Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 21 of 26
Found at i:2929824 original size:24 final size:23
Alignment explanation
Indices: 2929792--2929852 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
2929782 TTATTATTAT
* *
2929792 TTTATAAAAATAAAATTATTTAAA
1 TTTAAAAAAATAAAA-AATTTAAA
2929816 TTTAAAAAAATAAAAAATTTAAA
1 TTTAAAAAAATAAAAAATTTAAA
*
2929839 --AAAAAAAATAAAAA
1 TTTAAAAAAATAAAAA
2929853 TCATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.38
23 7 0.21
24 14 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TTTAAAAAAATAAAAAATTTAAA
Found at i:2929839 original size:16 final size:16
Alignment explanation
Indices: 2929813--2929846 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
2929803 AAAATTATTT
2929813 AAATTTAAAAAAATAAA
1 AAATTTAAAAAAA-AAA
2929830 AAATTTAAAAAAAAAA
1 AAATTTAAAAAAAAAA
2929846 A
1 A
2929847 TAAAAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATTTAAAAAAAAAA
Found at i:2929981 original size:20 final size:21
Alignment explanation
Indices: 2929958--2930000 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2929948 GGATATTTAT
*
2929958 AAAAT-TTTTTATTTTATTAA
1 AAAATATTTTTATTTTAATAA
2929978 AAAATATTTTTATTTTAATAA
1 AAAATATTTTTATTTTAATAA
2929999 AA
1 AA
2930001 TTTTAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATATTTTTATTTTAATAA
Found at i:2930446 original size:36 final size:33
Alignment explanation
Indices: 2930377--2930454 Score: 84
Period size: 36 Copynumber: 2.2 Consensus size: 33
2930367 CATGAATTAA
* ***
2930377 TTAATAATTATTTATTATTTAAATTTTTTAAAT
1 TTAATAATTATTTAATATTTAAATTTAAAAAAT
2930410 TTAATATATTATTATAATATATTAAATTTAAAAAAT
1 TTAATA-ATTATT-TAATAT-TTAAATTTAAAAAAT
2930446 TTAAATAAT
1 TT-AATAAT
2930455 AAATAATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 6 0.16
34 6 0.16
35 5 0.14
36 16 0.43
37 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTAATAATTATTTAATATTTAAATTTAAAAAAT
Found at i:2932993 original size:10 final size:10
Alignment explanation
Indices: 2932978--2933041 Score: 60
Period size: 10 Copynumber: 6.6 Consensus size: 10
2932968 TATATATGTT
2932978 TATGTATATG
1 TATGTATATG
2932988 TATGTATATG
1 TATGTATATG
*
2932998 TATGTACA--
1 TATGTATATG
**
2933006 TATACATATG
1 TATGTATATG
* * *
2933016 TATATATGTT
1 TATGTATATG
2933026 TATGTATATG
1 TATGTATATG
2933036 TATGTA
1 TATGTA
2933042 CATATACATA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
8 5 0.12
10 37 0.88
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (10 bp):
TATGTATATG
Found at i:2933009 original size:38 final size:38
Alignment explanation
Indices: 2932963--2933071 Score: 137
Period size: 38 Copynumber: 2.8 Consensus size: 38
2932953 ATACATATAC
* *
2932963 ACATATATATATGTTTATGTATATGTATGTATATGTATGT
1 ACATATACATATG--TATATATATGTATGTATATGTATGT
* *
2933003 ACATATACATATGTATATATGTTTATGTATATGTATGT
1 ACATATACATATGTATATATATGTATGTATATGTATGT
*
2933041 ACATATACATATGCATATATGTATGTATGTA
1 ACATATACATATG--TATATATATGTATGTA
2933072 CATATACATA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
38 35 0.58
40 25 0.42
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.46
Consensus pattern (38 bp):
ACATATACATATGTATATATATGTATGTATATGTATGT
Found at i:2933066 original size:30 final size:30
Alignment explanation
Indices: 2933032--2933089 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
2933022 TGTTTATGTA
2933032 TATGTATGTACATATACATATGCATATATG
1 TATGTATGTACATATACATATGCATATATG
*
2933062 TATGTATGTACATATACATATGTATATA
1 TATGTATGTACATATACATATGCATATA
2933090 GTGCCAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (30 bp):
TATGTATGTACATATACATATGCATATATG
Found at i:2934560 original size:26 final size:26
Alignment explanation
Indices: 2934531--2934587 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
2934521 CTAAACTAAT
2934531 TAGCAGTTAAAACTCCTACGAAGGTG
1 TAGCAGTTAAAACTCCTACGAAGGTG
**
2934557 TAGCCTTTTAAAACTCCTACGAAGGTG
1 TAG-CAGTTAAAACTCCTACGAAGGTG
2934584 TAGC
1 TAGC
2934588 CTTACTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (26 bp):
TAGCAGTTAAAACTCCTACGAAGGTG
Found at i:2934567 original size:27 final size:27
Alignment explanation
Indices: 2934537--2934590 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2934527 TAATTAGCAG
2934537 TTAAAACTCCTACGAAGGTGTAGCCTT
1 TTAAAACTCCTACGAAGGTGTAGCCTT
2934564 TTAAAACTCCTACGAAGGTGTAGCCTT
1 TTAAAACTCCTACGAAGGTGTAGCCTT
2934591 ACTTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (27 bp):
TTAAAACTCCTACGAAGGTGTAGCCTT
Found at i:2935868 original size:47 final size:47
Alignment explanation
Indices: 2935791--2935882 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 47
2935781 TTTCCTAAGT
* *
2935791 ATCTTTGGAAAATCACATCTCCTTACCTATGTCCAGATATGCATAGG
1 ATCTTTGGAAAATCACATCTCCATACCTATGTCCAAATATGCATAGG
* * *
2935838 ATCTTTGGAGAATCATATCTCCATATCTATGTCCAAATATGCATA
1 ATCTTTGGAAAATCACATCTCCATACCTATGTCCAAATATGCATA
2935883 AGACATGGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.34
Consensus pattern (47 bp):
ATCTTTGGAAAATCACATCTCCATACCTATGTCCAAATATGCATAGG
Found at i:2939652 original size:25 final size:27
Alignment explanation
Indices: 2939602--2939715 Score: 72
Period size: 32 Copynumber: 3.9 Consensus size: 27
2939592 GCATTTTTAT
* *
2939602 TAAAATTATATATTTTATAATTTTAAA
1 TAAAATTATATATTATATAATATTAAA
2939629 TAAAA-TATA-ATTATATAATATTAAAATA
1 TAAAATTATATATTATATAATATT--AA-A
*
2939657 TTAAAATTTATATGTTATA-AATTATTATTATA
1 -TAAAA-TTATATATTATATAA-TATTA--A-A
2939689 TTAAAATTTATATAATTATATAATATT
1 -TAAAA-TTATAT-ATTATATAATATT
2939716 TTAAATGTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 18
0.76 0.04 0.19
Matches are distributed among these distances:
25 11 0.15
26 4 0.06
27 7 0.10
28 1 0.01
29 5 0.07
30 1 0.01
31 6 0.08
32 25 0.35
33 9 0.13
34 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
TAAAATTATATATTATATAATATTAAA
Found at i:2939675 original size:32 final size:33
Alignment explanation
Indices: 2939633--2939715 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
2939623 TTTAAATAAA
2939633 ATATAATTATATAATATTAAAATATTAAAATTT
1 ATATAATTATATAATATTAAAATATTAAAATTT
* **
2939666 ATAT-GTTATA-AATTATTATTATATTAAAATTT
1 ATATAATTATATAA-TATTAAAATATTAAAATTT
2939698 ATATAATTATATAATATT
1 ATATAATTATATAATATT
2939716 TTAAATGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
31 2 0.05
32 26 0.60
33 13 0.30
34 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
ATATAATTATATAATATTAAAATATTAAAATTT
Found at i:2939719 original size:27 final size:25
Alignment explanation
Indices: 2939671--2939720 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
2939661 AATTTATATG
*
2939671 TTATAAATTATTATTATATTAAAAT
1 TTATAAATTATTAATATATTAAAAT
*
2939696 TTATATAATTATATAATATTTTAAA
1 TTATA-AATTAT-TAATATATTAAA
2939721 TGTAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 6 0.29
27 10 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATAAATTATTAATATATTAAAAT
Found at i:2946266 original size:8 final size:8
Alignment explanation
Indices: 2946253--2946288 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
2946243 TAACTGTGAT
2946253 AAAAATAA
1 AAAAATAA
2946261 AAAAAT-A
1 AAAAATAA
2946268 AAAAATAA
1 AAAAATAA
*
2946276 ATAAATAA
1 AAAAATAA
2946284 AAAAA
1 AAAAA
2946289 ACCCTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAATAA
Found at i:2946270 original size:7 final size:7
Alignment explanation
Indices: 2946253--2946287 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
2946243 TAACTGTGAT
2946253 AAAAATAA
1 AAAAAT-A
2946261 AAAAATA
1 AAAAATA
2946268 AAAAATA
1 AAAAATA
2946275 AATAAATA
1 AA-AAATA
2946283 AAAAA
1 AAAAA
2946288 AACCCTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 13 0.50
8 13 0.50
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:2946271 original size:15 final size:15
Alignment explanation
Indices: 2946253--2946287 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2946243 TAACTGTGAT
2946253 AAAAATAAAAAAATA
1 AAAAATAAAAAAATA
*
2946268 AAAAATAAATAAATA
1 AAAAATAAAAAAATA
2946283 AAAAA
1 AAAAA
2946288 AACCCTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:2948949 original size:2 final size:2
Alignment explanation
Indices: 2948942--2948987 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
2948932 AAAGGAGAAA
* * * *
2948942 AT AT AT AT AT AT AT AT AT AT AT TT GT AT TT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2948984 AT AT
1 AT AT
2948988 TAATAATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (2 bp):
AT
Found at i:2949002 original size:24 final size:24
Alignment explanation
Indices: 2948941--2949003 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
2948931 AAAAGGAGAA
* *
2948941 AATATATATATATATATATATATT
1 AATATTTATATTTATATATATATT
**
2948965 TGTATTTATATTTATATATATATT
1 AATATTTATATTTATATATATATT
2948989 AATAATTTAT-TTTAT
1 AAT-ATTTATATTTAT
2949004 TTTATGTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 26 0.81
25 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
AATATTTATATTTATATATATATT
Found at i:2949517 original size:23 final size:23
Alignment explanation
Indices: 2949491--2949550 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
2949481 TGTATTTAAA
2949491 ATATTATATTTTTATTTT-TTTAC
1 ATATTATATTTTTATTTTATTT-C
*
2949514 ATATTA-ATAATTTATTTTATTTC
1 ATATTATAT-TTTTATTTTATTTC
*
2949537 AT-GTATATTTTTAT
1 ATATTATATTTTTAT
2949551 ATGTACATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 9 0.29
23 19 0.61
24 3 0.10
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (23 bp):
ATATTATATTTTTATTTTATTTC
Found at i:2950705 original size:4 final size:4
Alignment explanation
Indices: 2950696--2950722 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2950686 GTCAGTTTAA
2950696 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
2950723 AAAAAGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2950778 original size:25 final size:26
Alignment explanation
Indices: 2950750--2950814 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
2950740 ATGTATTCGT
2950750 ATTTGTATTATTTTTTATAT-TTAA-A
1 ATTT-TATTATTTTTTATATATTAATA
2950775 ATTTTATATATTTTTTATATATTAATA
1 ATTTTAT-TATTTTTTATATATTAATA
*
2950802 ATTTATTTTATTT
1 ATTT-TATTATTT
2950815 CGTGTGTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
24 3 0.09
25 16 0.46
26 4 0.11
27 10 0.29
28 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (26 bp):
ATTTTATTATTTTTTATATATTAATA
Found at i:2951272 original size:26 final size:25
Alignment explanation
Indices: 2951242--2951306 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
2951232 ATTTTATATG
* * *
2951242 ATTAAATTTTAATTTTAAATTTATTT
1 ATTAAATTTTAA-ATAAAATTTATTA
2951268 ATTAAATATTTTAAATAAAATTTATTA
1 ATT-AA-ATTTTAAATAAAATTTATTA
2951295 ATTATAATTTTA
1 ATTA-AATTTTA
2951307 TAAATATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 10 0.30
27 16 0.48
28 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTAAATTTTAAATAAAATTTATTA
Found at i:2951288 original size:27 final size:28
Alignment explanation
Indices: 2951258--2951312 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
2951248 TTTTAATTTT
*
2951258 AAATTTATTTATTA-AATATTT-TAAATA
1 AAATTTATTAATTATAAT-TTTATAAATA
2951285 AAATTTATTAATTATAATTTTATAAATA
1 AAATTTATTAATTATAATTTTATAAATA
2951313 TTAAAATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AAATTTATTAATTATAATTTTATAAATA
Found at i:2951502 original size:31 final size:32
Alignment explanation
Indices: 2951450--2951525 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 32
2951440 ATTTAAAGTG
* * *
2951450 TTTAAAATT-AAATTATTTTATTTTATAATAA
1 TTTAATATTAAAATTATGTTATTATATAATAA
**
2951481 TTTAATATTAAAATT-TGTTATTATATTTTAA
1 TTTAATATTAAAATTATGTTATTATATAATAA
*
2951512 TTTTATCATTAAAA
1 TTTAAT-ATTAAAA
2951526 AGTAATACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 25 0.68
32 12 0.32
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (32 bp):
TTTAATATTAAAATTATGTTATTATATAATAA
Found at i:2952055 original size:2 final size:2
Alignment explanation
Indices: 2952050--2952081 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2952040 GTGTACGTAC
2952050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2952082 TTTCAAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2952197 original size:6 final size:6
Alignment explanation
Indices: 2952186--2952217 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2952176 TTGATTAATT
2952186 AATTTA AATTTA AATTT- AATTT- AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT
2952218 AATAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:2952206 original size:11 final size:11
Alignment explanation
Indices: 2952184--2952217 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2952174 ATTTGATTAA
2952184 TTAATTTAAAT
1 TTAATTTAAAT
2952195 TTAAATTT-AAT
1 TT-AATTTAAAT
2952206 TTAATTTAAAT
1 TTAATTTAAAT
2952217 T
1 T
2952218 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAATTTAAAT
Found at i:2953187 original size:15 final size:14
Alignment explanation
Indices: 2953168--2953206 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2953158 ATTTTAAAAC
*
2953168 TTAAAATAATTTAA
1 TTAAAATAATTCAA
2953182 TCTAAAATAATTCAA
1 T-TAAAATAATTCAA
2953197 TTCAAAATAA
1 TT-AAAATAA
2953207 CTCCGATCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAAATAATTCAA
Found at i:2953691 original size:23 final size:25
Alignment explanation
Indices: 2953645--2953703 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
2953635 CAATTGATAT
*
2953645 TTTTATTTAAATTTAAGTTGATTTTAAAA
1 TTTTATTTAAA-TTAA-TT--TTTAAAAA
2953674 TTTTATTTAAATTAATTTTTAAAAA
1 TTTTATTTAAATTAATTTTTAAAAA
2953699 TTTTA
1 TTTTA
2953704 AATTTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 12 0.41
27 2 0.07
28 4 0.14
29 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTTATTTAAATTAATTTTTAAAAA
Found at i:2954069 original size:26 final size:24
Alignment explanation
Indices: 2954022--2954080 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
2954012 ATTATGATGT
2954022 AATATTAAAAATAAATAAAATTATA
1 AATATTAAAAATAAATAAAATT-TA
** *
2954047 AATATATAAAAATTTATATAATTTA
1 AATAT-TAAAAATAAATAAAATTTA
2954072 AATTATTAA
1 AA-TATTAA
2954081 TATTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATATTAAAAATAAATAAAATTTA
Found at i:2954100 original size:32 final size:33
Alignment explanation
Indices: 2954022--2954102 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 33
2954012 ATTATGATGT
*
2954022 AATATTAAAAATAAATAAAATTATAAATATATAA
1 AATA-TAAAAATAATTAAAATTATAAATATATAA
** * * *
2954056 AA-ATTTATATAATTTAAATTATTAATAT-TAA
1 AATATAAAAATAATTAAAATTATAAATATATAA
2954087 AATATAAAAATAATTA
1 AATATAAAAATAATTA
2954103 TATTTATCTA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
31 5 0.14
32 28 0.78
33 1 0.03
34 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (33 bp):
AATATAAAAATAATTAAAATTATAAATATATAA
Found at i:2954340 original size:20 final size:21
Alignment explanation
Indices: 2954312--2954350 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2954302 ATTATTTTAA
2954312 TAAAAAAATTTA-ATTAATTT
1 TAAAAAAATTTATATTAATTT
2954332 TAAAAAAATTTATATTAAT
1 TAAAAAAATTTATATTAAT
2954351 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAAAAATTTATATTAATTT
Found at i:2954349 original size:25 final size:24
Alignment explanation
Indices: 2954284--2954355 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
2954274 ATTTTTAATA
*
2954284 AATAATAATATATTAATTATTATTTT
1 AATAAAAATATATTAATTA--ATTTT
*
2954310 AATAAAAAAAT-TTAATTAATTTT
1 AATAAAAATATATTAATTAATTTT
*
2954333 AA-AAAAATTTATATTAATAAATT
1 AATAAAAA--TATATTAATTAATT
2954356 AAAATATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.13
23 7 0.18
24 2 0.05
25 16 0.41
26 9 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATAAAAATATATTAATTAATTTT
Found at i:2954350 original size:38 final size:40
Alignment explanation
Indices: 2954303--2954378 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
2954293 ATATTAATTA
*
2954303 TTATTTTAATAAA-AAAAT-TTAATTAATTTTAAAAAAAT
1 TTATATTAATAAATAAAATATTAATTAATTTTAAAAAAAT
* *
2954341 TTATATTAATAAATTAAAATATTTATTATTTTTAAAAA
1 TTATATTAATAAA-TAAAATATTAATTAATTTTAAAAA
2954379 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 12 0.38
40 5 0.16
41 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (40 bp):
TTATATTAATAAATAAAATATTAATTAATTTTAAAAAAAT
Found at i:2954447 original size:131 final size:128
Alignment explanation
Indices: 2954370--2954612 Score: 321
Period size: 128 Copynumber: 1.9 Consensus size: 128
2954360 TATTTATTAT
* **
2954370 TTTTAAAAATAAAAAATAAAAAGGGTTTATTATTATTAGTTTTT-AGTAAAAT-TTAAATAATAT
1 TTTT-AAAATAAAAAATAAAAA-GGTTT-TTATTA-TAATTTTTGA-TAAAATAAAAAATAATAT
* **
2954433 TTAATTAAGTTAAAAAAA-TTACATTAATAAATTAAAATATTAATTATTATTTTTATAAAAATAA
61 TTAATTAAGTTAAAAAAATTTACATTAATAAA-TAAAATATTAATTAATATAATTATAAAAATAA
2954497 AAAA
125 AAAA
2954501 TTTTAAAATAAAAAATAAAAAGGTTTTTATTATAATTTTTGATAAAATAAAAAATAATATTTAAT
1 TTTTAAAATAAAAAATAAAAAGGTTTTTATTATAATTTTTGATAAAATAAAAAATAATATTTAAT
* * *
2954566 TAAGTTTAAAAAATTTACATTAACAAAATAAAATATTAATTATTATA
66 TAAGTTAAAAAAATTTACATTAA-TAAATAAAATATTAATTAATATA
2954613 TTTTTTTTCA
Statistics
Matches: 102, Mismatches: 6, Indels: 10
0.86 0.05 0.08
Matches are distributed among these distances:
127 13 0.13
128 33 0.32
129 32 0.31
130 20 0.20
131 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (128 bp):
TTTTAAAATAAAAAATAAAAAGGTTTTTATTATAATTTTTGATAAAATAAAAAATAATATTTAAT
TAAGTTAAAAAAATTTACATTAATAAATAAAATATTAATTAATATAATTATAAAAATAAAAAA
Found at i:2954601 original size:129 final size:132
Alignment explanation
Indices: 2954370--2954644 Score: 373
Period size: 129 Copynumber: 2.1 Consensus size: 132
2954360 TATTTATTAT
* **
2954370 TTTTAAAAATAAAAAATAAAAAGGGTTTATTATTATTAGTTTTTAGTAAAATTTAAATAATATTT
1 TTTT-AAAATAAAAAATAAAAAGGGTTTATTATTATTAATTTTTAGTAAAATAAAAATAATATTT
* * *
2954435 AATTAAGTTAAAAAAATTACATTAATAAATTAAAATATTAATTA-T-TATTTTTATAAAAATAAA
65 AATTAAGTTAAAAAAATTACATTAACAAAATAAAATATTAATTATTATATTTTTATAAAAACAAA
2954498 AAA
130 AAA
2954501 TTTTAAAATAAAAAATAAAAA-GGTTT-TTATTA-TAATTTTT-GATAAAATAAAAAATAATATT
1 TTTTAAAATAAAAAATAAAAAGGGTTTATTATTATTAATTTTTAG-TAAAAT-AAAAATAATATT
* * **
2954562 TAATTAAGTTTAAAAAATTTACATTAACAAAATAAAATATTAATTATTATATTTTTTTTCAAACA
64 TAATTAAG-TTAAAAAAATTACATTAACAAAATAAAATATTAATTATTATATTTTTATAAAAACA
2954627 AAAAA
128 AAAAA
*
2954632 TTTTAAATTAAAA
1 TTTTAAAATAAAA
2954645 TTTTATTAAT
Statistics
Matches: 128, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
126 1 0.01
127 13 0.10
128 24 0.19
129 39 0.30
130 18 0.14
131 33 0.26
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (132 bp):
TTTTAAAATAAAAAATAAAAAGGGTTTATTATTATTAATTTTTAGTAAAATAAAAATAATATTTA
ATTAAGTTAAAAAAATTACATTAACAAAATAAAATATTAATTATTATATTTTTATAAAAACAAAA
AA
Found at i:2958168 original size:27 final size:28
Alignment explanation
Indices: 2958138--2958213 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
2958128 AAAATAATCA
* *
2958138 TATAAAATAATGATTTATCAAAA-TA-TT
1 TATAAAA-AATTATTTATAAAAACTATTT
2958165 TATAAAAAATTATTT-TAAAAACTATTT
1 TATAAAAAATTATTTATAAAAACTATTT
2958192 TATAAAAAAATTATTTA-AAAAA
1 TAT-AAAAAATTATTTATAAAAA
2958214 TAAAAAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 5 0.12
26 9 0.21
27 12 0.28
28 17 0.40
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (28 bp):
TATAAAAAATTATTTATAAAAACTATTT
Found at i:2958172 original size:12 final size:13
Alignment explanation
Indices: 2958150--2958199 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
2958140 TAAAATAATG
*
2958150 ATTTATCAAAA-T
1 ATTTATAAAAACT
*
2958162 ATTTATAAAAAATT
1 ATTTAT-AAAAACT
2958176 ATTT-TAAAAACT
1 ATTTATAAAAACT
2958188 ATTTTATAAAAA
1 A-TTTATAAAAA
2958200 AATTATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 13 0.41
13 8 0.25
14 11 0.34
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTTATAAAAACT
Found at i:2958183 original size:13 final size:13
Alignment explanation
Indices: 2958157--2958214 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
2958147 ATGATTTATC
2958157 AAAA-TATTTATAA
1 AAAATTATTT-TAA
2958170 AAAATTATTTTAA
1 AAAATTATTTTAA
*
2958183 AAACTATT-TTATAAA
1 AAA--ATTATT-TTAA
2958198 AAAATTA-TTTAA
1 AAAATTATTTTAA
2958210 AAAAT
1 AAAAT
2958215 AAAAAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
12 8 0.21
13 14 0.37
14 7 0.18
15 9 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTATTTTAA
Found at i:2958677 original size:6 final size:6
Alignment explanation
Indices: 2958666--2958734 Score: 52
Period size: 6 Copynumber: 11.2 Consensus size: 6
2958656 GTCAGATTGA
* *
2958666 TTAATT TTAATT TTAATT TTAATT TAAAAATT TTAATT AATTAA-T TTAAGT
1 TTAATT TTAATT TTAATT TTAATT T--TAATT TTAATT --TTAATT TTAATT
* *
2958717 TTAAAT TTGA-T TTAATT T
1 TTAATT TTAATT TTAATT T
2958735 AAATAGATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
5 8 0.15
6 34 0.65
7 1 0.02
8 9 0.17
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (6 bp):
TTAATT
Found at i:2958699 original size:20 final size:21
Alignment explanation
Indices: 2958674--2958714 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2958664 GATTAATTTT
2958674 AATTTTAATT-TTAATTTAAA
1 AATTTTAATTATTAATTTAAA
2958694 AATTTTAATTAATTAATTTAA
1 AATTTTAATT-ATTAATTTAA
2958715 GTTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTTAATTATTAATTTAAA
Found at i:2958711 original size:14 final size:14
Alignment explanation
Indices: 2958665--2958712 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2958655 AGTCAGATTG
2958665 ATTAATTTTAATT-
1 ATTAATTTTAATTA
2958678 -TTAATTTTAATTTA
1 ATTAATTTTAA-TTA
*
2958692 A-AAATTTTAATTA
1 ATTAATTTTAATTA
2958705 ATTAATTT
1 ATTAATTT
2958713 AAGTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 10 0.34
13 6 0.21
14 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTAATTTTAATTA
Found at i:2958719 original size:28 final size:26
Alignment explanation
Indices: 2958668--2958721 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
2958658 CAGATTGATT
2958668 AATTTTAATTTTAATTTTAATTTAAA
1 AATTTTAATTTTAATTTTAATTTAAA
2958694 AATTTTAATTAATTAA-TTTAAGTTTAAA
1 AATTTTAATT--TTAATTTTAA-TTTAAA
2958722 TTTGATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 10 0.40
27 5 0.20
28 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
AATTTTAATTTTAATTTTAATTTAAA
Found at i:2958784 original size:22 final size:22
Alignment explanation
Indices: 2958749--2958800 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
2958739 AGATAAAAAA
*
2958749 TTAATAATTCAAAATTGATCG-AT
1 TTAA-AATTCAAAA-TAATCGAAT
*
2958772 TTAAAATTTAAAATAATCGAAT
1 TTAAAATTCAAAATAATCGAAT
2958794 TTAAAAT
1 TTAAAAT
2958801 AATTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 5 0.19
22 17 0.65
23 4 0.15
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (22 bp):
TTAAAATTCAAAATAATCGAAT
Found at i:2958806 original size:32 final size:33
Alignment explanation
Indices: 2958770--2958846 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
2958760 AAATTGATCG
*
2958770 ATTTAAAATTTAAAATAA-TCGAATTTAAAATA
1 ATTTAAAATTTAAAATAACTCAAATTTAAAATA
* *
2958802 ATTT-AAATTTAAAATAACTCAAATTTTAAATG
1 ATTTAAAATTTAAAATAACTCAAATTTAAAATA
*
2958834 A-TCAAAATTTAAA
1 ATTTAAAATTTAAA
2958847 TTAAGTATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 14 0.36
32 25 0.64
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
ATTTAAAATTTAAAATAACTCAAATTTAAAATA
Found at i:2958812 original size:16 final size:16
Alignment explanation
Indices: 2958775--2958846 Score: 76
Period size: 16 Copynumber: 4.6 Consensus size: 16
2958765 GATCGATTTA
2958775 AAATTTAAAATAA-TC
1 AAATTTAAAATAATTC
* *
2958790 GAATTTAAAATAATTT
1 AAATTTAAAATAATTC
*
2958806 AAATTTAAAATAACTC
1 AAATTTAAAATAATTC
* *
2958822 AAATTTTAAATGA-TC
1 AAATTTAAAATAATTC
2958837 AAAATTTAAA
1 -AAATTTAAA
2958847 TTAAGTATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
15 14 0.30
16 33 0.70
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATTTAAAATAATTC
Found at i:2958847 original size:15 final size:16
Alignment explanation
Indices: 2958806--2958847 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2958796 AAAATAATTT
2958806 AAATTTAAAATAACTCA
1 AAATTT-AAATAACTCA
* *
2958823 AATTTTAAATGA-TCA
1 AAATTTAAATAACTCA
2958838 AAATTTAAAT
1 AAATTTAAAT
2958848 TAAGTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 5 0.23
17 5 0.23
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (16 bp):
AAATTTAAATAACTCA
Found at i:2959725 original size:26 final size:27
Alignment explanation
Indices: 2959668--2959725 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
2959658 TAACTCGAAT
* *
2959668 CTAAAATGATTTAAACTTAAAAATAAT
1 CTAAAATGATTTAAAATTAAAAATAAC
* * *
2959695 TTAAAAT-TTTTAAAATTTAAAATAAC
1 CTAAAATGATTTAAAATTAAAAATAAC
2959721 CTAAA
1 CTAAA
2959726 CTAAAATTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (27 bp):
CTAAAATGATTTAAAATTAAAAATAAC
Found at i:2959748 original size:15 final size:16
Alignment explanation
Indices: 2959730--2959759 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2959720 CCTAAACTAA
2959730 AATTTAAAA-TAATTT
1 AATTTAAAATTAATTT
2959745 AATTTAAAATTAATT
1 AATTTAAAATTAATT
2959760 CGATTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAAAATTAATTT
Found at i:2959752 original size:22 final size:22
Alignment explanation
Indices: 2959676--2959755 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
2959666 ATCTAAAATG
* *
2959676 ATTTAAACTTAAAAATAATTTAAA
1 ATTTAAAATTTAAAATAATTT--A
**
2959700 ATTTTTAAAATTTAAAATAACCTA
1 A--TTTAAAATTTAAAATAATTTA
**
2959724 AACTAAAATTTAAAATAATTTA
1 ATTTAAAATTTAAAATAATTTA
2959746 ATTTAAAATT
1 ATTTAAAATT
2959756 AATTCGATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
22 25 0.57
24 3 0.07
26 16 0.36
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTAAAATTTAAAATAATTTA
Found at i:2964656 original size:25 final size:24
Alignment explanation
Indices: 2964628--2964694 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
2964618 TCTCAATTTA
*
2964628 ATAATATTAAATTAAATAAAATTAT
1 ATAATATGAAA-TAAATAAAATTAT
* *
2964653 ATAAATATGATATAAATAATATTAT
1 AT-AATATGAAATAAATAAAATTAT
2964678 ATAAATAT-AATATAAAT
1 AT-AATATGAA-ATAAAT
2964695 TATTAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.03
25 28 0.78
26 7 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (24 bp):
ATAATATGAAATAAATAAAATTAT
Found at i:2964667 original size:11 final size:11
Alignment explanation
Indices: 2964628--2964755 Score: 83
Period size: 11 Copynumber: 11.7 Consensus size: 11
2964618 TCTCAATTTA
2964628 ATAATATTAAAT
1 ATAATA-TAAAT
2964640 -TAA-ATAAA-
1 ATAATATAAAT
*
2964648 ATTATATAAAT
1 ATAATATAAAT
*
2964659 ATGATATAAAT
1 ATAATATAAAT
2964670 AATATTATATAAAT
1 -ATA--ATATAAAT
2964684 ATAATATAAATT
1 ATAATATAAA-T
2964696 ATTAATATAAAT
1 A-TAATATAAAT
*
2964708 ATAAT-T-ATT
1 ATAATATAAAT
2964717 AT-ATAATAAAT
1 ATAAT-ATAAAT
* *
2964728 -T-TTATTAAT
1 ATAATATAAAT
2964737 ATAATATAAAT
1 ATAATATAAAT
*
2964748 ATTATATA
1 ATAATATA
2964756 TAACATGAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 27
0.72 0.08 0.21
Matches are distributed among these distances:
8 2 0.02
9 15 0.16
10 11 0.12
11 39 0.42
12 6 0.06
13 12 0.13
14 8 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:2964669 original size:20 final size:22
Alignment explanation
Indices: 2964635--2964722 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 22
2964625 TTAATAATAT
2964635 TAAAT-TAAAT-A-AAATTATA
1 TAAATATAAATAATAAATTATA
*
2964654 TAAATATGATATAAATAATATTATA
1 TAAATAT-AAAT-AATAA-ATTATA
2964679 TAAATAT-AAT-ATAAATTAT-
1 TAAATATAAATAATAAATTATA
2964698 T-AATATAAAT-ATAATTATTATA
1 TAAATATAAATAATAA--ATTATA
2964720 TAA
1 TAA
2964723 TAAATTTTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
18 5 0.09
19 13 0.23
20 6 0.11
21 12 0.21
22 1 0.02
23 4 0.07
24 2 0.04
25 13 0.23
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
TAAATATAAATAATAAATTATA
Found at i:2964687 original size:6 final size:6
Alignment explanation
Indices: 2964651--2964711 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
2964641 AAATAAAATT
* * *
2964651 ATATAA ATAT-G ATATAA ATAATATT ATATAA ATAT-A ATATAA ATTATTA
1 ATATAA ATATAA ATATAA AT-ATA-A ATATAA ATATAA ATATAA A-TATAA
2964700 ATATAA ATATAA
1 ATATAA ATATAA
2964712 TTATTATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
5 9 0.20
6 22 0.50
7 11 0.25
8 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:2964701 original size:13 final size:13
Alignment explanation
Indices: 2964662--2964707 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
2964652 TATAAATATG
2964662 ATATAAATAATATT-
1 ATATAAAT--TATTA
2964676 ATATAAA-TA-TA
1 ATATAAATTATTA
2964687 ATATAAATTATTA
1 ATATAAATTATTA
2964700 ATATAAAT
1 ATATAAAT
2964708 ATAATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 9 0.31
12 2 0.07
13 10 0.34
14 7 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATAAATTATTA
Found at i:2964709 original size:35 final size:35
Alignment explanation
Indices: 2964629--2964740 Score: 83
Period size: 35 Copynumber: 3.2 Consensus size: 35
2964619 CTCAATTTAA
* * *
2964629 TAATATTAA-ATTAAATAAA-ATTATATAAATATGAT
1 TAATATAAATATTATATAAATATAATATAAAT-T-AT
2964664 ATAA-AT-AATATTATATAAATATAATATAAATTAT
1 -TAATATAAATATTATATAAATATAATATAAATTAT
* * *
2964698 TAATATAAATATAAT-TATTATATAATA-AATTTTAT
1 TAATATAAATATTATATA-AATATAATATAA-ATTAT
2964733 TAATATAA
1 TAATATAA
2964741 TATAAATATT
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
33 3 0.05
34 10 0.15
35 39 0.60
36 13 0.20
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (35 bp):
TAATATAAATATTATATAAATATAATATAAATTAT
Found at i:2964710 original size:55 final size:53
Alignment explanation
Indices: 2964651--2964758 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 53
2964641 AAATAAAATT
2964651 ATATAAATATGATATAAATAATATTATATAAATATAATATAAATTATTA-ATATAA
1 ATATAAATATGATAT-AATAA-ATTATATAAATATAATATAAA-TATTATATATAA
* * * *
2964706 ATATAATTATTATATAATAAATTTTATTAATATAATATAAATATTATATATAA
1 ATATAAATATGATATAATAAATTATATAAATATAATATAAATATTATATATAA
2964759 CATGAATAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
52 5 0.10
53 25 0.52
54 5 0.10
55 13 0.27
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (53 bp):
ATATAAATATGATATAATAAATTATATAAATATAATATAAATATTATATATAA
Found at i:2964719 original size:15 final size:15
Alignment explanation
Indices: 2964688--2964741 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
2964678 ATAAATATAA
*
2964688 TATAAAT-T-ATTAA
1 TATAAATATAATTAT
2964701 TATAAATATAATTAT
1 TATAAATATAATTAT
2964716 TATATAATA-AATT-T
1 TATA-AATATAATTAT
*
2964730 TATTAATATAAT
1 TATAAATATAAT
2964742 ATAAATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 11 0.31
14 8 0.23
15 12 0.34
16 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAAATATAATTAT
Found at i:2964766 original size:18 final size:17
Alignment explanation
Indices: 2964676--2964766 Score: 55
Period size: 18 Copynumber: 5.2 Consensus size: 17
2964666 AAATAATATT
* *
2964676 ATATAAATATAATATAA
1 ATATTAATATAACATAA
2964693 ATTATTAATATAA-ATATA
1 A-TATTAATATAACATA-A
2964711 ATTATT-ATAT-A-ATAA
1 A-TATTAATATAACATAA
*
2964726 ATTTTATTAATATAATATAA
1 A---TATTAATATAACATAA
*
2964746 ATATTATATATAACATGA
1 ATATTA-ATATAACATAA
2964764 ATA
1 ATA
2964767 GTCTAAGTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
15 2 0.03
16 4 0.06
17 18 0.29
18 33 0.52
19 1 0.02
20 5 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
ATATTAATATAACATAA
Found at i:2965263 original size:12 final size:13
Alignment explanation
Indices: 2965229--2965267 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
2965219 GTAATTTGTA
2965229 TATTTATATATTATT
1 TATTTATATA--ATT
2965244 TATTTATATAATT
1 TATTTATATAATT
2965257 T-TTTATATAAT
1 TATTTATATAAT
2965268 GATTGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.42
13 4 0.17
15 10 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTATATAATT
Found at i:2968966 original size:10 final size:10
Alignment explanation
Indices: 2968951--2969003 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
2968941 ATAAAGTAAA
2968951 TATTAAAATT
1 TATTAAAATT
2968961 TATTAAAATT
1 TATTAAAATT
2968971 TAATTAAAATT
1 T-ATTAAAATT
*
2968982 TATTTAAA--
1 TATTAAAATT
*
2968990 TATTAAAATA
1 TATTAAAATT
2969000 TATT
1 TATT
2969004 TTAAAATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 7 0.18
10 21 0.55
11 10 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TATTAAAATT
Found at i:2968976 original size:21 final size:22
Alignment explanation
Indices: 2968952--2968995 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2968942 TAAAGTAAAT
2968952 ATTAAAATTTATTAAAAT-TTA
1 ATTAAAATTTATTAAAATATTA
*
2968973 ATTAAAATTTATTTAAATATTA
1 ATTAAAATTTATTAAAATATTA
2968995 A
1 A
2968996 AATATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAAAATTTATTAAAATATTA
Found at i:2968978 original size:11 final size:11
Alignment explanation
Indices: 2968952--2968989 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
2968942 TAAAGTAAAT
2968952 ATTAAAATTT-
1 ATTAAAATTTA
2968962 ATTAAAATTTA
1 ATTAAAATTTA
2968973 ATTAAAATTTA
1 ATTAAAATTTA
*
2968984 TTTAAA
1 ATTAAA
2968990 TATTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTAAAATTTA
Found at i:2968996 original size:18 final size:18
Alignment explanation
Indices: 2968947--2969013 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 18
2968937 TCTGATAAAG
2968947 TAAATATTAAAATTTATT
1 TAAATATTAAAATTTATT
*
2968965 AAAATTTAATTAAAATTTATT
1 TAAA--T-ATTAAAATTTATT
*
2968986 TAAATATTAAAATATATTT
1 TAAATATTAAAATTTA-TT
2969005 TAAA-ATTAA
1 TAAATATTAA
2969014 TTTTATCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 18 0.43
19 7 0.17
20 1 0.02
21 16 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAATATTAAAATTTATT
Found at i:2974183 original size:20 final size:20
Alignment explanation
Indices: 2974160--2974206 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2974150 TATTAAATAT
2974160 AATATAAATA-AAATAATTAA
1 AATA-AAATATAAATAATTAA
*
2974180 AATAAAATATAAATTATTAA
1 AATAAAATATAAATAATTAA
*
2974200 TATAAAA
1 AATAAAA
2974207 CGTAATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAAATATAAATAATTAA
Found at i:2974188 original size:25 final size:23
Alignment explanation
Indices: 2974146--2974193 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
2974136 AGAAAGTTTA
*
2974146 AAAATATTAAATATAATATAAAT
1 AAAATATTAAATAAAATATAAAT
2974169 AAAATAATTAAAATAAAATATAAAT
1 AAAAT-ATT-AAATAAAATATAAAT
2974194 TATTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 3 0.14
25 14 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATATTAAATAAAATATAAAT
Found at i:2979236 original size:26 final size:26
Alignment explanation
Indices: 2979181--2979236 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
2979171 TACAAATCAA
* *
2979181 AAAGTTTGGCAAAAAAATGACAGAAG
1 AAAGTTTGGCAAAAAAATGACAAAAC
2979207 AAAGTTTGGCAAAAAAA-GACAAAAAC
1 AAAGTTTGGCAAAAAAATGAC-AAAAC
2979233 AAAG
1 AAAG
2979237 GTAGGTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.59, C:0.09, G:0.20, T:0.12
Consensus pattern (26 bp):
AAAGTTTGGCAAAAAAATGACAAAAC
Found at i:2980849 original size:19 final size:19
Alignment explanation
Indices: 2980822--2980859 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2980812 TTCTGCACTT
*
2980822 CTTTCTTTTTCTTTTCTAG
1 CTTTATTTTTCTTTTCTAG
*
2980841 CTTTATTTTTTTTTTCTAG
1 CTTTATTTTTCTTTTCTAG
2980860 GAGGAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.71
Consensus pattern (19 bp):
CTTTATTTTTCTTTTCTAG
Found at i:2983186 original size:3 final size:3
Alignment explanation
Indices: 2983178--2983220 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2983168 TATATAAGAA
2983178 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2983221 GCAAAAGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2989307 original size:34 final size:34
Alignment explanation
Indices: 2989269--2989336 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
2989259 AAGAAAAAGT
2989269 AAAAATGTAGAGCATCAGAAGCAAACTTACAAAA
1 AAAAATGTAGAGCATCAGAAGCAAACTTACAAAA
2989303 AAAAATGTAGAGCATCAGAAGCAAACTTACAAAA
1 AAAAATGTAGAGCATCAGAAGCAAACTTACAAAA
2989337 TCTGCTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (34 bp):
AAAAATGTAGAGCATCAGAAGCAAACTTACAAAA
Found at i:2991902 original size:31 final size:30
Alignment explanation
Indices: 2991867--2991955 Score: 83
Period size: 34 Copynumber: 2.8 Consensus size: 30
2991857 TTTTTTAATA
2991867 ATTTAAATTATTATTTATATAATAATTTTTT
1 ATTTAAATTATTATTTATA-AATAATTTTTT
* *
2991898 ATTTAAATTTAATATTTAATAAAAATATTTTTTT
1 ATTTAAA-TTATTATTT-AT--AAATAATTTTTT
*
2991932 ATTTTTAA-TATTATTT-TAAATAAT
1 A-TTTAAATTATTATTTATAAATAAT
2991956 GATATGAATC
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
29 6 0.12
31 8 0.17
32 8 0.17
33 9 0.19
34 11 0.23
35 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTAAATTATTATTTATAAATAATTTTTT
Found at i:2991941 original size:30 final size:32
Alignment explanation
Indices: 2991867--2991943 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
2991857 TTTTTTAATA
* * *
2991867 ATTTAAA-TTATTATTTATATAATAATTTTTT
1 ATTTAAATTTAATATTTATATAAAAATATTTT
2991898 ATTTAAATTTAATATTTA-ATAAAAATATTTT
1 ATTTAAATTTAATATTTATATAAAAATATTTT
**
2991929 -TTTATTTTTAATATT
1 ATTTAAATTTAATATT
2991944 ATTTTAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 13 0.32
31 18 0.45
32 9 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTTAAATTTAATATTTATATAAAAATATTTT
Found at i:2992024 original size:20 final size:20
Alignment explanation
Indices: 2991976--2992024 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2991966 AAAAATTAAT
2991976 ATAATTTAA-ATTTAAATTA
1 ATAATTTAATATTTAAATTA
** **
2991995 ATAAAATAATATTTTTATTA
1 ATAATTTAATATTTAAATTA
2992015 ATAATTTAAT
1 ATAATTTAAT
2992025 TTAATTTATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAATTTAATATTTAAATTA
Found at i:2992273 original size:34 final size:33
Alignment explanation
Indices: 2992210--2992302 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
2992200 ATATTATAAT
**
2992210 TTATATAA-TTTTTTATACGTTAATAATTTATA
1 TTATATAATTTTTTTATATATTAATAATTTATA
*
2992242 TTATATAATTTTTTTATATATTTATATATTTATA
1 TTATATAATTTTTTTATATATTAATA-ATTTATA
* * *
2992276 ATATGTTGATTTTTTTATTATATTAAT
1 TTAT-ATAATTTTTTTA-TATATTAAT
2992303 TTTAGCTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 8 0.16
33 14 0.28
34 10 0.20
35 10 0.20
36 8 0.16
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (33 bp):
TTATATAATTTTTTTATATATTAATAATTTATA
Found at i:2992292 original size:19 final size:16
Alignment explanation
Indices: 2992249--2992305 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 16
2992239 ATATTATATA
2992249 ATTTTTTTATATATTT
1 ATTTTTTTATATATTT
* *
2992265 ATATATTTATAATATGTT
1 ATTTTTTTAT-ATAT-TT
*
2992283 GATTTTTTTATTATATTA
1 -ATTTTTTTA-TATATTT
2992301 ATTTT
1 ATTTT
2992306 AGCTAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 8 0.25
17 9 0.28
18 3 0.09
19 11 0.34
20 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (16 bp):
ATTTTTTTATATATTT
Found at i:2992961 original size:24 final size:24
Alignment explanation
Indices: 2992914--2992962 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2992904 CAAAGATAAT
*
2992914 AAATTTTAAATATATTTTTTATTA
1 AAATTTTAAATATATTTTTGATTA
*
2992938 AAATTTTAGAT-TATATTTTGATTA
1 AAATTTTAAATATAT-TTTTGATTA
2992962 A
1 A
2992963 CATATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
AAATTTTAAATATATTTTTGATTA
Found at i:2994528 original size:2 final size:2
Alignment explanation
Indices: 2994521--2994550 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2994511 TTTCTGCTGT
2994521 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2994551 CGCCTCGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3000312 original size:28 final size:28
Alignment explanation
Indices: 3000268--3000341 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
3000258 ATTGCCTTCT
*
3000268 GTATTAAGTACATATTGTTTTGTTCATA
1 GTATTAAGTACAAATTGTTTTGTTCATA
*
3000296 GTATTAAGTCCAAATTGTTTTGTTCATA
1 GTATTAAGTACAAATTGTTTTGTTCATA
3000324 GTATTAAGTACAAATTGT
1 GTATTAAGTACAAATTGT
3000342 AGTTTATTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (28 bp):
GTATTAAGTACAAATTGTTTTGTTCATA
Found at i:3000572 original size:2 final size:2
Alignment explanation
Indices: 3000565--3000602 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3000555 CAAACATGAA
*
3000565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3000603 TTTGTTCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3000858 original size:28 final size:29
Alignment explanation
Indices: 3000800--3000858 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
3000790 AAATATGGTA
*
3000800 AAATTATATTACAAATATAATATATAAAT
1 AAATTATATTACAAATATAATAAATAAAT
* *
3000829 AAATT-TATTA-AAATTTATATAAATATAT
1 AAATTATATTACAAATATA-ATAAATAAAT
3000857 AA
1 AA
3000859 TATACTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 15 0.58
29 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AAATTATATTACAAATATAATAAATAAAT
Found at i:3003782 original size:14 final size:12
Alignment explanation
Indices: 3003750--3003774 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3003740 TATATCAATT
3003750 TTTATTTTTTAA
1 TTTATTTTTTAA
3003762 TTTATTTTTTAA
1 TTTATTTTTTAA
3003774 T
1 T
3003775 ATATATTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTTTAA
Found at i:3007573 original size:95 final size:94
Alignment explanation
Indices: 3007417--3007593 Score: 318
Period size: 95 Copynumber: 1.9 Consensus size: 94
3007407 AGCTGACTTA
3007417 ATGGTCTTGAACAGGCTGTCATCTGTTCTGGGCTGCTGACAGGAAGGCCATGGCCAGGAGGATTT
1 ATGGTCTTGAACAGGCTGTCATCTGTTCTGGGCTGCTGACAGGAAGGCCATGGCCAGGAGGATTT
*
3007482 TGCTTGAAAGCTGTTCTTTAAGCCGAGTCG
66 TGCTTGAAA-CCGTTCTTTAAGCCGAGTCG
* *
3007512 ATGGTCTTGAGCAGGCTGTCATCTGTTCTGGGCTGCTGACAGGAAGGCCATGGCCATGAGGATTT
1 ATGGTCTTGAACAGGCTGTCATCTGTTCTGGGCTGCTGACAGGAAGGCCATGGCCAGGAGGATTT
3007577 TGCTTGAAACCGTTCTT
66 TGCTTGAAACCGTTCTT
3007594 GCAGTTAGAG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
94 7 0.09
95 72 0.91
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.29
Consensus pattern (94 bp):
ATGGTCTTGAACAGGCTGTCATCTGTTCTGGGCTGCTGACAGGAAGGCCATGGCCAGGAGGATTT
TGCTTGAAACCGTTCTTTAAGCCGAGTCG
Found at i:3011439 original size:16 final size:16
Alignment explanation
Indices: 3011418--3011448 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3011408 CCAGGCCCCT
3011418 GGTTTTCAGTGATTCA
1 GGTTTTCAGTGATTCA
3011434 GGTTTTCAGTGATTC
1 GGTTTTCAGTGATTC
3011449 CAACTGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.13, G:0.26, T:0.45
Consensus pattern (16 bp):
GGTTTTCAGTGATTCA
Found at i:3016697 original size:2 final size:2
Alignment explanation
Indices: 3016690--3016727 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3016680 TTGGTCAGAA
* *
3016690 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3016728 TTGAGGTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3017334 original size:34 final size:33
Alignment explanation
Indices: 3017283--3017350 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
3017273 TTATTATTTT
**
3017283 ATTATAAAAATTGTA-TTTAAAATTAATTTATAAA
1 ATTATAAAAATAATATTTTAAAATT-A-TTATAAA
*
3017317 ATTATAAAAATAATATTTTAATATTATTATAAA
1 ATTATAAAAATAATATTTTAAAATTATTATAAA
3017350 A
1 A
3017351 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 8 0.27
34 14 0.47
35 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (33 bp):
ATTATAAAAATAATATTTTAAAATTATTATAAA
Found at i:3017342 original size:22 final size:21
Alignment explanation
Indices: 3017296--3017343 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
3017286 ATAAAAATTG
*
3017296 TATT-TAAAATTAATTTATAA
1 TATTATAAAAATAATTTATAA
* *
3017316 AATTATAAAAATAATATTTTAA
1 TATTATAAAAATAAT-TTATAA
3017338 TATTAT
1 TATTAT
3017344 TATAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 9 0.41
22 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTATAAAAATAATTTATAA
Found at i:3020285 original size:2 final size:2
Alignment explanation
Indices: 3020278--3020311 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3020268 TTAATTCGAA
3020278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3020312 CTTCGATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3021754 original size:14 final size:15
Alignment explanation
Indices: 3021735--3021787 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 15
3021725 AAATAATTTT
3021735 ATTATTATTTAA-AA
1 ATTATTATTTAATAA
*
3021749 ATTATTTATTTAATAT
1 ATTA-TTATTTAATAA
*
3021765 ATTATT-TTTATTAA
1 ATTATTATTTAATAA
3021779 ATTAATTAT
1 ATT-ATTAT
3021788 ATTTTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 13 0.41
15 13 0.41
16 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTTAATAA
Found at i:3021774 original size:18 final size:18
Alignment explanation
Indices: 3021733--3021797 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
3021723 AAAAATAATT
* *
3021733 TTATTATTATTTAA-AAA
1 TTATTTTTATTTAATATA
3021750 TTA--TTTATTTAATATA
1 TTATTTTTATTTAATATA
*
3021766 TTATTTTTATTAAAT-TAA
1 TTATTTTTATTTAATAT-A
*
3021784 TTATATTT-TTTAAT
1 TTATTTTTATTTAAT
3021798 TAAAATAACT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
15 8 0.21
16 5 0.13
17 9 0.23
18 17 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTTATTTAATATA
Found at i:3021803 original size:23 final size:22
Alignment explanation
Indices: 3021758--3021801 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3021748 AATTATTTAT
*
3021758 TTAATATATTATTTTTATTAAA
1 TTAATATATTATTTTAATTAAA
3021780 TTAATTATATT-TTTTAATTAAA
1 TTAA-TATATTATTTTAATTAAA
3021802 ATAACTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAATATATTATTTTAATTAAA
Found at i:3021954 original size:19 final size:20
Alignment explanation
Indices: 3021914--3021971 Score: 91
Period size: 19 Copynumber: 2.9 Consensus size: 20
3021904 ATATTATTCC
3021914 AATTTATTTAAAATAATAAATA
1 AATTTATTTAAAAT--TAAATA
3021936 AATTTATTT-AAATTAAATA
1 AATTTATTTAAAATTAAATA
3021955 AATTTATTTAAAATTAA
1 AATTTATTTAAAATTAA
3021972 GTTAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.43
20 7 0.20
21 4 0.11
22 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTATTTAAAATTAAATA
Found at i:3021998 original size:42 final size:41
Alignment explanation
Indices: 3021914--3022024 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 41
3021904 ATATTATTCC
*
3021914 AATTTATTTAAAATAATAAATAAATTTATTTAAATTAAATA
1 AATTTATTTAAAATAATAAATAAATTTATTTAAAATAAATA
3021955 AATTTATTTAAAATTAAGTTAAA-AAA-TTATTTATAAAT-AATA
1 AATTTATTTAAAA-TAA--TAAATAAATTTATTTA-AAATAAATA
** * *
3021997 AATAAATTTTAAATAAATAAATCAATTT
1 AATTTATTTAAAAT-AATAAATAAATTT
3022025 TAATTACTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
40 4 0.07
41 16 0.28
42 28 0.48
43 6 0.10
44 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (41 bp):
AATTTATTTAAAATAATAAATAAATTTATTTAAAATAAATA
Found at i:3022015 original size:19 final size:18
Alignment explanation
Indices: 3021983--3022027 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
3021973 TTAAAAAATT
3021983 ATTTATAAATAATAAATAA
1 ATTT-TAAATAATAAATAA
*
3022002 ATTTTAAATAAATAAATCA
1 ATTTTAAAT-AATAAATAA
3022021 ATTTTAA
1 ATTTTAA
3022028 TTACTATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTTAAATAATAAATAA
Found at i:3027307 original size:2 final size:2
Alignment explanation
Indices: 3027300--3027338 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
3027290 ACACAACTTC
* *
3027300 AT AT AT AT AG AT AT AT AT TT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3027339 TAAGGTGAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3028074 original size:3 final size:3
Alignment explanation
Indices: 3028066--3028098 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3028056 AGACAATATA
3028066 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3028099 ATAACCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3028426 original size:17 final size:16
Alignment explanation
Indices: 3028406--3028457 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
3028396 TAAATTTTAA
3028406 TTTATTAATAATTTATT
1 TTTATTAAT-ATTTATT
*
3028423 TTTATAAATATTAATATT
1 TTTATTAATATT--TATT
3028441 TTTATT-ATATTTATT
1 TTTATTAATATTTATT
3028456 TT
1 TT
3028458 ATTTTTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 6 0.19
16 3 0.10
17 13 0.42
18 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTAATATTTATT
Found at i:3028442 original size:18 final size:18
Alignment explanation
Indices: 3028419--3028485 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
3028409 ATTAATAATT
3028419 TATTTTTATAAATATTAA
1 TATTTTTATAAATATTAA
* *
3028437 TATTTTTAT-TATATTTATTT
1 TATTTTTATAAATA-TTA--A
3028457 TATTTTTATAACATATT-A
1 TATTTTTATAA-ATATTAA
*
3028475 TATTTTAATAA
1 TATTTTTATAA
3028486 TTTTTTTTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 3 0.08
18 22 0.56
20 9 0.23
21 2 0.05
22 3 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTTATAAATATTAA
Found at i:3028475 original size:21 final size:20
Alignment explanation
Indices: 3028417--3028475 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 20
3028407 TTATTAATAA
3028417 TTTATTTTTATAAATATTA-
1 TTTATTTTTATAAATATTAT
* *
3028436 -ATATTTTTAT-TATATTTAT
1 TTTATTTTTATAAATA-TTAT
3028455 TTTATTTTTATAACATATTAT
1 TTTATTTTTATAA-ATATTAT
3028476 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
17 3 0.10
18 12 0.39
20 9 0.29
21 4 0.13
22 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATTTTTATAAATATTAT
Found at i:3028660 original size:6 final size:6
Alignment explanation
Indices: 3028649--3028681 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3028639 TCGAAGGATT
*
3028649 TTTTTA TTTTTA TTTTTA TTTTCA TTTTT- TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
3028682 CAGAGTCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:3029377 original size:2 final size:2
Alignment explanation
Indices: 3029370--3029399 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3029360 TATTCGTGCA
*
3029370 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3029400 GTCACAGTCA
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:3030222 original size:2 final size:2
Alignment explanation
Indices: 3030215--3030240 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3030205 AATTACCCAA
3030215 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
3030241 TTGTGTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3031475 original size:16 final size:17
Alignment explanation
Indices: 3031447--3031483 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
3031437 TGAATTACTT
3031447 TATTAATTTTTTTAATA
1 TATTAATTTTTTTAATA
3031464 TATTAA-TTTTTTAATA
1 TATTAATTTTTTTAATA
3031480 TATT
1 TATT
3031484 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTAATTTTTTTAATA
Found at i:3031484 original size:29 final size:29
Alignment explanation
Indices: 3031411--3031486 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 29
3031401 ATTAATTTTT
3031411 TTAA-TTTTT-ATATA-TTTTTCAAGATA
1 TTAATTTTTTAATATATTTTTTCAAGATA
* * * * *
3031437 TGAATTACTTTATTA-ATTTTTTTAATATA
1 TTAATT-TTTTAATATATTTTTTCAAGATA
3031466 TTAATTTTTTAATATATTTTT
1 TTAATTTTTTAATATATTTTT
3031487 AAATTTTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
26 3 0.08
27 1 0.03
28 10 0.27
29 23 0.62
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (29 bp):
TTAATTTTTTAATATATTTTTTCAAGATA
Found at i:3031670 original size:8 final size:8
Alignment explanation
Indices: 3031657--3031682 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3031647 ATAAAATTAA
3031657 TTTTAATT
1 TTTTAATT
3031665 TTTTAATT
1 TTTTAATT
3031673 TTTTAATT
1 TTTTAATT
3031681 TT
1 TT
3031683 AATAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTAATT
Found at i:3049320 original size:8 final size:8
Alignment explanation
Indices: 3049307--3049386 Score: 67
Period size: 8 Copynumber: 9.6 Consensus size: 8
3049297 ATATTTATAT
3049307 TATATTTA
1 TATATTTA
3049315 TATATTTA
1 TATATTTA
3049323 TATATATTA
1 TATAT-TTA
3049332 TATATTTA
1 TATATTTA
3049340 TATAAATTTA
1 TAT--ATTTA
*
3049350 TATTAAATTA
1 TA-T-ATTTA
3049360 -ATAATTTA
1 TAT-ATTTA
3049368 TA-A-TTA
1 TATATTTA
*
3049374 TATATTTT
1 TATATTTA
3049382 TATAT
1 TATAT
3049387 GATAATTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
6 5 0.08
7 2 0.03
8 32 0.52
9 10 0.16
10 12 0.19
11 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATTTA
Found at i:3049323 original size:25 final size:25
Alignment explanation
Indices: 3049295--3049380 Score: 79
Period size: 25 Copynumber: 3.3 Consensus size: 25
3049285 TACTACGTTA
3049295 TTATATTTATATTATATTTATATAT
1 TTATATTTATATTATATTTATATAT
*
3049320 TTATATATAT-TATATATTTATATAAAT
1 TTATATTTATAT-TATATTTATAT--AT
*
3049347 TTATA-TTAAATTAATAATTTATA-AT
1 TTATATTTATATT-AT-ATTTATATAT
3049372 TATATATTT
1 T-TATATTT
3049381 TTATATGATA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
24 1 0.02
25 23 0.46
26 7 0.14
27 12 0.24
28 7 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTATATTTATATTATATTTATATAT
Found at i:3049371 original size:10 final size:9
Alignment explanation
Indices: 3049299--3049369 Score: 60
Period size: 8 Copynumber: 7.8 Consensus size: 9
3049289 ACGTTATTAT
3049299 ATTTATATTA
1 ATTTATA-TA
3049309 TATTTATAT-
1 -ATTTATATA
3049318 ATTTATAT-
1 ATTTATATA
3049326 ATATTATAT-
1 AT-TTATATA
3049335 ATTTATATAA
1 ATTTATAT-A
3049345 ATTTATATTA
1 ATTTATA-TA
*
3049355 AATTA-ATA
1 ATTTATATA
3049363 ATTTATA
1 ATTTATA
3049370 ATTATATATT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
8 22 0.42
9 10 0.19
10 13 0.25
11 8 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTATATA
Found at i:3049394 original size:46 final size:46
Alignment explanation
Indices: 3049299--3049396 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 46
3049289 ACGTTATTAT
* *
3049299 ATTTATATTATATTTATATATTTATATATATTATATATTTATATAA
1 ATTTATATTAAATTAATATATTTATATATATTATATATTTATATAA
*
3049345 ATTTATATTAAATTAATA-ATTTATA-AT-TATATATTTTTATATGATA
1 ATTTATATTAAATTAATATATTTATATATAT-TATATATTTATAT-A-A
3049391 ATTTAT
1 ATTTAT
3049397 CATATTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
43 1 0.02
44 14 0.30
45 8 0.17
46 23 0.50
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (46 bp):
ATTTATATTAAATTAATATATTTATATATATTATATATTTATATAA
Found at i:3050563 original size:21 final size:22
Alignment explanation
Indices: 3050539--3050579 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3050529 TTTCCGAGAT
*
3050539 GAAAAGGCGAA-GGAAAGAAGA
1 GAAAAGGAGAAGGGAAAGAAGA
*
3050560 GAAAATGAGAAGGGAAAGAA
1 GAAAAGGAGAAGGGAAAGAA
3050580 CACTGGGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.59, C:0.02, G:0.37, T:0.02
Consensus pattern (22 bp):
GAAAAGGAGAAGGGAAAGAAGA
Found at i:3051736 original size:2 final size:2
Alignment explanation
Indices: 3051729--3051768 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3051719 CACTATCTAT
*
3051729 TA TA TA TA TA TA TA TA TG 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 TA TA
3051769 AGAGTGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3052159 original size:22 final size:22
Alignment explanation
Indices: 3052134--3052179 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3052124 CTTATTTTAC
3052134 TATTTATAA-TAATATTAAATAT
1 TATTTATAATTAATATT-AATAT
*
3052156 TATTTTTAATTAATATTAATAT
1 TATTTATAATTAATATTAATAT
3052178 TA
1 TA
3052180 ATATTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTATAATTAATATTAATAT
Found at i:3052189 original size:22 final size:22
Alignment explanation
Indices: 3052134--3052190 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
3052124 CTTATTTTAC
3052134 TATTTATAATAATATTAAATATTA
1 TATTTAT--TAATATTAAATATTA
*
3052158 TTTTTAATTAATATT-AATATTAA
1 TATTT-ATTAATATTAAATATT-A
3052181 TATTTATTAA
1 TATTTATTAA
3052191 ATAATAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 11 0.38
23 12 0.41
24 4 0.14
25 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTATTAATATTAAATATTA
Found at i:3052198 original size:29 final size:25
Alignment explanation
Indices: 3052139--3052198 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 25
3052129 TTTACTATTT
*
3052139 ATAATAATATTAAATATTATTTTTA
1 ATAATAATATTAAATAATATTTTTA
3052164 AT--TAATATTAATATTAATATTTATTAA
1 ATAATAATATTAA-A-TAATATTT-TT-A
3052191 ATAATAAT
1 ATAATAAT
3052199 TCGAACAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
23 9 0.32
24 1 0.04
25 9 0.32
26 2 0.07
27 3 0.11
29 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAATAATATTAAATAATATTTTTA
Found at i:3052476 original size:72 final size:73
Alignment explanation
Indices: 3052358--3052492 Score: 209
Period size: 72 Copynumber: 1.9 Consensus size: 73
3052348 AATTAGAAAC
* * *
3052358 AAAAAATGAGAGAATTTGAGTTCTTCTATTTCTTAATTCTTAATTTCTCA-CATCTCATTATCCG
1 AAAAAATGAGAGAATTTAAGTTCCTCTATTTCTTAATTCTTAATTTCTCATAATCTCATTATCCG
3052422 TTCAAATA
66 TTCAAATA
* * *
3052430 AAAAAATGATAGAATTTAAGTTCCTCTATTTCTTAATTTTTGATTTCTCATAATCTCATTATC
1 AAAAAATGAGAGAATTTAAGTTCCTCTATTTCTTAATTCTTAATTTCTCATAATCTCATTATC
3052493 TATTAGAGTG
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
72 45 0.80
73 11 0.20
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (73 bp):
AAAAAATGAGAGAATTTAAGTTCCTCTATTTCTTAATTCTTAATTTCTCATAATCTCATTATCCG
TTCAAATA
Found at i:3053155 original size:2 final size:2
Alignment explanation
Indices: 3053148--3053185 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3053138 GCCACCTGCC
*
3053148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3053186 TTACCACCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3060033 original size:5 final size:5
Alignment explanation
Indices: 3060023--3060047 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3060013 TCTCAAGTCC
3060023 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
3060048 TGTTTATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:3060707 original size:15 final size:16
Alignment explanation
Indices: 3060682--3060719 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3060672 ACCCATAAAT
3060682 AAAAT-AATAATA-TA
1 AAAATAAATAATAGTA
3060696 AAAATAAATAATAGTA
1 AAAATAAATAATAGTA
*
3060712 AACATAAA
1 AAAATAAA
3060720 ATTAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 7 0.33
16 9 0.43
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAATAAATAATAGTA
Found at i:3062194 original size:13 final size:14
Alignment explanation
Indices: 3062167--3062200 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
3062157 TAAAATTTAA
3062167 AATTTATGTTAATT
1 AATTTATGTTAATT
3062181 AATTTATG-TAATT
1 AATTTATGTTAATT
3062194 AATTTAT
1 AATTTAT
3062201 ACTTAATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (14 bp):
AATTTATGTTAATT
Found at i:3062433 original size:16 final size:15
Alignment explanation
Indices: 3062414--3062455 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
3062404 AGATATAAAA
3062414 ATAATATAATAATTTT
1 ATAA-ATAATAATTTT
*
3062430 ATAAAAAAATAATTTT
1 AT-AAATAATAATTTT
3062446 -TAAATAATAA
1 ATAAATAATAA
3062456 AAAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 8 0.35
15 1 0.04
16 12 0.52
17 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATAATAATTTT
Found at i:3062476 original size:19 final size:19
Alignment explanation
Indices: 3062426--3062481 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
3062416 AATATAATAA
* *
3062426 TTTTATAAAAAAATAATTT
1 TTTTAAAAAAAAATTATTT
* *
3062445 TTAAATAATAAAAAATTATTT
1 TT--TTAAAAAAAAATTATTT
3062466 TTTTAAAAAAAAATTA
1 TTTTAAAAAAAAATTA
3062482 ATCTAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 14 0.48
21 15 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTAAAAAAAAATTATTT
Done.