Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 3 of 125
Found at i:785726 original size:70 final size:67
Alignment explanation
Indices: 785603--785735 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 67
785593 ATAAACAATA
* * * *
785603 TAATGGTTTTGCCTTTTAACTTAATGGATAAACATTTATCAAAATGATATAATTTTACCTTTTAA
1 TAATGATTTTGACTTTTAACTTAAAGGATAAACATTTATCAAAACGATATAATTTTACCTTTTAA
785668 CT
66 CT
*
785670 TAATGATTTTGACTTTTAACTTTAGAAAGGATAAACATTTATCAAAACGATGTAATTTTACCTTT
1 TAATGATTTTGACTTTTAAC-TT--AAAGGATAAACATTTATCAAAACGATATAATTTTACCTTT
785735 T
63 T
785736 CTTATTCGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
67 18 0.31
68 2 0.03
70 38 0.66
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (67 bp):
TAATGATTTTGACTTTTAACTTAAAGGATAAACATTTATCAAAACGATATAATTTTACCTTTTAA
CT
Found at i:786308 original size:29 final size:30
Alignment explanation
Indices: 786258--786318 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
786248 AATCTATATC
786258 TTTATAATTTTTAAAAAATTAAAT-TAAATT
1 TTTATAATTTTTAAAAAATTAAATAT-AATT
* * *
786288 TTTAT-ATTTTTTAGAATTTAAATATAATT
1 TTTATAATTTTTAAAAAATTAAATATAATT
786317 TT
1 TT
786319 ATCATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTATAATTTTTAAAAAATTAAATATAATT
Found at i:791281 original size:16 final size:16
Alignment explanation
Indices: 791257--791302 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
791247 ATTTCCCCCC
791257 AAAACTTTTACTCTCT
1 AAAACTTTTACTCTCT
***
791273 CTCACTTTT-CTC-CT
1 AAAACTTTTACTCTCT
791287 AAAACTTTTACTCTCT
1 AAAACTTTTACTCTCT
791303 TCCCATCCAA
Statistics
Matches: 22, Mismatches: 6, Indels: 4
0.69 0.19 0.12
Matches are distributed among these distances:
14 8 0.36
15 6 0.27
16 8 0.36
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAACTTTTACTCTCT
Found at i:791404 original size:166 final size:159
Alignment explanation
Indices: 791088--791404 Score: 347
Period size: 166 Copynumber: 1.9 Consensus size: 159
791078 TTACTTTTCT
* *
791088 CCCAAAACTTTTACTCTTTCCCACTTGTGCCCCAAAACTTTTACTCTCCTTCCATCTCTCCCTCA
1 CCCAAAACTTTTACTCTCTCCCACTTGTGCCCCAAAACTTTTACTCTCCTTCCATCTCACCCTCA
* *
791153 TTTACCCCAAACCCATTTCCCCTCAATTTTTTTAATATTTTCCCTCCAAAATTTTACTCTCTCAT
66 TCTACCCCAAACCCATTTCCCCCCAATTTTTTTAATATTTTCCCTCCAAAATTTTACTCTCTCAT
*
791218 TTTTTTCCCCAAAACCCTCAACACTCTTTATTTCCC
131 TTCTTT-------ACCCTCAACACTCTTTATTTCCC
* * *
791254 CCCAAAACTTTTACTCTCTCTCACTT-TTCTCCTAAAACTTTTACTCT-CTTCCCATC-CAACCC
1 CCCAAAACTTTTACTCTCTCCCACTTGTGC-CCCAAAACTTTTACTCTCCTT-CCATCTC-ACCC
*
791316 TCCATCTACCCCAAACCCATTCCTCCCTCCCAATTTTTTTTTGAATATTTTCCTTCCAAAATTTT
63 T-CATCTACCCCAAACCCATT--TCCC-CCCAA--TTTTTTT-AATATTTTCCCTCCAAAATTTT
791381 ACTCTC-CTATTTACTTT-CCCTCAA
121 ACTCTCTC-ATTT-CTTTACCCTCAA
791405 AATTTTACTC
Statistics
Matches: 130, Mismatches: 9, Indels: 24
0.80 0.06 0.15
Matches are distributed among these distances:
165 6 0.05
166 56 0.43
167 18 0.14
169 4 0.03
170 4 0.03
172 8 0.06
173 31 0.24
174 3 0.02
ACGTcount: A:0.22, C:0.37, G:0.01, T:0.39
Consensus pattern (159 bp):
CCCAAAACTTTTACTCTCTCCCACTTGTGCCCCAAAACTTTTACTCTCCTTCCATCTCACCCTCA
TCTACCCCAAACCCATTTCCCCCCAATTTTTTTAATATTTTCCCTCCAAAATTTTACTCTCTCAT
TTCTTTACCCTCAACACTCTTTATTTCCC
Found at i:792185 original size:21 final size:21
Alignment explanation
Indices: 792161--792205 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
792151 AACATTATTT
792161 TTATAAAAACATTTAATACTA
1 TTATAAAAACATTTAATACTA
* * * *
792182 TTATCAGAACATTTATTATTA
1 TTATAAAAACATTTAATACTA
792203 TTA
1 TTA
792206 ATGTTTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (21 bp):
TTATAAAAACATTTAATACTA
Found at i:792954 original size:6 final size:6
Alignment explanation
Indices: 792931--793005 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
792921 TTAGTATGTT
* * **
792931 AATTTT AATTTT AATTTA AATTT- AAGGTA AATTTA AATAATTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT--TTA AATTTA
* *
792980 AATTTA AA--TC AATTTA ACTTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
793006 AAAACAAGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
4 3 0.05
5 3 0.05
6 43 0.78
8 6 0.11
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:792954 original size:11 final size:11
Alignment explanation
Indices: 792929--793008 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
792919 AATTAGTATG
*
792929 TTAATTTTAATT
1 TTAA-TTTAAAT
792941 TTAATTTAAAT
1 TTAATTTAAAT
**
792952 TTAAGGTAAAT
1 TTAATTTAAAT
792963 TTAAATAATTAAAT
1 TT-AAT--TTAAAT
792977 TTAAATTTAAA-
1 TT-AATTTAAAT
* *
792988 TCAATTTAACT
1 TTAATTTAAAT
*
792999 TTAAATTAAA
1 TTAATTTAAA
793009 ACAAGAAGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
10 7 0.13
11 25 0.46
12 11 0.20
14 11 0.20
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (11 bp):
TTAATTTAAAT
Found at i:792995 original size:16 final size:16
Alignment explanation
Indices: 792943--793004 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
792933 TTTTAATTTT
*
792943 AATTTAAATTTAAGGTA
1 AATTTAAATTTAA-ATA
*
792960 AATTTAAA--TAATTA
1 AATTTAAATTTAAATA
*
792974 AATTTAAATTTAAATC
1 AATTTAAATTTAAATA
*
792990 AATTTAACTTTAAAT
1 AATTTAAATTTAAAT
793005 TAAAACAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
14 10 0.26
15 3 0.08
16 18 0.46
17 8 0.21
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:795521 original size:22 final size:23
Alignment explanation
Indices: 795496--795543 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
795486 CTCTCTGTTC
*
795496 TTCCTTC-T-TTTATTTCTTTTGT
1 TTCCTTCTTCTTTA-TTCTTTTAT
795518 TTCCTTCTTCTTTATTCTTTTAT
1 TTCCTTCTTCTTTATTCTTTTAT
795541 TTC
1 TTC
795544 ATATACATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 12 0.52
24 4 0.17
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.71
Consensus pattern (23 bp):
TTCCTTCTTCTTTATTCTTTTAT
Found at i:795621 original size:13 final size:12
Alignment explanation
Indices: 795551--795632 Score: 51
Period size: 13 Copynumber: 6.6 Consensus size: 12
795541 TTCATATACA
*
795551 TATATATATTAGT
1 TATA-ATATTAAT
*
795564 TAATAATAATAA-
1 T-ATAATATTAAT
* *
795576 TATTATACTAAT
1 TATAATATTAAT
*
795588 TA-AATAATAATT
1 TATAATATTAA-T
*
795600 TATATTATTATAT
1 TATAATATTA-AT
795613 TATAATATTAAT
1 TATAATATTAAT
795625 TAATAATA
1 T-ATAATA
795633 AATTTAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
11 14 0.26
12 9 0.17
13 27 0.50
14 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:801652 original size:22 final size:23
Alignment explanation
Indices: 801627--801674 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
801617 CTCTCTGTTC
*
801627 TTCCTTC-T-TTTATTTCTTTTGT
1 TTCCTTCTTCTTTA-TTCTTTTAT
801649 TTCCTTCTTCTTTATTCTTTTAT
1 TTCCTTCTTCTTTATTCTTTTAT
801672 TTC
1 TTC
801675 ATATACATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 12 0.52
24 4 0.17
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.71
Consensus pattern (23 bp):
TTCCTTCTTCTTTATTCTTTTAT
Found at i:801752 original size:13 final size:12
Alignment explanation
Indices: 801682--801763 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
801672 TTCATATACA
*
801682 TATATATATTAGT
1 TATA-ATATTAAT
*
801695 TAATAATAATAA-
1 T-ATAATATTAAT
*
801707 TATAATACTAAT
1 TATAATATTAAT
*
801719 TA-AATAATAATT
1 TATAATATTAA-T
*
801731 TATATTATTATAT
1 TATAATATTA-AT
801744 TATAATATTAAT
1 TATAATATTAAT
801756 TAATAATA
1 T-ATAATA
801764 AATTTAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:803436 original size:30 final size:30
Alignment explanation
Indices: 803397--803480 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
803387 ATTTAACTCC
* *
803397 TGAAATTTCTAAAAATTGCATTTTGGCCCA
1 TGAAATTTCTAAAAATTGCATTTTGACACA
* * * *
803427 TGAACTTTCTAAAAATTTCATTTTTACACT
1 TGAAATTTCTAAAAATTGCATTTTGACACA
*
803457 TAAAATTTCTAAAAATTGCATTTT
1 TGAAATTTCTAAAAATTGCATTTT
803481 AACTCCAAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (30 bp):
TGAAATTTCTAAAAATTGCATTTTGACACA
Found at i:807809 original size:21 final size:21
Alignment explanation
Indices: 807783--807835 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
807773 AAAATCGAAA
**
807783 TAAAAAAATATTAACTTCTAT
1 TAAAAAAATATTAACACCTAT
* * *
807804 TAAAAACATATTAGCACCTGT
1 TAAAAAAATATTAACACCTAT
807825 TAAAAAAATAT
1 TAAAAAAATAT
807836 AGAAACAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (21 bp):
TAAAAAAATATTAACACCTAT
Found at i:810898 original size:17 final size:17
Alignment explanation
Indices: 810878--810925 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
810868 ATTTTTTTAG
810878 TTTTAATCTTTTAAATT-
1 TTTTAAT-TTTTAAATTA
*
810895 TTTTTATTTATTAAATTA
1 TTTTAATTT-TTAAATTA
810913 TTTATAATTTTTA
1 TTT-TAATTTTTA
810926 GGATTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.08
17 13 0.50
18 6 0.23
19 5 0.19
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATTTTTAAATTA
Found at i:823892 original size:31 final size:32
Alignment explanation
Indices: 823856--823925 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
823846 TTATAATATG
*
823856 ATCATTGAATTATTTGAAAG-TTTTCATTTAA
1 ATCATTAAATTATTTGAAAGTTTTTCATTTAA
*
823887 ATCATTAAATTATTTGAAAGTTTTTTATTTAA
1 ATCATTAAATTATTTGAAAGTTTTTCATTTAA
*
823919 ACCATTA
1 ATCATTA
823926 GGATGTTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 19 0.54
32 16 0.46
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (32 bp):
ATCATTAAATTATTTGAAAGTTTTTCATTTAA
Found at i:826268 original size:19 final size:19
Alignment explanation
Indices: 826216--826255 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
826206 GCTCTTTTAT
*
826216 TTTTTAT-ACATTTTATAA
1 TTTTTATAAAATTTTATAA
826234 TTTTTATAAAATTTTATAA
1 TTTTTATAAAATTTTATAA
826253 TTT
1 TTT
826256 ATTACAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTATAAAATTTTATAA
Found at i:826346 original size:16 final size:17
Alignment explanation
Indices: 826327--826358 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
826317 AATTTTAATT
826327 TTTTTTATA-TTTTTTA
1 TTTTTTATAGTTTTTTA
826343 TTTTTTATAGTTTTTT
1 TTTTTTATAGTTTTTT
826359 TGTCACATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTTTATAGTTTTTTA
Found at i:826348 original size:26 final size:27
Alignment explanation
Indices: 826301--826359 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
826291 TTTTAATGAA
* *
826301 TTTTATATATTATTTTAATTTTA-ATT
1 TTTTTTATATTATTTTAATTTTATAGT
*
826327 TTTTTTATATT-TTTTATTTTTTATAGT
1 TTTTTTATATTATTTTA-ATTTTATAGT
826354 TTTTTT
1 TTTTTT
826360 GTCACATGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.18
26 15 0.54
27 8 0.29
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTTTATATTATTTTAATTTTATAGT
Found at i:833153 original size:2 final size:2
Alignment explanation
Indices: 833146--833178 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
833136 TTTAAGATGT
833146 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
833179 AATTTTGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:835700 original size:78 final size:78
Alignment explanation
Indices: 835613--835763 Score: 214
Period size: 78 Copynumber: 1.9 Consensus size: 78
835603 TCTGCTTGGA
*
835613 GAGGTAAAGTAAACTCTGGCTATTTCTTTGATTTAAT-TTTCTGGGTTTCTTTTTGGTGTTTGTT
1 GAGGTAAAGTAAACTCTGGCTATTTCTTTGATTT-ATCTTTCTGGGATTCTTTTTGGTGTTTGTT
*
835677 CGGTGAGAAAAATG
65 CGATGAGAAAAATG
* * * * * *
835691 GAGGTAAAGTTAATTCTGGGTGTTTCTTTGATTTTTCTTTCTGGGATTCTTTTTGGTGTTTGTTT
1 GAGGTAAAGTAAACTCTGGCTATTTCTTTGATTTATCTTTCTGGGATTCTTTTTGGTGTTTGTTC
835756 GATGAGAA
66 GATGAGAA
835764 TATGAAGGTA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 1 0.02
78 63 0.98
ACGTcount: A:0.19, C:0.08, G:0.25, T:0.48
Consensus pattern (78 bp):
GAGGTAAAGTAAACTCTGGCTATTTCTTTGATTTATCTTTCTGGGATTCTTTTTGGTGTTTGTTC
GATGAGAAAAATG
Found at i:844815 original size:15 final size:16
Alignment explanation
Indices: 844770--844813 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
844760 AGATTATTAT
844770 ATAAAAAATCA-AT-AA
1 ATAAAAAAT-ATATAAA
844785 ATAAAAAATATATAAA
1 ATAAAAAATATATAAA
844801 ATAAAATAATATA
1 ATAAAA-AATATA
844814 AATATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.04
15 11 0.42
16 8 0.31
17 6 0.23
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
ATAAAAAATATATAAA
Found at i:844823 original size:23 final size:21
Alignment explanation
Indices: 844783--844837 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
844773 AAAAATCAAT
844783 AAATAAAAAATATATAAAATA
1 AAATAAAAAATATATAAAATA
*
844804 AAATAATATAAATATTTAAAA-A
1 AAATAA-A-AAATATATAAAATA
*
844826 AATTAAAAAATA
1 AAATAAAAAATA
844838 ATATGGGCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 5 0.17
21 7 0.23
22 7 0.23
23 11 0.37
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAAAAATATATAAAATA
Found at i:849309 original size:31 final size:30
Alignment explanation
Indices: 849272--849342 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
849262 AGTTTTAGGT
849272 TCTTTAAAAGTTGAAGAAAAAAAATTTAAG
1 TCTTTAAAAGTTGAAGAAAAAAAATTTAAG
** * *
849302 TCTTTTAAAAGTTGGTGAAAAAAATTTTGAG
1 TC-TTTAAAAGTTGAAGAAAAAAAATTTAAG
*
849333 TCCTTAAAAG
1 TCTTTAAAAG
849343 CTAAAAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 9 0.26
31 26 0.74
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (30 bp):
TCTTTAAAAGTTGAAGAAAAAAAATTTAAG
Found at i:850767 original size:35 final size:33
Alignment explanation
Indices: 850715--850789 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 33
850705 TTTAAAAAAC
850715 TATATATCCTAAACTAAA-ATTATA-ACTACTATA
1 TATATATCCTAAACTAAACATTATATA-TA-TATA
*
850748 TATATATCCTAAACTCTAAACTTTATATATATATA
1 TATATATCCTAAA--CTAAACATTATATATATATA
850783 TATATAT
1 TATATAT
850790 ATGCACGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 13 0.35
35 16 0.43
36 7 0.19
37 1 0.03
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.41
Consensus pattern (33 bp):
TATATATCCTAAACTAAACATTATATATATATA
Found at i:850959 original size:31 final size:31
Alignment explanation
Indices: 850898--850962 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
850888 GGTATTTAAA
** * *
850898 TTTGATTTCAATATTTGATTTGATACTTGAG
1 TTTGATTTCAATATTCAAATTGAGACTTGAG
*
850929 TTTGATTTCAATATTCAAATTGAGATTTGAG
1 TTTGATTTCAATATTCAAATTGAGACTTGAG
850960 TTT
1 TTT
850963 TCTCAATTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (31 bp):
TTTGATTTCAATATTCAAATTGAGACTTGAG
Found at i:850973 original size:22 final size:22
Alignment explanation
Indices: 850943--850985 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
850933 ATTTCAATAT
850943 TCAAATTGAGATTTGAGTTTTC
1 TCAAATTGAGATTTGAGTTTTC
* *
850965 TCAATTTGATATTTGAGTTTT
1 TCAAATTGAGATTTGAGTTTT
850986 TTTTTTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (22 bp):
TCAAATTGAGATTTGAGTTTTC
Found at i:855389 original size:13 final size:13
Alignment explanation
Indices: 855371--855395 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
855361 TTAAAGTAAT
855371 TTCAAATTATTTA
1 TTCAAATTATTTA
855384 TTCAAATTATTT
1 TTCAAATTATTT
855396 TAGATTGAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
TTCAAATTATTTA
Found at i:861317 original size:244 final size:228
Alignment explanation
Indices: 860314--861425 Score: 999
Period size: 225 Copynumber: 4.8 Consensus size: 228
860304 TTGATCTCAA
* *** * * *
860314 TGCTTATATTATTGTTTTGCAACGAATTAAATGGTTTGAAAAGAGTAAGGTTAATCGGTTAGGAG
1 TGCTTATGTTATTGTTTCATAATGAATTAAATGGTTTG-AAAGAGTAAGGTTAATTGATTAGGAG
* * * * * * **
860379 GATTTAATGTTTTATGTTTGATTATAGATTTTGATTTTCAAGGAAAATTTGAATTTTTTGTTTTG
65 GATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTG-ATATATT-TTTCA
* * * * * **
860444 TTTTGTTCGAATTAGATGCTCGAATTAGTAAAG-TACAATACATTTGGA-TACAGAATTTAG---
128 TTTGGTT-GAAATAGATGTTTGAATTAGTAAAGTTTC-ATACATTTGGATTACAGAATACAGAAA
** ** * * *
860504 AATT-T-TTTTTTTTTTTATAAAT-TAAGTTGATCTCAA-
191 AATTGTGAATTTTAATTAAAAAATATCAGTT-ATCT-AAG
* ** * * * * * *
860540 TGCTTATATTATTGTTTTGTAACGAGTTAAAAGGTTTGAAGGAGTAAGGTTAATCGGTTAGGAGG
1 TGCTTATGTTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
* *
860605 ATTTAGTGTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTT-AT-T-TATTT--TTT
66 ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGATATATTTTTCATTT
* * * * *
860665 GGTTGAAATAAATGTTTGAATTAGT-AAGCTTT-ATGCATTTGGATTACAGAATGCGGAAAATTT
131 GGTTGAAATAGATGTTTGAATTAGTAAAG-TTTCATACATTTGGATTACAGAATACAGAAAAATT
* * * *
860728 TTGAGTTTTAAATTTTTTTTAAGAAAAAAATCAGTTAACTAAG
195 GTGAATTTT-AA------TT-A-AAAAATATCAGTTATCTAAG
* * *
860771 TGCTTATGTTATCGTTTCATAGTGAATTAAATGTTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
1 TGCTTATGTTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
**
860836 ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAT-T-TTTTTTTTTT
66 ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGATATATTTTTCATTT
* * * * *
860899 GGTTGAAATAGATGTTTGAATTAGT-AAG-CTCTATGCATTTGGATTACAGAATGCGGAAAATTT
131 GGTTGAAATAGATGTTTGAATTAGTAAAGTTTC-ATACATTTGGATTACAGAATACAGAAAAATT
* *
860962 TTGAGTTTTAATTAAAAAATATCAGTTATCTAAG
195 GTGAATTTTAATTAAAAAATATCAGTTATCTAAG
* *
860996 TGCTTATGTTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGTTTACGAGG
1 TGCTTATGTTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
*
861061 ATTTAGTCTTTTATGTTTGATTCTATATTTTGATTTTCAGGGAAAATTTGATATATATATATACA
66 ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGATATAT-T-T-T---
861126 CATACATTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGGA-TACAGAATACA
125 --T-CATTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGGATTACAGAATACA
861190 GAAAAATTGTGAACATTTTACATTGAAAAAAATAATTTCAGTTATCTAAG
187 GAAAAATTGTG-A-ATTTTA-ATT--AAAAAAT-A--TCAGTTATCTAAG
* * * * * * *
861240 TGCTTTTTTTATTGTTTCATAATGAACTAAACGGTTTGAAAGAGTAAGGTTAATCGATGAGGAAG
1 TGCTTATGTTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
** * * * **
861305 ATTTAGTCTTTTATG-CAGATTCTAGATTTTGATTTTCAGTGAAAATTTGAAATTTTTTTGTTTT
66 ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGATATATTTTTCATTT
* * *
861369 GATTTGGTAAATAGATGTTTGAATTCGTAAAGTTTTATACATTTGGATTACAGAATA
131 G-GTT-G-AAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGGATTACAGAATA
861426 TGGGAAATTT
Statistics
Matches: 756, Mismatches: 81, Indels: 86
0.82 0.09 0.09
Matches are distributed among these distances:
216 13 0.02
217 26 0.03
218 7 0.01
220 6 0.01
221 2 0.00
222 5 0.01
223 2 0.00
225 201 0.27
226 37 0.05
227 3 0.00
228 1 0.00
229 3 0.00
230 3 0.00
231 108 0.14
232 13 0.02
233 2 0.00
234 74 0.10
235 4 0.01
236 47 0.06
237 51 0.07
238 16 0.02
239 3 0.00
240 1 0.00
241 8 0.01
242 2 0.00
243 34 0.04
244 84 0.11
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.44
Consensus pattern (228 bp):
TGCTTATGTTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGATATATTTTTCATTT
GGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGGATTACAGAATACAGAAAAATTG
TGAATTTTAATTAAAAAATATCAGTTATCTAAG
Found at i:861452 original size:244 final size:242
Alignment explanation
Indices: 860662--861533 Score: 692
Period size: 225 Copynumber: 3.6 Consensus size: 242
860652 TTATTTATTT
* * * *
860662 TTTGGTTGAAATAAATGTTTGAATTAGT-AAGCTTT-ATGCATTTGGATTACAGAATGCGGAAAA
1 TTTGGTTGAAATAGATGTTTGAATTAGTAAAG-TTTCATACATTTGGA-TACAGAATACAGAAAA
* * * * * * * *
860725 TTTTTGAGTTTTAAATTTTTTTTAAGAAAAA-AA--TCAGTTAACTAAGTGCTTATGTTATCGTT
64 ATTGTGA-----ACATTTTATTGAA-AAAAATAATTTCAGTTATCTAAGTGCTTATATTATTGTT
* * * * * * *
860787 TCATAGTGAATTAAATGTTTTGAAAGAGTAAGGTTAATTGATTAGGAGGATTTAGTCTTTTATGT
123 TCATAATGAATTAAAAGGTTTGAAAGAGTAAGGTTAATCGATGACGAAGATTTAGTCTTTTATGT
** **
860852 TTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAT-T-T-T-T-T-----T-TT
188 CAGATTCTAGATTTTGATTTTCAGGGAAAATTTGATATATATATATACACATACA
* * * *
860896 TTTGGTTGAAATAGATGTTTGAATTAGT-AAG-CTCTATGCATTTGGATTACAGAATGCGGAAAA
1 TTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTC-ATACATTTGGA-TACAGAATACAGAAAA
* * * *
860959 TTTTTG-A-GTTTTAATT--AAAAAAT-A--TCAGTTATCTAAGTGCTTATGTTATTGTTTCATA
64 ATTGTGAACATTTT-ATTGAAAAAAATAATTTCAGTTATCTAAGTGCTTATATTATTGTTTCATA
* * * * * **
861017 ATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGTTTACGAGGATTTAGTCTTTTATGTTTGAT
128 ATGAATTAAAAGGTTTGAAAGAGTAAGGTTAATCGATGACGAAGATTTAGTCTTTTATGTCAGAT
*
861082 TCTATATTTTGATTTTCAGGGAAAATTTGATATATATATATACACATACA
193 TCTAGATTTTGATTTTCAGGGAAAATTTGATATATATATATACACATACA
861132 TTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGGATACAGAATACAGAAAAAT
1 TTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGGATACAGAATACAGAAAAAT
* *
861197 TGTGAACATTTTACATTGAAAAAAATAATTTCAGTTATCTAAGTGCTTTTTTTATTGTTTCATAA
66 TGTGAACATTTT--ATTGAAAAAAATAATTTCAGTTATCTAAGTGCTTATATTATTGTTTCATAA
* * *
861262 TGAACTAAACGGTTTGAAAGAGTAAGGTTAATCGATGAGGAAGATTTAGTCTTTTATG-CAGATT
129 TGAATTAAAAGGTTTGAAAGAGTAAGGTTAATCGATGACGAAGATTTAGTCTTTTATGTCAGATT
* * ***** **
861326 CTAGATTTTGATTTTCAGTGAAAATTTGA-A-AT-T-TTTTTGTTTTGA
194 CTAGATTTTGATTTTCAGGGAAAATTTGATATATATATATACACATACA
* * ** * *
861371 TTTGG-T-AAATAGATGTTTGAATTCGTAAAGTTTTATACATTTGGATTACAGAATATGGGAAAT
1 TTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGGA-TACAGAATACAGAAAAA
* * ***** * *
861434 TTTTGAACGTTTACATTTTTTTGTTTTTAATAATTTCTGTTTATCTACGTGCTTATATTATTGTT
65 TTGTG-A-----ACATTTTATTGAAAAAAATAATTTCAG-TTATCTAAGTGCTTATATTATTGTT
* * *
861499 CCGTAATGAATTAAAAGGTTGGAAAGAGTAAGGTT
123 TCATAATGAATTAAAAGGTTTGAAAGAGTAAGGTT
861534 TGATTCTAGA
Statistics
Matches: 541, Mismatches: 64, Indels: 57
0.82 0.10 0.09
Matches are distributed among these distances:
225 129 0.24
226 2 0.00
227 5 0.01
228 4 0.01
229 1 0.00
230 1 0.00
232 1 0.00
234 64 0.12
235 1 0.00
236 46 0.09
237 51 0.09
238 24 0.04
239 13 0.02
240 1 0.00
241 9 0.02
242 15 0.03
243 83 0.15
244 91 0.17
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.43
Consensus pattern (242 bp):
TTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGGATACAGAATACAGAAAAAT
TGTGAACATTTTATTGAAAAAAATAATTTCAGTTATCTAAGTGCTTATATTATTGTTTCATAATG
AATTAAAAGGTTTGAAAGAGTAAGGTTAATCGATGACGAAGATTTAGTCTTTTATGTCAGATTCT
AGATTTTGATTTTCAGGGAAAATTTGATATATATATATACACATACA
Found at i:861526 original size:243 final size:244
Alignment explanation
Indices: 860758--861533 Score: 703
Period size: 225 Copynumber: 3.3 Consensus size: 244
860748 AAGAAAAAAA
* * * * * *
860758 TCAGTTAACTAAGTGCTTATGTTATCGTTTCATAGTGAATTAAATGTTTTGAAAGAGTAAGGTTA
1 TCAGTTATCTAAGTGCTTATATTATTGTTTCATAATGAATTAAAAGGTTTGAAAGAGTAAGGTTA
* * * * **
860823 ATTGATTAGGAGGATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAT
66 ATCGATGACGAAGATTTAGTCTTTTATGTCAGATTCTAGATTTTGATTTTCAGGGAAAATTTGAT
** * *
860888 -T-T-T-T-T-----T-TTTTTGGTTGAAATAGATGTTTGAATTAGT-AAG-CTCTATGCATTTG
131 ATATATATATACACATACATTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTC-ATACATTTG
* * * *
860940 GATTACAGAATGCGGAAAATTTTTG---AGTTTTA-ATT--AAAAAAT-A--
195 GA-TACAGAATACAGAAAAATTGTGAACAG-TTTACATTGAAAAAAATAATT
* *
860983 TCAGTTATCTAAGTGCTTATGTTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTA
1 TCAGTTATCTAAGTGCTTATATTATTGTTTCATAATGAATTAAAAGGTTTGAAAGAGTAAGGTTA
* * * * ** *
861048 ATTGTTTACGAGGATTTAGTCTTTTATGTTTGATTCTATATTTTGATTTTCAGGGAAAATTTGAT
66 ATCGATGACGAAGATTTAGTCTTTTATGTCAGATTCTAGATTTTGATTTTCAGGGAAAATTTGAT
861113 ATATATATATACACATACATTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGG
131 ATATATATATACACATACATTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGG
*
861178 ATACAGAATACAGAAAAATTGTGAACATTTTACATTGAAAAAAATAATT
196 ATACAGAATACAGAAAAATTGTGAACAGTTTACATTGAAAAAAATAATT
* * * *
861227 TCAGTTATCTAAGTGCTTTTTTTATTGTTTCATAATGAACTAAACGGTTTGAAAGAGTAAGGTTA
1 TCAGTTATCTAAGTGCTTATATTATTGTTTCATAATGAATTAAAAGGTTTGAAAGAGTAAGGTTA
* *
861292 ATCGATGAGGAAGATTTAGTCTTTTATG-CAGATTCTAGATTTTGATTTTCAGTGAAAATTTGA-
66 ATCGATGACGAAGATTTAGTCTTTTATGTCAGATTCTAGATTTTGATTTTCAGGGAAAATTTGAT
* ***** ** * *
861355 A-AT-T-TTTTTGTTTTGATTTGG-T-AAATAGATGTTTGAATTCGTAAAGTTTTATACATTTGG
131 ATATATATATACACATACATTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGG
** * * * *****
861415 ATTACAGAATATGGGAAATTTTTGAAC-GTTTACATTTTTTTGTTTTTAATAATT
196 A-TACAGAATACAGAAAAATTGTGAACAGTTTACA-----TTGAAAAAAATAATT
* * * * *
861469 TCTGTTTATCTACGTGCTTATATTATTGTTCCGTAATGAATTAAAAGGTTGGAAAGAGTAAGGTT
1 TCAG-TTATCTAAGTGCTTATATTATTGTTTCATAATGAATTAAAAGGTTTGAAAGAGTAAGGTT
861534 TGATTCTAGA
Statistics
Matches: 463, Mismatches: 59, Indels: 40
0.82 0.10 0.07
Matches are distributed among these distances:
225 123 0.27
226 1 0.00
227 1 0.00
228 1 0.00
229 1 0.00
230 1 0.00
235 1 0.00
236 46 0.10
237 56 0.12
238 27 0.06
239 13 0.03
240 1 0.00
241 9 0.02
242 15 0.03
243 83 0.18
244 84 0.18
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (244 bp):
TCAGTTATCTAAGTGCTTATATTATTGTTTCATAATGAATTAAAAGGTTTGAAAGAGTAAGGTTA
ATCGATGACGAAGATTTAGTCTTTTATGTCAGATTCTAGATTTTGATTTTCAGGGAAAATTTGAT
ATATATATATACACATACATTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTTCATACATTTGG
ATACAGAATACAGAAAAATTGTGAACAGTTTACATTGAAAAAAATAATT
Found at i:866629 original size:23 final size:23
Alignment explanation
Indices: 866603--866649 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
866593 TTAACTTAAC
*
866603 TTAGAAATT-ATTTAAAAAATCAA
1 TTAGAAATTGA-TTAAAAAACCAA
866626 TTAGAAATTGATTAAAAAACCAA
1 TTAGAAATTGATTAAAAAACCAA
866649 T
1 T
866650 ATCTTACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (23 bp):
TTAGAAATTGATTAAAAAACCAA
Found at i:867176 original size:19 final size:18
Alignment explanation
Indices: 867114--867173 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
867104 AAAAGATTTA
*
867114 AAAATTTAAAATAAGTTTTT
1 AAAATTCAAAAT-AG-TTTT
*
867134 AACATTCAAAATAGTTTT
1 AAAATTCAAAATAGTTTT
867152 AAAATTCAAAATA-TTTAT
1 AAAATTCAAAATAGTTT-T
867170 AAAA
1 AAAA
867174 ATTTTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 3 0.08
18 21 0.58
19 2 0.06
20 10 0.28
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAATTCAAAATAGTTTT
Found at i:871561 original size:153 final size:153
Alignment explanation
Indices: 871331--871744 Score: 354
Period size: 164 Copynumber: 2.6 Consensus size: 153
871321 CTCGAAATTA
* * * * * *
871331 TACTTTACTCAAACTCTTC-TTTTACTCT-AAATACCCATGTTTGAAACTTGTTTTTGACACGTA
1 TACTTTACTCAAACTTTTCATTTT-CTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCA
* * * **
871394 TTCAATTACA--GGTTTTGATTGTTTTTAGACATAACACTTGCTCGAGTTTGGCTAATGCAAGAA
65 TGCAA--ACATGGGTTTTGATTGTTTTTAGACAT-ACACTTACTCAAGTTCAGCTAATGCAAGAA
* *
871457 GTG-TCATGAGTTCTCCGAACTGTGCT
127 GTGATCATGAATTCTCCGAACTATGCT
* *
871483 TACTTTGCTCAATCTTTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCAT
1 TACTTTACTCAAACTTTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCAT
* * * * *
871548 GCAAGCATGGGTTTTTGGTTGGTCATGTATACTCGTATCATTCACTTACTCAAGTTCAGTTAATG
66 GCAAACATGGG-TTTTGATT-GT--T-T-T--TAG-A-CATACACTTACTCAAGTTCAGCTAATG
* * *
871613 TACGAAGTGTATCATGAATTCTCCGATCTATGCT
121 CAAGAAGTG-ATCATGAATTCTCCGAACTATGCT
* * ** *
871647 TACTTTACTCAAACTTTTCAGTTTT-TTTAAAATATCCATGCTCAATATCTGTTTTTGACATGCA
1 TACTTTACTCAAACTTTTCA-TTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCA
* *
871711 TGCAAACATGCGTTTTTTTATTGTTTTTAGACAT
65 TGCAAACATG-G-GTTTTGATTGTTTTTAGACAT
871745 GTATACTCAT
Statistics
Matches: 208, Mismatches: 35, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
151 2 0.01
152 20 0.10
153 40 0.19
154 7 0.03
155 2 0.01
156 3 0.01
157 2 0.01
158 3 0.01
159 1 0.00
160 1 0.00
161 3 0.01
162 27 0.13
163 3 0.01
164 83 0.40
165 11 0.05
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (153 bp):
TACTTTACTCAAACTTTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCAT
GCAAACATGGGTTTTGATTGTTTTTAGACATACACTTACTCAAGTTCAGCTAATGCAAGAAGTGA
TCATGAATTCTCCGAACTATGCT
Found at i:871850 original size:170 final size:163
Alignment explanation
Indices: 871481--871851 Score: 399
Period size: 170 Copynumber: 2.2 Consensus size: 163
871471 CCGAACTGTG
* * ** *
871481 CTTACTTTGCTCAATCTTTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGC
1 CTTACTTTACTCAAACTTTTCATTTTCTCTAAAATACCCATGCTCAATATCTGTTTTTGACATGC
* * * * *
871546 ATGCAAGCATGGGTTTTTGGTTGGTCATGTATACTCGTATCATTCACTTACTCAAGTTCAGTTAA
66 ATGCAAACATGGGTTTTTGGTTAGACATGTATACTCATATCA-TCACTTACTCAAGTTCAGCTAA
* * * * *
871611 TGTACGAAGTGTATCATGAATTCTCCGATCTATG
130 AGTAAGAAGTGTATCATGAATTATACGATCTATA
* *
871645 CTTACTTTACTCAAACTTTTCAGTTTT-TTTAAAATATCCATGCTCAATATCTGTTTTTGACATG
1 CTTACTTTACTCAAACTTTTCA-TTTTCTCTAAAATACCCATGCTCAATATCTGTTTTTGACATG
* *
871709 CATGCAAACATGCGTTTTTTTATTGTTTTTAGACATGTATACTCATATCA-CACTCTACTCGAA-
65 CATGCAAACATG-G---GTTT-TTG--GTTAGACATGTATACTCATATCATCACT-TACTC-AAG
* *
871772 TTCTGCTAAAGTAAGAAGTGTGTCATGAATTATACGAAT-TATA
121 TTCAGCTAAAGTAAGAAGTGTATCATGAATTATACG-ATCTATA
* *
871815 TTTACTTTACTCAAACTCTTCATTTTCTCTAAAATAC
1 CTTACTTTACTCAAACTTTTCATTTTCTCTAAAATAC
871852 TCATTTATTG
Statistics
Matches: 170, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
164 63 0.37
165 5 0.03
168 3 0.02
169 11 0.06
170 65 0.38
171 23 0.14
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (163 bp):
CTTACTTTACTCAAACTTTTCATTTTCTCTAAAATACCCATGCTCAATATCTGTTTTTGACATGC
ATGCAAACATGGGTTTTTGGTTAGACATGTATACTCATATCATCACTTACTCAAGTTCAGCTAAA
GTAAGAAGTGTATCATGAATTATACGATCTATA
Found at i:875967 original size:20 final size:20
Alignment explanation
Indices: 875942--875986 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
875932 TGTTTATATG
*
875942 TAAAATT-TTAATATATTATA
1 TAAAATTATTAA-ATATTAAA
*
875962 TAAAATTATTAACTATTAAA
1 TAAAATTATTAAATATTAAA
875982 TAAAA
1 TAAAA
875987 AATATCATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATTATTAAATATTAAA
Found at i:880351 original size:5 final size:5
Alignment explanation
Indices: 880343--880393 Score: 93
Period size: 5 Copynumber: 10.2 Consensus size: 5
880333 CTCCCTCCCT
*
880343 CACCC CACCC CACCC CACCC CACCC CACCC CACCC CACCC TACCC CACCC
1 CACCC CACCC CACCC CACCC CACCC CACCC CACCC CACCC CACCC CACCC
880393 C
1 C
880394 CAAATGGTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.20, C:0.78, G:0.00, T:0.02
Consensus pattern (5 bp):
CACCC
Found at i:892791 original size:16 final size:16
Alignment explanation
Indices: 892741--892792 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
892731 GTTAACAAAT
*
892741 AATTTAAAATTTATAAA
1 AATTCAAAA-TTATAAA
*
892758 ATATTCATAAAATA-AAA
1 A-ATTCA-AAATTATAAA
892775 AATTCAAAATTATAAA
1 AATTCAAAATTATAAA
892791 AA
1 AA
892793 AAAAGTCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 5 0.17
16 10 0.34
17 5 0.17
18 6 0.21
19 3 0.10
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTCAAAATTATAAA
Found at i:892796 original size:20 final size:20
Alignment explanation
Indices: 892765--892814 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
892755 AAAATATTCA
*
892765 TAAAATAAAAAATTCA-AAAT
1 TAAAA-AAAAAAGTCATAAAT
892785 TATAAAAAAAAAGTCATAAAT
1 TA-AAAAAAAAAGTCATAAAT
892806 TAAAAAAAA
1 TAAAAAAAA
892815 CACGAAGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (20 bp):
TAAAAAAAAAAGTCATAAAT
Found at i:897053 original size:18 final size:18
Alignment explanation
Indices: 897014--897049 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
897004 GACAAAATCT
897014 ACTCATAATGAAACCTAA
1 ACTCATAATGAAACCTAA
*
897032 ACTCATAAT-AAATCTAA
1 ACTCATAATGAAACCTAA
897049 A
1 A
897050 ACTCGAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (18 bp):
ACTCATAATGAAACCTAA
Found at i:900673 original size:17 final size:16
Alignment explanation
Indices: 900630--900682 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
900620 GCAAATTGTG
900630 AACTGCGAGCTCACCA
1 AACTGCGAGCTCACCA
* *
900646 AATGTGTGAGCTCACCA
1 AA-CTGCGAGCTCACCA
*
900663 AGACTGCGAGCTCTCCA
1 A-ACTGCGAGCTCACCA
900680 AAC
1 AAC
900683 ATTAGAGCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.13
17 25 0.83
18 1 0.03
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (16 bp):
AACTGCGAGCTCACCA
Found at i:902398 original size:10 final size:11
Alignment explanation
Indices: 902372--902403 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
902362 TTCTTTAGAA
902372 TTTTTTAAATT
1 TTTTTTAAATT
902383 TTTTTTAAATT
1 TTTTTTAAATT
*
902394 TTTTTAAAAT
1 TTTTTTAAAT
902404 ATAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAAATT
Found at i:902446 original size:19 final size:19
Alignment explanation
Indices: 902416--902462 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
902406 AAAATTTAAC
*
902416 TTTTTTATAAA-TATTTTGAA
1 TTTTTTA-AAATTATTTAG-A
902436 TTTTTTAAAATTATTTAGA
1 TTTTTTAAAATTATTTAGA
902455 TTTTTTAA
1 TTTTTTAA
902463 TTTTGTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTTTAAAATTATTTAGA
Found at i:904005 original size:8 final size:8
Alignment explanation
Indices: 903992--904016 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
903982 CACTTTTAAA
903992 TTTAAAAT
1 TTTAAAAT
904000 TTTAAAAT
1 TTTAAAAT
904008 TTTAAAAT
1 TTTAAAAT
904016 T
1 T
904017 CAGTCTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:912597 original size:3 final size:3
Alignment explanation
Indices: 912589--912627 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
912579 CCATATCTCC
912589 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
912628 GGTTTCATTC
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:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:912966 original size:16 final size:17
Alignment explanation
Indices: 912939--912971 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
912929 ATTTAGGCCC
912939 TTTAAAATTTTTAAATT
1 TTTAAAATTTTTAAATT
912956 TTTAAAA-TTTTAAATT
1 TTTAAAATTTTTAAATT
912972 AATAAACGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAAATTTTTAAATT
Found at i:919849 original size:72 final size:72
Alignment explanation
Indices: 919763--919964 Score: 246
Period size: 64 Copynumber: 2.9 Consensus size: 72
919753 GCACCATACC
* *** *
919763 TCCA-CCATACATACATACATACATTA-TCTTAACCGTTTCATAAT-AGCTCTTCGTTACGTAGT
1 TCCATCCATACATACATACATACATTATTC-TAACCGTTTCACAATGA-CTAGCCGTTACATAGT
919825 GTACATCCA
64 GTACATCCA
919834 TCCATCCATACATACATACATACATTATTCTAACCGTTTCACAATGACTAGCCGTTACATAGTGT
1 TCCATCCATACATACATACATACATTATTCTAACCGTTTCACAATGACTAGCCGTTACATAGTGT
919899 --A--CA
66 ACATCCA
* *
919902 TCCAT-C---CATACATACATACATTATTCTAACCATTTCACAATGACTGGCCGTTACATAGTGT
1 TCCATCCATACATACATACATACATTATTCTAACCGTTTCACAATGACTAGCCGTTACATAGTGT
919963 AC
66 AC
919965 CTAAGTTGAA
Statistics
Matches: 119, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
64 53 0.45
67 1 0.01
68 7 0.06
70 1 0.01
71 4 0.03
72 50 0.42
73 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.32
Consensus pattern (72 bp):
TCCATCCATACATACATACATACATTATTCTAACCGTTTCACAATGACTAGCCGTTACATAGTGT
ACATCCA
Found at i:921335 original size:26 final size:27
Alignment explanation
Indices: 921287--921339 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
921277 CTTGAAAGCT
921287 ATTTGAGTTTGACTCGAAAAAATTCAA
1 ATTTGAGTTTGACTCGAAAAAATTCAA
*
921314 ATTTGA-TTTGA-TCGAATTAAATTCAA
1 ATTTGAGTTTGACTCGAA-AAAATTCAA
921340 GCATTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 13 0.54
27 6 0.25
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (27 bp):
ATTTGAGTTTGACTCGAAAAAATTCAA
Found at i:921402 original size:2 final size:2
Alignment explanation
Indices: 921395--921426 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
921385 TTTCATTCTA
921395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
921427 AAATTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:921723 original size:12 final size:12
Alignment explanation
Indices: 921699--921731 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
921689 TTATTTTAAA
921699 TTTAAAATATTTT
1 TTTAAAAT-TTTT
921712 TTT-AAATTTTT
1 TTTAAAATTTTT
921723 TTTAAAATT
1 TTTAAAATT
921732 CAAGTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.37
12 9 0.47
13 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTAAAATTTTT
Found at i:927448 original size:3 final size:3
Alignment explanation
Indices: 927442--927481 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
927432 ACCACCACAG
927442 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
927482 ATTTAATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:927844 original size:17 final size:16
Alignment explanation
Indices: 927796--927845 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
927786 GGTATTTTTC
*
927796 ATTTTTTTAATATATGA
1 ATTTTTTTAATAT-TTA
*
927813 ATTTTATTTATTATTTA
1 ATTTT-TTTAATATTTA
927830 ATTTTTTTAGATATTT
1 ATTTTTTTA-ATATTT
927846 TTTAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 4 0.14
17 17 0.61
18 7 0.25
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (16 bp):
ATTTTTTTAATATTTA
Found at i:934398 original size:27 final size:26
Alignment explanation
Indices: 934368--934420 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
934358 CATTAGAATC
* * *
934368 CAAGTTCAATGAGCAAATCAAAAGTTT
1 CAAGTTCAAAGAACAAA-AAAAAGTTT
934395 CAAGTTCAAAGAACAAAAAAAAGTTT
1 CAAGTTCAAAGAACAAAAAAAAGTTT
934421 AAAACAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (26 bp):
CAAGTTCAAAGAACAAAAAAAAGTTT
Found at i:935497 original size:24 final size:22
Alignment explanation
Indices: 935438--935502 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
935428 TAGTAGAATT
935438 AATTTGTATATTTTTATAATAAA
1 AATTT-TATATTTTTATAATAAA
* * *
935461 AATTTGA-AATTTTATCATTATAA
1 AATTTTATATTTTTAT-AATA-AA
935484 AATTTTATATTTTTATAAT
1 AATTTTATATTTTTATAAT
935503 TTTTAAAGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 7 0.21
22 4 0.12
23 15 0.45
24 7 0.21
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (22 bp):
AATTTTATATTTTTATAATAAA
Found at i:935900 original size:21 final size:21
Alignment explanation
Indices: 935871--935910 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
935861 AATAGCATTA
*
935871 TAAAGTTTAGAAATCCAAAAG
1 TAAAATTTAGAAATCCAAAAG
*
935892 TAAAATTTATAAATCCAAA
1 TAAAATTTAGAAATCCAAA
935911 GATAAAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (21 bp):
TAAAATTTAGAAATCCAAAAG
Found at i:935916 original size:21 final size:20
Alignment explanation
Indices: 935870--935917 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
935860 TAATAGCATT
*
935870 ATAAAGTTTAGAAATCCAAA
1 ATAAAATTTAGAAATCCAAA
*
935890 AGTAAAATTTATAAATCCAAA
1 A-TAAAATTTAGAAATCCAAA
935911 GATAAAA
1 -ATAAAA
935918 CCATGGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.25
Consensus pattern (20 bp):
ATAAAATTTAGAAATCCAAA
Found at i:936723 original size:29 final size:29
Alignment explanation
Indices: 936668--936725 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
936658 TCAAGCAAAG
*
936668 ATAAAACGGTTACTTAACTTTAGAAAATT
1 ATAAAACGGTTACTTAACTTTACAAAATT
* *
936697 ATAAAATGGTTATTTAACTATT-CAAAATT
1 ATAAAACGGTTACTTAACT-TTACAAAATT
936726 TTCTGTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (29 bp):
ATAAAACGGTTACTTAACTTTACAAAATT
Found at i:942191 original size:17 final size:17
Alignment explanation
Indices: 942169--942202 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
942159 GAATAAATCT
*
942169 TTAATTAAATAATTTAA
1 TTAATTAAAAAATTTAA
942186 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
942203 ACCCTAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:942800 original size:21 final size:20
Alignment explanation
Indices: 942761--942810 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
942751 CAGTTTACCC
*
942761 TAAAAATAATTTATATTAAA
1 TAAAAATAATATATATTAAA
942781 TTAAAAATAATATACT-TTAAA
1 -TAAAAATAATATA-TATTAAA
942802 TAAATAATA
1 TAAA-AATA
942811 TTAGCGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 21 0.81
22 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATAATATATATTAAA
Found at i:943194 original size:62 final size:59
Alignment explanation
Indices: 943098--943236 Score: 165
Period size: 62 Copynumber: 2.3 Consensus size: 59
943088 TTTAGCTTTC
* *
943098 TAATATTTAC-ATATTCTATCAATTTGATATAAATTCTAAAAAATTCAATAAATTTAATCCAT
1 TAATATTTACAAAATT-TATCAATTTAATATAAATT-TAAAAAATTCAATAAATTTAA-CC-T
* *
943160 TAATATTTACAAAATTTATCATTTTAAT-TCAAATTTTAAAAATTCAATAAATTTAACCT
1 TAATATTTACAAAATTTATCAATTTAATAT-AAATTTAAAAAATTCAATAAATTTAACCT
*
943219 TCAACATTTACAAAATTT
1 T-AATATTTACAAAATTT
943237 CTTAATATAA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
59 2 0.03
60 17 0.25
61 21 0.30
62 25 0.36
63 4 0.06
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (59 bp):
TAATATTTACAAAATTTATCAATTTAATATAAATTTAAAAAATTCAATAAATTTAACCT
Found at i:943262 original size:61 final size:62
Alignment explanation
Indices: 943128--943264 Score: 163
Period size: 60 Copynumber: 2.2 Consensus size: 62
943118 AATTTGATAT
* * *
943128 AAATTCTAAAAAATTCAATAAATTTAATCCATTAATATTTACAAAATTTATCATTTTAATTC
1 AAATTCTAAAAAATTCAATAAATTTAATCCATTAACATTTACAAAATTTATCAATATAATTC
* * * *
943190 AAATT-TTAAAAATTCAATAAATTTAA-CC-TTCAACATTTACAAAATTTCTTAATATAATTG
1 AAATTCTAAAAAATTCAATAAATTTAATCCATT-AACATTTACAAAATTTATCAATATAATTC
* *
943250 TAATTCAAAAAAATT
1 AAATTCTAAAAAATT
943265 AAAAGGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
59 2 0.03
60 29 0.46
61 27 0.43
62 5 0.08
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (62 bp):
AAATTCTAAAAAATTCAATAAATTTAATCCATTAACATTTACAAAATTTATCAATATAATTC
Found at i:943554 original size:32 final size:33
Alignment explanation
Indices: 943493--943572 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 33
943483 TTTCCGATTT
*
943493 TCTCCGATTCGATTTTGGGAAAAAAAAAAGGAA
1 TCTCCGCTTCGATTTTGGGAAAAAAAAAAGGAA
943526 TCTCCGCTTCGATTTTGGG-AAAAAAAAAGGAA
1 TCTCCGCTTCGATTTTGGGAAAAAAAAAAGGAA
*
943558 TCGCCGCTTCGATTT
1 TCTCCGCTTCGATTT
943573 CAAAATTCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (33 bp):
TCTCCGCTTCGATTTTGGGAAAAAAAAAAGGAA
Found at i:947530 original size:2 final size:2
Alignment explanation
Indices: 947523--947547 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
947513 AGTGCTGTTT
947523 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
947548 CCATACTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:948440 original size:19 final size:19
Alignment explanation
Indices: 948412--948449 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
948402 AATGGACGTA
* *
948412 TTTCTTATTTTCTTTTCTC
1 TTTCTAATTTTCTGTTCTC
948431 TTTCTAATTTTCTGTTCTC
1 TTTCTAATTTTCTGTTCTC
948450 CTTTTCCGTG
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:0.08, C:0.21, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTCTAATTTTCTGTTCTC
Found at i:950559 original size:10 final size:10
Alignment explanation
Indices: 950544--950583 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
950534 ATCAATATTT
*
950544 TTTTAAAATA
1 TTTTAAATTA
950554 TTTTAAATTA
1 TTTTAAATTA
*
950564 TATTTATATTA
1 T-TTTAAATTA
950575 TTTTAAATT
1 TTTTAAATT
950584 TAATATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTAAATTA
Found at i:950569 original size:21 final size:23
Alignment explanation
Indices: 950545--950601 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
950535 TCAATATTTT
950545 TTTAAAATATTTTAAA-TT-ATA
1 TTTAAAATATTTTAAATTTAATA
* *
950566 TTTATATTATTTTAAATTTAATA
1 TTTAAAATATTTTAAATTTAATA
*
950589 TTTAATA-ATTTTA
1 TTTAAAATATTTTA
950602 TAGAAACAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.48
22 8 0.28
23 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTAAAATATTTTAAATTTAATA
Found at i:953177 original size:48 final size:47
Alignment explanation
Indices: 953111--953259 Score: 147
Period size: 48 Copynumber: 3.1 Consensus size: 47
953101 ATACATGAAC
*
953111 TCTCGCTAATGGTCTGGTGGTTAGAGATGTTCACTCCAAAGAACTTAT
1 TCTCGCTAAT-GACTGGTGGTTAGAGATGTTCACTCCAAAGAACTTAT
* * *
953159 TCTCGCTAATGACATGGTGGTTAGGGATGTTGACTTCATAA-AACTTAT
1 TCTCGCTAATGAC-TGGTGGTTAGAGATGTTCACTCCA-AAGAACTTAT
* * * * * *
953207 TCTCCCAAATGATTTGGTGGTTAAAAGGATATTCACTCTAAAGAACTTAT
1 TCTCGCTAATGA-CTGGTGGTT-AGA-GATGTTCACTCCAAAGAACTTAT
953257 TCT
1 TCT
953260 TAGTTCTCGC
Statistics
Matches: 82, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
47 2 0.02
48 56 0.68
49 5 0.06
50 19 0.23
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (47 bp):
TCTCGCTAATGACTGGTGGTTAGAGATGTTCACTCCAAAGAACTTAT
Found at i:953582 original size:31 final size:31
Alignment explanation
Indices: 953547--953607 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
953537 ATATAGAAGA
* *
953547 TTGAATTAAAATTAAAATTTCATATATATAT
1 TTGAATCAAAATCAAAATTTCATATATATAT
* *
953578 TTGAATCACAATCAAAATTTCATATGTATA
1 TTGAATCAAAATCAAAATTTCATATATATA
953608 ATTGTACTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (31 bp):
TTGAATCAAAATCAAAATTTCATATATATAT
Found at i:956013 original size:126 final size:126
Alignment explanation
Indices: 955788--956152 Score: 509
Period size: 126 Copynumber: 2.9 Consensus size: 126
955778 CTAACCTGAG
* * *
955788 AAGAATCATCACTAGTAAACATCGAAAGTGCAACTACTATGCTAGTTCAATGAAGAACATATTGA
1 AAGAATCATCACTAGTAAACATCGAAAGTGCAACTGCTATGCTAGTGCAATGAAGAACATATCGA
* *
955853 CATTGAACTCGAGATATGCAAAAGAATAACAACATATGCAGCAAA-TGGCATAAGAACCGGA
66 CATTAAACTCGAGATATGCAAAAGAATAACAACATATGCAGCAAACT-GCATAAGAACCAGA
* * * * *
955914 AAGAACCATCACTAGTAAACATCGAAAGCGCAACCGCTGTGCTAGTGCAATGAAGAACATATCAA
1 AAGAATCATCACTAGTAAACATCGAAAGTGCAACTGCTATGCTAGTGCAATGAAGAACATATCGA
*
955979 CATTAAACTCGAGATATGCAAACA-AATAACAACATATGCAGCAAACTGCGTAAGAACCAGA
66 CATTAAACTCGAGATATGCAAA-AGAATAACAACATATGCAGCAAACTGCATAAGAACCAGA
* * * * *
956040 AAGAATCATCACTAGTATACATTGAGAGTGCAACTGCAATGCCAGTGCAATGAAGAACATATCGA
1 AAGAATCATCACTAGTAAACATCGAAAGTGCAACTGCTATGCTAGTGCAATGAAGAACATATCGA
* *
956105 CATTAAACTCGAGATGTGCAAATTGATAATAACAACATATGCAGCAAA
66 CATTAAACTCGAGATATGCAAA---AGAATAACAACATATGCAGCAAA
956153 ATCGTATGAG
Statistics
Matches: 211, Mismatches: 23, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
126 187 0.89
127 2 0.01
128 1 0.00
129 21 0.10
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (126 bp):
AAGAATCATCACTAGTAAACATCGAAAGTGCAACTGCTATGCTAGTGCAATGAAGAACATATCGA
CATTAAACTCGAGATATGCAAAAGAATAACAACATATGCAGCAAACTGCATAAGAACCAGA
Found at i:962600 original size:23 final size:23
Alignment explanation
Indices: 962574--962620 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
962564 CTTTGCCTAA
*
962574 TTTTCTTATTGGAATTAATGCTT
1 TTTTCTTATTGAAATTAATGCTT
* *
962597 TTTTTTTCTTGAAATTAATGCTT
1 TTTTCTTATTGAAATTAATGCTT
962620 T
1 T
962621 GTTGCCTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.11, T:0.60
Consensus pattern (23 bp):
TTTTCTTATTGAAATTAATGCTT
Found at i:962656 original size:54 final size:53
Alignment explanation
Indices: 962545--962657 Score: 120
Period size: 54 Copynumber: 2.1 Consensus size: 53
962535 ATTGCAAATA
* * ** * *
962545 TTTTTCTTGATATTAATGCCTTTGCCTAATTTTCTTATTGGAATTAATGCTTTT
1 TTTTTCTTGAAATTAATGCCTTTGCCTAATTTCCTTATTCAAATAAATGC-TCT
* *
962599 TTTTTCTTGAAATTAATGCTTTGTTGCCTAATTTCCTTCTTCAAATAAATG-TCT
1 TTTTTCTTGAAATTAATGC-CT-TTGCCTAATTTCCTTATTCAAATAAATGCTCT
962653 TTTTT
1 TTTTT
962658 GGATGCTTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
54 25 0.51
55 1 0.02
56 23 0.47
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (53 bp):
TTTTTCTTGAAATTAATGCCTTTGCCTAATTTCCTTATTCAAATAAATGCTCT
Found at i:962657 original size:56 final size:54
Alignment explanation
Indices: 962545--962657 Score: 136
Period size: 56 Copynumber: 2.0 Consensus size: 54
962535 ATTGCAAATA
* * ** *
962545 TTTTTCTTGATATTAATGCCTTTGCCTAATTTTCTTATTGGAATTAATGCTTTT
1 TTTTTCTTGAAATTAATGCCTTTGCCTAATTTCCTTATTCAAATAAATGCTTTT
* *
962599 TTTTTCTTGAAATTAATGCTTTGTTGCCTAATTTCCTTCTTCAAATAAATGTCTTTT
1 TTTTTCTTGAAATTAATGC-CT-TTGCCTAATTTCCTTATTCAAATAAATG-CTTTT
962656 TT
1 TT
962658 GGATGCTTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
54 18 0.37
55 1 0.02
56 23 0.47
57 7 0.14
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (54 bp):
TTTTTCTTGAAATTAATGCCTTTGCCTAATTTCCTTATTCAAATAAATGCTTTT
Found at i:967225 original size:79 final size:79
Alignment explanation
Indices: 967137--967296 Score: 302
Period size: 79 Copynumber: 2.0 Consensus size: 79
967127 AAGCTACAAA
*
967137 ATCAGCACAGTGAAATTCCCAGACAGAATCCATAAAATATAAGCATTTTTAAGGTGGGTTTTTGT
1 ATCAGCACAGTGAAATTCCCAAACAGAATCCATAAAATATAAGCATTTTTAAGGTGGGTTTTTGT
967202 TTATATATACATAT
66 TTATATATACATAT
967216 ATCAGCACAGTGAAATTCCCAAACAGAATCCATAAAATATAAGCATTTTTAAGGTGGGTTTTTGT
1 ATCAGCACAGTGAAATTCCCAAACAGAATCCATAAAATATAAGCATTTTTAAGGTGGGTTTTTGT
*
967281 TTATATATATATAT
66 TTATATATACATAT
967295 AT
1 AT
967297 GTGTGGCCAT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (79 bp):
ATCAGCACAGTGAAATTCCCAAACAGAATCCATAAAATATAAGCATTTTTAAGGTGGGTTTTTGT
TTATATATACATAT
Found at i:969964 original size:56 final size:54
Alignment explanation
Indices: 969854--969972 Score: 159
Period size: 53 Copynumber: 2.2 Consensus size: 54
969844 AAAGAAAAAC
* * *
969854 ACTCAAGTATCAAATTGAAAAAAAAAATTCAAGCACCATTGAATATGAAGCCAA
1 ACTCAGGTACCAAATTGAAAAAAAAAACTCAAGCACCATTGAATATGAAGCCAA
*
969908 ACTCAGGTACCAAATTG-AAAAAAAAACTCAAGTACCAAATTGAATATTGAAGCCAA
1 ACTCAGGTACCAAATTGAAAAAAAAAACTCAAGCACC--ATTGAATA-TGAAGCCAA
*
969964 AATCAGGTA
1 ACTCAGGTA
969973 TAAAATATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
53 17 0.30
54 15 0.26
55 8 0.14
56 17 0.30
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (54 bp):
ACTCAGGTACCAAATTGAAAAAAAAAACTCAAGCACCATTGAATATGAAGCCAA
Found at i:970121 original size:18 final size:18
Alignment explanation
Indices: 970098--970133 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
970088 AAAAACCCAC
*
970098 CATATATATACACATATA
1 CATATACATACACATATA
970116 CATATACATACACATATA
1 CATATACATACACATATA
970134 GTTCTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (18 bp):
CATATACATACACATATA
Found at i:975547 original size:9 final size:9
Alignment explanation
Indices: 975517--975551 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
975507 TAAACCCATC
975517 TCTTCTTCA
1 TCTTCTTCA
*
975526 TCTTCATCA
1 TCTTCTTCA
*
975535 TCTTCTTCT
1 TCTTCTTCA
975544 TCTTCTTC
1 TCTTCTTC
975552 CCTTTTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.09, C:0.34, G:0.00, T:0.57
Consensus pattern (9 bp):
TCTTCTTCA
Found at i:978405 original size:2 final size:2
Alignment explanation
Indices: 978398--978423 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
978388 CTCCGCTCTC
978398 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
978424 TGAATACGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:979709 original size:3 final size:3
Alignment explanation
Indices: 979664--979690 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
979654 TTTTGGCCCC
979664 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
979691 CACTTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:980982 original size:2 final size:2
Alignment explanation
Indices: 980975--981016 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
980965 GTCATATCAA
980975 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
981017 GCATTTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:988609 original size:33 final size:33
Alignment explanation
Indices: 988564--988628 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
988554 CCCTAAGAAG
988564 GTTCTACCCTGTGCAAACACTCTTTTAATGGAA
1 GTTCTACCCTGTGCAAACACTCTTTTAATGGAA
*
988597 GTTCTACGCTGTGCAAACACTCTTTTAATGGA
1 GTTCTACCCTGTGCAAACACTCTTTTAATGGA
988629 TCATTAGCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (33 bp):
GTTCTACCCTGTGCAAACACTCTTTTAATGGAA
Found at i:992596 original size:148 final size:149
Alignment explanation
Indices: 992320--992616 Score: 515
Period size: 148 Copynumber: 2.0 Consensus size: 149
992310 TATCATTTAA
* * **
992320 CTTTGGTTTTCTTTATTCATAATTAAAAACCATAAATTTTTGAATTGAATCAAATTTTATTTTTA
1 CTTTGGTTTCCTTTATTCATAATTAAAAACCATAAATATTTGAATTGAATCAAAAATTATTTTTA
*
992385 TAAGATCAAAATAAAATATTTTATTTCTAAATGAGCGAAAAAACTTAAAAGTAACTTTAACAAAA
66 TAAAATCAAAATAAAATATTTTATTTCTAAATGAGCGAAAAAACTTAAAAGTAACTTTAACAAAA
*
992450 GGGATGAACCGAAGCAATG
131 GGGATGAACCAAAGCAATG
992469 CTTTGGTTTCCTTTATTCATAATTAAAAACCATAAATATTTGAATTGAATCAAAAATTA-TTTTA
1 CTTTGGTTTCCTTTATTCATAATTAAAAACCATAAATATTTGAATTGAATCAAAAATTATTTTTA
* *
992533 TAAAATCAAAATAAAATATTTTATTTCTAAATTAGTGAAAAAACTTAAAAGTAACTTTAACAAAA
66 TAAAATCAAAATAAAATATTTTATTTCTAAATGAGCGAAAAAACTTAAAAGTAACTTTAACAAAA
992598 GGGATGAACCAAAGCAATG
131 GGGATGAACCAAAGCAATG
992617 AAATTCAATT
Statistics
Matches: 140, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
148 85 0.61
149 55 0.39
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (149 bp):
CTTTGGTTTCCTTTATTCATAATTAAAAACCATAAATATTTGAATTGAATCAAAAATTATTTTTA
TAAAATCAAAATAAAATATTTTATTTCTAAATGAGCGAAAAAACTTAAAAGTAACTTTAACAAAA
GGGATGAACCAAAGCAATG
Found at i:993823 original size:22 final size:21
Alignment explanation
Indices: 993781--993827 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
993771 TTGCTGCTAT
*
993781 TTTTCCATTGTTTTATTATTA
1 TTTTCCATTGTTTTATCATTA
993802 TTTTCCTATTGTTTT-TCCATTA
1 TTTTCC-ATTGTTTTAT-CATTA
993824 TTTT
1 TTTT
993828 ATTGTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTCCATTGTTTTATCATTA
Found at i:996636 original size:18 final size:19
Alignment explanation
Indices: 996615--996656 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
996605 ATAATATTTT
*
996615 AAAAATATAATACA-TAAA
1 AAAAATATAAAACATTAAA
996633 AAAAA-ATAAAACATTAAA
1 AAAAATATAAAACATTAAA
*
996651 ATAAAT
1 AAAAAT
996657 GTTTCTCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAATATAAAACATTAAA
Found at i:996858 original size:22 final size:22
Alignment explanation
Indices: 996817--996858 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
996807 TAGTGAAATG
* *
996817 ACAATAAAATAATGAGAAAACA
1 ACAATAAAATAATAAAAAAACA
*
996839 ACAATAAAATAGTAAAAAAA
1 ACAATAAAATAATAAAAAAA
996859 AGGAAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (22 bp):
ACAATAAAATAATAAAAAAACA
Found at i:1004048 original size:68 final size:69
Alignment explanation
Indices: 1003938--1004080 Score: 243
Period size: 68 Copynumber: 2.1 Consensus size: 69
1003928 TGAGGTGAAA
* *
1003938 AAAAAATTAATTTATAAAAAACCATACATATACATGTGCATATGCATATACATATAGTAATCATC
1 AAAAAATTAATTTATAAAAAACCATACATATACATATGCATATACATATACATATAGTAATCATC
1004003 ATAT
66 ATAT
* *
1004007 AAAAAATTAATTTA-AAAAAACCATACATATTCATATTCATATACATATACATATAGTAATCATC
1 AAAAAATTAATTTATAAAAAACCATACATATACATATGCATATACATATACATATAGTAATCATC
1004071 ATAT
66 ATAT
1004075 AAAAAA
1 AAAAAA
1004081 ACAACATCAA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
68 56 0.80
69 14 0.20
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.31
Consensus pattern (69 bp):
AAAAAATTAATTTATAAAAAACCATACATATACATATGCATATACATATACATATAGTAATCATC
ATAT
Found at i:1004208 original size:83 final size:85
Alignment explanation
Indices: 1004047--1004217 Score: 222
Period size: 83 Copynumber: 2.0 Consensus size: 85
1004037 TCATATTCAT
1004047 ATACATATACATATAGTAATCATCATATAAAAAAACAACATCAAACTAGCATATAGTACTGATAA
1 ATACATATACATATAGTAATCATCATATAAAAAAACAACATCAAACTAG-ATATAGTACTGATAA
* *
1004112 TAGATTGAATAAACTACACAC
65 TAGATTCAATAAACTAAACAC
* * * *** *
1004133 ATACATATACATATA-TAGTGATTATATAGGCAAACAACATCAAACTAG-TATAGTACTGGTCAA
1 ATACATATACATATAGTAATCATCATATAAAAAAACAACATCAAACTAGATATAGTACTGAT-AA
1004196 -AGATTCAATAAACTAAACAC
65 TAGATTCAATAAACTAAACAC
1004216 AT
1 AT
1004218 GTACATGTAC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
83 31 0.41
84 2 0.03
85 27 0.36
86 15 0.20
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (85 bp):
ATACATATACATATAGTAATCATCATATAAAAAAACAACATCAAACTAGATATAGTACTGATAAT
AGATTCAATAAACTAAACAC
Found at i:1007957 original size:15 final size:15
Alignment explanation
Indices: 1007939--1007971 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1007929 GTAAAACTTT
1007939 TTTATAT-TTTATTAA
1 TTTATATATTT-TTAA
1007954 TTTATATATTTTTAA
1 TTTATATATTTTTAA
1007969 TTT
1 TTT
1007972 CATAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATATATTTTTAA
Found at i:1009844 original size:19 final size:19
Alignment explanation
Indices: 1009820--1009879 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
1009810 ATCCTAATTC
1009820 TAAAAATTTTAAAAATATA
1 TAAAAATTTTAAAAATATA
** *
1009839 TAAAAAAATTAAAAATACA
1 TAAAAATTTTAAAAATATA
* *
1009858 TAAATATTTTCAAAAAAATA
1 TAAAAATTTT-AAAAATATA
1009878 TA
1 TA
1009880 TAAGATACCC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 23 0.72
20 9 0.28
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATTTTAAAAATATA
Found at i:1013040 original size:58 final size:58
Alignment explanation
Indices: 1012956--1013085 Score: 197
Period size: 58 Copynumber: 2.2 Consensus size: 58
1012946 CCCGGGGGCA
* * * *
1012956 AAATGGTAGATTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGGAGTTTGAGGGTG
1 AAATGGTA-ATTTTAGTGAAATCGGGGTTAAAAAGGGGATTTAGGGAAGTTTGAGGGTC
* *
1013015 AAATGGTAATTTTAGTGAAATCGGGGTTTAAAAGGGGATTTAGGGAAGTTTGGGGGTC
1 AAATGGTAATTTTAGTGAAATCGGGGTTAAAAAGGGGATTTAGGGAAGTTTGAGGGTC
1013073 AAATGGTAATTTT
1 AAATGGTAATTTT
1013086 TGAAAGTTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
58 57 0.88
59 8 0.12
ACGTcount: A:0.30, C:0.02, G:0.35, T:0.32
Consensus pattern (58 bp):
AAATGGTAATTTTAGTGAAATCGGGGTTAAAAAGGGGATTTAGGGAAGTTTGAGGGTC
Found at i:1013084 original size:29 final size:29
Alignment explanation
Indices: 1012994--1013084 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 29
1012984 TAAAAATGGG
* * *
1012994 ATTTAGGGGAGTTTGAGGGTGAAATGGTA
1 ATTTAGGGAAGTTTGGGGGTCAAATGGTA
* * * * * * **
1013023 ATTTTAGTGAA-ATCGGGGTTTAAAAGGGG
1 A-TTTAGGGAAGTTTGGGGGTCAAATGGTA
1013052 ATTTAGGGAAGTTTGGGGGTCAAATGGTA
1 ATTTAGGGAAGTTTGGGGGTCAAATGGTA
1013081 ATTT
1 ATTT
1013085 TTGAAAGTTT
Statistics
Matches: 42, Mismatches: 18, Indels: 4
0.66 0.28 0.06
Matches are distributed among these distances:
28 8 0.19
29 27 0.64
30 7 0.17
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.33
Consensus pattern (29 bp):
ATTTAGGGAAGTTTGGGGGTCAAATGGTA
Found at i:1013092 original size:29 final size:30
Alignment explanation
Indices: 1013060--1013261 Score: 225
Period size: 30 Copynumber: 6.8 Consensus size: 30
1013050 GGATTTAGGG
*
1013060 AAGTTTGGGGGTC-AAATGGTAATTTTTG-A
1 AAGTTTTGGGGTCAAAAT-GTAATTTTTGAA
** *
1013089 AAGTTTCAGGGT-AAAATGTAATTTTTGGA
1 AAGTTTTGGGGTCAAAATGTAATTTTTGAA
* * *
1013118 AA-TTTTGGGGTCAAAATATGATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTTGAA
* *
1013147 AAGTTTTGGGGTCAAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTTGAA
** *
1013177 AAGTTTTAAGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTTGAA
*
1013207 AAGTTTTGGGGTCAAAATATAATTTTT-AGA
1 AAGTTTTGGGGTCAAAATGTAATTTTTGA-A
*
1013237 AAGTTTTGAGGTCAAAATGTAATTT
1 AAGTTTTGGGGTCAAAATGTAATTT
1013262 ATGGACAATT
Statistics
Matches: 148, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
28 17 0.11
29 33 0.22
30 98 0.66
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTTGAA
Found at i:1013552 original size:162 final size:162
Alignment explanation
Indices: 1013359--1013673 Score: 551
Period size: 162 Copynumber: 1.9 Consensus size: 162
1013349 ATTTGAAAGT
* *
1013359 CTTGAAAAAATTTTGGACCAATTTTGTAATTAAATAAAAGTTAATTTAAGGACTAAATTAAAACA
1 CTTGAAAAAATTTTGGACCAATTTGGTAATTAAATAAAAGTTAATTTAAAGACTAAATTAAAACA
*
1013424 AATTAAAAATGTCAGGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAGCCTCTAGTA
66 AATTAAAAAAGTCAGGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAGCCTCTAGTA
1013489 CAGTCAAACAGTCAAAGGACTAATTTATAAAC
131 CAGTCAAACAGTCAAAGGACTAATTTATAAAC
* * *
1013521 CTTG-AAAAATTCTTGGGCCAATTTGGTAATTAAATAAAAGTTGATTTAAAGATTAAATTAAAAC
1 CTTGAAAAAATT-TTGGACCAATTTGGTAATTAAATAAAAGTTAATTTAAAGACTAAATTAAAAC
*
1013585 AAATTAAAAAAGTCAGGGACTAAATGCATAAATAATCTAAAAAGTGACACGTGGCAGCCTCTAGT
65 AAATTAAAAAAGTCAGGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAGCCTCTAGT
1013650 ACAGTCAAACAGTCAAAGGACTAA
130 ACAGTCAAACAGTCAAAGGACTAA
1013674 ATTGAAAGCT
Statistics
Matches: 145, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
161 7 0.05
162 138 0.95
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.26
Consensus pattern (162 bp):
CTTGAAAAAATTTTGGACCAATTTGGTAATTAAATAAAAGTTAATTTAAAGACTAAATTAAAACA
AATTAAAAAAGTCAGGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAGCCTCTAGTA
CAGTCAAACAGTCAAAGGACTAATTTATAAAC
Found at i:1014528 original size:9 final size:9
Alignment explanation
Indices: 1014490--1014521 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1014480 ATTACCATTG
*
1014490 TTATTAATA
1 TTATTGATA
1014499 TTATTGATA
1 TTATTGATA
1014508 TTATTGATA
1 TTATTGATA
1014517 TTATT
1 TTATT
1014522 ATTATTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (9 bp):
TTATTGATA
Found at i:1015231 original size:6 final size:6
Alignment explanation
Indices: 1015220--1015275 Score: 78
Period size: 6 Copynumber: 9.2 Consensus size: 6
1015210 AATGTTTAGT
*
1015220 ATTTAA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA
1015269 ATTTAA A
1 ATTTAA A
1015276 ATCAATTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
5 4 0.09
6 35 0.78
8 6 0.13
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:1015266 original size:31 final size:29
Alignment explanation
Indices: 1015220--1015285 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 29
1015210 AATGTTTAGT
*
1015220 ATTTAAATTTAAATTTAAATTTAAAGTAA
1 ATTTAAATTTAAATTTAAATTTAAAATAA
*
1015249 ATTTAAATAATTAAATTTAAATTTAAAATCA
1 ATTTAAAT--TTAAATTTAAATTTAAAATAA
1015280 ATTTAA
1 ATTTAA
1015286 CTCCAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 8 0.24
31 25 0.76
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTTAAATTTAAATTTAAATTTAAAATAA
Found at i:1022926 original size:37 final size:37
Alignment explanation
Indices: 1022884--1022958 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
1022874 ACATGCAATG
* *
1022884 TGTAACTAT-TTGATTATTACATTAACCACGCCAATTT
1 TGTAACTATCTAG-TTATTACATTAACCACACCAATTT
* *
1022921 TGTAACTGTCTAGTTATTACATTAGCCACACCAATTT
1 TGTAACTATCTAGTTATTACATTAACCACACCAATTT
1022958 T
1 T
1022959 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (37 bp):
TGTAACTATCTAGTTATTACATTAACCACACCAATTT
Found at i:1030142 original size:20 final size:19
Alignment explanation
Indices: 1030104--1030164 Score: 50
Period size: 22 Copynumber: 2.9 Consensus size: 19
1030094 GTTCAGTGAC
*
1030104 AGAGAGACAGAGAATAAAGAA
1 AGAGAGA-AGA-AAAAAAGAA
1030125 ATGAGAGAAGAAAAAAAGGTGAA
1 A-GAGAGAAGAAAAAAA---GAA
*
1030148 AGAGAGAAAAAAAAAAG
1 AGAGAGAAGAAAAAAAG
1030165 GATAATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 4 0.12
22 20 0.59
23 4 0.12
ACGTcount: A:0.66, C:0.02, G:0.28, T:0.05
Consensus pattern (19 bp):
AGAGAGAAGAAAAAAAGAA
Found at i:1030152 original size:22 final size:23
Alignment explanation
Indices: 1030122--1030165 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1030112 AGAGAATAAA
*
1030122 GAAATGAGAGAAGAAAAAAAGGT
1 GAAATGAGAGAAAAAAAAAAGGT
1030145 GAAA-GAGAGAAAAAAAAAAGG
1 GAAATGAGAGAAAAAAAAAAGG
1030166 ATAATGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.05
Consensus pattern (23 bp):
GAAATGAGAGAAAAAAAAAAGGT
Found at i:1033963 original size:21 final size:21
Alignment explanation
Indices: 1033939--1033983 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1033929 ATAAAATTAT
*
1033939 ATAAAACTATCTTAAAGATAA
1 ATAAAACTATCATAAAGATAA
* * *
1033960 ATAATATTATCATAAATATAA
1 ATAAAACTATCATAAAGATAA
1033981 ATA
1 ATA
1033984 TTATTTATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAAACTATCATAAAGATAA
Found at i:1033988 original size:21 final size:21
Alignment explanation
Indices: 1033946--1033988 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1033936 TATATAAAAC
*
1033946 TATCTTAAAGATAAATAATAT
1 TATCATAAAGATAAATAATAT
* *
1033967 TATCATAAATATAAATATTAT
1 TATCATAAAGATAAATAATAT
1033988 T
1 T
1033989 TATCTTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (21 bp):
TATCATAAAGATAAATAATAT
Found at i:1033998 original size:21 final size:20
Alignment explanation
Indices: 1033946--1033999 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
1033936 TATATAAAAC
*
1033946 TATCTTAAAGATAAATAATAT
1 TATCTT-AATATAAATAATAT
* *
1033967 TATCATAAATATAAATATTATT
1 TATC-TTAATATAAATAATA-T
1033989 TATCTTAATAT
1 TATCTTAATAT
1034000 TTAAATTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (20 bp):
TATCTTAATATAAATAATAT
Found at i:1048680 original size:15 final size:16
Alignment explanation
Indices: 1048655--1048709 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 16
1048645 ATTACATCAT
1048655 ATATAAAAATAATATA
1 ATATAAAAATAATATA
*
1048671 ATAT-AAAATACTATAA
1 ATATAAAAATAATAT-A
*
1048687 ACTTTAAAAATAATA-A
1 A-TATAAAAATAATATA
1048703 A-ATAAAA
1 ATATAAAA
1048710 CCAAGCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 5 0.16
15 9 0.28
16 8 0.25
17 2 0.06
18 8 0.25
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
ATATAAAAATAATATA
Found at i:1053252 original size:25 final size:24
Alignment explanation
Indices: 1053223--1053286 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 24
1053213 AAATTATGAA
1053223 ATTTTTAATAAAAAAAATTAATTT
1 ATTTTTAATAAAAAAAATTAATTT
* **
1053247 ATTTTTTATTTAAAATTAATTAATTT
1 A-TTTTTA-ATAAAAAAAATTAATTT
*
1053273 ATTTTTAATTAAAA
1 ATTTTTAATAAAAA
1053287 TTGATAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 5 0.16
25 12 0.38
26 15 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTTTAATAAAAAAAATTAATTT
Found at i:1053264 original size:22 final size:21
Alignment explanation
Indices: 1053236--1053280 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1053226 TTTAATAAAA
* *
1053236 AAAATTAATTTATTTTTTATTT
1 AAAATTAATTAATTTATT-TTT
1053258 AAAATTAATTAATTTATTTTT
1 AAAATTAATTAATTTATTTTT
1053279 AA
1 AA
1053281 TTAAAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AAAATTAATTAATTTATTTTT
Found at i:1053287 original size:25 final size:25
Alignment explanation
Indices: 1053223--1053288 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
1053213 AAATTATGAA
**
1053223 ATTTTTAA-TAAAAAAAATTAATTT
1 ATTTTTAATTAAAATTAATTAATTT
*
1053247 ATTTTTTATTTAAAATTAATTAATTT
1 A-TTTTTAATTAAAATTAATTAATTT
1053273 ATTTTTAATTAAAATT
1 ATTTTTAATTAAAATT
1053289 GATAAAATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 1 0.03
25 20 0.56
26 15 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTTTAATTAAAATTAATTAATTT
Found at i:1053978 original size:30 final size:31
Alignment explanation
Indices: 1053931--1053997 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
1053921 GTTGAAATGC
* **
1053931 AATTTTATCATTATAATAAAAT-TAAATTAT
1 AATTTTATAATTATAATAAAATCTAAACAAT
*
1053961 AATTTTATAAATT-TAATAGAATCTAAACAAT
1 AATTTTAT-AATTATAATAAAATCTAAACAAT
1053992 AATTTT
1 AATTTT
1053998 TCCAACCCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (31 bp):
AATTTTATAATTATAATAAAATCTAAACAAT
Found at i:1054105 original size:15 final size:16
Alignment explanation
Indices: 1054080--1054111 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1054070 TATTTAGAAA
1054080 TAATAAAAATATATAT
1 TAATAAAAATATATAT
1054096 TAAT-AAAATATATAT
1 TAATAAAAATATATAT
1054111 T
1 T
1054112 TTAGAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAAAAATATATAT
Found at i:1054425 original size:20 final size:20
Alignment explanation
Indices: 1054391--1054456 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
1054381 AACTTTGAAC
*
1054391 TTTAAACTT-GAGTTTGA-G
1 TTTAAATTTAGAGTTTGAGG
*
1054409 TTTAAGATTTAGAGTTTTAGG
1 TTTAA-ATTTAGAGTTTGAGG
*
1054430 TTTAAATTTTGAGGTTTG-GG
1 TTTAAATTTAGA-GTTTGAGG
1054450 ATTTAAA
1 -TTTAAA
1054457 GCTCTGGGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 5 0.13
19 3 0.08
20 15 0.38
21 16 0.41
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.47
Consensus pattern (20 bp):
TTTAAATTTAGAGTTTGAGG
Found at i:1061118 original size:15 final size:15
Alignment explanation
Indices: 1061098--1061126 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1061088 GCTTCTTTTA
1061098 ACCATCATCATCATC
1 ACCATCATCATCATC
1061113 ACCATCATCATCAT
1 ACCATCATCATCAT
1061127 ATTCAAGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (15 bp):
ACCATCATCATCATC
Found at i:1062931 original size:14 final size:15
Alignment explanation
Indices: 1062893--1062924 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1062883 TCTTAATGAA
1062893 CACATTGTTTCTTTG
1 CACATTGTTTCTTTG
1062908 CACATTGTTTCTTTG
1 CACATTGTTTCTTTG
1062923 CA
1 CA
1062925 TTTGTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (15 bp):
CACATTGTTTCTTTG
Found at i:1064095 original size:14 final size:14
Alignment explanation
Indices: 1064064--1064115 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
1064054 ATAAAATGAT
1064064 AATATAAATAATTAA
1 AATAT-AATAATTAA
* *
1064079 AATATAATATTTTA
1 AATATAATAATTAA
1064093 AATATAATAATTAA
1 AATATAATAATTAA
*
1064107 AATGTAATA
1 AATATAATA
1064116 TGATACAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 27 0.84
15 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
AATATAATAATTAA
Found at i:1070008 original size:30 final size:31
Alignment explanation
Indices: 1069963--1070022 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
1069953 ATTTATTAAC
1069963 AAAATAATCAAATTAGTC-TTTATTAGTTAAAT
1 AAAATAATCAAATTAGTCATTT-TT-GTTAAAT
1069995 AAAA-AAT-AAATTAGTCATTTTTGTTAAA
1 AAAATAATCAAATTAGTCATTTTTGTTAAA
1070023 AATTTTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 6 0.22
30 11 0.41
31 6 0.22
32 4 0.15
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (31 bp):
AAAATAATCAAATTAGTCATTTTTGTTAAAT
Found at i:1072238 original size:12 final size:12
Alignment explanation
Indices: 1072221--1072255 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
1072211 TGAAAATGCA
1072221 AAGAAGAAAAAG
1 AAGAAGAAAAAG
1072233 AAGAAGAAAAAG
1 AAGAAGAAAAAG
1072245 AAGAAGAAAAA
1 AAGAAGAAAAA
1072256 AATCTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:1076542 original size:6 final size:6
Alignment explanation
Indices: 1076531--1076560 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1076521 ATAACACCCC
1076531 TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA
1076561 ATTAGTTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:1078488 original size:36 final size:39
Alignment explanation
Indices: 1078425--1078498 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 39
1078415 AATTTATATT
1078425 TTATATATAATTATATTAAATTATTT-AAATATTATTTA
1 TTATATATAATTATATTAAATTATTTAAAATATTATTTA
* *
1078463 TTATATTTAATT-T-TTAAA-TATTTTAAAATTTTATTT
1 TTATATATAATTATATTAAATTA-TTTAAAATATTATTT
1078499 TAATTACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 2 0.06
36 8 0.25
37 11 0.34
38 11 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (39 bp):
TTATATATAATTATATTAAATTATTTAAAATATTATTTA
Found at i:1079598 original size:361 final size:361
Alignment explanation
Indices: 1078934--1081464 Score: 4825
Period size: 361 Copynumber: 7.0 Consensus size: 361
1078924 TACAATAATA
* *
1078934 TACTTTGGATAGTTGTCCTCATATGATTTTTGCATGTAAAACAAAATAAAAGCAAATGTTGTTCA
1 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
1078999 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
66 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
1079064 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
131 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
1079129 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
196 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
1079194 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
261 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
1079259 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
326 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
1079295 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
1 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
*
1079360 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACATGTTCAGACTGTAATACAAAATGA
66 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
1079425 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
131 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
1079490 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
196 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
*
1079555 TGATTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
261 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
1079620 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
326 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
1079656 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
1 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
1079721 CTGATTGTCTAATGTTTAAACT-A-A-TAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
66 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
1079783 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
131 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
1079848 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
196 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
*
1079913 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGAACTAACAATACATCGGACTAGATCCA
261 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
1079978 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
326 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
1080014 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
1 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
1080079 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
66 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
1080144 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
131 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
*
1080209 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGACATCGGAGCGAA
196 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
1080274 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
261 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
1080339 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
326 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
*
1080375 TACTTTGTATAGTTGTCCTCATATGATTTTTGCAAGTAAAACAAAATAAAAGCAAATGTTGTTCA
1 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
1080440 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
66 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
1080505 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
131 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
*
1080570 AGAGACTAATATGTCGTCTATCAAGTCCAGTTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
196 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
*
1080635 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGAACTAACAATACATCGGACTAGATCCA
261 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
1080700 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
326 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
*
1080736 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGTAAATGTTGTTCA
1 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
1080801 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
66 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
1080866 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
131 CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
1080931 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
196 AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
*
1080996 TGACTTCCAAAATATAGAGACAGAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
261 TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
1081061 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
326 AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
*
1081097 TACTTTGTATAGTTGTCCTCATATGATTTTTGCAAGTAAAACAAAATAAAAGCAAATGTTGTTCA
1 TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
* *
1081162 CTGATTGTCTAATGTTTAAACTAATACTAAGCGTTATTATGTGTTCAGACTGTAATACAAAATGA
66 CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
* *
1081227 CAACTTATATATTAATAGACGAACTTAAATATTTCTTTAGACTAATCGAAAATGAGCAAACGAAT
131 CAAC-T-TATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAAT
* *
1081292 TGAGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGACATCAGAGCG
194 TGAGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCG
* * * *
1081357 AATGACTTCCAAAATATAGAGACAGAGATGTGATTGACTGGACTAACAATACATTGGATTAGATC
259 AATGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATC
1081422 CAAGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
324 CAAGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
1081460 TACTT
1 TACTT
1081465 GTGACGTTCA
Statistics
Matches: 2136, Mismatches: 29, Indels: 8
0.98 0.01 0.00
Matches are distributed among these distances:
358 353 0.17
359 2 0.00
360 2 0.00
361 1554 0.73
362 1 0.00
363 224 0.10
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (361 bp):
TACTTTGTATAGTTGTCCTCATATGATTTTTGCACGTAAAACAAAATAAAAGCAAATGTTGTTCA
CTGATTGTCTAATGTTTAAACTAATACTAAGCGGTATTACGTGTTCAGACTGTAATACAAAATGA
CAACTTATATTAGTAGACGAACTTAAATATTTCTTTAGACTAATCGGAAATGAGCAAACGAATTG
AGAGACTAATATGTCGTCTATCAAGTCCAATTTGAGAGATGTTTTGTCTTGGGCATCGGAGCGAA
TGACTTCCAAAATATAGAGACATAGATGTGACTGACTGGACTAACAATACATCGGACTAGATCCA
AGAAGAATAGATCCTAAATTAGTTTATGGATTTATT
Found at i:1081893 original size:42 final size:43
Alignment explanation
Indices: 1081810--1081895 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1081800 TAAAATATAA
*
1081810 TCATATTGAGAGAACGGATATTATCCCAAAAAGATTAAAGATT
1 TCATATTGAGAGAACGAATATTATCCCAAAAAGATTAAAGATT
*
1081853 TCATATTGAGAGACCGAATATTA-CCCAAAAAGATTAAAGATT
1 TCATATTGAGAGAACGAATATTATCCCAAAAAGATTAAAGATT
1081895 T
1 T
1081896 TCTATAAGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 20 0.49
43 21 0.51
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (43 bp):
TCATATTGAGAGAACGAATATTATCCCAAAAAGATTAAAGATT
Found at i:1084835 original size:25 final size:25
Alignment explanation
Indices: 1084776--1084836 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 25
1084766 TAATATATGC
**
1084776 ATATAAAA-ATTTTATAAATATCAA
1 ATATAAAATATTGAATAAATATCAA
** * *
1084800 ATATATTATATTGAATAAATTTTAA
1 ATATAAAATATTGAATAAATATCAA
1084825 ATATAAAATATT
1 ATATAAAATATT
1084837 TATCAATTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
ATATAAAATATTGAATAAATATCAA
Found at i:1086910 original size:3 final size:3
Alignment explanation
Indices: 1086904--1086934 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1086894 GTATTTTCAG
1086904 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1086935 GTTCAAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1087980 original size:61 final size:60
Alignment explanation
Indices: 1087887--1088048 Score: 177
Period size: 61 Copynumber: 2.7 Consensus size: 60
1087877 TTCAAGTATC
* * * * * * *
1087887 AAATTAGACCAAAATAAAAGATTAGGTGCCAAATTAAAAAAAAAAGATTATGTTTAGGCATT
1 AAATTGGACCAAAA-AAAAGATTAAGTACCAAATTAAAAAAAAAAG-TCAAGTTCAGACATT
** *
1087949 AAATTGGACCAAAAAAAAGATTAAGTACCAAATTAGGAAAAAATGTCAAGTTCAGACATT
1 AAATTGGACCAAAAAAAAGATTAAGTACCAAATTAAAAAAAAAAGTCAAGTTCAGACATT
*
1088009 AAATTGAATCC--AAAAAAGATTAAGTACCAAA-TAAAAAAAA
1 AAATTGGA-CCAAAAAAAAGATTAAGTACCAAATTAAAAAAAA
1088049 GGGCTAATTT
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
58 7 0.08
59 20 0.23
60 18 0.21
61 28 0.33
62 13 0.15
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.22
Consensus pattern (60 bp):
AAATTGGACCAAAAAAAAGATTAAGTACCAAATTAAAAAAAAAAGTCAAGTTCAGACATT
Done.