Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 61 of 125
Found at i:12163693 original size:17 final size:17
Alignment explanation
Indices: 12163673--12163757 Score: 73
Period size: 17 Copynumber: 5.0 Consensus size: 17
12163663 TACAAATTTG
12163673 AAAATCTTGTGAATCTT
1 AAAATCTTGTGAATCTT
12163690 AAAATCTTGTGAATCTT
1 AAAATCTTGTGAATCTT
* * * *
12163707 CAATTCTTGT-AGATATG
1 AAAATCTTGTGA-ATCTT
** *
12163724 AAAATCTTGCAAACCTT
1 AAAATCTTGTGAATCTT
* *
12163741 CATATCTTGTGAATCTT
1 AAAATCTTGTGAATCTT
12163758 TAATTCTTGC
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
16 1 0.02
17 49 0.96
18 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
AAAATCTTGTGAATCTT
Found at i:12163703 original size:51 final size:51
Alignment explanation
Indices: 12163647--12163800 Score: 182
Period size: 51 Copynumber: 3.0 Consensus size: 51
12163637 TTTAATTCTA
* * *
12163647 GTGAATCTTCAATTCTTACAAATTTGAAAATCTTGTGAATCTTAAAATCTT
1 GTGAATCTTCAATTCTTGCAAATATGAAAATCTTGCGAATCTTAAAATCTT
* * * * * *
12163698 GTGAATCTTCAATTCTTGTAGATATGAAAATCTTGCAAACCTTCATATCTT
1 GTGAATCTTCAATTCTTGCAAATATGAAAATCTTGCGAATCTTAAAATCTT
* * * *
12163749 GTGAATCTTTAATTCTTGCAAATATGAAAGTCTTACGAATCTTTGAAATCTT
1 GTGAATCTTCAATTCTTGCAAATATGAAAATCTTGCGAATC-TTAAAATCTT
12163801 ACAAACCTTT
Statistics
Matches: 84, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
51 76 0.90
52 8 0.10
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (51 bp):
GTGAATCTTCAATTCTTGCAAATATGAAAATCTTGCGAATCTTAAAATCTT
Found at i:12163715 original size:34 final size:34
Alignment explanation
Indices: 12163676--12163770 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 34
12163666 AAATTTGAAA
** *
12163676 ATCTTGTGAATCTTAAAATCTTGTGAATCTTCA-
1 ATCTTGTGAATCTTAAAATCTTGCAAACCTTCAT
* *
12163709 ATTCTTGT-AGATATGAAAATCTTGCAAACCTTCAT
1 A-TCTTGTGA-ATCTTAAAATCTTGCAAACCTTCAT
* *
12163744 ATCTTGTGAATCTTTAATTCTTGCAAA
1 ATCTTGTGAATCTTAAAATCTTGCAAA
12163771 TATGAAAGTC
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
33 2 0.04
34 45 0.92
35 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (34 bp):
ATCTTGTGAATCTTAAAATCTTGCAAACCTTCAT
Found at i:12163802 original size:18 final size:18
Alignment explanation
Indices: 12163773--12163831 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
12163763 CTTGCAAATA
*
12163773 TGAAAGTCTTACGAATCTT
1 TGAAA-TCTTACGAACCTT
*
12163792 TGAAATCTTACAAACCTT
1 TGAAATCTTACGAACCTT
* * *
12163810 TGTAACCTTATGAACCTT
1 TGAAATCTTACGAACCTT
12163828 TGAA
1 TGAA
12163832 TTTCAAAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
18 28 0.85
19 5 0.15
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.36
Consensus pattern (18 bp):
TGAAATCTTACGAACCTT
Found at i:12163998 original size:92 final size:92
Alignment explanation
Indices: 12163890--12164071 Score: 267
Period size: 92 Copynumber: 2.0 Consensus size: 92
12163880 ATTTTGCATA
* *
12163890 TTTGGGTTTCAAGTTGAGAACCTTTA-AATTTGAAATCTTTGAAATTTTTATACATAGCTAAATT
1 TTTGGATTTCAAGTTGAGAACCTTTACAATTTG-AATCTTTGAAATTGTTATACATAGCTAAATT
*
12163954 GTGAAGCTGTATTGCAATGAGAATCTTT
65 GTGAAGCTGTATTGCAATAAGAATCTTT
* * * *
12163982 TTTGGATTTCAAGTTGAGAACTTTTACATTTTGAATCTTTGAAATTGTTGTACATAGCTAAATTT
1 TTTGGATTTCAAGTTGAGAACCTTTACAATTTGAATCTTTGAAATTGTTATACATAGCTAAATTG
* *
12164047 TGAATCTGTATTTCAATAAGAATCT
66 TGAAGCTGTATTGCAATAAGAATCT
12164072 CTAGAGTTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
92 75 0.94
93 5 0.06
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (92 bp):
TTTGGATTTCAAGTTGAGAACCTTTACAATTTGAATCTTTGAAATTGTTATACATAGCTAAATTG
TGAAGCTGTATTGCAATAAGAATCTTT
Found at i:12164276 original size:13 final size:12
Alignment explanation
Indices: 12164243--12164343 Score: 70
Period size: 11 Copynumber: 8.4 Consensus size: 12
12164233 GATTTTTATT
12164243 TTTAT-TTTTCTA
1 TTTATCTTTT-TA
12164255 TTCTATCTTTTGTA
1 TT-TATCTTTT-TA
*
12164269 TTTATC-TTTCA
1 TTTATCTTTTTA
*
12164280 TTT-TCTTATTA
1 TTTATCTTTTTA
*
12164291 TATATCTTTTTTA
1 TTTATC-TTTTTA
*
12164304 TTTATC-TCTTA
1 TTTATCTTTTTA
12164315 TTTATCTTTTT-
1 TTTATCTTTTTA
12164326 TTT-TCTTTCTTA
1 TTTATCTTT-TTA
12164338 TCTTAT
1 T-TTAT
12164344 TCTTATTCTA
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
10 7 0.10
11 24 0.34
12 11 0.16
13 19 0.27
14 9 0.13
ACGTcount: A:0.16, C:0.13, G:0.01, T:0.70
Consensus pattern (12 bp):
TTTATCTTTTTA
Found at i:12164343 original size:24 final size:24
Alignment explanation
Indices: 12164288--12164343 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
12164278 CATTTTCTTA
*
12164288 TTATATATCTTTTTTATTTATCTC
1 TTATTTATCTTTTTTATTTATCTC
* *
12164312 TTATTTATCTTTTTT-TTTCTTTC
1 TTATTTATCTTTTTTATTTATCTC
12164335 TTATCTTAT
1 TTAT-TTAT
12164344 TCTTATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.71
Consensus pattern (24 bp):
TTATTTATCTTTTTTATTTATCTC
Found at i:12164968 original size:13 final size:13
Alignment explanation
Indices: 12164950--12165007 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
12164940 TTTTGGTGAG
*
12164950 TTTATTATTTTAT
1 TTTATTAATTTAT
12164963 TTTATTAATTTAT
1 TTTATTAATTTAT
12164976 TTTATGTTAATTT-T
1 TTTA--TTAATTTAT
*
12164990 ATTTATTCAAATTAT
1 -TTTATT-AATTTAT
12165005 TTT
1 TTT
12165008 TTTGTTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 18 0.47
14 8 0.21
15 12 0.32
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTATTAATTTAT
Found at i:12167649 original size:58 final size:55
Alignment explanation
Indices: 12167587--12167860 Score: 189
Period size: 58 Copynumber: 4.7 Consensus size: 55
12167577 AAACTACTGC
* *
12167587 TTTATTTAAGGAAAAATTGATACTTTCAATTTTTTCCTCAA-ATGTTTTTGAAATATTT
1 TTTATTTAAAG-AAAATTGATA-TTTCAA-CTTTTCCTCAACATGTTTTT-AAATATTT
* * * * * * *
12167645 TTTATTTGAGGAAAATTAATATTTCAAAATTTCCCTAAAACATTTTTTTAAATATATATTT
1 TTTATTTAAAGAAAATTGATATTTC-AACTTTTCCT-CAACATGTTTTT--A-A-ATATTT
* *
12167706 TTTATTT-AAGAAAAATTGATATTTTAACTTTTCCTCATAACATATTTTTAAA-ATTAT
1 TTTATTTAAAG-AAAATTGATATTTCAACTTTTCCTC--AACATGTTTTTAAATATT-T
* *
12167763 TATTGTTTAAAGAAAATTGATATTTCAACTTTTCCTCAAAGCACAT-TTTTTAAAAAGTTT
1 T-TTATTTAAAGAAAATTGATATTTCAACTTTTCCTC--A--ACATGTTTTTAAATA-TTT
* *
12167823 TTTATTTAAAGAAAATTGATACTTT-AATTTTTCTTCAA
1 TTTATTTAAAGAAAATTGATA-TTTCAACTTTTCCTCAA
12167861 AACACATTTT
Statistics
Matches: 179, Mismatches: 20, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
55 1 0.01
56 13 0.07
57 17 0.09
58 49 0.27
59 41 0.23
60 21 0.12
61 37 0.21
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (55 bp):
TTTATTTAAAGAAAATTGATATTTCAACTTTTCCTCAACATGTTTTTAAATATTT
Found at i:12167739 original size:61 final size:60
Alignment explanation
Indices: 12167587--12167883 Score: 235
Period size: 59 Copynumber: 5.0 Consensus size: 60
12167577 AAACTACTGC
* * * *
12167587 TTTATTTAAGGAAAAATTGATACTTTCAATTTTTTCCTC--AA-ATGTTTTT-GAA-ATATTT
1 TTTATTTAAAG-AAAATTGATA-TTTCAA-CTTTTCCTCAAAACATTTTTTTAAAATATATTT
* * * **
12167645 TTTATTTGAGGAAAATTAATATTTCAAAATTTCC-CTAAAACATTTTTTTAAATATATATTT
1 TTTATTTAAAGAAAATTGATATTTCAACTTTTCCTC-AAAACATTTTTTTAAA-ATATATTT
* * *
12167706 TTTATTT-AAGAAAAATTGATATTTTAACTTTTCCTCATAACATATTTTTAAAAT-TA-TT
1 TTTATTTAAAG-AAAATTGATATTTCAACTTTTCCTCAAAACATTTTTTTAAAATATATTT
* * *
12167764 ATTGTTTAAAGAAAATTGATATTTCAACTTTTCCTCAAAGCACA-TTTTTTAAAA-A-GTTT
1 TTTATTTAAAGAAAATTGATATTTCAACTTTTCCTCAAA--ACATTTTTTTAAAATATATTT
* * * *
12167823 TTTATTTAAAGAAAATTGATACTTT-AATTTTTCTTCAAAACACATTTTTTGAAAT-TATTT
1 TTTATTTAAAGAAAATTGATA-TTTCAACTTTTCCTCAAAACA-TTTTTTTAAAATATATTT
12167883 T
1 T
12167884 AAGAAAATTA
Statistics
Matches: 195, Mismatches: 25, Indels: 36
0.76 0.10 0.14
Matches are distributed among these distances:
54 1 0.01
55 5 0.03
56 6 0.03
57 14 0.07
58 50 0.26
59 57 0.29
60 15 0.08
61 46 0.24
62 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (60 bp):
TTTATTTAAAGAAAATTGATATTTCAACTTTTCCTCAAAACATTTTTTTAAAATATATTT
Found at i:12167778 original size:119 final size:114
Alignment explanation
Indices: 12167587--12167884 Score: 284
Period size: 117 Copynumber: 2.5 Consensus size: 114
12167577 AAACTACTGC
* *
12167587 TTTATTTAAGGAAAAATTGATACTTTCAATTTTTTCCTC-AA-ATGTTTTTGAAATATT-TTTTA
1 TTTATTTAA-GAAAAATTGATA-TTTTAA-TTTTTCCTCAAACATATTTTT-AAA-ATTATTTTA
* *
12167649 TTTGAGGAAAATTAATATTTCAAAATTTCCCT-AAA-ACATTTTTTTAAATATATATTT
61 TTTAAAGAAAATTAATATTTC-AAATTTCCCTCAAACACA-TTTTTTAAA-A-A-ATTT
* *
12167706 TTTATTTAAGAAAAATTGATATTTTAACTTTTCCTCATAACATATTTTTAAAATTATTATTGTTT
1 TTTATTTAAGAAAAATTGATATTTTAATTTTTCCTCA-AACATATTTTTAAAATTATT-TTATTT
* * * *
12167771 AAAGAAAATTGATATTTCAACTTTTCCTCAAAGCACATTTTTTAAAAAGTTT
64 AAAGAAAATTAATATTTCAAATTTCCCTCAAA-CACATTTTTTAAAAAATTT
* * * *
12167823 TTTATTTAA-AGAAAATTGATACTTTAATTTTTCTTCAAAACACATTTTTTGAAATTATTTTA
1 TTTATTTAAGA-AAAATTGATATTTTAATTTTTCCTC-AAACATA-TTTTTAAAATTATTTTA
12167885 AGAAAATTAT
Statistics
Matches: 152, Mismatches: 16, Indels: 24
0.79 0.08 0.12
Matches are distributed among these distances:
116 9 0.06
117 49 0.32
118 42 0.28
119 40 0.26
120 9 0.06
121 3 0.02
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (114 bp):
TTTATTTAAGAAAAATTGATATTTTAATTTTTCCTCAAACATATTTTTAAAATTATTTTATTTAA
AGAAAATTAATATTTCAAATTTCCCTCAAACACATTTTTTAAAAAATTT
Found at i:12174532 original size:22 final size:22
Alignment explanation
Indices: 12174502--12174555 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
12174492 CTCCTTTTTG
*
12174502 TTTATGCTCTTTATATCAAATA
1 TTTAAGCTCTTTATATCAAATA
*
12174524 TTTAAGCTC-CTATATCAAATA
1 TTTAAGCTCTTTATATCAAATA
*
12174545 TTTAAACTCTT
1 TTTAAGCTCTT
12174556 ATAGCAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
TTTAAGCTCTTTATATCAAATA
Found at i:12174955 original size:16 final size:16
Alignment explanation
Indices: 12174934--12174968 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12174924 ATACAAACTC
*
12174934 ATACCAATTGTTAAGG
1 ATACCAATTGTTAAAG
12174950 ATACCAATTGTTAAAG
1 ATACCAATTGTTAAAG
12174966 ATA
1 ATA
12174969 TGTTACCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (16 bp):
ATACCAATTGTTAAAG
Found at i:12184214 original size:58 final size:57
Alignment explanation
Indices: 12184074--12184304 Score: 229
Period size: 58 Copynumber: 4.0 Consensus size: 57
12184064 AAACTAATGC
* * *
12184074 TTTATTAAAGGAAAAATTGATACTTTCAACTTTTTCCTC--AA-ATATTTTTGATATT-T
1 TTTATTTAAGG-AAAATTGATAC-TTCAAC-TTTTCCTCAAAACATATTTTTAAAATTAT
* * *
12184130 TTTATTTAAGGAAATTTGATATTTCAACTTTTCCTCAAAACATTTTTTTAAAATTACT
1 TTTATTTAAGGAAAATTGATACTTCAACTTTTCCTCAAAACATATTTTTAAAATTA-T
* * * **
12184188 TTTGTTTAAGGAAAATTGATACTTCAACTTTTCCTCAAAGCACATTTTTAAAAAAAAT
1 TTTATTTAAGGAAAATTGATACTTCAACTTTTCCTCAAAACATATTTTT-AAAATTAT
* * ** *
12184246 TTTATTTAAGAAAAATTGATAATTCAAC-TTTCCTCAAAATGTATTTTTTGAAATTAT
1 TTTATTTAAGGAAAATTGATACTTCAACTTTTCCTCAAAACATA-TTTTTAAAATTAT
12184303 TT
1 TT
12184305 AAAAAAATTC
Statistics
Matches: 144, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
53 8 0.06
54 6 0.04
55 11 0.08
56 21 0.15
57 18 0.12
58 75 0.52
59 5 0.03
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (57 bp):
TTTATTTAAGGAAAATTGATACTTCAACTTTTCCTCAAAACATATTTTTAAAATTAT
Found at i:12184360 original size:10 final size:10
Alignment explanation
Indices: 12184345--12184369 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12184335 TGAAGTTATT
12184345 TTTATTTTTC
1 TTTATTTTTC
12184355 TTTATTTTTC
1 TTTATTTTTC
12184365 TTTAT
1 TTTAT
12184370 CTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:12185209 original size:18 final size:19
Alignment explanation
Indices: 12185176--12185213 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12185166 ATTATCATTT
12185176 TTATTAGTATACTATAGTG
1 TTATTAGTATACTATAGTG
*
12185195 TTATTA-TATATTATAGTG
1 TTATTAGTATACTATAGTG
12185213 T
1 T
12185214 GTTAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (19 bp):
TTATTAGTATACTATAGTG
Found at i:12185289 original size:3 final size:3
Alignment explanation
Indices: 12185276--12185355 Score: 61
Period size: 3 Copynumber: 26.7 Consensus size: 3
12185266 TATACTATAG
* * * * * * * * *
12185276 TTA TCA TTA TTA TTA TTA TTA TTA CTA CTA CTA CTA CTA CTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
12185324 CTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12185356 TACGTTTATG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:12186194 original size:6 final size:6
Alignment explanation
Indices: 12186183--12186229 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
12186173 GTTTTATAGG
*
12186183 TTTTTC TTTTTC TTTTCC TTTTT- TGTTTTC TTTTTC TTTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC -TTTTTC TTTT
12186230 ATTTATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 1 0.03
6 28 0.78
7 7 0.19
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:12186211 original size:18 final size:18
Alignment explanation
Indices: 12186183--12186229 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
12186173 GTTTTATAGG
12186183 TTTTTCTTTTTCTTTTCCT
1 TTTTTC-TTTTCTTTTCCT
* *
12186202 TTTTTGTTTTCTTTTTCT
1 TTTTTCTTTTCTTTTCCT
12186220 TTTTTCTTTT
1 TTTTTCTTTT
12186230 ATTTATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTCTTTTCCT
Found at i:12186634 original size:37 final size:37
Alignment explanation
Indices: 12186584--12186667 Score: 168
Period size: 37 Copynumber: 2.3 Consensus size: 37
12186574 ATAAAATTTA
12186584 ACCAAACTATTGGAAGATTTGCTTCAAAGTAAGTCCT
1 ACCAAACTATTGGAAGATTTGCTTCAAAGTAAGTCCT
12186621 ACCAAACTATTGGAAGATTTGCTTCAAAGTAAGTCCT
1 ACCAAACTATTGGAAGATTTGCTTCAAAGTAAGTCCT
12186658 ACCAAACTAT
1 ACCAAACTAT
12186668 CGAAAGACTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (37 bp):
ACCAAACTATTGGAAGATTTGCTTCAAAGTAAGTCCT
Found at i:12189853 original size:5 final size:5
Alignment explanation
Indices: 12189843--12189872 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
12189833 AGGGCAAATA
*
12189843 TTTTC TTTTC TTTTC TTTCC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
12189873 CATGCATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:12195444 original size:340 final size:339
Alignment explanation
Indices: 12194820--12195501 Score: 1121
Period size: 340 Copynumber: 2.0 Consensus size: 339
12194810 GTCAACAAGA
* * *
12194820 TGAATCTAGCAAGAAAAATAGAGCTATTTATAACTTAAGCAAGAAGTTCACAAAAGTACAAATTC
1 TGAATCTAGCAAGAAAAAGAGAGATATTTATAACTTAAGCAAGAAGTTCACAAAAGTACAAATCC
* *
12194885 AAGATTCATCACTAGAAAAAATGTGTTGTGCTTTGGCATAGACAACTAAAAGGCTCAGGTTGTAT
66 AAGATTCATCACTAGAAAAAATGTATTGTGCTTTAGCATAGACAACTAAAAGGCTCAGGTTGTAT
*
12194950 ATGCTCTATCATACAACTTGGCTTATAGCTAAACTAAACCCAATCAAATACATTTTTGAGAAGCC
131 ATGCTCTATCATACAACTTGGCTTATAGCCAAACTAAACCCAATCAAATACATTTTTGAGAAGCC
*
12195015 ATCGCTATCAAGAAGAATGGCAAGATGGAAAGTGATGCTTTTGGAATATAACATAGTTTATGTAA
196 ATCGCTATCAAAAAGAATGGCAAGATGGAAAGTGATGCTTTTGGAATATAACATAGTTTATGTAA
* * **
12195080 GCCAAAAAGCAATCAAGGGAAGTGTCATTGTTGAATTCCTTGCAGATAGGGTTGTTAACGATTAT
261 GCCAAAAAGCAATCAAGAGAAGTGTCATTGTTGAATTCCTTACAGATAGGGTTACTAACGATTAT
12195145 AAACCTATAAAACT
326 AAACCTATAAAACT
* * *
12195159 TGAATCTGGTAAGAAAAAGAGAGATATTTATTACTTAAGCAAGAAGTTCACAAAAGTACAAATCC
1 TGAATCTAGCAAGAAAAAGAGAGATATTTATAACTTAAGCAAGAAGTTCACAAAAGTACAAATCC
* * ** *
12195224 AAGTATTCATCACTAGAAAAAATGTATTGTGCTTTAGCTTAGACAACTAAGAGTTTTAGGTTGTA
66 AAG-ATTCATCACTAGAAAAAATGTATTGTGCTTTAGCATAGACAACTAAAAGGCTCAGGTTGTA
12195289 TATGCTCTATCATACAACTTGGCTTATAGCCAAACTAAACCCAATCAAATACATTTTTGAGAAGC
130 TATGCTCTATCATACAACTTGGCTTATAGCCAAACTAAACCCAATCAAATACATTTTTGAGAAGC
* * * *
12195354 CATTGCTATCAAAAAGAATGGCAAGATGGCAAGTGATGCTTTTGGAATATAACATTGTTTATGTG
195 CATCGCTATCAAAAAGAATGGCAAGATGGAAAGTGATGCTTTTGGAATATAACATAGTTTATGTA
* *
12195419 AGCCACAAAGCAATCAAGAGAAGTGTCATTGTTGAATTCTTTACAGATAGGGTTACTAACGATTA
260 AGCCAAAAAGCAATCAAGAGAAGTGTCATTGTTGAATTCCTTACAGATAGGGTTACTAACGATTA
*
12195484 TGAACCTATAAAACT
325 TAAACCTATAAAACT
12195499 TGA
1 TGA
12195502 CTTTTCAGAT
Statistics
Matches: 316, Mismatches: 26, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
339 62 0.20
340 254 0.80
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (339 bp):
TGAATCTAGCAAGAAAAAGAGAGATATTTATAACTTAAGCAAGAAGTTCACAAAAGTACAAATCC
AAGATTCATCACTAGAAAAAATGTATTGTGCTTTAGCATAGACAACTAAAAGGCTCAGGTTGTAT
ATGCTCTATCATACAACTTGGCTTATAGCCAAACTAAACCCAATCAAATACATTTTTGAGAAGCC
ATCGCTATCAAAAAGAATGGCAAGATGGAAAGTGATGCTTTTGGAATATAACATAGTTTATGTAA
GCCAAAAAGCAATCAAGAGAAGTGTCATTGTTGAATTCCTTACAGATAGGGTTACTAACGATTAT
AAACCTATAAAACT
Found at i:12198763 original size:18 final size:16
Alignment explanation
Indices: 12198740--12198778 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
12198730 ATTAGTATAC
12198740 TATAGTGTTGTTATGTAT
1 TATAGTG-TGTTA-GTAT
12198758 TATAGTGTGTTAGTAT
1 TATAGTGTGTTAGTAT
12198774 T-TAGT
1 TATAGT
12198779 ATAGTACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 5 0.24
17 5 0.24
18 7 0.33
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (16 bp):
TATAGTGTGTTAGTAT
Found at i:12198836 original size:3 final size:3
Alignment explanation
Indices: 12198828--12198859 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12198818 TATACTATAG
*
12198828 TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12198860 TATGTTTATG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12198846 original size:15 final size:15
Alignment explanation
Indices: 12198823--12198855 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12198813 TACTGTATAC
*
12198823 TATAGTTATTATTAT
1 TATAATTATTATTAT
12198838 TATAATTATTATTAT
1 TATAATTATTATTAT
12198853 TAT
1 TAT
12198856 TATTTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TATAATTATTATTAT
Found at i:12199333 original size:19 final size:18
Alignment explanation
Indices: 12199311--12199346 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12199301 GAAAAATTTA
12199311 GGATTTTTCTAAATTTTTT
1 GGATTTTT-TAAATTTTTT
*
12199330 GGATTTTTTAAGTTTTT
1 GGATTTTTTAAATTTTT
12199347 CTAGGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.19, C:0.03, G:0.14, T:0.64
Consensus pattern (18 bp):
GGATTTTTTAAATTTTTT
Found at i:12199716 original size:15 final size:16
Alignment explanation
Indices: 12199696--12199725 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12199686 TCTTTTTCCT
12199696 TTTATTTTAT-TTTTA
1 TTTATTTTATATTTTA
12199711 TTTATTTTATATTTT
1 TTTATTTTATATTTT
12199726 TAATTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTTATATTTTA
Found at i:12199895 original size:12 final size:12
Alignment explanation
Indices: 12199845--12199897 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
12199835 AAAGGAAAAA
12199845 AAAAATAATAAT
1 AAAAATAATAAT
* *
12199857 AATAATAACAAT
1 AAAAATAATAAT
* * * *
12199869 GAGAATGAGAAT
1 AAAAATAATAAT
12199881 AAAAATAATAAT
1 AAAAATAATAAT
12199893 AAAAA
1 AAAAA
12199898 AATCTTTTCA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:12201548 original size:18 final size:20
Alignment explanation
Indices: 12201508--12201549 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
12201498 TAATAATAAT
*
12201508 AATATAAGCAAAAATAAATA
1 AATATAAGCAAAAATAAACA
*
12201528 AATA-AAGCAATAA-AAACA
1 AATATAAGCAAAAATAAACA
12201546 AATA
1 AATA
12201550 GGCTTGCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (20 bp):
AATATAAGCAAAAATAAACA
Found at i:12202557 original size:11 final size:11
Alignment explanation
Indices: 12202534--12202562 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12202524 TCAAAAACTC
12202534 CAAGAAT-TAT
1 CAAGAATATAT
12202544 CAAGAATATAT
1 CAAGAATATAT
12202555 CAAGAATA
1 CAAGAATA
12202563 GTCAAAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.24
Consensus pattern (11 bp):
CAAGAATATAT
Found at i:12207545 original size:2 final size:2
Alignment explanation
Indices: 12207534--12207568 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
12207524 GGTATCCACT
12207534 TA TA -A TA TA TA TA TA TA TA TA 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 TA
12207569 AATTGATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12211446 original size:10 final size:10
Alignment explanation
Indices: 12211424--12211514 Score: 64
Period size: 10 Copynumber: 9.4 Consensus size: 10
12211414 TTGTAAAAAG
*
12211424 AAAAAA-TTC
1 AAAAAATTTT
12211433 AAAAAATTTT
1 AAAAAATTTT
*
12211443 -AAAAA-TTC
1 AAAAAATTTT
12211451 ATAAAAATTTT
1 A-AAAAATTTT
*
12211462 AAAAAATTCT
1 AAAAAATTTT
*
12211472 CAAAAATTTT
1 AAAAAATTTT
* *
12211482 GAAAAATTCT
1 AAAAAATTTT
*
12211492 -AAAATTTTT
1 AAAAAATTTT
* *
12211501 TAAAATTTTT
1 AAAAAATTTT
12211511 AAAA
1 AAAA
12211515 TCTAAAAGAA
Statistics
Matches: 66, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
8 2 0.03
9 18 0.27
10 43 0.65
11 3 0.05
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.37
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:12211507 original size:18 final size:19
Alignment explanation
Indices: 12211425--12211505 Score: 101
Period size: 20 Copynumber: 4.2 Consensus size: 19
12211415 TGTAAAAAGA
*
12211425 AAAAATTC-AAAAAATTTT
1 AAAAATTCTAAAAATTTTT
*
12211443 AAAAATTCATAAAAATTTTA
1 AAAAATTC-TAAAAATTTTT
*
12211463 AAAAATTCTCAAAAATTTTG
1 AAAAATTCT-AAAAATTTTT
*
12211483 AAAAATTCTAAAATTTTTT
1 AAAAATTCTAAAAATTTTT
12211502 AAAA
1 AAAA
12211506 TTTTTAAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.15
19 13 0.24
20 34 0.62
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (19 bp):
AAAAATTCTAAAAATTTTT
Found at i:12211561 original size:9 final size:9
Alignment explanation
Indices: 12211425--12211565 Score: 54
Period size: 9 Copynumber: 15.0 Consensus size: 9
12211415 TGTAAAAAGA
12211425 AAAAATTCA-
1 AAAAATT-AT
*
12211434 AAAAATTTT
1 AAAAATTAT
12211443 AAAAATTCAT
1 AAAAATT-AT
*
12211453 AAAAATTTT
1 AAAAATTAT
*
12211462 AAAAAATTCT
1 -AAAAATTAT
*
12211472 CAAAAATTTT
1 -AAAAATTAT
*
12211482 GAAAAATTCT
1 -AAAAATTAT
* *
12211492 AAAATTTTT
1 AAAAATTAT
* *
12211501 TAAAATTTT
1 AAAAATTAT
* *
12211510 TAAAATCTAA
1 AAAAAT-TAT
12211520 AAGAAATTA-
1 AA-AAATTAT
12211529 AAAAA-TAT
1 AAAAATTAT
* * *
12211537 GACATATTTTT
1 -A-AAAATTAT
12211548 AAAAATTAT
1 AAAAATTAT
12211557 AAAAATTAT
1 AAAAATTAT
12211566 GATAATTTTA
Statistics
Matches: 102, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
7 2 0.02
8 3 0.03
9 52 0.51
10 39 0.38
11 6 0.06
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAAATTAT
Found at i:12211586 original size:26 final size:26
Alignment explanation
Indices: 12211523--12211586 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
12211513 AATCTAAAAG
*
12211523 AAATTAAAAAATATGACATATTTTTAA
1 AAATTAAAAAATATGA-ATAATTTTAA
12211550 AAATTATAAAAATTATG-ATAATTTT-A
1 AAATTA-AAAAA-TATGAATAATTTTAA
*
12211576 AAATTCAAAAA
1 AAATTAAAAAA
12211587 CTTTTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 5 0.15
26 6 0.18
27 13 0.39
28 5 0.15
29 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (26 bp):
AAATTAAAAAATATGAATAATTTTAA
Found at i:12211688 original size:18 final size:19
Alignment explanation
Indices: 12211657--12211708 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
12211647 CTATTTTCTT
*
12211657 AAAATTAAAAAAAATCAC-G
1 AAAATT-AAAAAAATAACTG
*
12211676 AAAATTGAAAAAA-AACTG
1 AAAATTAAAAAAATAACTG
12211694 AAAATTAAAAAAATA
1 AAAATTAAAAAAATA
12211709 TAAAAAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.07
18 19 0.68
19 7 0.25
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAATTAAAAAAATAACTG
Found at i:12211727 original size:21 final size:20
Alignment explanation
Indices: 12211701--12211764 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
12211691 CTGAAAATTA
12211701 AAAAAATATAAAAAGTTTTT
1 AAAAAATATAAAAAGTTTTT
*
12211721 GAAAAAATAT-GAAAGTTTTT
1 -AAAAAATATAAAAAGTTTTT
*
12211741 AAAAAAATTTAAAAA-TTTTT
1 -AAAAAATATAAAAAGTTTTT
12211761 AAAA
1 AAAA
12211765 TCTTTTGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.11
20 22 0.58
21 12 0.32
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (20 bp):
AAAAAATATAAAAAGTTTTT
Found at i:12211880 original size:9 final size:10
Alignment explanation
Indices: 12211849--12211883 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
12211839 ATAAAAACTT
*
12211849 AAAATTTAATA
1 AAAATTCAA-A
12211860 AAAATTCAAA
1 AAAATTCAAA
12211870 AAAATTCAAA
1 AAAATTCAAA
12211880 AAAA
1 AAAA
12211884 CAATATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAATTCAAA
Found at i:12211948 original size:21 final size:20
Alignment explanation
Indices: 12211919--12211969 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
12211909 ATTAAAAAAG
12211919 AAAAATTTTCATA-ATTTTTT
1 AAAAATTTT-ATATATTTTTT
12211939 AAAAACTTTTATATATTTTTT
1 AAAAA-TTTTATATATTTTTT
12211960 AAAAATTTTA
1 AAAAATTTTA
12211970 GATTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAAATTTTATATATTTTTT
Found at i:12211957 original size:20 final size:19
Alignment explanation
Indices: 12211919--12211977 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
12211909 ATTAAAAAAG
* *
12211919 AAAAATTTTCATAATTTTTT
1 AAAAATTTT-AGATTTTTTT
*
12211939 AAAAACTTTTATATATTTTTT
1 AAAAA-TTTTAGAT-TTTTTT
12211960 AAAAATTTTAGATTTTTT
1 AAAAATTTTAGATTTTTT
12211978 ATGTTGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.14
20 15 0.43
21 15 0.43
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (19 bp):
AAAAATTTTAGATTTTTTT
Found at i:12212218 original size:11 final size:10
Alignment explanation
Indices: 12212187--12212236 Score: 59
Period size: 11 Copynumber: 5.0 Consensus size: 10
12212177 TTAAAAAAAA
12212187 TAGAATTTTT
1 TAGAATTTTT
*
12212197 TGGAA--TTT
1 TAGAATTTTT
12212205 TAGAAATTTTT
1 TAG-AATTTTT
12212216 TAGAATTCTTT
1 TAGAATT-TTT
12212227 TAGAATTTTT
1 TAGAATTTTT
12212237 AAAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 5 0.15
9 2 0.06
10 11 0.32
11 16 0.47
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (10 bp):
TAGAATTTTT
Found at i:12212287 original size:40 final size:43
Alignment explanation
Indices: 12212211--12212296 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 43
12212201 ATTTTAGAAA
*
12212211 TTTTTTAGAATTCTTTTAGAATTTTTAAAAAAATTTTACATTT
1 TTTTTTAGAATTCTTTTAGAATTTTTAAAAAAATTTTACAATT
* *
12212254 TTTTTTA-AATT-TTTT-GAA-TTTTAAAAATTATTTTTCAATT
1 TTTTTTAGAATTCTTTTAGAATTTTTAAAAA-AATTTTACAATT
12212294 TTT
1 TTT
12212297 ATAATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
39 9 0.23
40 15 0.38
41 4 0.10
42 4 0.10
43 7 0.18
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (43 bp):
TTTTTTAGAATTCTTTTAGAATTTTTAAAAAAATTTTACAATT
Found at i:12212315 original size:29 final size:29
Alignment explanation
Indices: 12212255--12212315 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
12212245 TTTACATTTT
* **
12212255 TTTTTAAATTTTTTGAATTTTAAAAATTA
1 TTTTTAAATTTTTTGAATTTAAAAAAAAA
*
12212284 TTTTTCAATTTTTAT-AATTTAAAAAAAAA
1 TTTTTAAATTTTT-TGAATTTAAAAAAAAA
12212313 TTT
1 TTT
12212316 AGAATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTTTAAATTTTTTGAATTTAAAAAAAAA
Found at i:12216647 original size:21 final size:20
Alignment explanation
Indices: 12216600--12216653 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
12216590 CTTAAGTTTT
* * *
12216600 CAATTTAATTCAATTTCTTT
1 CAATTTAATTTAAATTCTTG
12216620 CAATTTAATTTAAATTCTTG
1 CAATTTAATTTAAATTCTTG
12216640 CAAGTTTAATTTAA
1 CAA-TTTAATTTAA
12216654 GTTTTCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (20 bp):
CAATTTAATTTAAATTCTTG
Found at i:12217310 original size:23 final size:22
Alignment explanation
Indices: 12217267--12217332 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
12217257 AAATTTTGGT
*
12217267 TTTAGGTTTTTAGCTTGTTTAA
1 TTTAGGTTTTTAGCTTATTTAA
* *
12217289 TTTAGTTTTTTTGCATTATTTAA
1 TTTAGGTTTTTAGC-TTATTTAA
12217312 TTTA--TTGTTTAGCTTAGTTTA
1 TTTAGGTT-TTTAGCTTA-TTTA
12217333 GTAATTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 5 0.14
22 21 0.57
23 11 0.30
ACGTcount: A:0.20, C:0.05, G:0.14, T:0.62
Consensus pattern (22 bp):
TTTAGGTTTTTAGCTTATTTAA
Found at i:12227037 original size:40 final size:40
Alignment explanation
Indices: 12226993--12227075 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
12226983 AGAATTTAAT
* * * *
12226993 AAAAAT-GACACTTCTAAGATAAATACGTAGTTTTTGTTGA
1 AAAAATAG-CACTTCTAAGATAAAAACATAATTTTTATTGA
**
12227033 AAAAATAGCGTTTCTAAGATAAAAACATAATTTTTATTGA
1 AAAAATAGCACTTCTAAGATAAAAACATAATTTTTATTGA
12227073 AAA
1 AAA
12227076 CATAAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
40 35 0.97
41 1 0.03
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (40 bp):
AAAAATAGCACTTCTAAGATAAAAACATAATTTTTATTGA
Found at i:12227139 original size:112 final size:112
Alignment explanation
Indices: 12226967--12227169 Score: 282
Period size: 112 Copynumber: 1.8 Consensus size: 112
12226957 GAAAATATGA
* * * * * *
12226967 AAAAAATATAATTTTTAGAATTTAATAAAAATGACACTTCTAAGATAAATACGTAGTTTTTGTTG
1 AAAAAATATAATTTTTAGAATTCAATAAAAATAACACTTCGAAGATAAAAACGAAATTTTTGTTG
12227032 AAAAAAT-AGCGTTTCTAAGATAAAAACATAATTTTTATTGAAAACAT
66 AAAAAATGA-CGTTTCTAAGATAAAAACATAATTTTTATTGAAAACAT
* *** *
12227079 AAAAAATATATTTTTTAGAATTCAATAAAAATAATGTTTCGAAGATAAAAATGAAATTTTTGTTG
1 AAAAAATATAATTTTTAGAATTCAATAAAAATAACACTTCGAAGATAAAAACGAAATTTTTGTTG
*
12227144 AAAAAATGACTTTTCTAAGATAAAAA
66 AAAAAATGACGTTTCTAAGATAAAAA
12227170 TGCAATTTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
112 77 0.99
113 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (112 bp):
AAAAAATATAATTTTTAGAATTCAATAAAAATAACACTTCGAAGATAAAAACGAAATTTTTGTTG
AAAAAATGACGTTTCTAAGATAAAAACATAATTTTTATTGAAAACAT
Found at i:12227164 original size:40 final size:40
Alignment explanation
Indices: 12227115--12227192 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
12227105 AAAAATAATG
12227115 TTTCGAAGATAAAAATGAAATTTTTGTTGAAAAAATGACT
1 TTTCGAAGATAAAAATGAAATTTTTGTTGAAAAAATGACT
* * * *
12227155 TTTCTAAGATAAAAATGCAATTTTTGTTGGAAATATGA
1 TTTCGAAGATAAAAATGAAATTTTTGTTGAAAAAATGA
12227193 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.37
Consensus pattern (40 bp):
TTTCGAAGATAAAAATGAAATTTTTGTTGAAAAAATGACT
Found at i:12227177 original size:112 final size:113
Alignment explanation
Indices: 12226957--12227198 Score: 281
Period size: 112 Copynumber: 2.1 Consensus size: 113
12226947 AATCTTTGTG
* * * * * *
12226957 GAAAATATGAAAAAAATATAATTTTTAGAATTTAATAAAAATGACACTTCTAAGATAAATACGTA
1 GAAAACATG-AAAAAATATAATTTTTAGAATTCAATAAAAATAACACTTCGAAGATAAAAACGAA
* *
12227022 GTTTTTGTTGAAAAAATAGCGTTTCTAAGATAAAAACATAATTTTTATT
65 ATTTTTGTTGAAAAAATAGCGTTTCTAAGATAAAAACACAATTTTTATT
* *** *
12227071 GAAAACAT-AAAAAATATATTTTTTAGAATTCAATAAAAATAATGTTTCGAAGATAAAAATGAAA
1 GAAAACATGAAAAAATATAATTTTTAGAATTCAATAAAAATAACACTTCGAAGATAAAAACGAAA
* ** *
12227135 TTTTTGTTGAAAAAAT-GACTTTTCTAAGATAAAAATGCAATTTTTGTT
66 TTTTTGTTGAAAAAATAG-CGTTTCTAAGATAAAAACACAATTTTTATT
* *
12227183 GGAAATATGAAAAAAT
1 GAAAACATGAAAAAAT
12227199 TAAAATGTAA
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
111 1 0.01
112 92 0.86
113 7 0.07
114 7 0.07
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.35
Consensus pattern (113 bp):
GAAAACATGAAAAAATATAATTTTTAGAATTCAATAAAAATAACACTTCGAAGATAAAAACGAAA
TTTTTGTTGAAAAAATAGCGTTTCTAAGATAAAAACACAATTTTTATT
Found at i:12231060 original size:14 final size:14
Alignment explanation
Indices: 12231041--12231069 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12231031 GCAATGACTT
12231041 ATCGTGGTATTGGG
1 ATCGTGGTATTGGG
12231055 ATCGTGGTATTGGG
1 ATCGTGGTATTGGG
12231069 A
1 A
12231070 ACTATCACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.41, T:0.34
Consensus pattern (14 bp):
ATCGTGGTATTGGG
Found at i:12241625 original size:29 final size:27
Alignment explanation
Indices: 12241576--12241629 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
12241566 TTTTATATTT
*
12241576 ATATTTTTAATATTTTATTATTTAGAC
1 ATATTTTTAATATTTAATTATTTAGAC
12241603 ATATTTTTAAATAGTTTAATTATTTAG
1 ATATTTTT-AATA-TTTAATTATTTAG
12241630 GTACTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.33
28 4 0.17
29 12 0.50
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (27 bp):
ATATTTTTAATATTTAATTATTTAGAC
Found at i:12242442 original size:168 final size:168
Alignment explanation
Indices: 12242143--12242450 Score: 438
Period size: 168 Copynumber: 1.8 Consensus size: 168
12242133 TTTATAGTCT
* * * * * * * *
12242143 CTTAGGCATTCTTTTTTCTTTCTTTTCTAAAAGGAGTTTTCTTACTTTCTATTGTTCTCTCTTTT
1 CTTAGACACTCTTTTGTCTTTCTTTTCAAAAAAGAGTTTTCTTACTTTATATTATTCTCTATTTT
* **
12242208 CTTTCCATCCTATGGTTTTTTGTCTAATTCTTTGAATACAATCCTTTTGTTCTTCAAGTCTAGGT
66 CTTTCCATCCCATGGTTTTTTGTCTAATTCTTTGAATACAATCCTTTTAATCTTCAAGTCTAGGT
12242273 CTTCTTTTATTGGTTCTTTCTTTTTTTCTCTAGAGTTC
131 CTTCTTTTATTGGTTCTTTCTTTTTTTCTCTAGAGTTC
*
12242311 CTTAGACACTCTTTTGTCTTTCTTTTCAAAAAAGAGTTTTCTTACTTTATCTTATTCTCTAATTT
1 CTTAGACACTCTTTTGTCTTTCTTTTCAAAAAAGAGTTTTCTTACTTTATATTATTCTCT-ATTT
* * * ** *
12242376 T-TTTGCATCCCATGGTTTTTTGTCTAATTTTTTTAATGTAATCCTTTTAATCTTCAAGTTTAGG
65 TCTTTCCATCCCATGGTTTTTTGTCTAATTCTTTGAATACAATCCTTTTAATCTTCAAGTCTAGG
12242440 TCTTCTTTTAT
130 TCTTCTTTTAT
12242451 CGATTTTTTC
Statistics
Matches: 121, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
168 117 0.97
169 4 0.03
ACGTcount: A:0.17, C:0.18, G:0.10, T:0.55
Consensus pattern (168 bp):
CTTAGACACTCTTTTGTCTTTCTTTTCAAAAAAGAGTTTTCTTACTTTATATTATTCTCTATTTT
CTTTCCATCCCATGGTTTTTTGTCTAATTCTTTGAATACAATCCTTTTAATCTTCAAGTCTAGGT
CTTCTTTTATTGGTTCTTTCTTTTTTTCTCTAGAGTTC
Found at i:12243827 original size:144 final size:140
Alignment explanation
Indices: 12243679--12244160 Score: 401
Period size: 141 Copynumber: 3.4 Consensus size: 140
12243669 AAATGTGATT
* * *
12243679 TTTGTTACAATTCAAGAATTTCGAAAATAAAGTTTTAACATTCACTACG-TTTTATGCTCAAAAT
1 TTTGTTA-AATTC-AGAATTTCAAAAATAAA-TTTCAACATTCACTAAGTTTTTATGCT-AAAAT
* * *
12243743 ATGGTTTTTATTAAAATTTTGAAAATTTGAAAATAAAGTTTAAACATCTACTATGTTTTTTTTAT
62 ATGATTTTTATTAAAATTTT-AGAATTTGAAAATAAAGTTTAAACATCCACTATGTTTTTTTTAT
* *
12243808 GTTCAAAACACAATC
126 CTTAAAAACACAATC
* * * *
12243823 TTTGTTAAAATTTTAGATTTTCAAAAATAAAATTTCAACATTCATTAAGTTTTTATGCTTAAATA
1 TTTGTT-AAA-TTCAGAATTTCAAAAAT-AAATTTCAACATTCACTAAGTTTTTATGCTAAAATA
* * * * * * **
12243888 CGATCTTTGTTACAATTCTAGAATTTCAAAAATAAAGTTTTCACATCCACTATG---TTTTTATC
63 TGATTTTTATTAAAATTTTAGAATTT-GAAAATAAAGTTTAAACATCCACTATGTTTTTTTTATC
*
12243950 TTAAAAACACAATT
127 TTAAAAACACAATC
* * *
12243964 TTTGTTAAACTTTCAGAATTTAAAAAATATAATATCAACATTCACTATGGTTTTTAT-CTTAAAA
1 TTTGTTAAA--TTCAGAATTTCAAAAATA-AATTTCAACATTCACTA-AGTTTTTATGC-TAAAA
* * *
12244028 T-TGCAATTTTTATTGAAATTTTAGAA-TTGAAAATAAAGTTTCAACATCCACTACG---TTTTT
61 TATG--ATTTTTATTAAAATTTTAGAATTTGAAAATAAAGTTTAAACATCCACTATGTTTTTTTT
* **
12244088 ATATTAAAAACATGATC
124 ATCTTAAAAACACAATC
* * * *
12244105 TTCGTTAAAATTCTA-AATTTTCAAAAATAAAGTTTCAACATCCAATATGTTTTTAT
1 TTTGTT-AAATTC-AGAA-TTTCAAAAATAAA-TTTCAACATTCACTAAGTTTTTAT
12244161 CTTAAAAATG
Statistics
Matches: 275, Mismatches: 48, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
140 19 0.07
141 126 0.46
142 18 0.07
143 22 0.08
144 75 0.27
145 15 0.05
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (140 bp):
TTTGTTAAATTCAGAATTTCAAAAATAAATTTCAACATTCACTAAGTTTTTATGCTAAAATATGA
TTTTTATTAAAATTTTAGAATTTGAAAATAAAGTTTAAACATCCACTATGTTTTTTTTATCTTAA
AAACACAATC
Found at i:12244054 original size:72 final size:68
Alignment explanation
Indices: 12243676--12244187 Score: 295
Period size: 71 Copynumber: 7.2 Consensus size: 68
12243666 TTAAAATGTG
** ** * * *
12243676 ATTTTTGTTACAATTCAAGAATTTCGAAAATAAAGTTTTAACATTCACTACG-TTTTATGCTCAA
1 ATTTTTGTTA-AATTTTAGAATTTAAAAAATAAA-TTTCAACATTCACTATGTTTTTAT-CTTAA
**
12243740 AATATG
63 AATACA
* * * * * *
12243746 GTTTTTATTAAAATTTTGAAAATTT-GAAAATAAAGTTTAAACA-TCTACTATGTTTTTTTTATG
1 ATTTTTGTT-AAATTTT-AGAATTTAAAAAATAAA-TTTCAACATTC-ACTATG---TTTTTATC
*
12243809 TTCAAAACACA
59 TT-AAAATACA
* * * * *
12243820 ATCTTTGTTAAAATTTTAGATTTTCAAAAATAAAATTTCAACATTCATTAAGTTTTTATGCTT-A
1 ATTTTTGTT-AAATTTTAGAATTTAAAAAAT-AAATTTCAACATTCACTATGTTTTTAT-CTTAA
*
12243884 AATACG
63 AATACA
* * * *
12243890 ATCTTTGTTACAATTCTAGAATTTCAAAAATAAAGTTTTC-ACATCCACTATGTTTTTATCTTAA
1 ATTTTTGTTA-AATTTTAGAATTTAAAAAATAAA--TTTCAACATTCACTATGTTTTTATCTT-A
*
12243954 AAACACA
62 AAATACA
* *
12243961 ATTTTTGTTAAACTTTCAGAATTTAAAAAATATAATATCAACATTCACTATGGTTTTTATCTTAA
1 ATTTTTGTTAAA-TTTTAGAATTTAAAAAATA-AATTTCAACATTCACTAT-GTTTTTATCTTAA
*
12244026 AATTGCA
63 AA-TACA
* * * * *
12244033 ATTTTTATTGAAATTTTAGAA-TT-GAAAATAAAGTTTCAACATCCACTACGTTTTTATATTAAA
1 ATTTTTGTT-AAATTTTAGAATTTAAAAAATAAA-TTTCAACATTCACTATGTTTTTATCTTAAA
12244096 A-ACA
64 ATACA
* * * * * *
12244100 TGATCTTCGTTAAAATTCTA-AATTTTCAAAAATAAAGTTTCAACATCCAATATGTTTTTATCTT
1 --ATTTTTGTT-AAATTTTAGAA-TTTAAAAAATAAA-TTTCAACATTCACTATGTTTTTATCTT
*
12244164 AAAAATGCA
61 -AAAATACA
*
12244173 ATATTTGTTGAAATT
1 ATTTTTGTT-AAATT
12244188 ATAAATAACA
Statistics
Matches: 351, Mismatches: 60, Indels: 61
0.74 0.13 0.13
Matches are distributed among these distances:
67 2 0.01
68 2 0.01
69 38 0.11
70 107 0.30
71 109 0.31
72 36 0.10
73 11 0.03
74 41 0.12
75 5 0.01
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (68 bp):
ATTTTTGTTAAATTTTAGAATTTAAAAAATAAATTTCAACATTCACTATGTTTTTATCTTAAAAT
ACA
Found at i:12244193 original size:71 final size:70
Alignment explanation
Indices: 12243679--12244187 Score: 338
Period size: 70 Copynumber: 7.2 Consensus size: 70
12243669 AAATGTGATT
* * * * * *
12243679 TTTGTTACAATTCAAGAATTTCGAAAATAAAGTTTTAACATTCACTACG-TTTTATGC-TCAAAA
1 TTTGTTA-AATTCTAGAATTTCAAAAATAAAGTTTCAACATCCACTATGTTTTTAT-CTTAAAAA
*** *
12243742 TATGGTT
64 TACAATA
* * * * * * * *
12243749 TTTATTAAAATTTTGAAAATTT-GAAAATAAAGTTTAAACATCTACTATGTTTTTTTTATGTTCA
1 TTTGTT-AAATTCT-AGAATTTCAAAAATAAAGTTTCAACATCCACTATG---TTTTTATCTTAA
* *
12243813 AAACACAATC
61 AAATACAATA
* * * * * *
12243823 TTTGTTAAAATTTTAGATTTTCAAAAATAAAATTTCAACATTCATTAAGTTTTTATGCTT--AAA
1 TTTGTT-AAATTCTAGAATTTCAAAAATAAAGTTTCAACATCCACTATGTTTTTAT-CTTAAAAA
* *
12243886 TACGATC
64 TACAATA
12243893 TTTGTTACAATTCTAGAATTTCAAAAATAAAGTTTTC-ACATCCACTATGTTTTTATCTTAAAAA
1 TTTGTTA-AATTCTAGAATTTCAAAAATAAAG-TTTCAACATCCACTATGTTTTTATCTTAAAAA
* *
12243957 CACAATT
64 TACAATA
* * *
12243964 TTTGTTAAACTT-TCAGAATTTAAAAAATATAA-TATCAACATTCACTATGGTTTTTATCTTAAA
1 TTTGTTAAA-TTCT-AGAATTTCAAAAATA-AAGTTTCAACATCCACTAT-GTTTTTATCTTAAA
* * *
12244027 ATTGCAATT
62 AATACAATA
* * * * * *
12244036 TTTATTGAAATTTTAGAA-TT-GAAAATAAAGTTTCAACATCCACTACGTTTTTATATTAAAAAC
1 TTTGTT-AAATTCTAGAATTTCAAAAATAAAGTTTCAACATCCACTATGTTTTTATCTTAAAAAT
** *
12244099 ATGATC
65 ACAATA
* *
12244105 TTCGTTAAAATTCTA-AATTTTCAAAAATAAAGTTTCAACATCCAATATGTTTTTATCTTAAAAA
1 TTTGTT-AAATTCTAGAA-TTTCAAAAATAAAGTTTCAACATCCACTATGTTTTTATCTTAAAAA
*
12244169 TGCAATA
64 TACAATA
12244176 TTTGTTGAAATT
1 TTTGTT-AAATT
12244188 ATAAATAACA
Statistics
Matches: 346, Mismatches: 69, Indels: 47
0.75 0.15 0.10
Matches are distributed among these distances:
68 2 0.01
69 33 0.10
70 110 0.32
71 110 0.32
72 35 0.10
73 9 0.03
74 47 0.14
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (70 bp):
TTTGTTAAATTCTAGAATTTCAAAAATAAAGTTTCAACATCCACTATGTTTTTATCTTAAAAATA
CAATA
Found at i:12244202 original size:141 final size:138
Alignment explanation
Indices: 12243772--12244190 Score: 407
Period size: 141 Copynumber: 3.0 Consensus size: 138
12243762 TGAAAATTTG
* * * *
12243772 AAAATAAAGTTTAAACATCTACTATGTTTTTTTTATGTTCAAAACACAATCTTTGTTAAAATTTT
1 AAAATAAAGTTTCAACATCCACTATG---TTTTTATATTAAAAACACAATCTTTGTTAAAA-TTT
* * * * * *
12243837 AGATTTTCAAAAATAAAATTTCAACATTCATTAAGTTTTTATGCTT--AAATACGATCTTTGTT-
62 AAATTTTCAAAAAT-AAATTTCAACATTCAATATGTTTTTAT-CTTAAAAATGCAATATTTGTTG
*
12243899 ACAATTCTAGAATTTCA
125 A-AATTATAGAA--TCA
* * *
12243916 AAAATAAAGTTTTC-ACATCCACTATGTTTTTATCTTAAAAACACAATTTTTGTTAAACTTTCAG
1 AAAATAAAG-TTTCAACATCCACTATGTTTTTATATTAAAAACACAATCTTTGTTAAAATTT-A-
* * * * * *
12243980 AA-TTTAAAAAATATAATATCAACATTCACTATGGTTTTTATCTTAAAATTGCAATTTTTATTGA
63 AATTTTCAAAAATA-AATTTCAACATTCAATAT-GTTTTTATCTTAAAAATGCAATATTTGTTGA
* **
12244044 AATTTTAGAATTG
126 AATTATAGAATCA
* ** *
12244057 AAAATAAAGTTTCAACATCCACTACGTTTTTATATTAAAAACATGATCTTCGTTAAAATTCTAAA
1 AAAATAAAGTTTCAACATCCACTATGTTTTTATATTAAAAACACAATCTTTGTTAAAATT-TAAA
*
12244122 TTTTCAAAAATAAAGTTTCAACATCCAATATGTTTTTATCTTAAAAATGCAATATTTGTTGAAAT
65 TTTTCAAAAATAAA-TTTCAACATTCAATATGTTTTTATCTTAAAAATGCAATATTTGTTGAAAT
12244187 TATA
129 TATA
12244191 AATAACAAAA
Statistics
Matches: 229, Mismatches: 34, Indels: 28
0.79 0.12 0.10
Matches are distributed among these distances:
140 46 0.20
141 129 0.56
142 10 0.04
143 20 0.09
144 21 0.09
145 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (138 bp):
AAAATAAAGTTTCAACATCCACTATGTTTTTATATTAAAAACACAATCTTTGTTAAAATTTAAAT
TTTCAAAAATAAATTTCAACATTCAATATGTTTTTATCTTAAAAATGCAATATTTGTTGAAATTA
TAGAATCA
Found at i:12244437 original size:18 final size:18
Alignment explanation
Indices: 12244416--12244450 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12244406 AAATCAACCT
* *
12244416 AAGGAATCAAATTAAGAA
1 AAGGAACCAAACTAAGAA
12244434 AAGGAACCAAACTAAGA
1 AAGGAACCAAACTAAGA
12244451 GACTTGTTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.11, G:0.17, T:0.11
Consensus pattern (18 bp):
AAGGAACCAAACTAAGAA
Found at i:12244864 original size:8 final size:8
Alignment explanation
Indices: 12244841--12244880 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
12244831 AATTCATAAA
12244841 TTAAATAT
1 TTAAATAT
12244849 TATAAATAT
1 T-TAAATAT
12244858 TTAAATAT
1 TTAAATAT
12244866 TTAAATAT
1 TTAAATAT
*
12244874 CTAAATA
1 TTAAATA
12244881 CGTAGTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (8 bp):
TTAAATAT
Found at i:12245839 original size:161 final size:161
Alignment explanation
Indices: 12245610--12247076 Score: 1136
Period size: 161 Copynumber: 9.0 Consensus size: 161
12245600 CGTACAAAAA
* ** * * * * **
12245610 CATGTTATTAAAGCTATCCAAATTGTTAAAACAAAATAATAACAATAAATTTGCGTTTTTATCTT
1 CATG-TATTTAAGCTATTGAAATTGTTAAAACAAAACAATAACAACAAATTTACATTTTTGCCTT
* * * * *
12245675 TTAATGGCA-TAAAAGTC-TTAAACAAACCCTAAATGATAACTTTTTCATACATATCG-ACTATG
65 TTAATGGCACAAAAAG-CATTAAACAAA-CGTAAATGGTAACTTTTTCACACATAT-GAACTGTG
** * *
12245737 AAAACTAAACTCAATAATTCGGACAAATTTAGTAT
127 AAAACTAAGTTCAATCATTCGGACAAGTTTAGTAT
* * * * * ** * *
12245772 CATATATTTAAGCTATCGAAATTGTTAAAACAGAACGATTACAGTAGATTTGCATTTTTGCCTTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAACAAAACAATAACAACAAATTTACATTTTTGCCTTT
**** * * * * * **
12245837 TAACAATACAAAAAGCACTAAACAAACGTAAACGGTAATTTTTTCATACATATGAACCGTGGGAA
66 TAATGGCACAAAAAGCATTAAACAAACGTAAATGGTAACTTTTTCACACATATGAACTGTGAAAA
*
12245902 -TCAAGTTCAATCATTTGGACAAGTTTAGTAT
131 CT-AAGTTCAATCATTCGGACAAGTTTAGTAT
* * * * *
12245933 CATGTATTTAAGCTATTG-AACTATTATAATAGAACAATAACAACAAATTTACATTTTTGCCTTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAACAAAACAATAACAACAAATTTACATTTTTGCCTTT
* * *
12245997 TAATGGCACAAAAAGCATTAAATAGACGTAAACAGTTACTTAT-TTACACATACTCATTCACACA
66 TAATGGCACAAAAAGCATT--A-A-AC--AAAC-G-TA--AATGGTA-AC-T--T-TTTCACACA
* * * * *
12246061 TATGAACTGTGAAAACCAAGTTCAATTATTCAGATAAGTTTAATAT
116 TATGAACTGTGAAAACTAAGTTCAATCATTCGGACAAGTTTAGTAT
* * * * * * ** *
12246107 CATATATTTAAGCTA-TCAAATCTATTAAAACATAACAATAATAGCATTTTTGCATTTTTGCCTT
1 CATGTATTTAAGCTATTGAAAT-TGTTAAAACAAAACAATAACAACAAATTTACATTTTTGCCTT
* * * * * *
12246171 TTAATGGCATAAAAAGCAGTAAACAAACGTAGACGGTAATTTTTTCACATATATGAACTGTGAAA
65 TTAATGGCACAAAAAGCATTAAACAAACGTAAATGGTAACTTTTTCACACATATGAACTGTGAAA
* * *
12246236 A-TCAAGTTCTATTATTTGGACAAGTTTAGTAT
130 ACT-AAGTTCAATCATTCGGACAAGTTTAGTAT
* * *
12246268 CATGTATTTAAGCTATTGAAATTGTTAAAATAAAACAATAACAACAAATTTATATTTTTGCATTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAACAAAACAATAACAACAAATTTACATTTTTGCCTTT
* * * ** * * ** *
12246333 TAATAGCATAAAAAGTATTAAACAGGCATAAACGGTAACTTTTTCACACATATGAACCATGAAAT
66 TAATGGCACAAAAAGCATTAAACAAACGTAAATGGTAACTTTTTCACACATATGAACTGTGAAAA
*
12246398 C-AAGTTCAATCATTCGAACAAGTTTAGTAT
131 CTAAGTTCAATCATTCGGACAAGTTTAGTAT
* * * * * * * * *
12246428 CATGTATTTAAGCTATGGAAACTATTAAAATAAAACAATAATAGCAATTTTGCATTTTTTTCCTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAACAAAACAATAACAACAAATTTACA-TTTTTGCCTT
* * * * * **
12246493 TTAATGGCACAAAAAGAACTAAACAAATGTAAATGGTAATTTTTTCACACATATGGACCATGAAA
65 TTAATGGCACAAAAAGCATTAAACAAACGTAAATGGTAACTTTTTCACACATATGAACTGTGAAA
* *
12246558 A-TCATGTTCAATCATTCGGACAACTTTAGTAT
130 ACT-AAGTTCAATCATTCGGACAAGTTTAGTAT
* * * * *
12246590 CATGTATATAAGCTATTGAAATTGTTAAAATAGAACAATAACAAAAAATTTACATTTTTTCCTTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAACAAAACAATAACAACAAATTTACATTTTTGCCTTT
*** * * * *
12246655 TAACAACACAAAAAGCATTAAACAAACGTAAATGGCAACTTTTTCAAATATATCAA-TCGTGAAA
66 TAATGGCACAAAAAGCATTAAACAAACGTAAATGGTAACTTTTTCACACATATGAACT-GTGAAA
* * **
12246719 ACCAAGTTCAATTATTCAAACAAGTTTAGTAT
130 ACTAAGTTCAATCATTCGGACAAGTTTAGTAT
* * * * **
12246751 CATATATTTAAGCTATTAAAACTGTTAAAACAAAATAATAACAACAAATTTACATTTTTATCTTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAACAAAACAATAACAACAAATTTACATTTTTGCCTTT
** * *
12246816 TAATGGCACAAAAAGTCA-TAAACAAACGTAAACAGTAACTTTTTCACACATATTAA-TCATGAA
66 TAATGGCACAAAAAG-CATTAAACAAACGTAAATGGTAACTTTTTCACACATATGAACT-GTGAA
* * ** *
12246879 AAC---CTT-AATAATTTAGACAAGTTTAATAT
129 AACTAAGTTCAATCATTCGGACAAGTTTAGTAT
* *** * * * * **
12246908 TATGTATTTAAGCTACCCAAATGGTTAAAACTAAACAATAACAAAAAATTTTCATTTTTAACTTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAACAAAACAATAACAACAAATTTACATTTTTGCCTTT
** * ** * * * *
12246973 TAATTACATAAAAAGCCCTAAACAGACGTAAATGGTAACCTTTTCACACATATCAA-TCAT-AGA
66 TAATGGCACAAAAAGCATTAAACAAACGTAAATGGTAACTTTTTCACACATATGAACT-GTGA-A
** *
12247036 AACTAAGTTCAATCATTCAAACAAGTTTAATAT
129 AACTAAGTTCAATCATTCGGACAAGTTTAGTAT
*
12247069 CTTGTATT
1 CATGTATT
12247077 ATTAAAATAG
Statistics
Matches: 1044, Mismatches: 223, Indels: 77
0.78 0.17 0.06
Matches are distributed among these distances:
156 2 0.00
157 125 0.12
158 2 0.00
160 125 0.12
161 551 0.53
162 95 0.09
163 1 0.00
164 3 0.00
165 2 0.00
166 6 0.01
167 3 0.00
168 3 0.00
169 6 0.01
170 2 0.00
171 3 0.00
172 1 0.00
173 3 0.00
174 59 0.06
175 52 0.05
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (161 bp):
CATGTATTTAAGCTATTGAAATTGTTAAAACAAAACAATAACAACAAATTTACATTTTTGCCTTT
TAATGGCACAAAAAGCATTAAACAAACGTAAATGGTAACTTTTTCACACATATGAACTGTGAAAA
CTAAGTTCAATCATTCGGACAAGTTTAGTAT
Found at i:12246588 original size:322 final size:320
Alignment explanation
Indices: 12245610--12247069 Score: 1355
Period size: 322 Copynumber: 4.5 Consensus size: 320
12245600 CGTACAAAAA
* ** * * * * * *
12245610 CATGTTATTAAAGCTATCCAAATTGTTAAAACAAAATAATAACAATAAATTTGCGTTTTTATC-T
1 CATG-TATTTAAGCTATTGAAATTGTTAAAATAAAACAATAACAAAAAATTTACATTTTT-GCAT
* * * * * *
12245674 TTTAATGGCAT-AAAAGTC-TTAAACAAACCCTAAATGATAACTTTTTCATACATATCG-ACTAT
64 TTTAATAGCATAAAAAG-CATTAAACAGA-CGTAAATGGTAACTTTTTCACACATAT-GAACCAT
* ** * ** * * *
12245736 GAAAACTAAACTCAATAATTCGGACAAATTTAGTATCATATATTTAAGCTATCGAAATTGTTAAA
126 G-AAACCAAGTTCAATCATTCAAACAAGTTTAGTATCATATATTTAAGCTAT-GAAACTATTAAA
* * * * ****
12245801 ACAGAACGATTACAGTAGA-TTTGCATTTTTGCCTTTTAACAATACAAAAAGCACTAAACAAACG
189 ACAAAACAATAACAGCA-ATTTTGCATTTTTGCCTTTTAATGGCACAAAAAGCACTAAACAAACG
* * **
12245865 TAAACGGTAATTTTTTCATACATATGAACCGTGGGAATCAAGTTCAATCATTTGGACAAGTTTAG
253 TAAACGGTAATTTTTTCACACATATGAACCATGAAAATCAAGTTCAATCATTTGGACAAGTTTAG
12245930 TAT
318 TAT
* * * * * *
12245933 CATGTATTTAAGCTATTG-AACTATTATAATAGAACAATAACAACAAATTTACATTTTTGCCTTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAATAAAACAATAACAAAAAATTTACATTTTTGCATTT
* * * ** *
12245997 TAATGGCACAAAAAGCATTAAATAGACGTAAACAGTTACTTATTTACACATACTCATTCACACAT
66 TAATAGCATAAAAAGCATTAAACAGACGT--A-A---A--T-GGTA-AC-T--T-TTTCACACAT
** * * * * *
12246062 ATGAACTGTGAAAACCAAGTTCAATTATTCAGATAAGTTTAATATCATATATTTAAGCTATCAAA
117 ATGAACCATG-AAACCAAGTTCAATCATTCAAACAAGTTTAGTATCATATATTTAAGCTATGAAA
* * * * *
12246127 TCTATTAAAACATAACAATAATAGCATTTTTGCATTTTTGCCTTTTAATGGCATAAAAAGCAGTA
181 -CTATTAAAACAAAACAATAACAGCAATTTTGCATTTTTGCCTTTTAATGGCACAAAAAGCACTA
* * ** * *
12246192 AACAAACGTAGACGGTAATTTTTTCACATATATGAACTGTGAAAATCAAGTTCTATTATTTGGAC
245 AACAAACGTAAACGGTAATTTTTTCACACATATGAACCATGAAAATCAAGTTCAATCATTTGGAC
12246257 AAGTTTAGTAT
310 AAGTTTAGTAT
* *
12246268 CATGTATTTAAGCTATTGAAATTGTTAAAATAAAACAATAACAACAAATTTATATTTTTGCATTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAATAAAACAATAACAAAAAATTTACATTTTTGCATTT
* * * * *
12246333 TAATAGCATAAAAAGTATTAAACAGGCATAAACGGTAACTTTTTCACACATATGAACCATGAAAT
66 TAATAGCATAAAAAGCATTAAACAGACGTAAATGGTAACTTTTTCACACATATGAACCATGAAAC
* * *
12246398 CAAGTTCAATCATTCGAACAAGTTTAGTATCATGTATTTAAGCTATGGAAACTATTAAAATAAAA
131 CAAGTTCAATCATTCAAACAAGTTTAGTATCATATATTTAAGCTAT-GAAACTATTAAAACAAAA
* * * * *
12246463 CAATAATAGCAATTTTGCATTTTTTTCCTTTTAATGGCACAAAAAGAACTAAACAAATGTAAATG
195 CAATAACAGCAATTTTGCA-TTTTTGCCTTTTAATGGCACAAAAAGCACTAAACAAACGTAAACG
* * * *
12246528 GTAATTTTTTCACACATATGGACCATGAAAATCATGTTCAATCATTCGGACAACTTTAGTAT
259 GTAATTTTTTCACACATATGAACCATGAAAATCAAGTTCAATCATTTGGACAAGTTTAGTAT
* * * *
12246590 CATGTATATAAGCTATTGAAATTGTTAAAATAGAACAATAACAAAAAATTTACATTTTTTCCTTT
1 CATGTATTTAAGCTATTGAAATTGTTAAAATAAAACAATAACAAAAAATTTACATTTTTGCATTT
* * * * * * * * * *
12246655 TAACAACACAAAAAGCATTAAACAAACGTAAATGGCAACTTTTTCAAATATATCAATCGTGAAAA
66 TAATAGCATAAAAAGCATTAAACAGACGTAAATGGTAACTTTTTCACACATATGAACCATG-AAA
* * *
12246720 CCAAGTTCAATTATTCAAACAAGTTTAGTATCATATATTTAAGCTATTAAAACTGTTAAAACAAA
130 CCAAGTTCAATCATTCAAACAAGTTTAGTATCATATATTTAAGCTA-TGAAACTATTAAAACAAA
* * * * **
12246785 ATAATAACAACAAATTTACATTTTTATCTTTTAATGGCACAAAAAGTCA-TAAACAAACGTAAAC
194 ACAATAACAGCAATTTTGCATTTTTGCCTTTTAATGGCACAAAAAG-CACTAAACAAACGTAAAC
* * * * * * * *
12246849 AGTAACTTTTTCACACATATTAATCATGAAAA-C--CTT-AATAATTTAGACAAGTTTAATAT
258 GGTAATTTTTTCACACATATGAACCATGAAAATCAAGTTCAATCATTTGGACAAGTTTAGTAT
* *** * * *
12246908 TATGTATTTAAGCTACCCAAATGGTTAAAACT-AAACAATAACAAAAAATTTTCATTTTT-AACT
1 CATGTATTTAAGCTATTGAAATTGTTAAAA-TAAAACAATAACAAAAAATTTACATTTTTGCA-T
** * * *
12246971 TTTAATTA-CATAAAAAGCCCTAAACAGACGTAAATGGTAACCTTTTCACACATATCAATCATAG
64 TTTAA-TAGCATAAAAAGCATTAAACAGACGTAAATGGTAACTTTTTCACACATATGAACCAT-G
* *
12247035 AAACTAAGTTCAATCATTCAAACAAGTTTAATATC
127 AAACCAAGTTCAATCATTCAAACAAGTTTAGTATC
12247070 TTGTATTATT
Statistics
Matches: 938, Mismatches: 169, Indels: 65
0.80 0.14 0.06
Matches are distributed among these distances:
318 150 0.16
319 5 0.01
320 1 0.00
321 119 0.13
322 304 0.32
323 81 0.09
324 2 0.00
325 1 0.00
326 2 0.00
327 3 0.00
329 1 0.00
330 3 0.00
331 2 0.00
332 1 0.00
333 1 0.00
334 6 0.01
335 193 0.21
336 63 0.07
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (320 bp):
CATGTATTTAAGCTATTGAAATTGTTAAAATAAAACAATAACAAAAAATTTACATTTTTGCATTT
TAATAGCATAAAAAGCATTAAACAGACGTAAATGGTAACTTTTTCACACATATGAACCATGAAAC
CAAGTTCAATCATTCAAACAAGTTTAGTATCATATATTTAAGCTATGAAACTATTAAAACAAAAC
AATAACAGCAATTTTGCATTTTTGCCTTTTAATGGCACAAAAAGCACTAAACAAACGTAAACGGT
AATTTTTTCACACATATGAACCATGAAAATCAAGTTCAATCATTTGGACAAGTTTAGTAT
Found at i:12252460 original size:7 final size:7
Alignment explanation
Indices: 12252448--12252473 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12252438 CGAATAAGAA
12252448 TGGAATT
1 TGGAATT
12252455 TGGAATT
1 TGGAATT
12252462 TGGAATT
1 TGGAATT
12252469 TGGAA
1 TGGAA
12252474 GACTAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (7 bp):
TGGAATT
Found at i:12256023 original size:22 final size:22
Alignment explanation
Indices: 12255996--12256039 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12255986 GTATTCTTAA
12255996 AAATTTATT-TTTGAAA-ATATAT
1 AAATTT-TTGTTT-AAATATATAT
12256018 AAATTTTTGTTTAAATATATAT
1 AAATTTTTGTTTAAATATATAT
12256040 TTAATTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
AAATTTTTGTTTAAATATATAT
Found at i:12256095 original size:25 final size:25
Alignment explanation
Indices: 12256069--12256117 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
12256059 AACGTTTAAT
12256069 TTTAAT-TC-AAATAAAATAAATATA
1 TTTAATCTCAAAAT-AAATAAATATA
*
12256093 TTTAATCTTAAAATAAATAAATATA
1 TTTAATCTCAAAATAAATAAATATA
12256118 ATGTGCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 12 0.55
26 4 0.18
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
TTTAATCTCAAAATAAATAAATATA
Found at i:12256119 original size:21 final size:21
Alignment explanation
Indices: 12256080--12256119 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12256070 TTAATTCAAA
* *
12256080 TAAAATAAATATATTTAATCT
1 TAAAATAAATAAATATAATCT
12256101 TAAAATAAATAAATATAAT
1 TAAAATAAATAAATATAAT
12256120 GTGCTAAAAT
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:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATAAATAAATATAATCT
Found at i:12258425 original size:10 final size:10
Alignment explanation
Indices: 12258407--12258452 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
12258397 TTTTTTCTTA
12258407 AATTAATTAT
1 AATTAATTAT
*
12258417 AATTTATTAT
1 AATTAATTAT
*
12258427 AA--AATGAT
1 AATTAATTAT
12258435 -ATTAATTAT
1 AATTAATTAT
12258444 AATTAATTA
1 AATTAATTA
12258453 ATAAAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
7 1 0.03
8 4 0.14
9 5 0.17
10 19 0.66
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (10 bp):
AATTAATTAT
Found at i:12258575 original size:40 final size:39
Alignment explanation
Indices: 12258500--12258575 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
12258490 ATTAATTATT
* *
12258500 AATTAATAAAATTAATTATTGATCATAATTAATTAACAA
1 AATTAATAAAATTAATTAATGATCATAAGTAATTAACAA
* *
12258539 AATTAATGATAATTAATTAATGATTATTAAGT-ATTAA
1 AATTAAT-AAAATTAATTAATGATCA-TAAGTAATTAA
12258576 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 7 0.23
40 20 0.65
41 4 0.13
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (39 bp):
AATTAATAAAATTAATTAATGATCATAAGTAATTAACAA
Found at i:12258679 original size:21 final size:20
Alignment explanation
Indices: 12258641--12258679 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12258631 AACTTTTTCT
*
12258641 TTTTTTTTCTTTCTCCTCCC
1 TTTTTTTTCTTTCCCCTCCC
12258661 TTTTTTTTCTCTTCCCCTC
1 TTTTTTTTCT-TTCCCCTC
12258680 TCGCAATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTTTCTTTCCCCTCCC
Found at i:12259431 original size:15 final size:15
Alignment explanation
Indices: 12259308--12259428 Score: 58
Period size: 15 Copynumber: 8.1 Consensus size: 15
12259298 TAATTAAGTT
12259308 TTAATT-AAATTAAA
1 TTAATTAAAATTAAA
*
12259322 TTAAGT-AAATT-AA
1 TTAATTAAAATTAAA
* *
12259335 TTGATTAATTATTAAA
1 TTAATTAA-AATTAAA
**
12259351 TT-ATTTTAA-TAAA
1 TTAATTAAAATTAAA
* *
12259364 TTAA-TAAAAATAATT
1 TTAATTAAAATTAA-A
*
12259379 TTAATTTTAAATT-AA
1 TTAA-TTAAAATTAAA
12259394 TTCAATTCAAAAATTAAA
1 TT-AATT--AAAATTAAA
12259412 TTAATTAAAATATAAA
1 TTAATTAAAAT-TAAA
12259428 T
1 T
12259429 AATATAAGTA
Statistics
Matches: 80, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
13 15 0.19
14 16 0.20
15 19 0.24
16 12 0.15
17 14 0.17
18 4 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (15 bp):
TTAATTAAAATTAAA
Found at i:12261216 original size:21 final size:21
Alignment explanation
Indices: 12261190--12261231 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12261180 GAAATTTTTG
12261190 TTTAAGTCATTCTATTGGTTT
1 TTTAAGTCATTCTATTGGTTT
* * *
12261211 TTTAAGTTATTTTGTTGGTTT
1 TTTAAGTCATTCTATTGGTTT
12261232 CATTGAACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.17, T:0.62
Consensus pattern (21 bp):
TTTAAGTCATTCTATTGGTTT
Found at i:12261769 original size:22 final size:22
Alignment explanation
Indices: 12261741--12261791 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
12261731 TTTTGTATTT
*
12261741 TGATTTTTTTC---ATGCATTG
1 TGATTTTTTTCTTAATGCATGG
*
12261760 TGTTTTTTTTCTTAATGCATGG
1 TGATTTTTTTCTTAATGCATGG
12261782 TGATTTTTTT
1 TGATTTTTTT
12261792 AGTTTAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 10 0.38
22 16 0.62
ACGTcount: A:0.14, C:0.08, G:0.16, T:0.63
Consensus pattern (22 bp):
TGATTTTTTTCTTAATGCATGG
Found at i:12270627 original size:19 final size:20
Alignment explanation
Indices: 12270600--12270644 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
12270590 ATAACATGAT
*
12270600 AACACTGATTTACATGAATA
1 AACACTGATATACATGAATA
12270620 AACA-TGATATACATGAAT-
1 AACACTGATATACATGAATA
12270638 AACACTG
1 AACACTG
12270645 TAAATACAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 15 0.65
20 4 0.17
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (20 bp):
AACACTGATATACATGAATA
Found at i:12273054 original size:45 final size:45
Alignment explanation
Indices: 12273004--12273094 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
12272994 ATTAAAAATG
* *
12273004 TATTAAAAACATACATTAGAAATTTATGAG-AAAAAACTATATATA
1 TATTAAAAACATACATTAAAAATGTATGAGTAAAAAAC-ATATATA
*
12273049 TATTAAAAACATATATTAAAAATGTATGAGTAAAAAACATATATA
1 TATTAAAAACATACATTAAAAATGTATGAGTAAAAAACATATATA
12273094 T
1 T
12273095 TAAAATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
45 35 0.83
46 7 0.17
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (45 bp):
TATTAAAAACATACATTAAAAATGTATGAGTAAAAAACATATATA
Found at i:12273064 original size:13 final size:13
Alignment explanation
Indices: 12273046--12273070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12273036 AAAACTATAT
12273046 ATATATTAAAAAC
1 ATATATTAAAAAC
12273059 ATATATTAAAAA
1 ATATATTAAAAA
12273071 TGTATGAGTA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATATTAAAAAC
Found at i:12273708 original size:21 final size:21
Alignment explanation
Indices: 12273682--12273728 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
12273672 CTGTAGATAA
12273682 TAAAAGTTAACCTTGAAAGTT
1 TAAAAGTTAACCTTGAAAGTT
* *
12273703 TAAAAGTTAGCTTTGAAAGTT
1 TAAAAGTTAACCTTGAAAGTT
12273724 TAAAA
1 TAAAA
12273729 ATCAGTCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (21 bp):
TAAAAGTTAACCTTGAAAGTT
Found at i:12274777 original size:102 final size:102
Alignment explanation
Indices: 12274654--12274859 Score: 376
Period size: 102 Copynumber: 2.0 Consensus size: 102
12274644 CATGATTCAT
12274654 TCTATTAAGATTATCAGATAGTTTCATATTATTATAAATGTTATTTATTATCATTATAATATATT
1 TCTATTAAGATTATCAGATAGTTTCATATTATTATAAATGTTATTTATTATCATTATAATATATT
12274719 ATGGTATATTCATGTAAATTAGATGTACTTTACTTTA
66 ATGGTATATTCATGTAAATTAGATGTACTTTACTTTA
* *
12274756 TCTATTAAGATTATTAGATAGTTTCATATTATTATAAATGTTATTTATTGTCATTATAATATATT
1 TCTATTAAGATTATCAGATAGTTTCATATTATTATAAATGTTATTTATTATCATTATAATATATT
* *
12274821 ATTGTATATTCATGTGAATTAGATGTACTTTACTTTA
66 ATGGTATATTCATGTAAATTAGATGTACTTTACTTTA
12274858 TC
1 TC
12274860 AATAACCATA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (102 bp):
TCTATTAAGATTATCAGATAGTTTCATATTATTATAAATGTTATTTATTATCATTATAATATATT
ATGGTATATTCATGTAAATTAGATGTACTTTACTTTA
Found at i:12275187 original size:14 final size:15
Alignment explanation
Indices: 12275152--12275187 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
12275142 TAATATATAT
*
12275152 ATATATATATATTTA
1 ATATATGTATATTTA
12275167 ATATATGTAT-TTTA
1 ATATATGTATATTTA
12275181 ATATATG
1 ATATATG
12275188 CCTTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATATGTATATTTA
Found at i:12281533 original size:6 final size:6
Alignment explanation
Indices: 12281522--12281546 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12281512 AGGACTCAAG
12281522 TTTAGA TTTAGA TTTAGA TTTAGA T
1 TTTAGA TTTAGA TTTAGA TTTAGA T
12281547 AAGGAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TTTAGA
Found at i:12282941 original size:28 final size:28
Alignment explanation
Indices: 12282907--12282973 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
12282897 TCTGATGTTA
*
12282907 TAATTTTGTTAAATAGCTATTAATATTC
1 TAATTTTGTTAAACAGCTATTAATATTC
* * * *
12282935 TATTTTTGTTAAACAGCTATTTATGTTT
1 TAATTTTGTTAAACAGCTATTAATATTC
12282963 TAATTTTGTTA
1 TAATTTTGTTA
12282974 GAAAAGACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (28 bp):
TAATTTTGTTAAACAGCTATTAATATTC
Found at i:12287050 original size:28 final size:28
Alignment explanation
Indices: 12287009--12287062 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
12286999 TATTTAATTG
* * *
12287009 ATTATTTGAGTATAATACTTAATTATTA
1 ATTATATGAATATAATACTGAATTATTA
12287037 ATTATATGAATATAATACTGAATTAT
1 ATTATATGAATATAATACTGAATTAT
12287063 GATATTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (28 bp):
ATTATATGAATATAATACTGAATTATTA
Found at i:12288257 original size:123 final size:121
Alignment explanation
Indices: 12288031--12288275 Score: 373
Period size: 123 Copynumber: 2.0 Consensus size: 121
12288021 GGAGAATAGG
* *
12288031 TTAAGTAAACTTCGCTGAGATAAAAATAAATAAATAACAAACAAAGCTTTACAATGCCTAAAGCC
1 TTAAGTAAACTCCACTGAGATAAAAATAAATAAATAACAAACAAAGCTTTACAATGCCTAAAGCC
* * *
12288096 AACCCTTTGATTGCTATTAATTTTTTGTGAGATATATATATATATATGTATGTATA
66 AACCCTTTGATTGCTATTAATTTTTTATGAGATATATATATATATATATATATATA
* *
12288152 TTAAGTAAACTCCATTGAGATAAATAAATAAATAAATAACAAACAAAGTTTTACAATGCCTAAAG
1 TTAAGTAAACTCCACTGAGAT-AA-AAATAAATAAATAACAAACAAAGCTTTACAATGCCTAAAG
* * * *
12288217 CCAACCCTTTTATTGCTATTGATTTTTTATGATATGTATATATATATATATATATATA
64 CCAACCCTTTGATTGCTATTAATTTTTTATGAGATATATATATATATATATATATATA
12288275 T
1 T
12288276 ATGTGTGTGT
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
121 18 0.16
122 2 0.02
123 91 0.82
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (121 bp):
TTAAGTAAACTCCACTGAGATAAAAATAAATAAATAACAAACAAAGCTTTACAATGCCTAAAGCC
AACCCTTTGATTGCTATTAATTTTTTATGAGATATATATATATATATATATATATA
Found at i:12288258 original size:2 final size:2
Alignment explanation
Indices: 12288248--12288277 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12288238 ATTTTTTATG
*
12288248 AT AT GT 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
12288278 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12289860 original size:30 final size:29
Alignment explanation
Indices: 12289790--12289857 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
12289780 AATATTGTCG
* **
12289790 CTATATTTTAATTTTGTTAAATTTTATTA
1 CTATATTTTAATTTTGTTTAATTTTACCA
* *
12289819 GTGTACTTTTAATTTTGTTTAATTTTACCA
1 CTATA-TTTTAATTTTGTTTAATTTTACCA
12289849 CTATATTTT
1 CTATATTTT
12289858 TAACTTTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.26, C:0.07, G:0.06, T:0.60
Consensus pattern (29 bp):
CTATATTTTAATTTTGTTTAATTTTACCA
Found at i:12290378 original size:42 final size:42
Alignment explanation
Indices: 12290323--12290411 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
12290313 CGTTGTATAG
* **
12290323 CATCAAAGCTTGTAGTTAATTTCTCTTTGTTATTCTCATTCC
1 CATCAAAGCTTGTAGTTAAATTCTCTTCATTATTCTCATTCC
* *
12290365 CATCAATGTTTGTAGTTAAATTCTCTTCATTATTCTCATTCC
1 CATCAAAGCTTGTAGTTAAATTCTCTTCATTATTCTCATTCC
12290407 CATCA
1 CATCA
12290412 CATCCACCTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (42 bp):
CATCAAAGCTTGTAGTTAAATTCTCTTCATTATTCTCATTCC
Found at i:12295715 original size:13 final size:13
Alignment explanation
Indices: 12295697--12295721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12295687 ATTATATATA
12295697 TTTACAAATTAAT
1 TTTACAAATTAAT
12295710 TTTACAAATTAA
1 TTTACAAATTAA
12295722 ATTAGTAAAT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTACAAATTAAT
Found at i:12298299 original size:25 final size:26
Alignment explanation
Indices: 12298271--12298319 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
12298261 ATGCAATTAG
* *
12298271 TTTTTGTATTTATATAA-AATTTGAA
1 TTTTAGTACTTATATAATAATTTGAA
*
12298296 TTTTAGTCCTTATATAATAATTTG
1 TTTTAGTACTTATATAATAATTTG
12298320 TAGAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (26 bp):
TTTTAGTACTTATATAATAATTTGAA
Found at i:12298604 original size:18 final size:18
Alignment explanation
Indices: 12298557--12298605 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
12298547 ACAAAAAAGG
* *
12298557 AAACTTATTTAAATAATT
1 AAACTAATTTAAATAATA
* * *
12298575 ATATTAAATTAAATAATA
1 AAACTAATTTAAATAATA
12298593 AAACTAATTTAAA
1 AAACTAATTTAAA
12298606 AACCAATACA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
AAACTAATTTAAATAATA
Found at i:12298838 original size:21 final size:22
Alignment explanation
Indices: 12298805--12298856 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
12298795 TTTTATTAAA
* *
12298805 ATTAAATAATGACAAATTTAT-
1 ATTATATATTGACAAATTTATG
12298826 ATTATATATTGACAAATTTATG
1 ATTATATATTGACAAATTTATG
12298848 A-TATATATT
1 ATTATATATT
12298857 TAATAGATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (22 bp):
ATTATATATTGACAAATTTATG
Found at i:12299404 original size:19 final size:20
Alignment explanation
Indices: 12299361--12299404 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
12299351 GGAAATCAAG
*
12299361 TAATATTGTTATCAATTAGAC
1 TAATATTGTTA-CAATTAAAC
*
12299382 TAATATTGTTA-AATTAAAT
1 TAATATTGTTACAATTAAAC
12299401 TAAT
1 TAAT
12299405 TAAGGATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (20 bp):
TAATATTGTTACAATTAAAC
Found at i:12299496 original size:31 final size:30
Alignment explanation
Indices: 12299432--12299496 Score: 71
Period size: 31 Copynumber: 2.1 Consensus size: 30
12299422 GTAAATTATT
*
12299432 ATATAGAGATTAAAATTTAAATTTTATATAA
1 ATATAGAGATT-AAATTTAAATTTGATATAA
12299463 ATATAGAGATT-AATTGTATAATTTGACTA-AA
1 ATATAGAGATTAAATT-TA-AATTTGA-TATAA
12299494 ATA
1 ATA
12299497 ATATAAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
29 4 0.13
30 2 0.07
31 22 0.73
32 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (30 bp):
ATATAGAGATTAAATTTAAATTTGATATAA
Found at i:12299784 original size:17 final size:17
Alignment explanation
Indices: 12299764--12299801 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
12299754 TATTTTATTG
*
12299764 TATAAAAATTTAA-AAAA
1 TATAAAAA-CTAATAAAA
12299781 TATAAAAACTAATAAAA
1 TATAAAAACTAATAAAA
12299798 TATA
1 TATA
12299802 TAATTTGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TATAAAAACTAATAAAA
Found at i:12299942 original size:20 final size:21
Alignment explanation
Indices: 12299909--12299953 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
12299899 AATTTTAACC
12299909 AAATCAAATATTAAATTT-TT
1 AAATCAAATATTAAATTTCTT
* * *
12299929 AAATCAATTTTTAATTTTCTT
1 AAATCAAATATTAAATTTCTT
12299950 AAAT
1 AAAT
12299954 TTATTTCCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATCAAATATTAAATTTCTT
Found at i:12301435 original size:24 final size:24
Alignment explanation
Indices: 12301408--12301479 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
12301398 GAAACCCTCT
12301408 CATAAAGATCCAATGAAAAAAAAG
1 CATAAAGATCCAATGAAAAAAAAG
12301432 CATAAAGATCCAATGAAAAAAAAG
1 CATAAAGATCCAATGAAAAAAAAG
12301456 CATAAAGATCCAATGAAAAAAAAG
1 CATAAAGATCCAATGAAAAAAAAG
12301480 AAAGTTAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12
Consensus pattern (24 bp):
CATAAAGATCCAATGAAAAAAAAG
Found at i:12301779 original size:21 final size:21
Alignment explanation
Indices: 12301733--12301780 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
12301723 GAGTTGAGAG
*
12301733 AAGAATTGGGCGAAACTAAAA
1 AAGATTTGGGCGAAACTAAAA
12301754 AAGATTTGGGCGAAACTAAAA
1 AAGATTTGGGCGAAACTAAAA
12301775 AAGATT
1 AAGATT
12301781 CGATAATCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.19
Consensus pattern (21 bp):
AAGATTTGGGCGAAACTAAAA
Found at i:12302512 original size:12 final size:12
Alignment explanation
Indices: 12302495--12302521 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12302485 TTAAGGAGTC
12302495 ATTATCAATACG
1 ATTATCAATACG
12302507 ATTATCAATACG
1 ATTATCAATACG
12302519 ATT
1 ATT
12302522 TAGTTCAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (12 bp):
ATTATCAATACG
Found at i:12302705 original size:18 final size:18
Alignment explanation
Indices: 12302682--12302736 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
12302672 CGAATTCATT
* *
12302682 ACTGAATCAAGAATATAA
1 ACTGAATCAAGAACAAAA
12302700 ACTGAATCAAGAACAAAA
1 ACTGAATCAAGAACAAAA
*
12302718 ACGGAATCAAGAACAAAA
1 ACTGAATCAAGAACAAAA
12302736 A
1 A
12302737 TATAAAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.60, C:0.15, G:0.13, T:0.13
Consensus pattern (18 bp):
ACTGAATCAAGAACAAAA
Found at i:12302795 original size:16 final size:14
Alignment explanation
Indices: 12302769--12302802 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 14
12302759 AACACTATAG
12302769 ATATAATTTATTAT
1 ATATAATTTATTAT
12302783 CATATATATTTATTAT
1 -ATATA-ATTTATTAT
12302799 ATAT
1 ATAT
12302803 CAAGATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATAATTTATTAT
Found at i:12302951 original size:9 final size:9
Alignment explanation
Indices: 12302937--12302964 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12302927 ATAATTATCT
12302937 AACGGGGAA
1 AACGGGGAA
12302946 AACGGGGAA
1 AACGGGGAA
12302955 AACGGGGAA
1 AACGGGGAA
12302964 A
1 A
12302965 TTTTCGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.43, T:0.00
Consensus pattern (9 bp):
AACGGGGAA
Found at i:12303072 original size:21 final size:21
Alignment explanation
Indices: 12303046--12303109 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
12303036 CTGGGTCGAT
*
12303046 ACCAGTACCAAGAGTAAGAAG
1 ACCAGTACCAAGAGTAAGAAA
12303067 ACCAGTACCAAGAGTAAGAAA
1 ACCAGTACCAAGAGTAAGAAA
12303088 ACCAGTACCAAGAGTAAGAAA
1 ACCAGTACCAAGAGTAAGAAA
12303109 A
1 A
12303110 ATATTAAGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.52, C:0.19, G:0.20, T:0.09
Consensus pattern (21 bp):
ACCAGTACCAAGAGTAAGAAA
Found at i:12303382 original size:24 final size:24
Alignment explanation
Indices: 12303355--12303874 Score: 386
Period size: 24 Copynumber: 23.0 Consensus size: 24
12303345 AGAAGATTAT
*
12303355 GGTAAATCATCCAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
*
12303379 GGTAAATCATCCAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
12303403 GGTAAATCATACAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
* ** * ** *
12303427 -G---AT-GTTGAA-GAAGATTAT
1 GGTAAATCATACAATCAAGAAAAA
*
12303445 GGTAAATCATCCAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
*
12303469 GGTAAATCATCCAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
12303493 GGTAAATCATACAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
* ** * ** *
12303517 -G---AT-GTTGAA-GAAGATTAT
1 GGTAAATCATACAATCAAGAAAAA
*
12303535 GGTAAATCATACAATGAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
12303559 GGTAAATCATACAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
* ** * ** *
12303583 -G---AT-GTTGAA-GAAGATTAT
1 GGTAAATCATACAATCAAGAAAAA
*
12303601 GGTAAATCATACAATGAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
12303625 GGTAAATCATACAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
* ** * ** *
12303649 -G---AT-GTTGAA-GAAGATTAT
1 GGTAAATCATACAATCAAGAAAAA
*
12303667 GGTAAATCATCCAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
12303691 GGTAAATCATACAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
* ** * ** *
12303715 -G---AT-GTTGAA-GAAGATTAT
1 GGTAAATCATACAATCAAGAAAAA
*
12303733 GGTAAATCATCCAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
12303757 GGTAAATCATACAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
*
12303781 GGTAAATCATCCAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
*
12303805 GGTAAATCATCCAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
*
12303829 GGTAAATC--A-GATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
*
12303850 GGTAAATCAGACAATCAAGAAAAA
1 GGTAAATCATACAATCAAGAAAAA
12303874 G
1 G
12303875 ATGTTGAAGA
Statistics
Matches: 385, Mismatches: 78, Indels: 66
0.73 0.15 0.12
Matches are distributed among these distances:
18 25 0.06
19 20 0.05
20 10 0.03
21 19 0.05
22 10 0.03
23 21 0.05
24 280 0.73
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.19
Consensus pattern (24 bp):
GGTAAATCATACAATCAAGAAAAA
Found at i:12303478 original size:90 final size:90
Alignment explanation
Indices: 12303325--12303583 Score: 491
Period size: 90 Copynumber: 2.9 Consensus size: 90
12303315 CGTTCTCTCA
12303325 AATCAAGAAAAAGATGTTGAAGAAGATTATGGTAAATCATCCAATCAAGAAAAAGGTAAATCATC
1 AATCAAGAAAAAGATGTTGAAGAAGATTATGGTAAATCATCCAATCAAGAAAAAGGTAAATCATC
12303390 CAATCAAGAAAAAGGTAAATCATAC
66 CAATCAAGAAAAAGGTAAATCATAC
12303415 AATCAAGAAAAAGATGTTGAAGAAGATTATGGTAAATCATCCAATCAAGAAAAAGGTAAATCATC
1 AATCAAGAAAAAGATGTTGAAGAAGATTATGGTAAATCATCCAATCAAGAAAAAGGTAAATCATC
12303480 CAATCAAGAAAAAGGTAAATCATAC
66 CAATCAAGAAAAAGGTAAATCATAC
* * *
12303505 AATCAAGAAAAAGATGTTGAAGAAGATTATGGTAAATCATACAATGAAGAAAAAGGTAAATCATA
1 AATCAAGAAAAAGATGTTGAAGAAGATTATGGTAAATCATCCAATCAAGAAAAAGGTAAATCATC
12303570 CAATCAAGAAAAAG
66 CAATCAAGAAAAAG
12303584 ATGTTGAAGA
Statistics
Matches: 166, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 166 1.00
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (90 bp):
AATCAAGAAAAAGATGTTGAAGAAGATTATGGTAAATCATCCAATCAAGAAAAAGGTAAATCATC
CAATCAAGAAAAAGGTAAATCATAC
Found at i:12303539 original size:66 final size:66
Alignment explanation
Indices: 12303469--12303781 Score: 590
Period size: 66 Copynumber: 4.7 Consensus size: 66
12303459 TCAAGAAAAA
12303469 GGTAAATCATCCAATCAAGAAAAAGGTAAATCATACAATCAAGAAAAAGATGTTGAAGAAGATTA
1 GGTAAATCATCCAATCAAGAAAAAGGTAAATCATACAATCAAGAAAAAGATGTTGAAGAAGATTA
12303534 T
66 T
* *
12303535 GGTAAATCATACAATGAAGAAAAAGGTAAATCATACAATCAAGAAAAAGATGTTGAAGAAGATTA
1 GGTAAATCATCCAATCAAGAAAAAGGTAAATCATACAATCAAGAAAAAGATGTTGAAGAAGATTA
12303600 T
66 T
* *
12303601 GGTAAATCATACAATGAAGAAAAAGGTAAATCATACAATCAAGAAAAAGATGTTGAAGAAGATTA
1 GGTAAATCATCCAATCAAGAAAAAGGTAAATCATACAATCAAGAAAAAGATGTTGAAGAAGATTA
12303666 T
66 T
12303667 GGTAAATCATCCAATCAAGAAAAAGGTAAATCATACAATCAAGAAAAAGATGTTGAAGAAGATTA
1 GGTAAATCATCCAATCAAGAAAAAGGTAAATCATACAATCAAGAAAAAGATGTTGAAGAAGATTA
12303732 T
66 T
12303733 GGTAAATCATCCAATCAAGAAAAAGGTAAATCATACAATCAAGAAAAAG
1 GGTAAATCATCCAATCAAGAAAAAGGTAAATCATACAATCAAGAAAAAG
12303782 GTAAATCATC
Statistics
Matches: 243, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 243 1.00
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (66 bp):
GGTAAATCATCCAATCAAGAAAAAGGTAAATCATACAATCAAGAAAAAGATGTTGAAGAAGATTA
T
Found at i:12304304 original size:16 final size:17
Alignment explanation
Indices: 12304274--12304309 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12304264 GAAATTAATC
12304274 AAAGACGCAAAAAAAAA
1 AAAGACGCAAAAAAAAA
12304291 AAAGACGCAAAAAAAAA
1 AAAGACGCAAAAAAAAA
12304308 AA
1 AA
12304310 CTATATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAGACGCAAAAAAAAA
Found at i:12307342 original size:17 final size:17
Alignment explanation
Indices: 12307320--12307353 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12307310 TATCCTTTGT
12307320 ATAGATTCCCATACATG
1 ATAGATTCCCATACATG
12307337 ATAGATTCCCATACATG
1 ATAGATTCCCATACATG
12307354 TATTGCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (17 bp):
ATAGATTCCCATACATG
Found at i:12309331 original size:22 final size:22
Alignment explanation
Indices: 12309306--12309348 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12309296 AAGGTTCCGT
*
12309306 TTTGGTTTAAGTTAAAAGAATA
1 TTTGGTTTAACTTAAAAGAATA
*
12309328 TTTGGTTTGACTTAAAAGAAT
1 TTTGGTTTAACTTAAAAGAAT
12309349 GAGGCCTTTA
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:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (22 bp):
TTTGGTTTAACTTAAAAGAATA
Found at i:12311675 original size:21 final size:21
Alignment explanation
Indices: 12311645--12311687 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12311635 TTTATTTATT
12311645 TATATATTTATATATATAAAA
1 TATATATTTATATATATAAAA
* *
12311666 TATATGTTTATTTATATAAAA
1 TATATATTTATATATATAAAA
12311687 T
1 T
12311688 GTGCTGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATATATTTATATATATAAAA
Found at i:12314492 original size:58 final size:58
Alignment explanation
Indices: 12314397--12314511 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
12314387 TTTGTGATTG
*
12314397 AGCATGTAGGTATGCATTAATGTAAGACATTATAGAACCAAATATTTGTTGAGAACTA
1 AGCATGTAGGTATGCATTAATGTAAGACATTACAGAACCAAATATTTGTTGAGAACTA
* * *
12314455 AGCATGTAGGTATTCATTCATGTAAGACATTACAGAACCAACTATTTGTTGAGAACT
1 AGCATGTAGGTATGCATTAATGTAAGACATTACAGAACCAAATATTTGTTGAGAACT
12314512 TCCTTTTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (58 bp):
AGCATGTAGGTATGCATTAATGTAAGACATTACAGAACCAAATATTTGTTGAGAACTA
Found at i:12319128 original size:19 final size:20
Alignment explanation
Indices: 12319097--12319134 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12319087 TAATGATGCA
12319097 AAAGAATGTTATGA-AATGT
1 AAAGAATGTTATGACAATGT
12319116 AAAG-ATGTCTATGACAATG
1 AAAGAATGT-TATGACAATG
12319135 GATTTTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (20 bp):
AAAGAATGTTATGACAATGT
Found at i:12319501 original size:37 final size:37
Alignment explanation
Indices: 12319440--12319532 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 37
12319430 AATAAGGTTG
* * *
12319440 ACACTACC-AGTAAGATGTGCATGAGATGGAAA-GCAT
1 ACACTACCTATTAAAATGTGAATGAGAT-GAAATGCAT
*
12319476 GCACTACCTATTAAAATGTGAATGAGATGAAATGCAT
1 ACACTACCTATTAAAATGTGAATGAGATGAAATGCAT
* * *
12319513 ATACCACCTGTTAAAATGTG
1 ACACTACCTATTAAAATGTG
12319533 CATAAAATGA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
36 11 0.23
37 36 0.77
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (37 bp):
ACACTACCTATTAAAATGTGAATGAGATGAAATGCAT
Found at i:12326032 original size:174 final size:174
Alignment explanation
Indices: 12325737--12326082 Score: 467
Period size: 174 Copynumber: 2.0 Consensus size: 174
12325727 TTTCTTTTTT
* * **
12325737 TTCCCTCATCTTCTTTCAATCTAAACATAACGTTAGTGTTTATGCTATGGATTGTGTGTCGATCG
1 TTCCCTCATCTTCTTTCAATCTAAACATAACGTTAGAGTTTATACTATGGACAGTGTGTCGATCG
* * * ** *
12325802 GCTAAAGGTCTGTTTATTTGTTGAGTTTGTGTTTAAAGTTTTTATGAAACATTGACAAATTGTTA
66 GCTAAAGGTCTGTTGATCTGTTGAGCTTGTGTTTAAAGTTTCCATAAAACATTGACAAATTGTTA
*** *
12325867 GGGGAAAGTTTGGGATAAACAGGAGGCTTTGGTTAAGATTTTCG
131 GACAAAAATTTGGGATAAACAGGAGGCTTTGGTTAAGATTTTCG
* **
12325911 TTCCCTCATCTTCTTTCAATCTAAACGTAGTGTTAGAGTTTATACTATGGACAGTGTGTCGATCG
1 TTCCCTCATCTTCTTTCAATCTAAACATAACGTTAGAGTTTATACTATGGACAGTGTGTCGATCG
* * *** *
12325976 GCTAAAGGTTTGTTGATCTGTTGGGCTTGTGTTTTTGGTTTCCATAAAATATTGACAAATTGTTA
66 GCTAAAGGTCTGTTGATCTGTTGAGCTTGTGTTTAAAGTTTCCATAAAACATTGACAAATTGTTA
* *
12326041 GACAAAAATTTGGGATAAACGGGAGGCTTTGGTTAAGGTTTT
131 GACAAAAATTTGGGATAAACAGGAGGCTTTGGTTAAGATTTT
12326083 GGACTATTTC
Statistics
Matches: 147, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
174 147 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (174 bp):
TTCCCTCATCTTCTTTCAATCTAAACATAACGTTAGAGTTTATACTATGGACAGTGTGTCGATCG
GCTAAAGGTCTGTTGATCTGTTGAGCTTGTGTTTAAAGTTTCCATAAAACATTGACAAATTGTTA
GACAAAAATTTGGGATAAACAGGAGGCTTTGGTTAAGATTTTCG
Found at i:12333899 original size:18 final size:17
Alignment explanation
Indices: 12333858--12333899 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
12333848 AAATTTTAAA
12333858 ATATAT-TTAAAAATAT
1 ATATATATTAAAAATAT
* *
12333874 TTAAATATTAATAAATAT
1 ATATATATTAA-AAATAT
12333892 ATATATAT
1 ATATATAT
12333900 ATTTTGAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 4 0.20
17 4 0.20
18 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATATTAAAAATAT
Found at i:12342800 original size:54 final size:55
Alignment explanation
Indices: 12342670--12342872 Score: 257
Period size: 55 Copynumber: 3.7 Consensus size: 55
12342660 TATATATTAA
* * *
12342670 AAATGTTATTTTCAATGAAAATTGATACTTTCAACTTTT-TTTAAAATGTTTTTGG
1 AAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTT-AAATGTTTTTGG
* * **
12342725 AAATTTTATTTTTAAAGAAAATTGATACTTTCAACTTTTCCTTAAA-GCATTTGG
1 AAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAATGTTTTTGG
* * * *
12342779 AAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTCCCTAAAATTTTTTTGA
1 AAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAATGTTTTTGG
* * *
12342834 AAATTTTATTTTTAAGAAAAATTGCTACTTTCAACTTTT
1 AAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTT
12342873 TTTCAAAAAT
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
54 48 0.38
55 78 0.61
56 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.47
Consensus pattern (55 bp):
AAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAATGTTTTTGG
Found at i:12342866 original size:109 final size:109
Alignment explanation
Indices: 12342670--12342872 Score: 318
Period size: 109 Copynumber: 1.9 Consensus size: 109
12342660 TATATATTAA
* *** *
12342670 AAATGTTATTTTCAATGAAAATTGATACTTTCAACTTTTTTTAAAATGTTTTTGGAAATTTTATT
1 AAATGTTATTTTCAAGGAAAATTGATACTTTCAACTTTCCCTAAAATGTTTTTGAAAATTTTATT
12342735 TTTAAAGAAAATTGATACTTTCAACTTTTCCTTAAAGCATTTGG
66 TTTAAAGAAAATTGATACTTTCAACTTTTCCTTAAAGCATTTGG
* *
12342779 AAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTCCCTAAAATTTTTTTGAAAATTTTATT
1 AAATGTTATTTTCAAGGAAAATTGATACTTTCAACTTTCCCTAAAATGTTTTTGAAAATTTTATT
*
12342844 TTT-AAGAAAAATTGCTACTTTCAACTTTT
66 TTTAAAG-AAAATTGATACTTTCAACTTTT
12342873 TTTCAAAAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
108 3 0.04
109 82 0.96
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.47
Consensus pattern (109 bp):
AAATGTTATTTTCAAGGAAAATTGATACTTTCAACTTTCCCTAAAATGTTTTTGAAAATTTTATT
TTTAAAGAAAATTGATACTTTCAACTTTTCCTTAAAGCATTTGG
Found at i:12344482 original size:12 final size:13
Alignment explanation
Indices: 12344465--12344497 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12344455 ACCACAATAA
12344465 AAATAAAAA-ATG
1 AAATAAAAATATG
*
12344477 AAATAAAAATTTG
1 AAATAAAAATATG
12344490 AAATAAAA
1 AAATAAAA
12344498 TGAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (13 bp):
AAATAAAAATATG
Found at i:12344674 original size:16 final size:15
Alignment explanation
Indices: 12344653--12344696 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
12344643 AACTCGACAT
*
12344653 TTTTTTTGCTTTTTTA
1 TTTTTTTG-TTGTTTA
12344669 TTTTTTTGTTGTTTA
1 TTTTTTTGTTGTTTA
*
12344684 TTTTTTTTTTGTT
1 TTTTTTTGTTGTT
12344697 AAAATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.05, C:0.02, G:0.09, T:0.84
Consensus pattern (15 bp):
TTTTTTTGTTGTTTA
Found at i:12344693 original size:18 final size:16
Alignment explanation
Indices: 12344652--12344696 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
12344642 CAACTCGACA
*
12344652 TTTTTTTTGCTTTTTT
1 TTTTTTTTGTTTTTTT
*
12344668 ATTTTTTTGTTGTTTATT
1 TTTTTTTTGTT-TTT-TT
12344686 TTTTTTTTGTT
1 TTTTTTTTGTT
12344697 AAAATTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 9 0.38
17 3 0.12
18 12 0.50
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTTTTTTGTTTTTTT
Found at i:12344905 original size:44 final size:44
Alignment explanation
Indices: 12344708--12345461 Score: 908
Period size: 44 Copynumber: 17.5 Consensus size: 44
12344698 AAATTTTGAT
* * *
12344708 CAAAGCTCCTCTAAGTAGAGGCTCAACGATTTTG-AGAAAT--A
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* * * *
12344749 -AATGCTCTTCTAAACAGAGGCTCAAAGACTTTG-AAAAAT--A
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* * *
12344789 -AATGCTCCTCTAAACAGAGGCTTAACGACTTTG---AAA-AAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* * * *
12344828 CAAAGCTCCTTTAATCAGAGGCTCAATGGCTTTGAAAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* * *
12344872 CAAAGCTCCTCTAAGCAGAAGCTCCACGACTTTGGAAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* * * * *
12344916 CAAAGCTCCTTTCAGCAGAGGCTTAACGACTTTGGAAAAGTAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* *
12344960 CAAAGCTCCTCTAATCAGAAGCTCAACGACTTTGAAAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
*
12345004 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* * * *
12345048 CAAAGTTCCTCTAAGCAGAGGTTCAACGACTTTGGAAAAGTAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* ** *
12345092 CAAAGCTCCTCTAATCAGAGGCTCCGCGACTTTGAGAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* *
12345136 CAAAGCTCCTCTAAGCAGAGGCTCAATGAC-TTGAAAAAACAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* * * *
12345179 CAAAGCTCCTCTTAGCAGAGGCTTAACGACTTTGGAAAAGTAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* *
12345223 CAAAGCTCCTCTAATCAGAGGCTCAATGACTTTGAAAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* *
12345267 TAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTTG-AAAAGTAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGAC-TTTGAAAAAATAAA
* * *
12345311 CAAAGCTCTTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAG
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
* * *
12345355 CAAAGCTTCTCTAATCAGAGGCTCAACAACTTTGAAAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
** * * *
12345399 CAAAGCTTTTCTAAGTAGAGGCTCAATGACTTAG-AAAAATAAA
1 CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
12345442 CAAAGCTCCTCTAAGCAGAG
1 CAAAGCTCCTCTAAGCAGAG
12345462 CTCCACAACT
Statistics
Matches: 613, Mismatches: 90, Indels: 18
0.85 0.12 0.02
Matches are distributed among these distances:
38 3 0.00
39 1 0.00
40 90 0.15
43 71 0.12
44 444 0.72
45 4 0.01
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.22
Consensus pattern (44 bp):
CAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAAAAAATAAA
Found at i:12344993 original size:132 final size:132
Alignment explanation
Indices: 12344708--12345461 Score: 1009
Period size: 132 Copynumber: 5.8 Consensus size: 132
12344698 AAATTTTGAT
* * * * *
12344708 CAAAGCTCCTCTAAGT-AGAGGCTCAACGATTTTG-AGAAAT--A-AATGCTCTTCTAAACAGAG
1 CAAAGCTCCTCTAA-TCAGAGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGAG
* * *
12344768 GCTCAAAGACTTT-GAAAAAT--A-AATGCTCCTCTAAACAGAGGCTTAACGACTTT-G-AAA--
65 GCTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTTAACGACTTTGGAAAAGT
12344825 AAA
130 AAA
* * * *
12344828 CAAAGCTCCTTTAATCAGAGGCTCAATGGCTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGAAG
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGAGG
* * *
12344893 CTCCACGACTTTGGAAAAATAAACAAAGCTCCTTTCAGCAGAGGCTTAACGACTTTGGAAAAGTA
66 CTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTTAACGACTTTGGAAAAGTA
12344958 AA
131 AA
*
12344960 CAAAGCTCCTCTAATCAGAAGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGAGG
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGAGG
*
12345025 CTCAACGACTTTGGAAAAATAAACAAAGTTCCTCTAAGCAGAGG-TTCAACGACTTTGGAAAAGT
66 CTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTT-AACGACTTTGGAAAAGT
12345089 AAA
130 AAA
** *
12345092 CAAAGCTCCTCTAATCAGAGGCTCCGCGACTTTGAGAAAATAAACAAAGCTCCTCTAAGCAGAGG
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGAGG
* * * *
12345157 CTCAATGAC-TTGAAAAAACAAACAAAGCTCCTCTTAGCAGAGGCTTAACGACTTTGGAAAAGTA
66 CTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTTAACGACTTTGGAAAAGTA
12345221 AA
131 AA
* *
12345223 CAAAGCTCCTCTAATCAGAGGCTCAATGACTTTGAAAAAATAAATAAAGCTCCTCTAAGCAGAGG
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGAGG
* * * * * * *
12345288 CTCAACGACTTTTGAAAAGTAAACAAAGCTCTTCTAATCAGAGGCTCAACGACTTTGAAAAAATA
66 CTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTTAACGACTTTGGAAAAGTA
*
12345353 AG
131 AA
* * ** *
12345355 CAAAGCTTCTCTAATCAGAGGCTCAACAACTTTGAAAAAATAAACAAAGCTTTTCTAAGTAGAGG
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGAGG
* *
12345420 CTCAATGAC-TTAGAAAAATAAACAAAGCTCCTCTAAGCAGAG
66 CTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAGCAGAG
12345462 CTCCACAACT
Statistics
Matches: 556, Mismatches: 62, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
119 1 0.00
120 28 0.05
121 5 0.01
123 1 0.00
124 26 0.05
125 7 0.01
127 1 0.00
128 28 0.05
129 1 0.00
130 3 0.01
131 149 0.27
132 306 0.55
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.22
Consensus pattern (132 bp):
CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAACAAAGCTCCTCTAAGCAGAGG
CTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTTAACGACTTTGGAAAAGTA
AA
Found at i:12345502 original size:41 final size:42
Alignment explanation
Indices: 12345446--12345534 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
12345436 AATAAACAAA
* * *
12345446 GCTCCTCTAAGCAGA-GCTCCACAACTTTTGAACAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATT
12345487 GCTCCTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATT
*
12345529 ACTCCT
1 GCTCCT
12345535 TGACAATCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 14 0.33
42 29 0.67
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.26
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACAACTTTTGAAAAATAAATT
Found at i:12347105 original size:9 final size:9
Alignment explanation
Indices: 12347082--12347124 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
12347072 TTTGAGTTTT
12347082 TCTTTTTC-
1 TCTTTTTCA
12347090 T-TTTTTCA
1 TCTTTTTCA
12347098 TCTTTTTCA
1 TCTTTTTCA
12347107 TCTTTTTTCA
1 TC-TTTTTCA
*
12347117 TTTTTTTC
1 TCTTTTTC
12347125 TTTTTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
7 6 0.19
8 2 0.06
9 15 0.48
10 8 0.26
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (9 bp):
TCTTTTTCA
Found at i:12347112 original size:19 final size:16
Alignment explanation
Indices: 12347084--12347166 Score: 82
Period size: 16 Copynumber: 5.1 Consensus size: 16
12347074 TGAGTTTTTC
12347084 TTTTTCTTTTTTCATCT
1 TTTTTCTTTTTTCAT-T
12347101 TTTTCATCTTTTTTCATT
1 TTTT--TCTTTTTTCATT
12347119 TTTTTCTTTTTTC-TT
1 TTTTTCTTTTTTCATT
** *
12347134 TCCTT-TTTCTTCATT
1 TTTTTCTTTTTTCATT
12347149 TGTTTT-TTTTTTCATT
1 T-TTTTCTTTTTTCATT
12347165 TT
1 TT
12347167 CTTCATTCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
14 6 0.11
15 9 0.16
16 21 0.38
17 4 0.07
18 5 0.09
19 11 0.20
ACGTcount: A:0.06, C:0.16, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTTCTTTTTTCATT
Done.