACTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCAGCGACAATAA
Found at i:12352504 original size:18 final size:19
Alignment explanation
Indices: 12352467--12352506 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12352457 GCACTTCGTA
*
12352467 TGCCAGTACGTACTTTACG
1 TGCCAGTACGCACTTTACG
*
12352486 TGCCAGTATGCAC-TTACG
1 TGCCAGTACGCACTTTACG
12352504 TGC
1 TGC
12352507 TAATTTCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30
Consensus pattern (19 bp):
TGCCAGTACGCACTTTACG
Found at i:12357797 original size:24 final size:25
Alignment explanation
Indices: 12357748--12357802 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
12357738 ATAAGTAATT
* *
12357748 TTAAACACAACACAAAATTATGTAA
1 TTAAAAACAACACAAAAATATGTAA
12357773 TTAAAAACTAACA-AAAAATAT-TAA
1 TTAAAAAC-AACACAAAAATATGTAA
12357797 TTAAAA
1 TTAAAA
12357803 TAAATCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 9 0.33
25 14 0.52
26 4 0.15
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.25
Consensus pattern (25 bp):
TTAAAAACAACACAAAAATATGTAA
Found at i:12358464 original size:19 final size:20
Alignment explanation
Indices: 12358427--12358464 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
12358417 CAAAAATCCT
* *
12358427 CAAAACTCTTTATTTTCTCC
1 CAAAACTCTTTACTCTCTCC
12358447 CAAAACT-TTTACTCTCTC
1 CAAAACTCTTTACTCTCTC
12358465 TCACTTTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (20 bp):
CAAAACTCTTTACTCTCTCC
Found at i:12359150 original size:19 final size:19
Alignment explanation
Indices: 12359126--12359170 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
12359116 AAAAAAATTT
12359126 AACTCGAACAAATATATTC
1 AACTCGAACAAATATATTC
12359145 AACTCGAACAAATATATTC
1 AACTCGAACAAATATATTC
*
12359164 AATTCGA
1 AACTCGA
12359171 TTCGATTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (19 bp):
AACTCGAACAAATATATTC
Found at i:12362097 original size:10 final size:10
Alignment explanation
Indices: 12362084--12362116 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
12362074 AGAAAAAACT
12362084 AAAAAAATAA
1 AAAAAAATAA
12362094 AAAAAAATAA
1 AAAAAAATAA
12362104 AAAAAAATAA
1 AAAAAAATAA
12362114 AAA
1 AAA
12362117 TCCATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:12362717 original size:11 final size:11
Alignment explanation
Indices: 12362703--12362733 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
12362693 ACATTTTGAT
12362703 TTTATTTTTTA
1 TTTATTTTTTA
12362714 TTTATTTTTTA
1 TTTATTTTTTA
12362725 TTTATTTTT
1 TTTATTTTT
12362734 ATATATACGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:12362786 original size:81 final size:82
Alignment explanation
Indices: 12362637--12362799 Score: 181
Period size: 81 Copynumber: 2.0 Consensus size: 82
12362627 TTTGTGTTTG
* * **
12362637 TTTTATTTTTATATATATATACGCATGTATATGTATATATATATATACATAGATATACATTTTGA
1 TTTTATTTTTATATATATATACGCATG-ATACGTATATATATATATACATACATATACATTTCAA
*
12362702 -TTTTATTTTTTATTTATT
65 TTTTTA-TTGTTATTTATT
* * **
12362720 TTTTATTTATT-TTTATATATACGCATG-TACGTATATATATAT-TAACATACATCTTGATTTCA
1 TTTTATTT-TTATATATATATACGCATGATACGTATATATATATAT-ACATACATATACATTTCA
12362782 ATTTTTATTGTTATTTAT
64 ATTTTTATTGTTATTTAT
12362800 ATACTTTCGT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
80 1 0.01
81 37 0.54
82 5 0.07
83 23 0.34
84 2 0.03
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.56
Consensus pattern (82 bp):
TTTTATTTTTATATATATATACGCATGATACGTATATATATATATACATACATATACATTTCAAT
TTTTATTGTTATTTATT
Found at i:12368483 original size:7 final size:7
Alignment explanation
Indices: 12368466--12368514 Score: 64
Period size: 7 Copynumber: 6.9 Consensus size: 7
12368456 ATTCCCCCCC
12368466 AAAAAAGG
1 AAAAAA-G
12368474 AAAAAAG
1 AAAAAAG
12368481 AAAAAA-
1 AAAAAAG
12368487 AAGAAAAG
1 AA-AAAAG
*
12368495 GAAAAAG
1 AAAAAAG
12368502 AAAAAAG
1 AAAAAAG
12368509 AAAAAA
1 AAAAAA
12368515 AGGAGATGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
6 2 0.05
7 28 0.76
8 7 0.19
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:12368493 original size:22 final size:23
Alignment explanation
Indices: 12368466--12368518 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
12368456 ATTCCCCCCC
12368466 AAAAAAGGAAAAAAGAAAAAA-A
1 AAAAAAGGAAAAAAGAAAAAAGA
*
12368488 AGAAAAGG-AAAAAGAAAAAAGA
1 AAAAAAGGAAAAAAGAAAAAAGA
12368510 AAAAAAGGA
1 AAAAAAGGA
12368519 GATGTCGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (23 bp):
AAAAAAGGAAAAAAGAAAAAAGA
Found at i:12369802 original size:98 final size:98
Alignment explanation
Indices: 12369631--12370265 Score: 833
Period size: 98 Copynumber: 6.5 Consensus size: 98
12369621 TACAGGTTTA
* * *
12369631 GAGGGAAAGGTTAAAGTCGTAATGGCGAACCTTGTACCTCAGAAACATGCTGGGAAAGATTGAAG
1 GAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGCTGGGAAAGATTGAAG
** ** *
12369696 CTATAACGGTGAATCTGGTACCACAAAGATATG
66 CTGCAACGACGAATCTGGTACCACGAAGATATG
* * * *
12369729 GAGGGAAAGGTTTAAGTCGTAACGGCAAACCTTGTACCTCAAAAACATGTTGGGAAAGATTGAAG
1 GAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGCTGGGAAAGATTGAAG
** *
12369794 CTGCAACGGTGAATCTAGTACCACGAAGATATG
66 CTGCAACGACGAATCTGGTACCACGAAGATATG
* *
12369827 GAGGGAAAGGTTTAAGTCACAATGGCGAACCTTGTACCTCAAAAACATGCTAGGAAAGATTGAAG
1 GAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGCTGGGAAAGATTGAAG
* *
12369892 -TCGCAACGGCGAATCTGGTACCACGAAGATACG
66 CT-GCAACGACGAATCTGGTACCACGAAGATATG
* * * * * * *
12369925 GAAGGAAAGGTTTAAGCCACAACGACGAACCTTGTACCTCAAAAACTTGCTAGGAAAGATTGAAG
1 GAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGCTGGGAAAGATTGAAG
* * *
12369990 CCGTAACGACAAATCTGGTACCA-GAAGATATG
66 CTGCAACGACGAATCTGGTACCACGAAGATATG
* * * *
12370022 GAGGGAAAGGTTGAAGTCGCAACGGTGAACCTTGTACCTCATAAACATGCTGGGAAAGATTGAAG
1 GAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGCTGGGAAAGATTGAAG
* * * *
12370087 CCGCAACAACGAATCTGGTACCACTAAGATACG
66 CTGCAACGACGAATCTGGTACCACGAAGATATG
* * *
12370120 GAAGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAACATGCTGGGAAAGATTGAAG
1 GAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGCTGGGAAAGATTGAAG
* ** *
12370185 ATGCAATAACGAATCTGGTACCACAAAGATATG
66 CTGCAACGACGAATCTGGTACCACGAAGATATG
* *
12370218 GAGGGAAACGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAGACAT
1 GAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACAT
12370266 AAAGGGAAAG
Statistics
Matches: 476, Mismatches: 58, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
97 85 0.18
98 391 0.82
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (98 bp):
GAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAAACATGCTGGGAAAGATTGAAG
CTGCAACGACGAATCTGGTACCACGAAGATATG
Found at i:12370168 original size:293 final size:294
Alignment explanation
Indices: 12369656--12370265 Score: 846
Period size: 293 Copynumber: 2.1 Consensus size: 294
12369646 GTCGTAATGG
* * * ***
12369656 CGAACCTTGTACCTCAGAAACATGCTGGGAAAGATTGAAGCTATAACGGTGAATCTGGTACCACA
1 CGAACCTTGTACCTCAAAAACATGCTAGGAAAGATTGAAGCCATAACGACAAATCTGGTACCACA
* * *
12369721 AAGATATGGAGGGAAAGGTTTAAGTCGTAACGGCAAACCTTGTACCTCAAAAACATGTTGGGAAA
66 AAGATATGGAGGGAAAGGTTGAAGTCGCAACGGCAAACCTTGTACCTCAAAAACATGCTGGGAAA
* *** * *
12369786 GATTGAAGCTGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAATG
131 GATTGAAGCCGCAACAACGAATCTAGTACCACGAAGATACGGAAGGAAAGGTTTAAGTCACAATG
* **
12369851 GCGAACCTTGTACCTCAAAAACATGCTAGGAAAGATTGAAG-TCGCAACGGCGAATCTGGTACCA
196 ACGAACCTTGTACCTCAAAAACATGCTAGGAAAGATTGAAGAT-GCAACAACGAATCTGGTACCA
* *
12369915 CGAAGATACGGAAGGAAAGGTTTAAGCCACAACGA
260 CAAAGATACGGAAGGAAACGTTTAAGCCACAACGA
* * *
12369950 CGAACCTTGTACCTCAAAAACTTGCTAGGAAAGATTGAAGCCGTAACGACAAATCTGGTACCA-G
1 CGAACCTTGTACCTCAAAAACATGCTAGGAAAGATTGAAGCCATAACGACAAATCTGGTACCACA
** *
12370014 AAGATATGGAGGGAAAGGTTGAAGTCGCAACGGTGAACCTTGTACCTCATAAACATGCTGGGAAA
66 AAGATATGGAGGGAAAGGTTGAAGTCGCAACGGCAAACCTTGTACCTCAAAAACATGCTGGGAAA
* * *
12370079 GATTGAAGCCGCAACAACGAATCTGGTACCACTAAGATACGGAAGGAAAGGTTTAAGTCGCAATG
131 GATTGAAGCCGCAACAACGAATCTAGTACCACGAAGATACGGAAGGAAAGGTTTAAGTCACAATG
* * *
12370144 ACGAACCTTGTACCTCAGAAACATGCTGGGAAAGATTGAAGATGCAATAACGAATCTGGTACCAC
196 ACGAACCTTGTACCTCAAAAACATGCTAGGAAAGATTGAAGATGCAACAACGAATCTGGTACCAC
* * * * * *
12370209 AAAGATATGGAGGGAAACGTTTAAGTCGCAATGG
261 AAAGATACGGAAGGAAACGTTTAAGCCACAACGA
*
12370243 CGAACCTTGTACCTCAAAGACAT
1 CGAACCTTGTACCTCAAAAACAT
12370266 AAAGGGAAAG
Statistics
Matches: 275, Mismatches: 40, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
293 219 0.80
294 56 0.20
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (294 bp):
CGAACCTTGTACCTCAAAAACATGCTAGGAAAGATTGAAGCCATAACGACAAATCTGGTACCACA
AAGATATGGAGGGAAAGGTTGAAGTCGCAACGGCAAACCTTGTACCTCAAAAACATGCTGGGAAA
GATTGAAGCCGCAACAACGAATCTAGTACCACGAAGATACGGAAGGAAAGGTTTAAGTCACAATG
ACGAACCTTGTACCTCAAAAACATGCTAGGAAAGATTGAAGATGCAACAACGAATCTGGTACCAC
AAAGATACGGAAGGAAACGTTTAAGCCACAACGA
Found at i:12370240 original size:49 final size:48
Alignment explanation
Indices: 12369706--12370280 Score: 266
Period size: 49 Copynumber: 11.8 Consensus size: 48
12369696 CTATAACGGT
* * *
12369706 GAATCTGGTACCACAAAGATATGGAGGGAAAGGTTTAAGTCGTAACGGC
1 GAATCTGGTACCACAAAGATATGGAGGGAAA-GTTGAAGTCGCAACGAC
* * * * * * ** **
12369755 AAACCTTGTACCTCAAAAACATGTTGGGAAAGATTGAAG-CTGCAACGGT
1 GAATCTGGTACCACAAAGATATGGAGGGAAAG-TTGAAGTC-GCAACGAC
* * * * * *
12369804 GAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAATGGC
1 GAATCTGGTACCACAAAGATATGGAGGGAAA-GTTGAAGTCGCAACGAC
* * * * * * *
12369853 GAACCTTGTACCTCAAAAACATGCTA-GGAAAGATTGAAGTCGCAACGGC
1 GAATCTGGTACCACAAAGATATG-GAGGGAAAG-TTGAAGTCGCAACGAC
* * * * * *
12369902 GAATCTGGTACCACGAAGATACGGAAGGAAAGGTTTAAGCCACAACGAC
1 GAATCTGGTACCACAAAGATATGGAGGGAAA-GTTGAAGTCGCAACGAC
* * * * * * *
12369951 GAACCTTGTACCTCAAAAACT-TGCTA-GGAAAGATTGAAGCCGTAACGAC
1 GAATCTGGTACCACAAAGA-TATG-GAGGGAAAG-TTGAAGTCGCAACGAC
* * **
12370000 AAATCTGGTACCA-GAAGATATGGAGGGAAAGGTTGAAGTCGCAACGGT
1 GAATCTGGTACCACAAAGATATGGAGGGAAA-GTTGAAGTCGCAACGAC
* * * * ** * *
12370048 GAACCTTGTACCTCATAA-ACATGCTGGGAAAGATTGAAGCCGCAACAAC
1 GAATCTGGTACCACA-AAGATATGGAGGGAAAG-TTGAAGTCGCAACGAC
* * * * *
12370097 GAATCTGGTACCACTAAGATACGGAAGGAAAGGTTTAAGTCGCAATGAC
1 GAATCTGGTACCACAAAGATATGGAGGGAAA-GTTGAAGTCGCAACGAC
* * * * ** **
12370146 GAACCTTGTACCTCAGAA-ACATGCTGGGAAAGATTGAAGAT-GCAATAAC
1 GAATCTGGTACCACA-AAGATATGGAGGGAAAG-TTGAAG-TCGCAACGAC
* * *
12370195 GAATCTGGTACCACAAAGATATGGAGGGAAACGTTTAAGTCGCAATGGC
1 GAATCTGGTACCACAAAGATATGGAGGGAAA-GTTGAAGTCGCAACGAC
* * * * **
12370244 GAACCTTGTACCTCAAAGACATAAAGGGAAAGGTTGA
1 GAATCTGGTACCACAAAGATATGGAGGGAAA-GTTGA
12370281 GGCCACCACG
Statistics
Matches: 381, Mismatches: 120, Indels: 50
0.69 0.22 0.09
Matches are distributed among these distances:
47 2 0.01
48 43 0.11
49 323 0.85
50 13 0.03
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (48 bp):
GAATCTGGTACCACAAAGATATGGAGGGAAAGTTGAAGTCGCAACGAC
Found at i:12370740 original size:38 final size:38
Alignment explanation
Indices: 12370618--12370897 Score: 173
Period size: 38 Copynumber: 7.3 Consensus size: 38
12370608 CCCGATCATG
* * *
12370618 AGGCACATTGAAGAATCTAATCTCTTACCCTAATCA-A
1 AGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGA
* * * **
12370655 AGGGCAGAAGTGAAGACATACCAATATCTTGCCCCAATCATG-
1 A-GGCAG-ATTGAAGA-AT-CCAATCTCTTACCTTAATCA-GA
* *
12370697 GGGCAGATTGAAGAATTCAATCTCTTACCTTAATCAGA
1 AGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGA
* *
12370735 AGGCAGATTGAAGACA-CCAATCTCTTTCCTCAATCATG-
1 AGGCAGATTGAAGA-ATCCAATCTCTTACCTTAATCA-GA
* * * * * *
12370773 AGGCAGATCGCAAGCATACAATCTTTTACCTTCATCAAA
1 AGGCAGATTG-AAGAATCCAATCTCTTACCTTAATCAGA
* ***
12370812 AGGTA-AGTTGAAGAA---AATCTCTTACCCCGATCATG-
1 AGGCAGA-TTGAAGAATCCAATCTCTTACCTTAATCA-GA
* * * *
12370847 AGGTAGATTGAAGCATCCAATCTTTTACCTTAATTAGA
1 AGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGA
12370885 AGGCAGATTGAAG
1 AGGCAGATTGAAG
12370898 CTACCATCTC
Statistics
Matches: 184, Mismatches: 40, Indels: 37
0.70 0.15 0.14
Matches are distributed among these distances:
35 26 0.14
36 1 0.01
37 3 0.02
38 89 0.48
39 35 0.19
40 9 0.05
41 21 0.11
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (38 bp):
AGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGA
Found at i:12371368 original size:18 final size:18
Alignment explanation
Indices: 12371345--12371389 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
12371335 GTCTGCTCTA
12371345 GAGACC-CTTCCTCTGCCC
1 GAGACCTCTT-CTCTGCCC
* *
12371363 GAGACCTCTTGTGTGCCC
1 GAGACCTCTTCTCTGCCC
12371381 GAGACCTCT
1 GAGACCTCT
12371390 CGTCTGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.13, C:0.40, G:0.22, T:0.24
Consensus pattern (18 bp):
GAGACCTCTTCTCTGCCC
Found at i:12371767 original size:66 final size:67
Alignment explanation
Indices: 12371642--12371786 Score: 163
Period size: 66 Copynumber: 2.1 Consensus size: 67
12371632 TTTGTGTTTG
* * *
12371642 TTTTATTTTTTTTATATATATACGCATGTATATGTATATATATACATAGATATACATTTCAATTT
1 TTTTATTTATTTTATATATATACGCATG-ATACGTATATATATACATACATATACATTTC-ATTT
12371707 TATT-
64 T-TTA
* **
12371711 TTTTATTTATTTT-TATATATACGCATG-TACGTATATAT-TAACATACATCTTGATTTCATTTT
1 TTTTATTTATTTTATATATATACGCATGATACGTATATATAT-ACATACATATACATTTCATTTT
12371773 TTA
65 TTA
12371776 TTGTTATTTAT
1 TT-TTATTTAT
12371787 ATACTTACGT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
64 2 0.03
65 8 0.12
66 31 0.46
68 14 0.21
69 12 0.18
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.55
Consensus pattern (67 bp):
TTTTATTTATTTTATATATATACGCATGATACGTATATATATACATACATATACATTTCATTTTT
TA
Found at i:12379647 original size:41 final size:41
Alignment explanation
Indices: 12379571--12379649 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
12379561 AATGCAGCAA
* *
12379571 GCACATTCTGTCCAGCATTGCAATAGTACTGTGGGTAGTTG
1 GCACATTCTGTCCAGCATTGCAATAATACTATGGGTAGTTG
* *
12379612 GCACATTTTGTCCAGCATTGCAATAATATTATGGGTAG
1 GCACATTCTGTCCAGCATTGCAATAATACTATGGGTAG
12379650 AATGCAGCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (41 bp):
GCACATTCTGTCCAGCATTGCAATAATACTATGGGTAGTTG
Found at i:12380637 original size:24 final size:25
Alignment explanation
Indices: 12380604--12380657 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
12380594 TTATTCCTGC
* *
12380604 AAAATTAAAGA-AACAAATTAA-AGT
1 AAAATAAAAGACAA-AAATTAACAGA
12380628 AAAATAAAAGACAAAAATTAACAGA
1 AAAATAAAAGACAAAAATTAACAGA
12380653 AAAAT
1 AAAAT
12380658 TACAATGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (25 bp):
AAAATAAAAGACAAAAATTAACAGA
Found at i:12380656 original size:13 final size:12
Alignment explanation
Indices: 12380604--12380656 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
12380594 TTATTCCTGC
12380604 AAAATTAAAGAA
1 AAAATTAAAGAA
*
12380616 ACAAATTAAAG-T
1 A-AAATTAAAGAA
*
12380628 AAAATAAAAGACA
1 AAAATTAAAGA-A
12380641 AAAATTAACAGAA
1 AAAATTAA-AGAA
12380654 AAA
1 AAA
12380657 TTACAATGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 8 0.24
12 2 0.06
13 20 0.61
14 3 0.09
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAATTAAAGAA
Found at i:12391017 original size:9 final size:9
Alignment explanation
Indices: 12391003--12391031 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
12390993 TGACACCTAT
12391003 AGAATTGAA
1 AGAATTGAA
12391012 AGAATTGAA
1 AGAATTGAA
12391021 AGAATTGAA
1 AGAATTGAA
12391030 AG
1 AG
12391032 TACAATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (9 bp):
AGAATTGAA
Found at i:12396367 original size:25 final size:25
Alignment explanation
Indices: 12396339--12396386 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
12396329 TGAATAATAA
*
12396339 AATAAAATAAATAACATTAATAACT
1 AATAAAATAAATAACATAAATAACT
* *
12396364 AATACAATTAATAACATAAATAA
1 AATAAAATAAATAACATAAATAA
12396387 ATAAAATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (25 bp):
AATAAAATAAATAACATAAATAACT
Found at i:12396562 original size:11 final size:10
Alignment explanation
Indices: 12396547--12396619 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
12396537 TGACATAAGA
12396547 AATAAATAAT
1 AATAAATAAT
*
12396557 AGATAAA-CA-
1 A-ATAAATAAT
*
12396566 AATACAAAAAT
1 AATA-AATAAT
*
12396577 AATATATAA-
1 AATAAATAAT
12396586 AATAAATACA-
1 AATAAATA-AT
12396596 AA-AAA-AAT
1 AATAAATAAT
12396604 AATAAATAAT
1 AATAAATAAT
12396614 AATAAA
1 AATAAA
12396620 GGAGAAAAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
7 1 0.02
8 6 0.12
9 16 0.32
10 18 0.36
11 9 0.18
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.22
Consensus pattern (10 bp):
AATAAATAAT
Found at i:12396576 original size:27 final size:27
Alignment explanation
Indices: 12396546--12396612 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 27
12396536 ATGACATAAG
*
12396546 AAATAAATAATAGATAAACAAATACAA
1 AAATAAATAATAAATAAACAAATACAA
* *
12396573 AAAT-AAT-ATATA-AAATAAATACAA
1 AAATAAATAATAAATAAACAAATACAA
12396597 AAA-AAATAATAAATAA
1 AAATAAATAATAAATAA
12396613 TAATAAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 17 0.50
25 8 0.24
26 5 0.15
27 4 0.12
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.21
Consensus pattern (27 bp):
AAATAAATAATAAATAAACAAATACAA
Found at i:12397700 original size:21 final size:22
Alignment explanation
Indices: 12397663--12397710 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
12397653 TATAGCCTAA
12397663 ATTTTTACATCTATATTT-TTCT
1 ATTTTTACATCTATATTTGTT-T
12397685 ATTTTGTAC-TCT-TATTTGTTT
1 ATTTT-TACATCTATATTTGTTT
12397706 ATTTT
1 ATTTT
12397711 CTCCTTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 11 0.46
22 10 0.42
23 3 0.12
ACGTcount: A:0.19, C:0.10, G:0.04, T:0.67
Consensus pattern (22 bp):
ATTTTTACATCTATATTTGTTT
Found at i:12397946 original size:17 final size:18
Alignment explanation
Indices: 12397926--12397963 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12397916 TTTTTTATTA
*
12397926 TTTTTAGTAT-TTTGGAC
1 TTTTTAGTATATGTGGAC
*
12397943 TTTTTATTATATGTGGAC
1 TTTTTAGTATATGTGGAC
12397961 TTT
1 TTT
12397964 ACTTATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (18 bp):
TTTTTAGTATATGTGGAC
Found at i:12398878 original size:15 final size:15
Alignment explanation
Indices: 12398858--12398888 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12398848 CGTAAAAAGT
*
12398858 GCCGCTAAAGATAAC
1 GCCGCTAAAAATAAC
12398873 GCCGCTAAAAATAAC
1 GCCGCTAAAAATAAC
12398888 G
1 G
12398889 GCGTTTATGA
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:0.42, C:0.26, G:0.19, T:0.13
Consensus pattern (15 bp):
GCCGCTAAAAATAAC
Found at i:12399047 original size:43 final size:43
Alignment explanation
Indices: 12398907--12399128 Score: 261
Period size: 43 Copynumber: 5.2 Consensus size: 43
12398897 GAGAAAAAAT
*
12398907 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-CCTACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
* * * * * * *
12398949 ACCACTAAAGAACATGGTCTTTAACGGCAG--TTACCTATAAAT
1 GCCGCTAAAGAACATGGTCTTTAGCGGC-GCTTTCCCCACAAAC
* * *
12398991 GCCTCTAAAGAACATAGTCTTTAGCGGTGCTTTCCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
* * *
12399034 GTCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCATAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
* *
12399077 GCCACTAAAGAACATGGTCTTTAGCGACGCTTTCCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
*
12399120 ACCGCTAAA
1 GCCGCTAAA
12399129 ATTAACAGAT
Statistics
Matches: 149, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
41 3 0.02
42 55 0.37
43 91 0.61
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAAC
Found at i:12399101 original size:86 final size:85
Alignment explanation
Indices: 12398911--12399128 Score: 296
Period size: 86 Copynumber: 2.6 Consensus size: 85
12398901 AAAAATGCCG
* *
12398911 CTAAAGAACATGGTCTTTAGCGGCGCTTT-CCTACAAACACCACTAAAGAACATGGTCTTTAACG
1 CTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAGAACATGGTCTTTAACG
* * *
12398975 GCAGTTACCTATAAATGCCT
66 GCAGTTACCCATAAACGCCA
* * ** *
12398995 CTAAAGAACATAGTCTTTAGCGGTGCTTTCCCCACAAACGTCGCTAAAGAACATGGTCTTTAGCG
1 CTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAGAACATGGTCTTTAACG
*
12399060 GC-GCTTTTCCCATAAACGCCA
66 GCAG--TTACCCATAAACGCCA
*
12399081 CTAAAGAACATGGTCTTTAGCGACGCTTTCCCCACAAACACCGCTAAA
1 CTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAA
12399129 ATTAACAGAT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
84 28 0.24
85 32 0.28
86 55 0.48
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (85 bp):
CTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAGAACATGGTCTTTAACG
GCAGTTACCCATAAACGCCA
Found at i:12403265 original size:41 final size:41
Alignment explanation
Indices: 12403048--12403264 Score: 308
Period size: 41 Copynumber: 5.3 Consensus size: 41
12403038 TTTAAATAAA
* * *
12403048 TTAGCGGTGCTTTCTCATAAACGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
12403089 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* * * *
12403130 TTAGCAGCGCTTTCCCATAAGTGTCGCTATTTCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* *
12403171 TTAGCTGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
* ** * *
12403212 TTAGCGGCGCTTACCCATAAATGCCGCTATTACTCTAACCT
1 TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
12403253 TTAGCGGCGCTT
1 TTAGCGGCGCTT
12403265 ATTGCTCTGA
Statistics
Matches: 158, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 158 1.00
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTCTGACCT
Found at i:12403272 original size:25 final size:25
Alignment explanation
Indices: 12403239--12403289 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
12403229 TAAATGCCGC
12403239 TATTACTCTAACCTTTAGCGGCGCT
1 TATTACTCTAACCTTTAGCGGCGCT
* * *
12403264 TATTGCTCTGACCTTTAGCGGTGCT
1 TATTACTCTAACCTTTAGCGGCGCT
12403289 T
1 T
12403290 GCCCATAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (25 bp):
TATTACTCTAACCTTTAGCGGCGCT
Found at i:12403304 original size:66 final size:66
Alignment explanation
Indices: 12403190--12403330 Score: 196
Period size: 66 Copynumber: 2.2 Consensus size: 66
12403180 CTTGCCCATA
* *
12403190 AGCGCCGC-TATTGCTCTGACCTTTAGCGGCGCTTACCCATAAATGCCGCTATTACTCT-AACCT
1 AGCGGCGCTTATTGCTCTGACCTTTAGCGGCGCTTACCCATAAACGCCGCTATTACTCTGAA-CT
12403253 TT
65 TT
* * * * *
12403255 AGCGGCGCTTATTGCTCTGACCTTTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTTTGAACTT
1 AGCGGCGCTTATTGCTCTGACCTTTAGCGGCGCTTACCCATAAACGCCGCTATTACTCTGAACTT
12403320 T
66 T
12403321 AGCGGCGCTT
1 AGCGGCGCTT
12403331 TCCCATAAGC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 7 0.10
66 58 0.87
67 2 0.03
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.31
Consensus pattern (66 bp):
AGCGGCGCTTATTGCTCTGACCTTTAGCGGCGCTTACCCATAAACGCCGCTATTACTCTGAACTT
T
Found at i:12403321 original size:41 final size:41
Alignment explanation
Indices: 12403255--12403606 Score: 481
Period size: 41 Copynumber: 8.6 Consensus size: 41
12403245 TCTAACCTTT
* *
12403255 AGCGGCGCTTATTGCTCTGACCTTTAGCGGTGCTTGCCCATA
1 AGCGCCGC-TATTGCTCTGACCTTTAGCGGCGCTTGCCCATA
* * *
12403297 AGCGCCGCTATTGCTTTGAACTTTAGCGGCGCTTTCCCATA
1 AGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATA
* * * **
12403338 AGCGCCGCTATTGCTTTGACCTTCAGCAGCGCTTTACCATA
1 AGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATA
* *
12403379 AGCGCCGCTATTGCTCTAACCTTTAGCGACGCTTGCCCATA
1 AGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATA
* **
12403420 AGCACCGCTATCACTCTGACCTTTAGCGGCGCTTGCCCATA
1 AGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATA
* *
12403461 AGCGCTGCTATTGCTCTGACCTTTAGCGACGCTTGCCCATA
1 AGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATA
* * *
12403502 AGCGTCACTATTGCTCTGACCTTTAGCGGCGCTTTCCCATA
1 AGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATA
* *
12403543 AGCGCCGCTATTGCTCTGACCTTTAGTGGCGCTTTCCCATA
1 AGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATA
*
12403584 AGCGCTGCTATTGCTCT-ACCTTT
1 AGCGCCGCTATTGCTCTGACCTTT
12403607 TGCCTATTGG
Statistics
Matches: 275, Mismatches: 35, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 6 0.02
41 262 0.95
42 7 0.03
ACGTcount: A:0.17, C:0.32, G:0.21, T:0.30
Consensus pattern (41 bp):
AGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCCATA
Found at i:12403348 original size:107 final size:107
Alignment explanation
Indices: 12403157--12403349 Score: 314
Period size: 107 Copynumber: 1.8 Consensus size: 107
12403147 TAAGTGTCGC
* * *
12403157 TATTTCTCTGACCTTTAGCTGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGAACTTTAGCGGCGC
*
12403222 TTACCCATAAATGCCGCTATTACTCTAACCTTTAGCGGCGCT
66 TTACCCATAAACGCCGCTATTACTCTAACCTTTAGCGGCGCT
* *
12403264 TATTGCTCTGACCTTTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTTTGAACTTTAGCGGCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGAACTTTAGCGGCGC
* *
12403329 TTTCCCATAAGCGCCGCTATT
66 TTACCCATAAACGCCGCTATT
12403350 GCTTTGACCT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 78 1.00
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.32
Consensus pattern (107 bp):
TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGAACTTTAGCGGCGC
TTACCCATAAACGCCGCTATTACTCTAACCTTTAGCGGCGCT
Found at i:12403360 original size:107 final size:107
Alignment explanation
Indices: 12403157--12403371 Score: 313
Period size: 107 Copynumber: 2.0 Consensus size: 107
12403147 TAAGTGTCGC
* * *
12403157 TATTTCTCTGACCTTTAGCTGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGAACTTTAGCGGCGC
* * *
12403222 TTACCCATAAATGCCGCTATTACTCTAACCTTTAGCGGCGCT
66 TTACCCATAAACGCCGCTATTACTCTAACCTTCAGCAGCGCT
* *
12403264 TATTGCTCTGACCTTTAGCGGTGCTTGCCCATAAGCGCCGCTATTGCTTTGAACTTTAGCGGCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGAACTTTAGCGGCGC
* * * * *
12403329 TTTCCCATAAGCGCCGCTATTGCTTTGACCTTCAGCAGCGCT
66 TTACCCATAAACGCCGCTATTACTCTAACCTTCAGCAGCGCT
12403371 T
1 T
12403372 TACCATAAGC
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
107 95 1.00
ACGTcount: A:0.17, C:0.31, G:0.20, T:0.32
Consensus pattern (107 bp):
TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGAACTTTAGCGGCGC
TTACCCATAAACGCCGCTATTACTCTAACCTTCAGCAGCGCT
Found at i:12403615 original size:19 final size:19
Alignment explanation
Indices: 12403591--12403628 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12403581 ATAAGCGCTG
12403591 CTATTGCTCTACCTTTTGC
1 CTATTGCTCTACCTTTTGC
* *
12403610 CTATTGGTTTACCTTTTGC
1 CTATTGCTCTACCTTTTGC
12403629 GGCTTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.26, G:0.13, T:0.50
Consensus pattern (19 bp):
CTATTGCTCTACCTTTTGC
Found at i:12405430 original size:21 final size:22
Alignment explanation
Indices: 12405404--12405445 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
12405394 ATCAAAAAGA
12405404 AAAAGAAAAATGAGT-AGAAAT
1 AAAAGAAAAATGAGTAAGAAAT
**
12405425 AAAAGAAGCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
12405446 ACATGTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAT
Found at i:12408743 original size:12 final size:12
Alignment explanation
Indices: 12408726--12408757 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
12408716 TGAAAAACAT
*
12408726 AAAATAAAGTAG
1 AAAATAAAATAG
12408738 AAAATAAAATAG
1 AAAATAAAATAG
12408750 AAAATAAA
1 AAAATAAA
12408758 TGCAAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAG
Found at i:12412394 original size:739 final size:739
Alignment explanation
Indices: 12410978--12414772 Score: 7473
Period size: 739 Copynumber: 5.1 Consensus size: 739
12410968 TGGTAATTAA
12410978 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
1 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
12411043 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
66 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
*
12411108 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTAGATGGTAAATATACCATATACTTATATTA
131 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
12411173 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
196 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
12411238 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
261 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
12411303 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
326 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
12411368 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
391 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
* *
12411433 ACTCGGGGACTAATTTGCACAATTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
456 ACTCGGGGACTAATTTGTACAACTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
12411498 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
521 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
12411563 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
586 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
12411628 TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTTTGCTTGAAAT
651 TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTTTGCTTGAAAT
12411693 TGGTTAAATTGCAAGTTTTGAGCT
716 TGGTTAAATTGCAAGTTTTGAGCT
12411717 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
1 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
12411782 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
66 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
12411847 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
131 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
12411912 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
196 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
*
12411977 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATGTTTTCTCTTTCTTCTTCC
261 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
12412042 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
326 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
12412107 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
391 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
12412172 ACTCGGGGACTAATTTGTACAACTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
456 ACTCGGGGACTAATTTGTACAACTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
12412237 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
521 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
12412302 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
586 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
*
12412367 TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTCTGCTTGAAAT
651 TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTTTGCTTGAAAT
12412432 TGGTTAAATTGCAAGTTTTGAGCT
716 TGGTTAAATTGCAAGTTTTGAGCT
12412456 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
1 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
12412521 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
66 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
12412586 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
131 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
12412651 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
196 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
12412716 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
261 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
12412781 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
326 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
12412846 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
391 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
12412911 ACTCGGGGACTAATTTGTACAACTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
456 ACTCGGGGACTAATTTGTACAACTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
12412976 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
521 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
12413041 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
586 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
*
12413106 TAACAGCATGTATGGACTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTTTGCTTGAAAT
651 TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTTTGCTTGAAAT
12413171 TGGTTAAATTGCAAGTTTTGAGCT
716 TGGTTAAATTGCAAGTTTTGAGCT
12413195 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
1 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
12413260 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
66 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
12413325 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
131 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
12413390 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
196 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
12413455 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
261 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
12413520 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
326 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
12413585 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
391 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
12413650 ACTCGGGGACTAATTTGTACAACTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
456 ACTCGGGGACTAATTTGTACAACTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
12413715 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
521 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
12413780 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
586 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
*
12413845 TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTCTGCTTGAAAT
651 TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTTTGCTTGAAAT
12413910 TGGTTAAATTGCAAGTTTTGAGCT
716 TGGTTAAATTGCAAGTTTTGAGCT
12413934 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
1 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
12413999 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
66 TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
12414064 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
131 AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
12414129 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
196 AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
12414194 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
261 ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
12414259 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
326 TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
*
12414324 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCATATTAGCTTGATTTGGATA
391 AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
*
12414389 ACTCGGGGACTAATTTGTACAATTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
456 ACTCGGGGACTAATTTGTACAACTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
*
12414454 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAAGACTATTTTGTAAAGTAGTTT
521 TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
12414519 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
586 TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
12414584 TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTTTGCTTGAAAT
651 TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTTTGCTTGAAAT
12414649 TGGTTAAATTGCAAGTTTTGAGCT
716 TGGTTAAATTGCAAGTTTTGAGCT
* *
12414673 AAAATGGTCAAAAATTCCAAGAGGTGGTGGATATGATTACCTTCCACTAACTTTTGGGTTATTTT
1 AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
12414738 TTTATTTAGTCCTAATTAGTTTAGGGACTAAATTG
66 TTTATTTAGTCCTAATTAGTTTA-GGACTAAATTG
12414773 CATAAAAGTA
Statistics
Matches: 3039, Mismatches: 16, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
739 3028 1.00
740 11 0.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (739 bp):
AAAATGGTCAAAAAGTCCAAGAGGTGGTGGATATGATTACCATCCACTAACTTTTGGGTTATTTT
TTTATTTAGTCCTAATTAGTTTAGGACTAAATTGGAATTAAGCTAGTTTAGTTAAAATTAAAGAT
AATTGAAGGACCAATGGTGCAATTAAACCTTCCTTGGATGGTAAATATACCATATACTTATATTA
AGGACATTTATGGGCATGTTTTAATGATTTTATATGTTAAAATTAAAAGGTTAATTTGGTAAAAG
ATTAAATGATAAGTTAAATTAAATAAGTTAAAAGTAATATTATCATTTTTTCTCTTTCTTCTTCC
TAAAAGTCGAAACACCATGGAAAGGAGAAAGTTTATTCAACCAAGCTAGGGTTTATTGTTTTGGT
AGTTAAATCTTACCTCTTTTTAGTAATTTTTATGTTTTTGAACTCGTATTAGCTTGATTTGGATA
ACTCGGGGACTAATTTGTACAACTGTCAAATGTTTTGGATTATTCCATTGATGAGTTTTGGATAT
TATTAAAGTTTTATGATGGATTATTAAGTTTGGTTGTTAAATAGGACTATTTTGTAAAGTAGTTT
TTGTTAATTTTAATGTTTAAAGACTAAAATGCTAAAGTGATAAAATTAAGAAGACTTGTATGAAA
TAACAGCATGTATGGGCTGTAGAGAACTATAGTATAATTTGGCTAAACTTAGTTTTGCTTGAAAT
TGGTTAAATTGCAAGTTTTGAGCT
Found at i:12415106 original size:27 final size:27
Alignment explanation
Indices: 12415068--12415272 Score: 197
Period size: 27 Copynumber: 7.6 Consensus size: 27
12415058 TAAGAAATAC
*
12415068 TCTGTAGT-TGGCTCGAACGAGCATTAT
1 TCTGTA-TCTGGCTCGAAAGAGCATTAT
* *
12415095 TCTGTATCTGGCTCAAAATAGCATTAT
1 TCTGTATCTGGCTCGAAAGAGCATTAT
*
12415122 TCTGTATCTGGCTTGAAAGAGCATTAT
1 TCTGTATCTGGCTCGAAAGAGCATTAT
12415149 TCTGTATCTGGCTCGAAAGAGCATTAT
1 TCTGTATCTGGCTCGAAAGAGCATTAT
* *
12415176 TCTGTGTCTGGCTCGAATA-AGCCAAT-T
1 TCTGTATCTGGCTCGAA-AGAG-CATTAT
* * * * *
12415203 TCTGAATCTAGCTCGAATGAGCAATAA
1 TCTGTATCTGGCTCGAAAGAGCATTAT
* *
12415230 TATGT-TCTGGGCTCGAATGAGC-TATAT
1 TCTGTATCT-GGCTCGAAAGAGCAT-TAT
*
12415257 TCTGTAAC-GGCTCGAA
1 TCTGTATCTGGCTCGAA
12415273 TAATCATATT
Statistics
Matches: 149, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
26 16 0.11
27 128 0.86
28 5 0.03
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (27 bp):
TCTGTATCTGGCTCGAAAGAGCATTAT
Found at i:12415206 original size:81 final size:81
Alignment explanation
Indices: 12415063--12415285 Score: 217
Period size: 81 Copynumber: 2.8 Consensus size: 81
12415053 AGGCTTAAGA
* * * *
12415063 AATACTCTGTAGT-TGGCTCGAACGAGCATTATTCTGTATCTGGCTC-AAAATAGCATTATTCTG
1 AATAATCTGTA-TCTGGCTCGAAAGAGCATTATTCTGTATCTGGCTCGAATA-AGCAATATTCTG
* * *
12415126 TATCTGGCTTGAAAGAGC
64 AATCTAGCTCGAAAGAGC
* * *
12415144 ATTATTCTGTATCTGGCTCGAAAGAGCATTATTCTGTGTCTGGCTCGAATAAGCCAAT-TTCTGA
1 AATAATCTGTATCTGGCTCGAAAGAGCATTATTCTGTATCTGGCTCGAATAAG-CAATATTCTGA
*
12415208 ATCTAGCTCGAATGAGC
65 ATCTAGCTCGAAAGAGC
* * * *
12415225 AATAATATGT-TCTGGGCTCGAATGAGC-TATATTCTGTAAC-GGCTCGAATAATC-ATATTCTG
1 AATAATCTGTATCT-GGCTCGAAAGAGCAT-TATTCTGTATCTGGCTCGAATAAGCAATATTCTG
12415286 TCACAGTGGA
Statistics
Matches: 119, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
78 2 0.02
79 6 0.05
80 16 0.13
81 89 0.75
82 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (81 bp):
AATAATCTGTATCTGGCTCGAAAGAGCATTATTCTGTATCTGGCTCGAATAAGCAATATTCTGAA
TCTAGCTCGAAAGAGC
Found at i:12417048 original size:30 final size:30
Alignment explanation
Indices: 12417013--12417078 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
12417003 TTTTTCGATC
12417013 TCTTCTTAGCTTCTTTAGGCTTGCTGGGTT
1 TCTTCTTAGCTTCTTTAGGCTTGCTGGGTT
* * ** *
12417043 TCTTCTTTGGTTCTTTAGGCTTTTTTGGTT
1 TCTTCTTAGCTTCTTTAGGCTTGCTGGGTT
12417073 TCTTCT
1 TCTTCT
12417079 CTGGCACCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.05, C:0.18, G:0.20, T:0.58
Consensus pattern (30 bp):
TCTTCTTAGCTTCTTTAGGCTTGCTGGGTT
Found at i:12425519 original size:36 final size:38
Alignment explanation
Indices: 12425467--12425538 Score: 114
Period size: 37 Copynumber: 1.9 Consensus size: 38
12425457 ATATTAGTTT
12425467 TTTAAAATATTTTAATGAAATT-TTTA-AAAATAATTAA
1 TTTAAAATATTTTAATGAAATTCTTTACAAAA-AATTAA
12425504 TTTAAAAT-TTTTAATGAAATTCTTTACAAAAAATT
1 TTTAAAATATTTTAATGAAATTCTTTACAAAAAATT
12425539 GAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 13 0.39
37 16 0.48
38 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (38 bp):
TTTAAAATATTTTAATGAAATTCTTTACAAAAAATTAA
Found at i:12428084 original size:25 final size:25
Alignment explanation
Indices: 12428056--12428106 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
12428046 GAAGTAACAT
*
12428056 AACTAATTGAGATCTCTTCGTTATC
1 AACTAATTGAGATCTCTTCATTATC
12428081 AACTAATTGAGATCTCTTCATTATC
1 AACTAATTGAGATCTCTTCATTATC
12428106 A
1 A
12428107 CCATTTTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (25 bp):
AACTAATTGAGATCTCTTCATTATC
Found at i:12440716 original size:25 final size:26
Alignment explanation
Indices: 12440688--12440744 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
12440678 GGTCTTTCAG
*
12440688 AAATTTAGCTCATA-GAGCCCAGACA
1 AAATTTAGCTCATACGAGCCCAAACA
*
12440713 AAA-TTAGCTCTTACGAGCCCAAACA
1 AAATTTAGCTCATACGAGCCCAAACA
*
12440738 AAGTTTA
1 AAATTTA
12440745 ACCATTATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 9 0.33
25 15 0.56
26 3 0.11
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (26 bp):
AAATTTAGCTCATACGAGCCCAAACA
Found at i:12446492 original size:20 final size:20
Alignment explanation
Indices: 12446467--12446515 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
12446457 GGAGACTACA
12446467 TGGTTAAAATGATTTTGACT
1 TGGTTAAAATGATTTTGACT
* *
12446487 TGGTTAAATTTATTTTGACT
1 TGGTTAAAATGATTTTGACT
*
12446507 TGTTTAAAA
1 TGGTTAAAA
12446516 ACATTTTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (20 bp):
TGGTTAAAATGATTTTGACT
Found at i:12446521 original size:20 final size:20
Alignment explanation
Indices: 12446467--12446528 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
12446457 GGAGACTACA
**
12446467 TGGTTAAAATGATTTTGACT
1 TGGTTAAAAACATTTTGACT
***
12446487 TGGTTAAATTTATTTTGACT
1 TGGTTAAAAACATTTTGACT
* *
12446507 TGTTTAAAAACATTTTAACT
1 TGGTTAAAAACATTTTGACT
12446527 TG
1 TG
12446529 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (20 bp):
TGGTTAAAAACATTTTGACT
Found at i:12449143 original size:24 final size:24
Alignment explanation
Indices: 12449048--12449144 Score: 74
Period size: 24 Copynumber: 4.0 Consensus size: 24
12449038 ACTGAGTCTT
*
12449048 CCAGA-AATTTAGCTCATACGAGC
1 CCAGATAAGTTAGCTCATACGAGC
* * * *
12449071 CCATACAAAATTAGTTCATACGAGC
1 CCAGA-TAAGTTAGCTCATACGAGC
* *
12449096 CCAAATAGGTTAGCTTTCAT--GAGC
1 CCAGATAAGTTAGC--TCATACGAGC
*
12449120 CCAGATAAGTTAGCTCATTCGAGC
1 CCAGATAAGTTAGCTCATACGAGC
12449144 C
1 C
12449145 TAGACAGAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
22 4 0.07
23 4 0.07
24 26 0.45
25 20 0.34
26 4 0.07
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (24 bp):
CCAGATAAGTTAGCTCATACGAGC
Found at i:12451356 original size:26 final size:26
Alignment explanation
Indices: 12451295--12451398 Score: 104
Period size: 26 Copynumber: 4.0 Consensus size: 26
12451285 AATCTACAAA
*
12451295 ATAGTATAGTATATCACTCTTACGAG
1 ATAGTATAGTATATCACTCTTTCGAG
*
12451321 -TCAGTTTAGTATATCACTCTTTCGAG
1 AT-AGTATAGTATATCACTCTTTCGAG
* * *
12451347 ATAGTATAGTAAATCGCTTTTTCGAG
1 ATAGTATAGTATATCACTCTTTCGAG
* **
12451373 CTAGT-TCAGTATATTGCTCTTTCGAG
1 ATAGTAT-AGTATATCACTCTTTCGAG
12451399 CCAATACAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
25 2 0.03
26 62 0.95
27 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (26 bp):
ATAGTATAGTATATCACTCTTTCGAG
Found at i:12451384 original size:52 final size:52
Alignment explanation
Indices: 12451295--12451398 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
12451285 AATCTACAAA
* *
12451295 ATAGTATAGTATATCACTCTTACGAGTCAGTTTAGTATATCACTCTTTCGAG
1 ATAGTATAGTAAATCACTCTTACGAGTCAGTTCAGTATATCACTCTTTCGAG
* * * **
12451347 ATAGTATAGTAAATCGCTTTTTCGAG-CTAGTTCAGTATATTGCTCTTTCGAG
1 ATAGTATAGTAAATCACTCTTACGAGTC-AGTTCAGTATATCACTCTTTCGAG
12451399 CCAATACAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 1 0.02
52 43 0.98
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (52 bp):
ATAGTATAGTAAATCACTCTTACGAGTCAGTTCAGTATATCACTCTTTCGAG
Found at i:12458285 original size:3 final size:3
Alignment explanation
Indices: 12458277--12458315 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12458267 ACATAGTCAT
12458277 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
12458316 ATCATCATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:12458320 original size:3 final size:3
Alignment explanation
Indices: 12458314--12458345 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12458304 CTCCTCCTCC
*
12458314 TCA TCA TCA TCA TCA TCA TCA TCA TCG TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
12458346 TTTATTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.03, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:12460194 original size:20 final size:20
Alignment explanation
Indices: 12460111--12460201 Score: 58
Period size: 20 Copynumber: 4.5 Consensus size: 20
12460101 TCCTGGAGCT
*
12460111 ATTTTGACTTGTTTGAAACAC
1 ATTTTGACTTGTTT-AAAAAC
* ** **
12460132 ATTTTTAAGTG-TTAAAATG
1 ATTTTGACTTGTTTAAAAAC
* * * **
12460151 ATTTTGACATGGTTCAAATT
1 ATTTTGACTTGTTTAAAAAC
12460171 ATTTTGACTTGTTTAAAAAC
1 ATTTTGACTTGTTTAAAAAC
*
12460191 ATTTTAACTTG
1 ATTTTGACTTG
12460202 ATTTTAAGAT
Statistics
Matches: 52, Mismatches: 17, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
19 11 0.21
20 33 0.63
21 8 0.15
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTTTGACTTGTTTAAAAAC
Found at i:12469044 original size:26 final size:27
Alignment explanation
Indices: 12469014--12469074 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 27
12469004 CAAAATTAAT
*
12469014 AAAATCAACTAAACCCGAAGAATAACAAA
1 AAAATCAACTAAACCCGAAGAA-AA-ACA
12469043 ATTAAATCAACTAAACCCGAAGAAAAACA
1 A--AAATCAACTAAACCCGAAGAAAAACA
12469072 AAA
1 AAA
12469075 TTAATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 2 0.07
29 4 0.14
30 2 0.07
31 21 0.72
ACGTcount: A:0.62, C:0.20, G:0.07, T:0.11
Consensus pattern (27 bp):
AAAATCAACTAAACCCGAAGAAAAACA
Found at i:12469084 original size:66 final size:69
Alignment explanation
Indices: 12469002--12469136 Score: 222
Period size: 66 Copynumber: 2.0 Consensus size: 69
12468992 CTTAACACTT
*
12469002 AACAAAATTAATAAAATCAACTAAACCCGAAGAATAACAAAA-T-T-AAATCAACTAAACCCGAA
1 AACAAAATTAATAAAATCAACTAAACCCGAAAAATAACAAAATTATAAAATCAACTAAACCCGAA
12469064 GAAA
66 GAAA
*
12469068 AACAAAATTAATAAAATCAACTAAACCCGAAAAATTACAAAATTAATAAAATCAACTAAACCCGA
1 AACAAAATTAATAAAATCAACTAAACCCGAAAAATAACAAAATT-ATAAAATCAACTAAACCCGA
12469133 AGAA
65 AGAA
12469137 TTACGGACGT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
66 40 0.63
67 1 0.02
69 1 0.02
70 21 0.33
ACGTcount: A:0.61, C:0.18, G:0.05, T:0.16
Consensus pattern (69 bp):
AACAAAATTAATAAAATCAACTAAACCCGAAAAATAACAAAATTATAAAATCAACTAAACCCGAA
GAAA
Found at i:12469140 original size:35 final size:35
Alignment explanation
Indices: 12469001--12469137 Score: 219
Period size: 35 Copynumber: 4.0 Consensus size: 35
12468991 GCTTAACACT
12469001 TAACAAAATTAATAAAATCAACTAAACCCGAAGAA
1 TAACAAAATTAATAAAATCAACTAAACCCGAAGAA
12469036 TAACAAAA-T--T-AAATCAACTAAACCCGAAGAA
1 TAACAAAATTAATAAAATCAACTAAACCCGAAGAA
* *
12469067 AAACAAAATTAATAAAATCAACTAAACCCGAAAAA
1 TAACAAAATTAATAAAATCAACTAAACCCGAAGAA
*
12469102 TTACAAAATTAATAAAATCAACTAAACCCGAAGAA
1 TAACAAAATTAATAAAATCAACTAAACCCGAAGAA
12469137 T
1 T
12469138 TACGGACGTT
Statistics
Matches: 93, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
31 28 0.30
32 2 0.02
34 2 0.02
35 61 0.66
ACGTcount: A:0.60, C:0.18, G:0.05, T:0.18
Consensus pattern (35 bp):
TAACAAAATTAATAAAATCAACTAAACCCGAAGAA
Found at i:12471007 original size:16 final size:16
Alignment explanation
Indices: 12470986--12471017 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12470976 ATCCTGCAAA
12470986 TGAAAAAGCAGATGAG
1 TGAAAAAGCAGATGAG
12471002 TGAAAAAGCAGATGAG
1 TGAAAAAGCAGATGAG
12471018 ATCGAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.31, T:0.12
Consensus pattern (16 bp):
TGAAAAAGCAGATGAG
Found at i:12471103 original size:2 final size:2
Alignment explanation
Indices: 12471096--12471124 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12471086 AGATACGGAT
12471096 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
12471125 GAATAGGGGA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12490051 original size:32 final size:32
Alignment explanation
Indices: 12490015--12490079 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
12490005 ATTAATGATG
12490015 AGTGACTAAAATGATAAAAATATAAAATGACA
1 AGTGACTAAAATGATAAAAATATAAAATGACA
* * **
12490047 AGTGACTAAAATGATTAAAGTATGTAATGACA
1 AGTGACTAAAATGATAAAAATATAAAATGACA
12490079 A
1 A
12490080 TGCTTACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.25
Consensus pattern (32 bp):
AGTGACTAAAATGATAAAAATATAAAATGACA
Found at i:12502369 original size:21 final size:21
Alignment explanation
Indices: 12502334--12502385 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
12502324 TTGCCCCCAC
* *
12502334 ACAAAGTTGCTAGAGGGTTCAG
1 ACAAAGGT-CTAGAGGGTTAAG
12502356 ACAAAGGTCTAGAGGGTTAAG
1 ACAAAGGTCTAGAGGGTTAAG
12502377 ACAAAGGTC
1 ACAAAGGTC
12502386 CTCCCGGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.19
Consensus pattern (21 bp):
ACAAAGGTCTAGAGGGTTAAG
Found at i:12510447 original size:43 final size:43
Alignment explanation
Indices: 12510359--12510658 Score: 284
Period size: 43 Copynumber: 7.0 Consensus size: 43
12510349 ACCCATGACA
* * * *
12510359 AAAGAACATGGTCTATAGTGGCGC-TTTCCCAAAAACGCCGCT
1 AAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGCT
* * * * * *
12510401 AAAGAACGTGGTTTTTAGCGGCACTTTTTCCACAAGCGCAGCT
1 AAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGCT
** * *
12510444 AAAGAACATGGTCTTTAGCGGTTCTTTTCCCACAAACGCCGTT
1 AAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGCT
* * * *
12510487 AAAAAACATGGTTTTTAGTGACGCTTTTACCACAAACGCCGCT
1 AAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGCT
* * *
12510530 AAAGAACATGGTCTTTAGCGGCGCTTTTATCACAAACGTCGTT
1 AAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGCT
* * * * *
12510573 ATAGAGCATGGTCTTTAACGGTG-TTTTCCCCACAAACGCCGCT
1 AAAGAACATGGTCTTTAGCGGCGCTTTT-ACCACAAACGCCGCT
* * * * *
12510616 ATAGAACATGTTCTTTAGCGGC-TTTTTCCCA-AAACGTCGCT
1 AAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGCT
12510657 AA
1 AA
12510659 CATTAACAGA
Statistics
Matches: 209, Mismatches: 46, Indels: 7
0.80 0.18 0.03
Matches are distributed among these distances:
41 10 0.05
42 27 0.13
43 172 0.82
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (43 bp):
AAAGAACATGGTCTTTAGCGGCGCTTTTACCACAAACGCCGCT
Found at i:12510624 original size:129 final size:128
Alignment explanation
Indices: 12510359--12510633 Score: 324
Period size: 129 Copynumber: 2.1 Consensus size: 128
12510349 ACCCATGACA
* * * * * *
12510359 AAAGAACATGGTCTATAGTGGCGCTTTCCCAAAAACGCCGCTAAAGAACGTGGTTTTTAGCGGCA
1 AAAGAACATGGTTTTTAGTGACGCTTTACCAAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCA
* * * *
12510424 CTTTTTCCACAAGCGCAGCTAAAGAACATGGTCTTTAGCGGTTCTTTTCCCACAAACGCCGTT
66 CTTTTTCCACAAACGCAGCTAAAGAACATGGTCTTTAACGGTTCTTTCCCCACAAACGCCGCT
* *
12510487 AAAAAACATGGTTTTTAGTGACGCTTTTACCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGC
1 AAAGAACATGGTTTTTAGTGACGC-TTTACCAAAAACGCCGCTAAAGAACATGGTCTTTAGCGGC
* * * *
12510552 GCTTTTAT-CACAAACGTC-GTTATAGAGCATGGTCTTTAACGGTGT-TTTCCCCACAAACGCCG
65 ACTTTT-TCCACAAACG-CAGCTAAAGAACATGGTCTTTAACGGT-TCTTTCCCCACAAACGCCG
12510614 CT
127 CT
*
12510616 ATAGAACAT-GTTCTTTAG
1 AAAGAACATGGTT-TTTAG
12510634 CGGCTTTTTC
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
128 23 0.19
129 98 0.79
130 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (128 bp):
AAAGAACATGGTTTTTAGTGACGCTTTACCAAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCA
CTTTTTCCACAAACGCAGCTAAAGAACATGGTCTTTAACGGTTCTTTCCCCACAAACGCCGCT
Found at i:12510744 original size:14 final size:14
Alignment explanation
Indices: 12510725--12510752 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12510715 TTTTCTTATA
12510725 AATTCAAATCCAAC
1 AATTCAAATCCAAC
12510739 AATTCAAATCCAAC
1 AATTCAAATCCAAC
12510753 GAAGAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
AATTCAAATCCAAC
Found at i:12513108 original size:58 final size:58
Alignment explanation
Indices: 12513045--12513243 Score: 214
Period size: 58 Copynumber: 3.4 Consensus size: 58
12513035 GATTTAAATA
12513045 TAATTAAATAATTAAATATTTTGAATTAAATATTTGGGTTTAGTGTTTAATAAATAAC
1 TAATTAAATAATTAAATATTTTGAATTAAATATTTGGGTTTAGTGTTTAATAAATAAC
* * *
12513103 TAATTAAATAATT-AA-A---T-AATTAAATATTTGGGTTTTTAATAATTTAATATTTATTTAAA
1 TAATTAAATAATTAAATATTTTGAATTAAATATTTGGG--TTTAGT-GTTTAATA---A-AT-AA
*
12513162 TA
58 -C
*
12513164 TAATTAAATAATTAAATATTTTGAATTAAATATTTGAGTTTAAG-GTTTAATAAATAAC
1 TAATTAAATAATTAAATATTTTGAATTAAATATTTGGGTTT-AGTGTTTAATAAATAAC
12513222 TAATTAAATAATTAAATATTTT
1 TAATTAAATAATTAAATATTTT
12513244 AATATTTGGG
Statistics
Matches: 116, Mismatches: 9, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
52 15 0.13
53 1 0.01
54 5 0.04
55 7 0.06
56 1 0.01
57 2 0.02
58 36 0.31
59 3 0.03
60 3 0.03
61 14 0.12
62 2 0.02
63 1 0.01
64 7 0.06
65 3 0.03
66 2 0.02
67 14 0.12
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (58 bp):
TAATTAAATAATTAAATATTTTGAATTAAATATTTGGGTTTAGTGTTTAATAAATAAC
Found at i:12513116 original size:8 final size:8
Alignment explanation
Indices: 12513093--12513128 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
12513083 TTTAGTGTTT
*
12513093 AATAAATA
1 AATAATTA
*
12513101 ACTAATTA
1 AATAATTA
12513109 AATAATTA
1 AATAATTA
12513117 AATAATTA
1 AATAATTA
12513125 AATA
1 AATA
12513129 TTTGGGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAATTA
Found at i:12513216 original size:119 final size:119
Alignment explanation
Indices: 12513036--12513255 Score: 397
Period size: 119 Copynumber: 1.8 Consensus size: 119
12513026 AATCAAATTG
*
12513036 ATTTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGGTTTAGTGTTTAATAAATA
1 ATTTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGAGTTTAGTGTTTAATAAATA
12513101 ACTAATTAAATAATTAAATAATTAAATATTTGGGTTTTTAATAATTTAATATTT
66 ACTAATTAAATAATTAAATAATTAAATATTTGGGTTTTTAATAATTTAATATTT
12513155 ATTTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGAGTTTAAG-GTTTAATAAAT
1 ATTTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGAGTTT-AGTGTTTAATAAAT
* *
12513219 AACTAATTAAATAATTAAATATTTTAATATTTGGGTT
65 AACTAATTAAATAATTAAATAATTAAATATTTGGGTT
12513256 GTTTTTTACA
Statistics
Matches: 97, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
119 95 0.98
120 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (119 bp):
ATTTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGAGTTTAGTGTTTAATAAATA
ACTAATTAAATAATTAAATAATTAAATATTTGGGTTTTTAATAATTTAATATTT
Found at i:12526820 original size:12 final size:12
Alignment explanation
Indices: 12526805--12526830 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12526795 AATTAAAGAA
12526805 ATAATAGCATTC
1 ATAATAGCATTC
12526817 ATAATAGCATTC
1 ATAATAGCATTC
12526829 AT
1 AT
12526831 CATGATGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:12532834 original size:13 final size:14
Alignment explanation
Indices: 12532813--12532842 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
12532803 AATATTTGTG
12532813 AAAGATATTAATCT
1 AAAGATATTAATCT
12532827 AAAG-TATTAATCT
1 AAAGATATTAATCT
12532840 AAA
1 AAA
12532843 CTAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAGATATTAATCT
Found at i:12555028 original size:12 final size:11
Alignment explanation
Indices: 12555007--12555056 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
12554997 TAGTCACTTG
12555007 AAAAAGA-AAA
1 AAAAAGAGAAA
*
12555017 AAAATGAGAAA
1 AAAAAGAGAAA
12555028 AAGAAAGAGAAA
1 AA-AAAGAGAAA
12555040 AGAAAAGAAGAAA
1 A-AAAAG-AGAAA
12555053 AAAA
1 AAAA
12555057 TTTTATTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.18
11 5 0.15
12 16 0.47
13 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:12555038 original size:24 final size:25
Alignment explanation
Indices: 12555006--12555054 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
12554996 TTAGTCACTT
12555006 GAAAAAGAAAA-AAAATG-AGAAAAA
1 GAAAAAGAAAAGAAAA-GAAGAAAAA
*
12555030 GAAAGAGAAAAGAAAAGAAGAAAAA
1 GAAAAAGAAAAGAAAAGAAGAAAAA
12555055 AATTTTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (25 bp):
GAAAAAGAAAAGAAAAGAAGAAAAA
Found at i:12557295 original size:12 final size:12
Alignment explanation
Indices: 12557280--12557305 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12557270 AATTAAAGAA
12557280 ATAATAGCATTC
1 ATAATAGCATTC
12557292 ATAATAGCATTC
1 ATAATAGCATTC
12557304 AT
1 AT
12557306 CATGATGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:12560612 original size:24 final size:24
Alignment explanation
Indices: 12560572--12560618 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12560562 GTTCAGAGTA
12560572 AAAATTGTCAGTACAAATGTAATAT
1 AAAATTGTCAGTACAAAT-TAATAT
12560597 AAAA-TGTCAG-AGCAAATTAATA
1 AAAATTGTCAGTA-CAAATTAATA
12560619 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 11 0.52
25 4 0.19
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (24 bp):
AAAATTGTCAGTACAAATTAATAT
Found at i:12562793 original size:17 final size:17
Alignment explanation
Indices: 12562763--12562835 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
12562753 ATAATAATGG
* * *
12562763 AAATGCAAATACAATTC
1 AAATGCAGAGACAATTA
*
12562780 AAATGCTAGA-ACAAATA
1 AAATGC-AGAGACAATTA
*
12562797 AAATGCAGAGACAATAAA
1 AAATGCAGAGACAAT-TA
12562815 AAATGCA-ATGACAATTA
1 AAATGCAGA-GACAATTA
12562832 AAAT
1 AAAT
12562836 TTTTTTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.07
17 27 0.59
18 16 0.35
ACGTcount: A:0.58, C:0.12, G:0.11, T:0.19
Consensus pattern (17 bp):
AAATGCAGAGACAATTA
Found at i:12562819 original size:18 final size:19
Alignment explanation
Indices: 12562796--12562834 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
12562786 TAGAACAAAT
12562796 AAAATGCAGA-GACAA-TAA
1 AAAATGCA-ATGACAATTAA
12562814 AAAATGCAATGACAATTAA
1 AAAATGCAATGACAATTAA
12562833 AA
1 AA
12562835 TTTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 13 0.68
19 5 0.26
ACGTcount: A:0.62, C:0.10, G:0.13, T:0.15
Consensus pattern (19 bp):
AAAATGCAATGACAATTAA
Found at i:12577237 original size:26 final size:26
Alignment explanation
Indices: 12577197--12577257 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
12577187 GATATATCAA
* *
12577197 TCATCTTCCTCTTGGAGTCCTCTTCT
1 TCATCTTTCTATTGGAGTCCTCTTCT
12577223 TCATCTTTCTATTGGAGTCCTCTTCT
1 TCATCTTTCTATTGGAGTCCTCTTCT
* *
12577249 CCTTCTTTC
1 TCATCTTTC
12577258 CTCCTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.08, C:0.33, G:0.10, T:0.49
Consensus pattern (26 bp):
TCATCTTTCTATTGGAGTCCTCTTCT
Found at i:12577730 original size:27 final size:30
Alignment explanation
Indices: 12577680--12577736 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 30
12577670 CAAATGATTT
*
12577680 TAAAATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAATTATTATTTTAAAATA
12577710 TAAAATTATT-AAA-T-TTATTTTAAAATA
1 TAAAATTATTAAAATTATTATTTTAAAATA
12577737 ATTTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 12 0.46
28 1 0.04
29 3 0.12
30 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTATTTTAAAATA
Found at i:12577744 original size:30 final size:30
Alignment explanation
Indices: 12577678--12577746 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
12577668 AGCAAATGAT
**
12577678 TTTAAAATTATTAAAATTATTTTTTTAAAA
1 TTTAAAATTATTAAAATTATTTTTAAAAAA
* *
12577708 TATAAAATTATTAAATTTA-TTTTAAAATAA
1 TTTAAAATTATTAAAATTATTTTTAAAA-AA
12577738 TTTAAAATT
1 TTTAAAATT
12577747 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAAAATTATTAAAATTATTTTTAAAAAA
Done.