Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 44 of 135
Found at i:16157813 original size:23 final size:23
Alignment explanation
Indices: 16157785--16157841 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
16157775 ATGAAATACA
16157785 AATTTTGAATATTT-TAAGTAA-TT
1 AATTTTGAATATTTATAA--AATTT
16157808 AATTTT-AATTATTTATAAAATTT
1 AATTTTGAA-TATTTATAAAATTT
16157831 AA-TTTGAATAT
1 AATTTTGAATAT
16157842 ATAAATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
22 10 0.33
23 17 0.57
24 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
AATTTTGAATATTTATAAAATTT
Found at i:16161931 original size:20 final size:20
Alignment explanation
Indices: 16161901--16161947 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
16161891 ATACACTCTA
16161901 AGAATATTTTGATATAA-CCTT
1 AGAA-ATTTTGATA-AATCCTT
16161922 AGAAATTTTGATAAATCCTT
1 AGAAATTTTGATAAATCCTT
*
16161942 AAAAAT
1 AGAAAT
16161948 ATTAGTATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 18 0.75
21 4 0.17
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (20 bp):
AGAAATTTTGATAAATCCTT
Found at i:16177066 original size:23 final size:25
Alignment explanation
Indices: 16177040--16177089 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
16177030 AATTACGATT
*
16177040 TTTATTTTTATT-TTTTAAT-ATAA
1 TTTATTTTAATTATTTTAATAATAA
16177063 TTTATTTTAATTATTTTAATAATAA
1 TTTATTTTAATTATTTTAATAATAA
16177088 TT
1 TT
16177090 AATTACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.46
24 7 0.29
25 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTATTTTAATTATTTTAATAATAA
Found at i:16177119 original size:16 final size:16
Alignment explanation
Indices: 16177100--16177136 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
16177090 AATTACATAA
*
16177100 ATAATTATAATAAAAT
1 ATAAATATAATAAAAT
*
16177116 ATAAATATCATAAAAT
1 ATAAATATAATAAAAT
16177132 ATAAA
1 ATAAA
16177137 CCCATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAATATAATAAAAT
Found at i:16177189 original size:9 final size:9
Alignment explanation
Indices: 16177160--16177215 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
16177150 GACTTTGTCA
*
16177160 TTATAATTT
1 TTATAATAT
* *
16177169 TTTTATTAT
1 TTATAATAT
16177178 TTATAATAT
1 TTATAATAT
*
16177187 TTATGATAT
1 TTATAATAT
*
16177196 TTATAAGAT
1 TTATAATAT
*
16177205 TTTTAAT-T
1 TTATAATAT
16177213 TTA
1 TTA
16177216 CTAAAATAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
8 3 0.08
9 33 0.92
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (9 bp):
TTATAATAT
Found at i:16177416 original size:18 final size:19
Alignment explanation
Indices: 16177390--16177427 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
16177380 TATTACTTTT
*
16177390 ATTTTAATTGTTTAT-TAA
1 ATTTAAATTGTTTATATAA
*
16177408 ATTTAAATTTTTTATATAA
1 ATTTAAATTGTTTATATAA
16177427 A
1 A
16177428 ATTTTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
ATTTAAATTGTTTATATAA
Found at i:16185253 original size:16 final size:17
Alignment explanation
Indices: 16185232--16185268 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
16185222 TTTTCTATAA
16185232 TAATTCAA-ATAAAAAT
1 TAATTCAATATAAAAAT
*
16185248 TAATTCAATATAAAATT
1 TAATTCAATATAAAAAT
16185265 TAAT
1 TAAT
16185269 CTTCTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATTCAATATAAAAAT
Found at i:16185747 original size:22 final size:22
Alignment explanation
Indices: 16185700--16185747 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
16185690 AAATATATAT
* *
16185700 AAAAAAAATTATGAGTGATTATC
1 AAAAAAAA-TATGAGTGACTACC
16185723 AAAAAAAA-ATGAGTGGACTACC
1 AAAAAAAATATGAGT-GACTACC
16185745 AAA
1 AAA
16185748 TAATGGTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 8 0.36
23 8 0.36
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.21
Consensus pattern (22 bp):
AAAAAAAATATGAGTGACTACC
Found at i:16186018 original size:39 final size:39
Alignment explanation
Indices: 16185970--16186058 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 39
16185960 AATACATGCT
* * * *
16185970 AAAATTTATGGGAGAATATAAAAAAAA-TTAGGAAA-TACA
1 AAAAATTATGAGAG-AT-TAAAAAAAACATAAGAAAGTACA
* *
16186009 AAAAATTATGAGTGATTAAAAAAAACATAAGAAAGTACG
1 AAAAATTATGAGAGATTAAAAAAAACATAAGAAAGTACA
16186048 AAAAATTATGA
1 AAAAATTATGA
16186059 AAGTATAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
37 9 0.21
38 8 0.19
39 25 0.60
ACGTcount: A:0.60, C:0.03, G:0.15, T:0.22
Consensus pattern (39 bp):
AAAAATTATGAGAGATTAAAAAAAACATAAGAAAGTACA
Found at i:16186060 original size:18 final size:18
Alignment explanation
Indices: 16185991--16186074 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
16185981 GAGAATATAA
*
16185991 AAAAAATTAGGAAA-TAC
1 AAAAAATTATGAAAGTAC
* * *
16186008 AAAAAATTATGAGTGATTAA
1 AAAAAATTATGA--AAGTAC
* *
16186028 AAAAAACATAAGAAAGTAC
1 AAAAAA-TTATGAAAGTAC
* *
16186047 GAAAAATTATGAAAGTAT
1 AAAAAATTATGAAAGTAC
16186065 AAAAAATTAT
1 AAAAAATTAT
16186075 AAGGGTGTAT
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
17 11 0.22
18 18 0.36
19 9 0.18
20 8 0.16
21 4 0.08
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.23
Consensus pattern (18 bp):
AAAAAATTATGAAAGTAC
Found at i:16186068 original size:39 final size:35
Alignment explanation
Indices: 16185986--16186070 Score: 89
Period size: 39 Copynumber: 2.3 Consensus size: 35
16185976 TATGGGAGAA
* *
16185986 TATAAAAAAAATTAGGAAATACAAAAAATTATGAG
1 TATAAAAAAAAATAAGAAATACAAAAAATTATGAG
*
16186021 TGATTAAAAAAAACATAAGAAAGTACGAAAAATTATGAAAG
1 T-A-TAAAAAAAA-ATAAGAAA-TACAAAAAATTATG--AG
16186062 TATAAAAAA
1 TATAAAAAA
16186071 TTATAAGGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
35 1 0.02
36 1 0.02
37 9 0.22
38 6 0.15
39 20 0.49
40 1 0.02
41 3 0.07
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.21
Consensus pattern (35 bp):
TATAAAAAAAAATAAGAAATACAAAAAATTATGAG
Found at i:16191202 original size:58 final size:59
Alignment explanation
Indices: 16191139--16191286 Score: 185
Period size: 58 Copynumber: 2.5 Consensus size: 59
16191129 TAATAAGATT
*
16191139 ATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATT-ATA-TTTTAACATAATA
1 ATTATTAAATATAATTTAATAAAAATAATAAATAATTT-ATTAACATTTTTAACATAATA
** * *
16191197 ATTATTAAATATAATTTAAT-AAAATAATGTATAATTTATTAACATTTTTAATATAATT
1 ATTATTAAATATAATTTAATAAAAATAATAAATAATTTATTAACATTTTTAACATAATA
* * *
16191255 ATTATTAAAATATAAATTAGTAAAAATCATAA
1 ATTATT-AAATATAATTTAATAAAAATAATAA
16191287 TATATAATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
56 3 0.04
57 17 0.22
58 37 0.49
59 12 0.16
60 7 0.09
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (59 bp):
ATTATTAAATATAATTTAATAAAAATAATAAATAATTTATTAACATTTTTAACATAATA
Found at i:16191204 original size:26 final size:27
Alignment explanation
Indices: 16191175--16191236 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
16191165 AATAAATAAT
*
16191175 TTAATTATATTTTAACATAATAAT-TA
1 TTAATTATATTTTAACAAAATAATGTA
* * *
16191201 TTAAATATAATTTAATAAAATAATGTA
1 TTAATTATATTTTAACAAAATAATGTA
16191228 -TAATT-TATT
1 TTAATTATATT
16191237 AACATTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 3 0.10
26 24 0.83
27 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAATTATATTTTAACAAAATAATGTA
Found at i:16191293 original size:24 final size:23
Alignment explanation
Indices: 16191264--16191313 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
16191254 TATTATTAAA
*
16191264 ATATAA-ATTAGTAAAAATCATAAT
1 ATATAATATTAG-AAAAATAAT-AT
16191288 ATATAATATTAGAAAAATAATAT
1 ATATAATATTAGAAAAATAATAT
16191311 ATA
1 ATA
16191314 ACCTACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 14 0.58
25 5 0.21
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAATATTAGAAAAATAATAT
Found at i:16193680 original size:8 final size:8
Alignment explanation
Indices: 16193648--16193681 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
16193638 AGCAACCAAC
16193648 CAGAGAAA
1 CAGAGAAA
*
16193656 AAGAGAAA
1 CAGAGAAA
*
16193664 CAGAAAAA
1 CAGAGAAA
16193672 CAGAGAAA
1 CAGAGAAA
16193680 CA
1 CA
16193682 AAGCTTTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.68, C:0.12, G:0.21, T:0.00
Consensus pattern (8 bp):
CAGAGAAA
Found at i:16196440 original size:2 final size:2
Alignment explanation
Indices: 16196435--16196462 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16196425 TATATATATT
16196435 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16196463 ATAGGTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:16196951 original size:27 final size:27
Alignment explanation
Indices: 16196916--16196976 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
16196906 AATACAGTGG
*
16196916 TAAAATAAAATAAAAGTAAAGTCCAAA
1 TAAACTAAAATAAAAGTAAAGTCCAAA
*
16196943 TAAACTAAAGTAAAAGTAAAGTCCAAA
1 TAAACTAAAATAAAAGTAAAGTCCAAA
16196970 TAAACTA
1 TAAACTA
16196977 GAGTTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.20
Consensus pattern (27 bp):
TAAACTAAAATAAAAGTAAAGTCCAAA
Found at i:16199981 original size:17 final size:17
Alignment explanation
Indices: 16199959--16199997 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
16199949 AGGTGGAGAA
* *
16199959 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
16199976 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
16199993 CTTGT
1 CTTGT
16199998 CAATGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:16204356 original size:3 final size:3
Alignment explanation
Indices: 16204350--16204381 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
16204340 TTTAATTGGT
16204350 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
16204382 TTTATACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:16208231 original size:19 final size:21
Alignment explanation
Indices: 16208207--16208246 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
16208197 TGATATTTTT
16208207 TTAAAA-AAAT-TTATAAACC
1 TTAAAAGAAATATTATAAACC
16208226 TTAAAATGAAATATTATAAAC
1 TTAAAA-GAAATATTATAAAC
16208247 TATAACATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (21 bp):
TTAAAAGAAATATTATAAACC
Found at i:16214481 original size:8 final size:8
Alignment explanation
Indices: 16214468--16214545 Score: 50
Period size: 8 Copynumber: 9.0 Consensus size: 8
16214458 AATTTCACCA
*
16214468 AAAAAAGT
1 AAAAAAGG
16214476 AAAAAAGG
1 AAAAAAGG
16214484 AAAAAAAAGG
1 --AAAAAAGG
16214494 AAAAAAGAG
1 AAAAAAG-G
*
16214503 AAAAAGAGAA
1 AAAAA-AG-G
*
16214513 AAAGAAAAG
1 AAA-AAAGG
*
16214522 AAAAAAAG
1 AAAAAAGG
16214530 AAGAAAA-G
1 AA-AAAAGG
16214538 AAAAAAGG
1 AAAAAAGG
16214546 GGAGGTCGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
7 4 0.07
8 25 0.42
9 13 0.22
10 15 0.25
11 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (8 bp):
AAAAAAGG
Found at i:16214489 original size:10 final size:9
Alignment explanation
Indices: 16214467--16214543 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
16214457 AAATTTCACC
*
16214467 AAAAAAAGT
1 AAAAAAAGA
*
16214476 AAAAAAGGA
1 AAAAAAAGA
16214485 AAAAAAAG-
1 AAAAAAAGA
*
16214493 GAAAAAAGA
1 AAAAAAAGA
*
16214502 GAAAAAGAGA
1 -AAAAAAAGA
16214512 AAAAGAAA-A
1 AAAA-AAAGA
16214521 GAAAAAAAG-
1 -AAAAAAAGA
*
16214530 AAGAAAAGA
1 AAAAAAAGA
16214539 AAAAA
1 AAAAA
16214544 GGGGAGGTCG
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
8 14 0.26
9 26 0.49
10 13 0.25
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:16214497 original size:27 final size:26
Alignment explanation
Indices: 16214467--16214543 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 26
16214457 AAATTTCACC
16214467 AAAAAAAGTAAAAAAGG-AAAAAAAAG
1 AAAAAAAG-AAAAAAGGAAAAAAAAAG
*
16214493 GAAAAAAGAGAAAAAGAGAAAAAGAAAAG
1 AAAAAAAGA-AAAAAG-GAAAAA-AAAAG
16214522 AAAAAAAGAAGAAAA-GAAAAAA
1 AAAAAAAGAA-AAAAGGAAAAAA
16214544 GGGGAGGTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
25 1 0.02
26 14 0.32
27 7 0.16
28 5 0.11
29 17 0.39
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (26 bp):
AAAAAAAGAAAAAAGGAAAAAAAAAG
Found at i:16214506 original size:16 final size:14
Alignment explanation
Indices: 16214487--16214543 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 14
16214477 AAAAAGGAAA
16214487 AAAAAGGAAAAAAGAG
1 AAAAA-GAAAAAA-AG
*
16214503 AAAAAGAGAAAAAG
1 AAAAAGAAAAAAAG
16214517 -AAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
16214530 AAGAAAAGAAAAAA
1 -A-AAAAGAAAAAA
16214544 GGGGAGGTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
13 12 0.33
14 2 0.06
15 6 0.17
16 16 0.44
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:16214522 original size:21 final size:21
Alignment explanation
Indices: 16214496--16214541 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
16214486 AAAAAAGGAA
*
16214496 AAAAGAGAAAAAG-AGAAAAAG
1 AAAAGAAAAAAAGAAG-AAAAG
16214517 AAAAGAAAAAAAGAAGAAAAG
1 AAAAGAAAAAAAGAAGAAAAG
16214538 AAAA
1 AAAA
16214542 AAGGGGAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAAGAAGAAAAG
Found at i:16215493 original size:50 final size:50
Alignment explanation
Indices: 16215401--16215533 Score: 142
Period size: 50 Copynumber: 2.7 Consensus size: 50
16215391 GTGATGGAAC
** * * * *
16215401 GACAAATCTTTTACCCCTAAAGCTGT-GAAGGTGCAGATTGAAGCCGCAAT
1 GACAAATCTCATACACCTAAAGCTGTAG-AGGGGAAGAATGAAGCCGCAAT
*
16215451 GGCAAATCTCATACACCTAAAGCTGTAGAGGGGAAGAATGAAGCCGCAAT
1 GACAAATCTCATACACCTAAAGCTGTAGAGGGGAAGAATGAAGCCGCAAT
* * * * *
16215501 GACGAATTTTATTCACCTAAAGCTATAGAGGGG
1 GACAAATCTCATACACCTAAAGCTGTAGAGGGG
16215534 TAAATTGAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
50 68 0.99
51 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (50 bp):
GACAAATCTCATACACCTAAAGCTGTAGAGGGGAAGAATGAAGCCGCAAT
Found at i:16215555 original size:50 final size:50
Alignment explanation
Indices: 16215455--16215562 Score: 119
Period size: 50 Copynumber: 2.2 Consensus size: 50
16215445 CGCAATGGCA
* * * * *
16215455 AATCTCATACACCTAAAGCTGTAGAGGGGAAGAATGAAGCCGCAATGACG
1 AATCTTATTCACCTAAAGCTATAGAGGGGAAGAATGAAGCCACAAGGACG
* * **
16215505 AATTTTATTCACCTAAAGCTATAGAGGGGTAA-ATTGAAGTTACAAGGACG
1 AATCTTATTCACCTAAAGCTATAGAGGGG-AAGAATGAAGCCACAAGGACG
16215555 AATCTTAT
1 AATCTTAT
16215563 ACTCTTGAAG
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 45 0.96
51 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (50 bp):
AATCTTATTCACCTAAAGCTATAGAGGGGAAGAATGAAGCCACAAGGACG
Found at i:16215733 original size:80 final size:80
Alignment explanation
Indices: 16215597--16216169 Score: 394
Period size: 80 Copynumber: 7.2 Consensus size: 80
16215587 AGTTACAACC
* *
16215597 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTACCCCAATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCAATCATGG
16215662 GGCAAATTGAAGAAA
66 GGCAAATTGAAGAAA
* * * *
16215677 TCTAATCTTTTACCTTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCGATCATAG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCAATCATGG
* *
16215742 GGTAGATTGAAGAAA
66 GGCAAATTGAAGAAA
* * * * *
16215757 TCCAATCTTTTACCCTAACCAGAGGGCAATATTGAATATCATCCGATCTTTTACCCTAACCA-GA
1 TCCAATCTTTTACCCTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCAATCATG-
*
16215821 GGGCAAAATTGAAGACCA
65 GGGC-AAATTGAAGA-AA
* * * * * * ** * * * *
16215839 TTCGATCTTTTACGCC-GATCATG-GGGC-AGATTGAAGA-AATCTAATTTTTTACCCTAATTAA
1 TCCAATCTTTTAC-CCTAACCA-GAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCAATCAT
* * *
16215900 AGGGCAAGATTAAAGACCA
64 GGGGCAA-ATTGAAGA-AA
* ** * * * * ** *
16215919 TCCGATCTTTTACCCCGATCATG-GGGC-AGATTGAAGA-AATCCAATCTTTTACCCTGATTATG
1 TCCAATCTTTTACCCTAACCA-GAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCAATCATG
* * *
16215981 GGGTATATTGAAGCAA
65 GGGCAAATTGAAGAAA
* * * * * * * *
16215997 TCCAATCTTTTACCCTAACTAAAAGG-TAGATTGAAGACCATCCGATCTCTTACCTCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCAATCATGG
* * * *
16216061 GACAGATTAAAGCAA
66 GGCAAATTGAAGAAA
* * * * * ** * * * *
16216076 TCCAATTTTTTACCTTAACCAGAAGGC-AGATTAAAGACCATCAAATCTCTTACCCCGACCATGA
1 TCCAATCTTTTACCCTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCAATCATGG
*
16216140 GGCAGATTGAA-ATAA
66 GGCAAATTGAAGA-AA
16216155 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
16216170 CTAAAATAAT
Statistics
Matches: 403, Mismatches: 77, Indels: 27
0.79 0.15 0.05
Matches are distributed among these distances:
78 29 0.07
79 118 0.29
80 217 0.54
81 17 0.04
82 19 0.05
83 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCAATCATGG
GGCAAATTGAAGAAA
Found at i:16215807 original size:121 final size:119
Alignment explanation
Indices: 16215625--16216050 Score: 437
Period size: 121 Copynumber: 3.5 Consensus size: 119
16215615 CCAGAAGGCA
* * * * * **
16215625 AGATTGAAGACCATCCGATCTTTTACCCCAATCATG-GGGCAAATTGAAGAAATCTAATCTTTTA
1 AGATTGAAGA-AATCCAATCTTTTACCCTAACCA-GAGGGCAAATTGAAGACATCCGATCTTTTA
* *
16215689 CCTTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCGATCATAGGGT
64 CCCTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGT
*
16215745 AGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAATATTGAATATCATCCGATCTTTTA
1 AGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAA-ATTGAAGA-CATCCGATCTTTTA
* * *
16215810 CCCTAACCAGAGGGCAAAATTGAAGACCATTCGATCTTTTACGCCGATCATGGGGC
64 CCCTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGT
* * ** * *
16215866 AGATTGAAGAAATCTAATTTTTTACCCTAATTAAAGGGCAAGATTAAAGACCATCCGATCTTTTA
1 AGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAA-ATTGAAGA-CATCCGATCTTTTA
** * * * * * *
16215931 CCCCGATCATG-GGGC-AGATTGAAGA-AATCCAATCTTTTACCCTGATTATGGGGT
64 CCCTAACCA-GAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGT
* * * * * * * *
16215985 ATATTGAAGCAATCCAATCTTTTACCCTAACTAAAAGGTAGATTGAAGACCATCCGATCTCTTAC
1 AGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGA-CATCCGATCTTTTAC
16216050 C
65 C
16216051 TCGATCATGG
Statistics
Matches: 259, Mismatches: 43, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
118 24 0.09
119 80 0.31
120 26 0.10
121 128 0.49
122 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (119 bp):
AGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACATCCGATCTTTTACC
CTAACCAGAGGGCAAAATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGT
Found at i:16215952 original size:201 final size:198
Alignment explanation
Indices: 16215597--16216169 Score: 726
Period size: 201 Copynumber: 2.9 Consensus size: 198
16215587 AGTTACAACC
*
16215597 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTACCCCAATCATGG
1 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTA-CCCGATCATGG
* * * * *
16215662 GGCAAATTGAAGAAATCTAATCTTTTACCTTAACCAGAGGGCAAAATTGAAGACCATCCGATCTT
65 GGCAGATTGAAGAAATCTAATTTTTTACCTTAACCAAAGGGCAAGATTAAAGACCATCCGATCTT
* *
16215727 TTACCCCGATCATAGGGTAGATTGAAGAAATCCAATCTTTTACCCTAACCA-GAGGGCAATATTG
130 TTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCATG-GGG-AATATTG
*
16215791 AA-TATCA
193 AAGCA--A
* * * *
16215798 TCCGATCTTTTACCCTAACCAGAGGGCAAAATTGAAGACCATTCGATCTTTTACGCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTAC-CCGATCATGG
* **
16215863 GGCAGATTGAAGAAATCTAATTTTTTACCCTAATTAAAGGGCAAGATTAAAGACCATCCGATCTT
65 GGCAGATTGAAGAAATCTAATTTTTTACCTTAACCAAAGGGCAAGATTAAAGACCATCCGATCTT
* ** *
16215928 TTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTGATTATGGGGTATATTGAA
130 TTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCATGGGGAATATTGAA
16215993 GCAA
195 GCAA
* * * *
16215997 TCCAATCTTTTACCCTAACTAAAAGG-TAGATTGAAGACCATCCGATCTCTTACCTCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTACC-CGATCATGG
* * * * **
16216061 GACAGATTAAAGCAATCCAATTTTTTACCTTAACCAGAA-GGC-AGATTAAAGACCATCAAATCT
65 GGCAGATTGAAGAAATCTAATTTTTTACCTTAACCA-AAGGGCAAGATTAAAGACCATCCGATCT
* * *
16216124 CTTACCCCGACCATGAGGCAGATTGAA-ATAATCCAATCTTTTACCC
129 TTTACCCCGATCATGGGGCAGATTGAAGA-AATCCAATCTTTTACCC
16216170 CTAAAATAAT
Statistics
Matches: 326, Mismatches: 40, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
196 1 0.00
197 61 0.19
198 64 0.20
199 25 0.08
200 9 0.03
201 165 0.51
202 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (198 bp):
TCCAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGACCATCCGATCTTTTACCCGATCATGGG
GCAGATTGAAGAAATCTAATTTTTTACCTTAACCAAAGGGCAAGATTAAAGACCATCCGATCTTT
TACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCATGGGGAATATTGAAG
CAA
Found at i:16216080 original size:79 final size:80
Alignment explanation
Indices: 16215987--16216169 Score: 230
Period size: 79 Copynumber: 2.3 Consensus size: 80
16215977 TATGGGGTAT
* * * **
16215987 ATTG-AAGCAATCCAATCTTTTACCCTAACTAAAAGGTAGATTGAAGACCATCCGATCTCTTACC
1 ATTGAAAGCAATCCAATCTTTTACCCTAACCAAAAGGCAGATTAAAGACCATCAAATCTCTTACC
* *
16216051 TCGATCATG-GGACAG
66 CCGACCATGAGG-CAG
* * *
16216066 ATT-AAAGCAATCCAATTTTTTACCTTAACCAGAAGGCAGATTAAAGACCATCAAATCTCTTACC
1 ATTGAAAGCAATCCAATCTTTTACCCTAACCAAAAGGCAGATTAAAGACCATCAAATCTCTTACC
16216130 CCGACCATGAGGCAG
66 CCGACCATGAGGCAG
*
16216145 ATTGAAA-TAATCCAATCTTTTACCC
1 ATTGAAAGCAATCCAATCTTTTACCC
16216170 CTAAAATAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
79 83 0.94
80 5 0.06
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27
Consensus pattern (80 bp):
ATTGAAAGCAATCCAATCTTTTACCCTAACCAAAAGGCAGATTAAAGACCATCAAATCTCTTACC
CCGACCATGAGGCAG
Found at i:16216170 original size:39 final size:40
Alignment explanation
Indices: 16215597--16216169 Score: 318
Period size: 39 Copynumber: 14.4 Consensus size: 40
16215587 AGTTACAACC
*
16215597 TCCAATCTTTTACCCTAACCA-GAAGGCAAGATTGAAGACCA
1 TCCAATCTTTTACCCTAACCATG-AGGC-AGATTGAAGACAA
* * * * *
16215638 TCCGATCTTTTACCCCAATCATGGGGCAAATTGAAGA-AA
1 TCCAATCTTTTACCCTAACCATGAGGCAGATTGAAGACAA
* * * *
16215677 TCTAATCTTTTACCTTAACCA-GAGGGCAAAATTGAAGACCA
1 TCCAATCTTTTACCCTAACCATGA-GGC-AGATTGAAGACAA
* ** * *
16215718 TCCGATCTTTTACCCCGATCAT-AGGGTAGATTGAAGA-AA
1 TCCAATCTTTTACCCTAACCATGA-GGCAGATTGAAGACAA
* *
16215757 TCCAATCTTTTACCCTAACCA-GAGGGCAATATTGAATATC-A
1 TCCAATCTTTTACCCTAACCATGA-GGC-AGATTGAAGA-CAA
* * *
16215798 TCCGATCTTTTACCCTAACCA-GAGGGCAAAATTGAAGACCA
1 TCCAATCTTTTACCCTAACCATGA-GGC-AGATTGAAGACAA
* * * * *
16215839 TTCGATCTTTTACGCC-GATCATGGGGCAGATTGAAGA-AA
1 TCCAATCTTTTAC-CCTAACCATGAGGCAGATTGAAGACAA
* * ** * * *
16215878 TCTAATTTTTTACCCTAATTA-AAGGGCAAGATTAAAGACCA
1 TCCAATCTTTTACCCTAACCATGA-GGC-AGATTGAAGACAA
* ** * *
16215919 TCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGA-AA
1 TCCAATCTTTTACCCTAACCATGAGGCAGATTGAAGACAA
* ** * * *
16215958 TCCAATCTTTTACCCTGATTATGGGGTATATTGAAG-CAA
1 TCCAATCTTTTACCCTAACCATGAGGCAGATTGAAGACAA
* ** * *
16215997 TCCAATCTTTTACCCTAACTAAAAGGTAGATTGAAGACCA
1 TCCAATCTTTTACCCTAACCATGAGGCAGATTGAAGACAA
* * * * *
16216037 TCCGATCTCTTA-CCTCGATCATG-GGACAGATTAAAG-CAA
1 TCCAATCTTTTACCCT-AACCATGAGG-CAGATTGAAGACAA
* * * *
16216076 TCCAATTTTTTACCTTAACCA-GAAGGCAGATTAAAGACCA
1 TCCAATCTTTTACCCTAACCATG-AGGCAGATTGAAGACAA
* * ** *
16216116 TCAAATCTCTTACCCCGACCATGAGGCAGATTGAA-ATAA
1 TCCAATCTTTTACCCTAACCATGAGGCAGATTGAAGACAA
16216155 TCCAATCTTTTACCC
1 TCCAATCTTTTACCC
16216170 CTAAAATAAT
Statistics
Matches: 408, Mismatches: 98, Indels: 54
0.73 0.17 0.10
Matches are distributed among these distances:
38 4 0.01
39 166 0.41
40 118 0.29
41 116 0.28
42 4 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (40 bp):
TCCAATCTTTTACCCTAACCATGAGGCAGATTGAAGACAA
Found at i:16216810 original size:67 final size:65
Alignment explanation
Indices: 16216691--16216865 Score: 227
Period size: 67 Copynumber: 2.7 Consensus size: 65
16216681 TCCATTTTTC
* *
16216691 TTATTATTTTTATTTATTTATTATTATTTTTATG-A-AT-AA-AAATAAATATAAAATAATATTA
1 TTATT-TTATTATTTATTTATTATTA--TTTATGAATATAAATAAATAAATATAAAAAAATATTA
16216752 ATT
63 ATT
*
16216755 TTATTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAAAAATATTAA
1 TTATTTTATTATTTATTTA-TTATTATT-TATGAATATAAATAAATAAATATAAAAAAATATTAA
16216820 TT
64 TT
*
16216822 TTGTTTTATTATTTATTTATTA-T-TTTATGAATATAAATAAATAA
1 TTATTTTATTATTTATTTATTATTATTTATGAATATAAATAAATAA
16216866 GAAACAAAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
62 2 0.02
63 36 0.36
64 14 0.14
65 3 0.03
66 5 0.05
67 41 0.41
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (65 bp):
TTATTTTATTATTTATTTATTATTATTTATGAATATAAATAAATAAATATAAAAAAATATTAATT
Found at i:16216875 original size:63 final size:62
Alignment explanation
Indices: 16216698--16216865 Score: 227
Period size: 63 Copynumber: 2.7 Consensus size: 62
16216688 TTCTTATTAT
* *
16216698 TTTTATTTATTTA-TTATTATTTTTATGAATAAAAATAAAT--ATAAAATAATATTAATTTTA
1 TTTTA-TTATTTATTTATTATTTTTATGAATATAAATAAATAAATAAAAAAATATTAATTTTA
16216758 TTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAAAAATATTAATTT
1 TTTTATTATTTATTTA-TTATT-TT-TATGAATATAAATAAATAAA--TAAAAAAATATTAATTT
*
16216823 TG
61 TA
16216825 TTTTATTATTTATTTATTA-TTTTATGAATATAAATAAATAA
1 TTTTATTATTTATTTATTATTTTTATGAATATAAATAAATAA
16216866 GAAACAAAAA
Statistics
Matches: 97, Mismatches: 3, Indels: 13
0.86 0.03 0.12
Matches are distributed among these distances:
59 7 0.07
60 8 0.08
61 5 0.05
62 2 0.02
63 35 0.36
64 2 0.02
65 2 0.02
66 3 0.03
67 33 0.34
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (62 bp):
TTTTATTATTTATTTATTATTTTTATGAATATAAATAAATAAATAAAAAAATATTAATTTTA
Found at i:16221823 original size:18 final size:20
Alignment explanation
Indices: 16221782--16221825 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
16221772 ACCCTCAACA
*
16221782 TCTTCTTCTTCTTCATCACCT
1 TCTTCTTCTTCTACATCA-CT
16221803 TCTTCTTCTTCTAC-TCA-T
1 TCTTCTTCTTCTACATCACT
16221821 TCTTC
1 TCTTC
16221826 CAACTTCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
20 3 0.14
21 13 0.59
ACGTcount: A:0.09, C:0.36, G:0.00, T:0.55
Consensus pattern (20 bp):
TCTTCTTCTTCTACATCACT
Found at i:16228598 original size:22 final size:22
Alignment explanation
Indices: 16228572--16228621 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
16228562 ATCTCCAGAG
16228572 GTACTTCTACTTCTCCCAAGAA
1 GTACTTCTACTTCTCCCAAGAA
16228594 GTACTTCTACTTCTCCCAAGAA
1 GTACTTCTACTTCTCCCAAGAA
16228616 GTACTT
1 GTACTT
16228622 GTACCCTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.10, T:0.34
Consensus pattern (22 bp):
GTACTTCTACTTCTCCCAAGAA
Found at i:16243274 original size:66 final size:66
Alignment explanation
Indices: 16243154--16243283 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 66
16243144 CCATTTTCTA
* *
16243154 ATAATTGAAAATTACCAGTCACGCAGAGTATACTCTAAGAACTTCATACAGAATATATTCAGACA
1 ATAATTGAAAATTACCAGTCAAGCAGAGTATACTCTAAGAACTTCATACAGAATACATTCAGACA
16243219 G
66 G
* * * * * * *
16243220 ATAATTGAAAATTACCGGTCAAGCGGAGTGTATTCTAAGAACTTCATGCTGAATACGTTCAGAC
1 ATAATTGAAAATTACCAGTCAAGCAGAGTATACTCTAAGAACTTCATACAGAATACATTCAGAC
16243284 TTCAGACAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (66 bp):
ATAATTGAAAATTACCAGTCAAGCAGAGTATACTCTAAGAACTTCATACAGAATACATTCAGACA
G
Found at i:16244802 original size:41 final size:40
Alignment explanation
Indices: 16244737--16244817 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
16244727 ATTTTTATTA
*
16244737 GATAGTTTTCTAGAGCGTTGGGTGTCTGTGAAAACGTATC
1 GATAGTTTTCTAGAGCATTGGGTGTCTGTGAAAACGTATC
* * *
16244777 GATAGTTTCTCTTGAGCATTGGGTGTTTGTGGAAACGTATC
1 GATAGTTT-TCTAGAGCATTGGGTGTCTGTGAAAACGTATC
16244818 ATTAGCTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 8 0.22
41 28 0.78
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.37
Consensus pattern (40 bp):
GATAGTTTTCTAGAGCATTGGGTGTCTGTGAAAACGTATC
Found at i:16253862 original size:29 final size:29
Alignment explanation
Indices: 16253799--16253862 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
16253789 ATAAAAGAAC
* * *
16253799 CATTAGAAGAATCACAAGAAAAACTGATT
1 CATTAAAAGAATCAAAAGAAAAACCGATT
** *
16253828 TGTTAAAAGAATCAAAAGAAAACCCGATT
1 CATTAAAAGAATCAAAAGAAAAACCGATT
16253857 CATTAA
1 CATTAA
16253863 CCAAAGGAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (29 bp):
CATTAAAAGAATCAAAAGAAAAACCGATT
Found at i:16256257 original size:21 final size:22
Alignment explanation
Indices: 16256233--16256276 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
16256223 ATTAAAATAA
16256233 TATTTATGTGTATGTTT-TTAT
1 TATTTATGTGTATGTTTATTAT
* * *
16256254 TATTTGTTTGTTTGTTTATTAT
1 TATTTATGTGTATGTTTATTAT
16256276 T
1 T
16256277 CATTAACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.16, C:0.00, G:0.14, T:0.70
Consensus pattern (22 bp):
TATTTATGTGTATGTTTATTAT
Found at i:16256346 original size:23 final size:23
Alignment explanation
Indices: 16256298--16256373 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
16256288 TTCGTGAGCG
* *
16256298 TGTTCAATTATATTTTCATGAACA
1 TGTTCGATTA-ATGTTCATGAACA
*
16256322 TGTTCGATTAATGTTCGTGAACA
1 TGTTCGATTAATGTTCATGAACA
*
16256345 TGTTCGATTAA-GTTAAATGAACA
1 TGTTCGATTAATGTT-CATGAACA
16256368 TGTTCG
1 TGTTCG
16256374 TGAACATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 3 0.07
23 34 0.74
24 9 0.20
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGATTAATGTTCATGAACA
Found at i:16256383 original size:23 final size:23
Alignment explanation
Indices: 16256339--16256384 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
16256329 TTAATGTTCG
* *
16256339 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
16256362 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
16256385 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:16257461 original size:28 final size:27
Alignment explanation
Indices: 16257430--16257523 Score: 125
Period size: 28 Copynumber: 3.4 Consensus size: 27
16257420 ATAGATATCT
*
16257430 CTTTTCATAATATCCTTACGGATATAAC
1 CTTTTCA-AATATCTTTACGGATATAAC
* *
16257458 CTTTTCAATATATTTTTACGGATACAAC
1 CTTTTCAA-ATATCTTTACGGATATAAC
* *
16257486 CTTTTCAAATATCTTTTCGAATATAAC
1 CTTTTCAAATATCTTTACGGATATAAC
16257513 CTTTTCAAATA
1 CTTTTCAAATA
16257524 ATTTTAGAGC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
27 27 0.47
28 31 0.53
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (27 bp):
CTTTTCAAATATCTTTACGGATATAAC
Found at i:16263126 original size:16 final size:16
Alignment explanation
Indices: 16263082--16263130 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
16263072 AAATACTCGA
16263082 AATTAATTACCAAAA-
1 AATTAATTACCAAAAT
* *
16263097 CA-TAATATA-AAAAAT
1 AATTAAT-TACCAAAAT
16263112 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
16263128 AAT
1 AAT
16263131 ATCTCCATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
14 8 0.31
15 6 0.23
16 12 0.46
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTAATTACCAAAAT
Found at i:16263197 original size:30 final size:30
Alignment explanation
Indices: 16263163--16263257 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
16263153 AAATGGTACA
16263163 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
** * * * * *
16263193 AAAT-AAT-GGTGTGTGGATATCATTTTGGT
1 AAATAAATATTTATTTTG-TACCATTTTAGT
* *
16263222 ATATAAATATTTATTTTGTACAATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
16263252 AAATAA
1 AAATAA
16263258 CCCATTTTGG
Statistics
Matches: 45, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
28 4 0.09
29 16 0.36
30 21 0.47
31 4 0.09
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (30 bp):
AAATAAATATTTATTTTGTACCATTTTAGT
Found at i:16264039 original size:43 final size:43
Alignment explanation
Indices: 16263957--16264041 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
16263947 ATTAACATGT
* * *
16263957 TAAATTATATTACTTGACTCGTGTAAATATGGTTGCATGTTAC
1 TAAAGTATATTACTTGACTCGTATAAATATGCTTGCATGTTAC
* * *
16264000 TAAAGTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAAGTATATTACTTGACTCGTATAAATATGCTTG-CATGTTA
16264042 TTAATTGTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.09
43 32 0.91
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (43 bp):
TAAAGTATATTACTTGACTCGTATAAATATGCTTGCATGTTAC
Found at i:16264668 original size:45 final size:45
Alignment explanation
Indices: 16264603--16264691 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
16264593 GCCTAGCTCA
*
16264603 TCAAGCCAAAGATATCAGCCTCAGTTTGACAACCCACCGCAATAC
1 TCAAGCCAAAGATACCAGCCTCAGTTTGACAACCCACCGCAATAC
* * * * *
16264648 TCAAGCTAAGGATACCAGCCTCATTTTGACGAGCCACCGCAATA
1 TCAAGCCAAAGATACCAGCCTCAGTTTGACAACCCACCGCAATA
16264692 TTCTACTCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (45 bp):
TCAAGCCAAAGATACCAGCCTCAGTTTGACAACCCACCGCAATAC
Found at i:16264731 original size:21 final size:21
Alignment explanation
Indices: 16264686--16264727 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
16264676 ACGAGCCACC
*
16264686 GCAATATTCTACTCCTCTCGG
1 GCAATACTCTACTCCTCTCGG
16264707 GCAATACTCTACTCCT-TCGG
1 GCAATACTCTACTCCTCTCGG
16264727 G
1 G
16264728 GCAAATAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.31
Consensus pattern (21 bp):
GCAATACTCTACTCCTCTCGG
Found at i:16269615 original size:24 final size:24
Alignment explanation
Indices: 16269562--16269615 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
16269552 TAATTAACAT
**
16269562 TTATAATTAAACATATCATTTTTA
1 TTATAATTAAACATATCATTTAAA
* *
16269586 TCATAATTAATCATAT-ATGTTAAA
1 TTATAATTAAACATATCAT-TTAAA
16269610 TTATAA
1 TTATAA
16269616 ACACTTTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (24 bp):
TTATAATTAAACATATCATTTAAA
Found at i:16274789 original size:18 final size:18
Alignment explanation
Indices: 16274751--16274794 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
16274741 TAAAAGATTA
16274751 TTAAAAATAAATAAAATT
1 TTAAAAATAAATAAAATT
* *
16274769 TTATAAATAAA-AAATTCT
1 TTAAAAATAAATAAAAT-T
16274787 TTAAAAAT
1 TTAAAAAT
16274795 TCTTTCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAAATAAATAAAATT
Found at i:16275499 original size:31 final size:31
Alignment explanation
Indices: 16275430--16275501 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
16275420 TAATCTAGTC
* *
16275430 CTCATAAAATAATAAAAGAATCAATTAAACT
1 CTCATAAAATAATAAAAAAATAAATTAAACT
* **
16275461 CTTATAAAATAA-AATAAAAATAAATTAAGTT
1 CTCATAAAATAATAA-AAAAATAAATTAAACT
16275492 CTCATAAAAT
1 CTCATAAAAT
16275502 TTTCACGTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (31 bp):
CTCATAAAATAATAAAAAAATAAATTAAACT
Found at i:16276177 original size:14 final size:14
Alignment explanation
Indices: 16276158--16276208 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
16276148 TAATAATTAT
*
16276158 TTATCAAATATAAA
1 TTATCAAATACAAA
16276172 TTATCAAATCACAAA
1 TTATCAAAT-ACAAA
16276187 -TATACAAGATACAAA
1 TTAT-CAA-ATACAAA
16276202 TTATCAA
1 TTATCAA
16276209 TATCGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.38
15 15 0.47
16 5 0.16
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (14 bp):
TTATCAAATACAAA
Found at i:16283171 original size:63 final size:65
Alignment explanation
Indices: 16283096--16283217 Score: 176
Period size: 63 Copynumber: 1.9 Consensus size: 65
16283086 AATAACATAC
* * **
16283096 AATTTATGAAGAAATTAAAAATTGGACTATAAATA-TATAT-CTTAAAAATATTTAAATATATAT
1 AATTTATCAAGAAATTAAAAATTAGACTATAAATAGTATATGCGAAAAAATATTTAAATATATAT
*
16283159 AATTTATCAAGAAATTGAAAATTAGACTATAAATATGTATATGCGAAAAAATATTTAAA
1 AATTTATCAAGAAATTAAAAATTAGACTATAAATA-GTATATGCGAAAAAATATTTAAA
16283218 AACAACGATA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
63 32 0.63
65 5 0.10
66 14 0.27
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.35
Consensus pattern (65 bp):
AATTTATCAAGAAATTAAAAATTAGACTATAAATAGTATATGCGAAAAAATATTTAAATATATAT
Found at i:16292816 original size:21 final size:21
Alignment explanation
Indices: 16292792--16292832 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16292782 CCCCTCCCCC
16292792 TCCCCCTCCTCCACCTCCACT
1 TCCCCCTCCTCCACCTCCACT
* *
16292813 TCCCCGTTCTCCACCTCCAC
1 TCCCCCTCCTCCACCTCCAC
16292833 CTGGAATCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.63, G:0.02, T:0.24
Consensus pattern (21 bp):
TCCCCCTCCTCCACCTCCACT
Found at i:16295737 original size:58 final size:59
Alignment explanation
Indices: 16295675--16295822 Score: 194
Period size: 58 Copynumber: 2.5 Consensus size: 59
16295665 TAATAAGATT
16295675 ATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATT-ATA-TTTTAACATAATA
1 ATTATTAAATATAATTTAATAAAAATAATAAATAATTT-ATTAATATTTTTAACATAATA
* * * *
16295733 ATTATTAAATATAATTTAAT-GAAATAATATATAATTTATTAATATTTTTAATATAATT
1 ATTATTAAATATAATTTAATAAAAATAATAAATAATTTATTAATATTTTTAACATAATA
* * *
16295791 ATTATTAAAATATAAATTAGTAAAAATCATAA
1 ATTATT-AAATATAATTTAATAAAAATAATAA
16295823 TATATAATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
56 3 0.04
57 18 0.23
58 37 0.48
59 12 0.16
60 7 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTAAATATAATTTAATAAAAATAATAAATAATTTATTAATATTTTTAACATAATA
Found at i:16295746 original size:16 final size:15
Alignment explanation
Indices: 16295674--16295814 Score: 52
Period size: 14 Copynumber: 9.7 Consensus size: 15
16295664 TTAATAAGAT
16295674 TATTATTAAATATAA
1 TATTATTAAATATAA
* *
16295689 T-TTAATAAAAATAA
1 TATTATTAAATATAA
* *
16295703 TAAATAATTTAAT-T-A
1 T--ATTATTAAATATAA
*
16295718 TATT-TT-AACATAA
1 TATTATTAAATATAA
16295731 TAATTATTAAATATAA
1 T-ATTATTAAATATAA
* *
16295747 T-TTAATGAA-ATAA
1 TATTATTAAATATAA
*
16295760 TA-TA-TAATTTATTAA
1 TATTATTAA-ATA-TAA
*
16295775 TATT-TTTAATATAA
1 TATTATTAAATATAA
16295789 TTATTATTAAAATATAA
1 -TATTATT-AAATATAA
*
16295806 -ATTAGTAAA
1 TATTATTAAA
16295815 AATCATAATA
Statistics
Matches: 92, Mismatches: 17, Indels: 35
0.64 0.12 0.24
Matches are distributed among these distances:
11 2 0.02
12 5 0.05
13 11 0.12
14 28 0.30
15 21 0.23
16 13 0.14
17 12 0.13
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (15 bp):
TATTATTAAATATAA
Found at i:16295829 original size:24 final size:23
Alignment explanation
Indices: 16295800--16295849 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
16295790 TATTATTAAA
*
16295800 ATATAA-ATTAGTAAAAATCATAAT
1 ATATAATATTAG-AAAAATAAT-AT
16295824 ATATAATATTAGAAAAATAATAT
1 ATATAATATTAGAAAAATAATAT
16295847 ATA
1 ATA
16295850 ACCTACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 14 0.58
25 5 0.21
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAATATTAGAAAAATAATAT
Found at i:16297364 original size:2 final size:2
Alignment explanation
Indices: 16297357--16297383 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16297347 ATGTATGTAT
16297357 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
16297384 CTTTAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16298907 original size:16 final size:14
Alignment explanation
Indices: 16298871--16298898 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16298861 AGATTTTTAA
16298871 ATAATTTATATTTT
1 ATAATTTATATTTT
16298885 ATAATTTATATTTT
1 ATAATTTATATTTT
16298899 TTACCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATAATTTATATTTT
Found at i:16299475 original size:24 final size:24
Alignment explanation
Indices: 16299441--16299486 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16299431 ATAGATGCTC
* *
16299441 AACCTTTCATCTCCCTTGACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
*
16299465 AACCTTCCATCTTCCTTAACCT
1 AACCTTCCATCTCCCTTAACCT
16299487 CCCTTGACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.39, G:0.02, T:0.39
Consensus pattern (24 bp):
AACCTTCCATCTCCCTTAACCTTT
Found at i:16299483 original size:17 final size:17
Alignment explanation
Indices: 16299463--16299518 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
16299453 CCCTTGACCT
16299463 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
16299480 TTAACC-TCC--CTTGACC
1 TTAACCTTCCATCTT--CC
*
16299496 TTTAACCTTTCATCTTCC
1 -TTAACCTTCCATCTTCC
16299514 TTAAC
1 TTAAC
16299519 TTTTCATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 3 0.09
16 5 0.16
17 17 0.53
18 4 0.12
20 3 0.09
ACGTcount: A:0.20, C:0.38, G:0.02, T:0.41
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:16299494 original size:34 final size:34
Alignment explanation
Indices: 16299451--16299518 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
16299441 AACCTTTCAT
16299451 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
1 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
*
16299485 CTCCCTTGACCTTTAACCTTTCATCTTCCTTAAC
1 CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
16299519 TTTTCATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.40, G:0.03, T:0.40
Consensus pattern (34 bp):
CTCCCTTGACCTTTAACCTTCCATCTTCCTTAAC
Found at i:16300034 original size:33 final size:34
Alignment explanation
Indices: 16299977--16300053 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
16299967 TATTTTTCTG
* * * *
16299977 TTATATTATGCTTGCAAGTTTTGTTAAGGGATTAC
1 TTATATT-TACTTGAAAGTTTTGTTAAAGGACTAC
*
16300012 TTATGTTTACTTGAAAG-TTTGTTAAAGGACTAC
1 TTATATTTACTTGAAAGTTTTGTTAAAGGACTAC
16300045 TTATATTTA
1 TTATATTTA
16300054 TATTAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 22 0.61
34 8 0.22
35 6 0.17
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.47
Consensus pattern (34 bp):
TTATATTTACTTGAAAGTTTTGTTAAAGGACTAC
Found at i:16304991 original size:17 final size:17
Alignment explanation
Indices: 16304946--16304994 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
16304936 TTTCATCTCC
*
16304946 CTTGACCTTTAACCTTT
1 CTTGACCTTTAACCTCT
**
16304963 CATTTTCC-TTAACCTCT
1 C-TTGACCTTTAACCTCT
16304980 CTTGACCTTTAACCT
1 CTTGACCTTTAACCT
16304995 TCCGTCTTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 4 0.16
17 17 0.68
18 4 0.16
ACGTcount: A:0.18, C:0.33, G:0.04, T:0.45
Consensus pattern (17 bp):
CTTGACCTTTAACCTCT
Found at i:16309151 original size:14 final size:14
Alignment explanation
Indices: 16309132--16309158 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16309122 TGCTTCCAGG
16309132 TCTGTGACTGTGAC
1 TCTGTGACTGTGAC
16309146 TCTGTGACTGTGA
1 TCTGTGACTGTGA
16309159 GCAACTAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.37
Consensus pattern (14 bp):
TCTGTGACTGTGAC
Found at i:16312499 original size:14 final size:14
Alignment explanation
Indices: 16312480--16312509 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16312470 AGCAATCTTC
16312480 CACAAAAAAAAAAT
1 CACAAAAAAAAAAT
16312494 CACAAAAAAAAAAT
1 CACAAAAAAAAAAT
16312508 CA
1 CA
16312510 ATCTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.17, G:0.00, T:0.07
Consensus pattern (14 bp):
CACAAAAAAAAAAT
Found at i:16312543 original size:36 final size:36
Alignment explanation
Indices: 16312503--16312572 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
16312493 TCACAAAAAA
16312503 AAAATCAATCTTATTT-TCTTCAAAATAAAAAAATTT
1 AAAATCAATCTTATTTAT-TTCAAAATAAAAAAATTT
* *
16312539 AAAATTAATCTTATTTATTTCAAATTAAAAAAAT
1 AAAATCAATCTTATTTATTTCAAAATAAAAAAAT
16312573 ATAACACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (36 bp):
AAAATCAATCTTATTTATTTCAAAATAAAAAAATTT
Found at i:16313193 original size:46 final size:46
Alignment explanation
Indices: 16313126--16313226 Score: 193
Period size: 46 Copynumber: 2.2 Consensus size: 46
16313116 AAGCAGTAAT
*
16313126 TGACCCTCTATGTTCTAATTGCTCAATTCTGAGTAGGAAGCTTCCC
1 TGACCCTCTATGTTCTAATTGCTCAATTCTGAGTAGGAAGCTCCCC
16313172 TGACCCTCTATGTTCTAATTGCTCAATTCTGAGTAGGAAGCTCCCC
1 TGACCCTCTATGTTCTAATTGCTCAATTCTGAGTAGGAAGCTCCCC
16313218 TGACCCTCT
1 TGACCCTCT
16313227 CCCTTTCCGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.34
Consensus pattern (46 bp):
TGACCCTCTATGTTCTAATTGCTCAATTCTGAGTAGGAAGCTCCCC
Found at i:16313339 original size:2 final size:2
Alignment explanation
Indices: 16313334--16313376 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
16313324 TCTTTTTTCC
16313334 TA TA TA TA TA TA 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 TA TA TA
16313376 T
1 T
16313377 TCACAGCTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16314871 original size:29 final size:29
Alignment explanation
Indices: 16314809--16314877 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
16314799 ATCATTATAT
* *
16314809 TTTTAATCTTATATTGAATTTTATTGATTTA
1 TTTTAAT-TT-TATTAAATTTTATTGATTAA
*
16314840 TTTTTATTTTATTAAATTTTATT-ATTCAA
1 TTTTAATTTTATTAAATTTTATTGATT-AA
16314869 TTTTAATTT
1 TTTTAATTT
16314878 AAAATAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 22 0.67
30 2 0.06
31 6 0.18
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTTAATTTTATTAAATTTTATTGATTAA
Found at i:16315234 original size:1 final size:1
Alignment explanation
Indices: 16315223--16315255 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
16315213 AGTCCATTGA
*
16315223 CCCCCCGCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
16315256 AAAACAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.97, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:16322262 original size:3 final size:3
Alignment explanation
Indices: 16322254--16322286 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
16322244 TTCCAACGGA
16322254 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
16322287 TTGGAGGCAG
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:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:16325917 original size:26 final size:26
Alignment explanation
Indices: 16325867--16325917 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
16325857 TTCATGATAT
* * *
16325867 TGAAAAAATATTGAATAATTCTTGTA
1 TGAAAAAATATTGAAAAAATATTGTA
16325893 TGAAAAAATATTGAAAAAATATTGT
1 TGAAAAAATATTGAAAAAATATTGT
16325918 TAATCAGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (26 bp):
TGAAAAAATATTGAAAAAATATTGTA
Found at i:16339258 original size:21 final size:20
Alignment explanation
Indices: 16339234--16339280 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
16339224 TAGACTATTT
16339234 TTATAATTAATTAAATTTTTA
1 TTATAATTAATT-AATTTTTA
**
16339255 TTATTTTTAATTAATTTTTA
1 TTATAATTAATTAATTTTTA
*
16339275 ATATAA
1 TTATAA
16339281 AGACGGAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATAATTAATTAATTTTTA
Found at i:16339271 original size:11 final size:11
Alignment explanation
Indices: 16339240--16339276 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16339230 ATTTTTATAA
16339240 TTAATTAAATTT
1 TTAATT-AATTT
16339252 TT-ATT-ATTT
1 TTAATTAATTT
16339261 TTAATTAATTT
1 TTAATTAATTT
16339272 TTAAT
1 TTAAT
16339277 ATAAAGACGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.26
10 3 0.13
11 12 0.52
12 2 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTAATTAATTT
Found at i:16341024 original size:18 final size:17
Alignment explanation
Indices: 16341001--16341035 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16340991 TATAAAAAAT
*
16341001 TAATTTAACTTTTAATAA
1 TAATTTAA-TATTAATAA
16341019 TAATTTAATATTAATAA
1 TAATTTAATATTAATAA
16341036 CGTTACCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTTAATATTAATAA
Found at i:16341428 original size:15 final size:15
Alignment explanation
Indices: 16341378--16341430 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
16341368 AATTGTACTC
16341378 ATATTAAATAATAAAAT
1 ATATTAAATAAT--AAT
* **
16341395 ATATTTAAATTATTTT
1 ATA-TTAAATAATAAT
16341411 ATATTAAATAATAAT
1 ATATTAAATAATAAT
16341426 ATATT
1 ATATT
16341431 TATGATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 14 0.48
16 4 0.14
17 3 0.10
18 8 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTAAATAATAAT
Found at i:16343408 original size:25 final size:25
Alignment explanation
Indices: 16343337--16343409 Score: 60
Period size: 25 Copynumber: 2.9 Consensus size: 25
16343327 ATAATAAATC
*
16343337 TAAACTAAAACTTATTACCAATATT
1 TAAACTAAAACTTATTACTAATATT
* * * **
16343362 TAGA-T-ATATTTATAATGGTAATATT
1 TAAACTAAAACTTAT--TACTAATATT
16343387 TAAACTAAAACTTATTACTAATA
1 TAAACTAAAACTTATTACTAATA
16343410 ATTAGGTCTG
Statistics
Matches: 33, Mismatches: 11, Indels: 8
0.63 0.21 0.15
Matches are distributed among these distances:
23 6 0.18
24 1 0.03
25 19 0.58
26 1 0.03
27 6 0.18
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.40
Consensus pattern (25 bp):
TAAACTAAAACTTATTACTAATATT
Found at i:16344988 original size:18 final size:17
Alignment explanation
Indices: 16344945--16344988 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
16344935 TTTATTTAGT
**
16344945 AGTATTTTTATCTTAAA
1 AGTATTTTTATCCCAAA
*
16344962 AATAATTTTTATCCCAAA
1 AGT-ATTTTTATCCCAAA
16344980 AGTATTTTT
1 AGTATTTTT
16344989 GAAAAGCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (17 bp):
AGTATTTTTATCCCAAA
Found at i:16346296 original size:32 final size:32
Alignment explanation
Indices: 16346260--16346333 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
16346250 TATGCAAAAA
*
16346260 TATATTATTTATAAAATGTGT-TA-TAGAAATTT
1 TATATTATTTA-AAAAT-TATATATTAGAAATTT
* *
16346292 TATATTATTTAAAGATTATATATTATAAATTT
1 TATATTATTTAAAAATTATATATTAGAAATTT
16346324 TATATTATTT
1 TATATTATTT
16346334 TTATTTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 2 0.05
31 6 0.16
32 29 0.78
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (32 bp):
TATATTATTTAAAAATTATATATTAGAAATTT
Found at i:16346299 original size:16 final size:15
Alignment explanation
Indices: 16346280--16346331 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 15
16346270 ATAAAATGTG
16346280 TTATAGAAATTTTATA
1 TTATA-AAATTTTATA
*
16346296 TTATTTAAAGATTATATA
1 TTA--TAAA-ATTTTATA
16346314 TTAT-AAATTTTATA
1 TTATAAAATTTTATA
16346328 TTAT
1 TTAT
16346332 TTTTATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 11 0.35
15 2 0.06
16 4 0.13
17 2 0.06
18 12 0.39
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
TTATAAAATTTTATA
Found at i:16351661 original size:17 final size:16
Alignment explanation
Indices: 16351608--16351665 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
16351598 AATTTAAGTA
*
16351608 AAAAATATTAAAATTAT
1 AAAAATA-TATAATTAT
** *
16351625 AAAATATATATTTTTTT
1 AAAA-ATATATAATTAT
16351642 AAAAATATATCAATTAT
1 AAAAATATAT-AATTAT
16351659 AAAAATA
1 AAAAATA
16351666 GTAAAAGATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 6 0.19
17 23 0.72
18 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAATATATAATTAT
Found at i:16370826 original size:14 final size:16
Alignment explanation
Indices: 16370807--16370840 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
16370797 TCAATTTCAA
16370807 ATATATT-TATT-TTT
1 ATATATTATATTATTT
16370821 ATATATTATATTATTT
1 ATATATTATATTATTT
16370837 ATAT
1 ATAT
16370841 CATATGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 4 0.22
16 7 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATATTATATTATTT
Found at i:16370845 original size:19 final size:19
Alignment explanation
Indices: 16370808--16370845 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
16370798 CAATTTCAAA
*
16370808 TATATTTATTTTTATATAT
1 TATATTTATTTATATATAT
16370827 TATA-TTATTTATATCATAT
1 TATATTTATTTATAT-ATAT
16370846 GAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTTATTTATATATAT
Found at i:16373350 original size:15 final size:15
Alignment explanation
Indices: 16373330--16373361 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16373320 TTTTTTGTAT
*
16373330 TATTTTAATATTAAA
1 TATTTTAAAATTAAA
16373345 TATTTTAAAATTAAA
1 TATTTTAAAATTAAA
16373360 TA
1 TA
16373362 ACATCAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAATTAAA
Found at i:16373922 original size:15 final size:16
Alignment explanation
Indices: 16373886--16373924 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
16373876 ATCGAAACTA
16373886 AATTTTAATTTTTAAT
1 AATTTTAATTTTTAAT
16373902 AATTTTAATTTTT-AT
1 AATTTTAATTTTTAAT
*
16373917 ATTTTTAA
1 AATTTTAA
16373925 AGAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATTTTAATTTTTAAT
Found at i:16375906 original size:11 final size:11
Alignment explanation
Indices: 16375892--16375933 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
16375882 ATTAAATGTT
16375892 TAATAAATAAA
1 TAATAAATAAA
*
16375903 TAATAAATATA
1 TAATAAATAAA
*
16375914 TAAT-AAT-TA
1 TAATAAATAAA
16375923 TAATAAATAAA
1 TAATAAATAAA
16375934 AAAGCAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 6 0.22
10 6 0.22
11 15 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:16377141 original size:23 final size:23
Alignment explanation
Indices: 16377067--16377280 Score: 142
Period size: 23 Copynumber: 9.5 Consensus size: 23
16377057 TAAACGGAAC
* * *
16377067 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
16377089 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
16377111 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
16377137 AAACAGAGAGTACACAAA-----
1 AAACAGAGAGCACACAAAGTGCT
* *
16377155 ATAC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
16377176 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
16377199 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
16377222 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
16377247 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
16377270 AATCAGAGAGC
1 AAACAGAGAGC
16377281 GCGCTAGTGT
Statistics
Matches: 149, Mismatches: 27, Indels: 31
0.72 0.13 0.15
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
21 2 0.01
22 18 0.12
23 78 0.52
24 2 0.01
25 28 0.19
26 8 0.05
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:16377234 original size:48 final size:46
Alignment explanation
Indices: 16377160--16377280 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
16377150 ACAAAATACT
* * *
16377160 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
16377206 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
16377254 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
16377281 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:16379808 original size:29 final size:29
Alignment explanation
Indices: 16379727--16380050 Score: 231
Period size: 30 Copynumber: 10.9 Consensus size: 29
16379717 TAGGTCCCTG
* * * * *
16379727 AACTTTCTAAAAATCATATTTTAACTCATA
1 AACTTT-TCAAAATTATATTTTGACCCTTA
* * * *
16379757 AACTTCTTTAATATTACATTTTGACTCTTA
1 AACTT-TTCAAAATTATATTTTGACCCTTA
*
16379787 AACTTTTCAAAATTATATTTTGACCCCTA
1 AACTTTTCAAAATTATATTTTGACCCTTA
* **
16379816 AACTTTTTCAAAATTATATTTTAACCCCAA
1 AAC-TTTTCAAAATTATATTTTGACCCTTA
* *
16379846 AAATTTTCCAAAATTATATTTTGACCCCTA
1 AACTTTT-CAAAATTATATTTTGACCCTTA
* * *
16379876 AACTTCTCTAAAATTACA-TTTAACCCTTA
1 AACTTTTC-AAAATTATATTTTGACCCTTA
* * *
16379905 AACTTCTCAAGATTATATTTTAACCC-TA
1 AACTTTTCAAAATTATATTTTGACCCTTA
* * *
16379933 AACCTTTCCAAAATTACATTTTAACCCTCTA
1 AA-CTTTTCAAAATTATATTTTGACCCT-TA
* * * *
16379964 AACTTCTCCAAAATCATGTTTTGACCCTCA
1 AACTT-TTCAAAATTATATTTTGACCCTTA
** * *
16379994 AACCTTCCCAAAATCACATTTTGA-CCTCTA
1 AA-CTTTTCAAAATTATATTTTGACCCT-TA
*
16380024 AACTTTTCCAAAATTATGTTTTGACCC
1 AACTTTT-CAAAATTATATTTTGACCC
16380051 CGTATTCTTC
Statistics
Matches: 240, Mismatches: 41, Indels: 25
0.78 0.13 0.08
Matches are distributed among these distances:
28 11 0.05
29 78 0.32
30 123 0.51
31 28 0.12
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (29 bp):
AACTTTTCAAAATTATATTTTGACCCTTA
Found at i:16379870 original size:60 final size:60
Alignment explanation
Indices: 16379769--16380051 Score: 299
Period size: 60 Copynumber: 4.8 Consensus size: 60
16379759 CTTCTTTAAT
* * * * **
16379769 ATTACATTTTGACTCTTAAACTTTT-CAAAATTATATTTTGACCCCTAAACTTTTTCAAA
1 ATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTGACCCCTAAACCTTCCCAAA
* * * *
16379828 ATTATATTTTAACCCCAAAAATTTTCCAAAATTATATTTTGACCCCTAAA-CTTCTCTAAA
1 ATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTGACCCCTAAACCTTC-CCAAA
* * * * *
16379888 ATTACA-TTTAACCCTTAAACTTCT-CAAGATTATATTTT-AACCCTAAACCTTTCCAAA
1 ATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTGACCCCTAAACCTTCCCAAA
* * *
16379945 ATTACATTTTAACCCTCTAAACTTCTCCAAAATCATGTTTTGA-CCCTCAAACCTTCCCAAA
1 ATTACATTTTAACCC-CTAAACTTTTCCAAAATTATATTTTGACCCCT-AAACCTTCCCAAA
* * * *
16380006 ATCACATTTTGACCTCTAAACTTTTCCAAAATTATGTTTTGACCCC
1 ATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTGACCCC
16380052 GTATTCTTCG
Statistics
Matches: 186, Mismatches: 29, Indels: 16
0.81 0.13 0.07
Matches are distributed among these distances:
57 18 0.10
58 24 0.13
59 44 0.24
60 72 0.39
61 28 0.15
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (60 bp):
ATTACATTTTAACCCCTAAACTTTTCCAAAATTATATTTTGACCCCTAAACCTTCCCAAA
Found at i:16379965 original size:88 final size:90
Alignment explanation
Indices: 16379722--16379977 Score: 263
Period size: 89 Copynumber: 2.9 Consensus size: 90
16379712 TCCAATAGGT
* * * * * ** * *
16379722 CCCTGAACTTTCTAAAAATCATATTTTAA-CTCATAAACTTCTTTAATATTACATTTTGACTCT-
1 CCCTAAACTTTCTCAAAATTATATTTTAACCCCAAAAACTT-TCCAAAATTACATTTTGACCCTC
* * *
16379785 TAAACTTTTCAAAATTATATTTTGAC
65 TAAACTTCTCAAAATTACATTTTAAC
* * *
16379811 CCCTAAACTTTTTCAAAATTATATTTTAACCCCAAAAATTTTCCAAAATTATATTTTGACCC-CT
1 CCCTAAACTTTCTCAAAATTATATTTTAACCCCAAAAACTTTCCAAAATTACATTTTGACCCTCT
16379875 AAACTTCTCTAAAATTACA-TTTAAC
66 AAACTTCTC-AAAATTACATTTTAAC
* * * * *
16379900 CCTTAAAC-TTCTCAAGATTATATTTTAA-CCCTAAACCTTTCCAAAATTACATTTTAACCCTCT
1 CCCTAAACTTTCTCAAAATTATATTTTAACCCCAAAAACTTTCCAAAATTACATTTTGACCCTCT
16379963 AAACTTCTCCAAAAT
66 AAACTTCT-CAAAAT
16379978 CATGTTTTGA
Statistics
Matches: 139, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
87 27 0.19
88 33 0.24
89 63 0.45
90 16 0.12
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.39
Consensus pattern (90 bp):
CCCTAAACTTTCTCAAAATTATATTTTAACCCCAAAAACTTTCCAAAATTACATTTTGACCCTCT
AAACTTCTCAAAATTACATTTTAAC
Found at i:16380007 original size:118 final size:118
Alignment explanation
Indices: 16379736--16380047 Score: 317
Period size: 118 Copynumber: 2.6 Consensus size: 118
16379726 GAACTTTCTA
* * * ** * * * *
16379736 AAAATCATATTTTAACTCATAAACTTCTTTAATATTACATTTTGACTCTTAAACTTTTCAAAATT
1 AAAATCATATTTTGACCCCTAAACTTCTCCAAAATTACA-TTTAACCCTTAAACTTCTCAAAATT
* * * * *
16379801 ATATTTTGACCCCTAAACTTTTTCAAAATTATATTTTAACCCCAAAAATTTTCC
65 ATATTTTGAACCCTAAACCTTTCCAAAATTACATTTTAACCCCAAAAATTCTCC
* * *
16379855 AAAATTATATTTTGACCCCTAAACTTCTCTAAAATTACATTTAACCCTTAAACTTCTCAAGATTA
1 AAAATCATATTTTGACCCCTAAACTTCTCCAAAATTACATTTAACCCTTAAACTTCTCAAAATTA
* *
16379920 TATTTT-AACCCTAAACCTTTCCAAAATTACATTTTAACCCTCTAAACTTCTCC
66 TATTTTGAACCCTAAACCTTTCCAAAATTACATTTTAACCC-CAAAAATTCTCC
* * * *
16379973 AAAATCATGTTTTGA-CCCTCAAACCTTC-CCAAAATCACATTTTGA-CCTCTAAACTTTTCCAA
1 AAAATCATATTTTGACCCCT-AAA-CTTCTCCAAAATTACA-TTTAACCCT-TAAACTTCT-CAA
*
16380035 AATTATGTTTTGA
61 AATTATATTTTGA
16380048 CCCCGTATTC
Statistics
Matches: 161, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
117 34 0.21
118 65 0.40
119 49 0.30
120 12 0.07
121 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (118 bp):
AAAATCATATTTTGACCCCTAAACTTCTCCAAAATTACATTTAACCCTTAAACTTCTCAAAATTA
TATTTTGAACCCTAAACCTTTCCAAAATTACATTTTAACCCCAAAAATTCTCC
Found at i:16380046 original size:30 final size:29
Alignment explanation
Indices: 16379769--16380050 Score: 246
Period size: 30 Copynumber: 9.5 Consensus size: 29
16379759 CTTCTTTAAT
* *
16379769 ATTACATTTTGACTCTTAAACTTTT-CAAA
1 ATTATATTTTGAC-CCTAAACTTTTCCAAA
*
16379798 ATTATATTTTGACCCCTAAACTTTTTCAAA
1 ATTATATTTTGA-CCCTAAACTTTTCCAAA
* * *
16379828 ATTATATTTTAACCCCAAAAATTTTCCAAA
1 ATTATATTTTGA-CCCTAAACTTTTCCAAA
* *
16379858 ATTATATTTTGACCCCTAAACTTCTCTAAA
1 ATTATATTTTGA-CCCTAAACTTTTCCAAA
* * * *
16379888 ATTACA-TTTAACCCTTAAACTTCT-CAAG
1 ATTATATTTTGACCC-TAAACTTTTCCAAA
* *
16379916 ATTATATTTTAACCCTAAACCTTTCCAAA
1 ATTATATTTTGACCCTAAACTTTTCCAAA
* * *
16379945 ATTACATTTTAACCCTCTAAACTTCTCCAAA
1 ATTATATTTTGA-CC-CTAAACTTTTCCAAA
* * * *
16379976 ATCATGTTTTGACCCTCAAACCTTCCCAAA
1 ATTATATTTTGACCCT-AAACTTTTCCAAA
* *
16380006 ATCACATTTTGACCTCTAAACTTTTCCAAA
1 ATTATATTTTGACC-CTAAACTTTTCCAAA
*
16380036 ATTATGTTTTGACCC
1 ATTATATTTTGACCC
16380051 CGTATTCTTC
Statistics
Matches: 208, Mismatches: 36, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
28 17 0.08
29 59 0.28
30 109 0.52
31 23 0.11
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTATATTTTGACCCTAAACTTTTCCAAA
Found at i:16384831 original size:20 final size:20
Alignment explanation
Indices: 16384806--16384847 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
16384796 TAAAAATCAC
16384806 TTAAAAATATTAAT-AATCG
1 TTAAAAATATTAATAAATCG
*
16384825 TTAAAAATATTGATAAATCG
1 TTAAAAATATTAATAAATCG
16384845 TTA
1 TTA
16384848 CTGGAACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
TTAAAAATATTAATAAATCG
Found at i:16393329 original size:18 final size:16
Alignment explanation
Indices: 16393296--16393343 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
16393286 CAATTGTAAA
*
16393296 TAATTTAAAA-TT-TT
1 TAATTAAAAATTTATT
16393310 TAATTAATTAAATTTATT
1 TAATTAA--AAATTTATT
16393328 TAATTAAAAATTTATT
1 TAATTAAAAATTTATT
16393344 CTTATCCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 6 0.21
16 12 0.41
17 2 0.07
18 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATTAAAAATTTATT
Found at i:16404290 original size:55 final size:56
Alignment explanation
Indices: 16404227--16404374 Score: 192
Period size: 55 Copynumber: 2.7 Consensus size: 56
16404217 AGTAGTTATG
* * *
16404227 TAGAAATCAAATTACTAAAAGATAATATCTCATAATAATA-TCTTATAATATCCCAT
1 TAGAAATCAAATTATTAAAAGATAATATCCCATAATAATACTC-TATAATATCCCAA
* * *
16404283 TAG-AATCAACTTATTAAAAGATAATATCCCATTATAATACTCTATAATCTCCCAA
1 TAGAAATCAAATTATTAAAAGATAATATCCCATAATAATACTCTATAATATCCCAA
* * *
16404338 TAGAAATTAAATTGTTAAAAGATAATATCGCATAATA
1 TAGAAATCAAATTATTAAAAGATAATATCCCATAATA
16404375 GTATTCTAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
55 46 0.58
56 33 0.42
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.33
Consensus pattern (56 bp):
TAGAAATCAAATTATTAAAAGATAATATCCCATAATAATACTCTATAATATCCCAA
Found at i:16407668 original size:2 final size:2
Alignment explanation
Indices: 16407655--16407698 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
16407645 TTCCAAAGCA
*
16407655 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16407697 AT
1 AT
16407699 TAATAATCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16421974 original size:22 final size:23
Alignment explanation
Indices: 16421949--16422011 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
16421939 TTAAAAATAA
*
16421949 TAAAATTTTAATTTAATTATT-T
1 TAAAATTATAATTTAATTATTGT
* *
16421971 TAAAATTATATTTTTATTATTGT
1 TAAAATTATAATTTAATTATTGT
*
16421994 AAAAATTATAATTTAATT
1 TAAAATTATAATTTAATT
16422012 TTGATCCCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TAAAATTATAATTTAATTATTGT
Found at i:16424057 original size:14 final size:15
Alignment explanation
Indices: 16424027--16424062 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
16424017 TAACCTAGAT
16424027 TAATTAAATTGAACA
1 TAATTAAATTGAACA
*
16424042 TAATTTAATT-AACA
1 TAATTAAATTGAACA
16424056 TAATTAA
1 TAATTAA
16424063 CCCTTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (15 bp):
TAATTAAATTGAACA
Found at i:16424991 original size:24 final size:24
Alignment explanation
Indices: 16424964--16425009 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
16424954 TAATATTTTA
*
16424964 ATATATGAAAT-ATTAATTTTAAAT
1 ATATAT-AAATAATTAATATTAAAT
*
16424988 ATATCTAAATAATTAATATTAA
1 ATATATAAATAATTAATATTAA
16425010 TTATTTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATATAAATAATTAATATTAAAT
Found at i:16425126 original size:19 final size:20
Alignment explanation
Indices: 16425104--16425143 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
16425094 CACAATTATA
16425104 TTATTTTAAA-AAATAATTT
1 TTATTTTAAATAAATAATTT
*
16425123 TTATTTTAAATTAATAATTT
1 TTATTTTAAATAAATAATTT
16425143 T
1 T
16425144 AATACATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTTTAAATAAATAATTT
Found at i:16433564 original size:16 final size:16
Alignment explanation
Indices: 16433543--16433577 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
16433533 GCTGCTAAAC
16433543 AAGTTAAGAATAAATT
1 AAGTTAAGAATAAATT
16433559 AAGTTAAGAATAAATT
1 AAGTTAAGAATAAATT
16433575 AAG
1 AAG
16433578 CTCTCAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (16 bp):
AAGTTAAGAATAAATT
Found at i:16443487 original size:10 final size:9
Alignment explanation
Indices: 16443476--16443549 Score: 69
Period size: 9 Copynumber: 7.8 Consensus size: 9
16443466 AATTTATGAT
16443476 TTTTTATAA
1 TTTTTATAA
16443485 TTTTTATAAA
1 TTTTTAT-AA
* *
16443495 CTTTTATGA
1 TTTTTATAA
*
16443504 TTTTAATTAA
1 TTTTTA-TAA
16443514 TTTTTAATAA
1 TTTTT-ATAA
16443524 -TTTTATAA
1 TTTTTATAA
16443532 TTTTTATGAA
1 TTTTTAT-AA
16443542 TATTTTAT
1 T-TTTTAT
16443550 TAAGTGGACG
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
8 4 0.08
9 22 0.42
10 20 0.38
11 7 0.13
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:16443490 original size:19 final size:19
Alignment explanation
Indices: 16443476--16443549 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
16443466 AATTTATGAT
16443476 TTTTTATAATTTTTATAAA
1 TTTTTATAATTTTTATAAA
* * * *
16443495 CTTTTATGATTTTAATTAA
1 TTTTTATAATTTTTATAAA
16443514 TTTTTAATAA-TTTTAT-AA
1 TTTTT-ATAATTTTTATAAA
16443532 TTTTTATGAATATTTTAT
1 TTTTTAT-AAT-TTTTAT
16443550 TAAGTGGACG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.05
18 9 0.20
19 24 0.55
20 9 0.20
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAA
Found at i:16443501 original size:29 final size:28
Alignment explanation
Indices: 16443468--16443549 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 28
16443458 TAATATGCAA
16443468 TTTATGATTTTTTATAATTTTTATA-AACT
1 TTTATGA-TTTTTATAATTTTTATATAA-T
*
16443497 TTTATGATTTTAATTAATTTTTA-ATAAT
1 TTTATGATTTTTA-TAATTTTTATATAAT
*
16443525 TTTATAATTTTTATGAATATTTTAT
1 TTTATGATTTTTAT-AAT-TTTTAT
16443550 TAAGTGGACG
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 1 0.02
28 21 0.47
29 23 0.51
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTATGATTTTTATAATTTTTATATAAT
Found at i:16448829 original size:26 final size:27
Alignment explanation
Indices: 16448800--16448853 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
16448790 GAATGTGAGG
*
16448800 AGAGTAAAAGCTTTGG-GGGAAAGTAA
1 AGAGTAAAAGCTTTGGAGGAAAAGTAA
*
16448826 AGAGTAAAAGTTTTGGAGGAAAAGTAA
1 AGAGTAAAAGCTTTGGAGGAAAAGTAA
16448853 A
1 A
16448854 AAGGTTTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.46, C:0.02, G:0.31, T:0.20
Consensus pattern (27 bp):
AGAGTAAAAGCTTTGGAGGAAAAGTAA
Found at i:16449370 original size:20 final size:20
Alignment explanation
Indices: 16449329--16449371 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
16449319 GAAAAATAAA
* *
16449329 ATAAACATGGAATATATTAT
1 ATAAACATGAAATATATCAT
16449349 ATAAA-ATGAAATATTATCAT
1 ATAAACATGAAATA-TATCAT
16449369 ATA
1 ATA
16449372 GAAAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (20 bp):
ATAAACATGAAATATATCAT
Found at i:16450141 original size:58 final size:56
Alignment explanation
Indices: 16450077--16450222 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 56
16450067 AATTTTAATG
*
16450077 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
16450135 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
16450193 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
16450223 TATAATATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 3 0.04
58 43 0.55
59 15 0.19
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:16454210 original size:25 final size:25
Alignment explanation
Indices: 16454178--16454226 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
16454168 TAAAACTTGT
16454178 AGTCTTATTTCTTAATCCTAAACTG
1 AGTCTTATTTCTTAATCCTAAACTG
16454203 AGTCTTATTTCTTAATCCTAAACT
1 AGTCTTATTTCTTAATCCTAAACT
16454227 AATATACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (25 bp):
AGTCTTATTTCTTAATCCTAAACTG
Found at i:16455297 original size:139 final size:139
Alignment explanation
Indices: 16455047--16455467 Score: 765
Period size: 139 Copynumber: 3.0 Consensus size: 139
16455037 TAAGCAACAC
16455047 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
1 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
16455112 TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
66 TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
16455177 AACAGAATG
131 AACAGAATG
*
16455186 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGAAACATAA
1 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
*
16455251 TATTTGTACAACCAGCAACACATTGAACCCCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
66 TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
*
16455316 AACAAAATG
131 AACAGAATG
*
16455325 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAAAATC-GAAAGCAACATA
1 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAG-AAGCAACATA
*
16455389 ATATTTGTACAA-CAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAACGTATCC
65 ATATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCC
16455453 TAACAGAATG
130 TAACAGAATG
*
16455463 GCAAT
1 TCAAT
16455468 GGATGATGAC
Statistics
Matches: 272, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
138 64 0.24
139 208 0.76
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (139 bp):
TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
AACAGAATG
Found at i:16458019 original size:30 final size:30
Alignment explanation
Indices: 16457985--16458048 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
16457975 TTAATTGAGA
*
16457985 TAAAAAAAATTCAAATACAAAATTTAATAT
1 TAAAAAAAATTCAAATACAAAATTAAATAT
* * **
16458015 TAAAATAAATTCAGATACTTAATTAAATAT
1 TAAAAAAAATTCAAATACAAAATTAAATAT
16458045 TAAA
1 TAAA
16458049 TTAAAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (30 bp):
TAAAAAAAATTCAAATACAAAATTAAATAT
Found at i:16464542 original size:3 final size:3
Alignment explanation
Indices: 16464536--16464565 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16464526 ACTATGAGGG
16464536 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
16464566 TGATGATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:16465514 original size:22 final size:23
Alignment explanation
Indices: 16465488--16465538 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
16465478 TATTTTGGAT
* *
16465488 AAATATGAA-TGAAATTAATTTA
1 AAATATCAATTGAAATAAATTTA
**
16465510 AAATATCAATTTTAATAAATTTA
1 AAATATCAATTGAAATAAATTTA
16465533 AAATAT
1 AAATAT
16465539 ATTTTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (23 bp):
AAATATCAATTGAAATAAATTTA
Found at i:16465545 original size:23 final size:23
Alignment explanation
Indices: 16465504--16465552 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
16465494 GAATGAAATT
*
16465504 AATTTAAAATATCAATTTTAATA
1 AATTTAAAATATCAATTTTAAAA
*
16465527 AATTTAAAATAT-ATTTTTTAAAA
1 AATTTAAAATATCA-ATTTTAAAA
16465550 AAT
1 AAT
16465553 AAATTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAAAATATCAATTTTAAAA
Found at i:16472008 original size:29 final size:28
Alignment explanation
Indices: 16471948--16472008 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
16471938 TTTTAATTTT
* *
16471948 AATCTTGATTTTTGAACTCTAAACTTTA
1 AATCTTGATTTTGGAACTCTAAACATTA
*
16471976 AATCTTGAAATTTTGGAA-TCTAAACATTG
1 AATCTTG--ATTTTGGAACTCTAAACATTA
16472005 AATC
1 AATC
16472009 CTAAAGTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 13 0.46
30 8 0.29
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (28 bp):
AATCTTGATTTTGGAACTCTAAACATTA
Found at i:16474003 original size:16 final size:16
Alignment explanation
Indices: 16473980--16474023 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
16473970 TACCTTTTTA
*
16473980 AATTAAAAAAAACCAC
1 AATTAAAAAAAAACAC
*
16473996 ATTTAAAAAAAAACAC
1 AATTAAAAAAAAACAC
*
16474012 AACTAAAAAAAA
1 AATTAAAAAAAA
16474024 GTAAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.14
Consensus pattern (16 bp):
AATTAAAAAAAAACAC
Found at i:16474042 original size:21 final size:19
Alignment explanation
Indices: 16474018--16474061 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
16474008 ACACAACTAA
16474018 AAAAAAGTAAAAAATAAAACT
1 AAAAAAG-AAAAAATAAAA-T
**
16474039 AAAAAAGATTAAATAAAAT
1 AAAAAAGAAAAAATAAAAT
16474058 AAAA
1 AAAA
16474062 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAAAGAAAAAATAAAAT
Found at i:16474051 original size:23 final size:24
Alignment explanation
Indices: 16474002--16474071 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 24
16473992 CCACATTTAA
* *
16474002 AAAAAAACACAACTAAAAAAAAGT
1 AAAAAAATAAAACTAAAAAAAAGT
* *
16474026 -AAAAAATAAAACTAAAAAAGATT
1 AAAAAAATAAAACTAAAAAAAAGT
16474049 AAATAAAATAAAA-TAAAATAAAA
1 AAA-AAAATAAAACTAAAA-AAAA
16474072 AGCTTTTAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 19 0.50
24 7 0.18
25 12 0.32
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (24 bp):
AAAAAAATAAAACTAAAAAAAAGT
Found at i:16474059 original size:5 final size:5
Alignment explanation
Indices: 16474028--16474071 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
16474018 AAAAAAGTAA
* *
16474028 AAAAT AAAACT AAAA- AAGAT TAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
16474072 AGCTTTTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.09
5 25 0.76
6 5 0.15
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Done.