Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 14 of 126
Found at i:4622759 original size:56 final size:56
Alignment explanation
Indices: 4622596--4622760 Score: 197
Period size: 56 Copynumber: 2.9 Consensus size: 56
4622586 TAATTATAAC
* * * * *
4622596 ATATTATGTCTTAGCAATTTGATTCCTAATGGGATATTATATGATATTATTACGGG
1 ATATTATCTTTTAGCAATTTGATTCCTAATGAGATATTATATGATATTATTATGAG
** **
4622652 ATATTATCTTTTATTAATTTGATTCCTAATGAGATATTATACAATATTATTATGAG
1 ATATTATCTTTTAGCAATTTGATTCCTAATGAGATATTATATGATATTATTATGAG
* * * *
4622708 ATATTATCTTTTAGCAATTTAATTTCTAATGATATATTATTATGAGA-TATTAT
1 ATATTATCTTTTAGCAATTTGATTCCTAATGAGATATTA-TATGATATTATTAT
4622761 CTCTTAGCAA
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
56 87 0.96
57 4 0.04
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (56 bp):
ATATTATCTTTTAGCAATTTGATTCCTAATGAGATATTATATGATATTATTATGAG
Found at i:4625520 original size:16 final size:16
Alignment explanation
Indices: 4625499--4625532 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4625489 TTCTATTAAT
*
4625499 TAAAAATTATAAAAAA
1 TAAAAAATATAAAAAA
*
4625515 TAAAAAATATTAAAAA
1 TAAAAAATATAAAAAA
4625531 TA
1 TA
4625533 TTAAAATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAAATATAAAAAA
Found at i:4625539 original size:8 final size:9
Alignment explanation
Indices: 4625497--4625538 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
4625487 TCTTCTATTA
4625497 ATTAAAAAT
1 ATTAAAAAT
4625506 -TATAAAAA-
1 AT-TAAAAAT
*
4625514 ATAAAAAAT
1 ATTAAAAAT
4625523 ATTAAAAAT
1 ATTAAAAAT
4625532 ATTAAAA
1 ATTAAAA
4625539 TTGATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:4628002 original size:10 final size:10
Alignment explanation
Indices: 4627957--4628004 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
4627947 AATAAATATT
4627957 AAAATTGATAA
1 AAAATT-ATAA
*
4627968 AAACTTAT-A
1 AAAATTATAA
4627977 AAAATTATTTAA
1 AAAATTA--TAA
4627989 AAAATTATAA
1 AAAATTATAA
4627999 AAAATT
1 AAAATT
4628005 TATCTAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 7 0.22
10 11 0.34
11 6 0.19
12 8 0.25
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAATTATAA
Found at i:4628978 original size:15 final size:15
Alignment explanation
Indices: 4628958--4628986 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4628948 AAGATTTGGT
4628958 TTGTTTATTTTATTG
1 TTGTTTATTTTATTG
4628973 TTGTTTATTTTATT
1 TTGTTTATTTTATT
4628987 ATTATTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (15 bp):
TTGTTTATTTTATTG
Found at i:4628994 original size:15 final size:15
Alignment explanation
Indices: 4628961--4628995 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4628951 ATTTGGTTTG
* *
4628961 TTTATTTTATTGTTG
1 TTTATTTTATTATTA
4628976 TTTATTTTATTATTA
1 TTTATTTTATTATTA
4628991 TTTAT
1 TTTAT
4628996 CATTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTATTTTATTATTA
Found at i:4629059 original size:21 final size:21
Alignment explanation
Indices: 4629015--4629073 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
4629005 ATATATAAAT
*
4629015 TATATAAATTAAAATATACTAA
1 TATATAAA-GAAAATATACTAA
*
4629037 TA-ATAGAGAATAATATA-TAAA
1 TATATAAAGAA-AATATACT-AA
4629058 TATATAAAGAAAATAT
1 TATATAAAGAAAATAT
4629074 GCGTTATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.10
21 19 0.61
22 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
TATATAAAGAAAATATACTAA
Found at i:4629490 original size:13 final size:13
Alignment explanation
Indices: 4629474--4629498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4629464 GATTTCGTTG
4629474 AAATCAATATAGT
1 AAATCAATATAGT
4629487 AAATCAATATAG
1 AAATCAATATAG
4629499 ATTTATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
AAATCAATATAGT
Found at i:4637299 original size:23 final size:23
Alignment explanation
Indices: 4637243--4637337 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
4637233 AGTGCTGGGT
*
4637243 AACAGAGGGTACACGA-AGTGCTAA
1 AACAGAGGGCACAC-ACAGTGCT-A
* *
4637267 TAACAGAGGGCACACACAGTGTTG
1 -AACAGAGGGCACACACAGTGCTA
* *
4637291 AACAAAGGGCACGAAAC-GTGCTA
1 AACAGAGGGCAC-ACACAGTGCTA
*
4637314 AACAGAGGGCACACACAGTTCTA
1 AACAGAGGGCACACACAGTGCTA
4637337 A
1 A
4637338 TAAGAGAGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
22 3 0.05
23 32 0.56
24 4 0.07
25 18 0.32
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.13
Consensus pattern (23 bp):
AACAGAGGGCACACACAGTGCTA
Found at i:4643263 original size:26 final size:26
Alignment explanation
Indices: 4643233--4643327 Score: 70
Period size: 26 Copynumber: 3.5 Consensus size: 26
4643223 TGGCTAAAGA
4643233 TATAATTTCAGAATCATCAAGCGGAT
1 TATAATTTCAGAATCATCAAGCGGAT
* * **
4643259 TATAATTT-AGTGACTGTAGCTCAAG-ATAT
1 TATAATTTCA--GAAT-CA--TCAAGCGGAT
*
4643288 AAATAATTTCAGAATCATCAAGCGGAT
1 -TATAATTTCAGAATCATCAAGCGGAT
4643315 TATAATTTC-GAAT
1 TATAATTTCAGAAT
4643328 TCTGTAGTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 17
0.65 0.13 0.22
Matches are distributed among these distances:
25 5 0.10
26 21 0.41
27 5 0.10
28 2 0.04
29 5 0.10
30 12 0.24
31 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (26 bp):
TATAATTTCAGAATCATCAAGCGGAT
Found at i:4643298 original size:56 final size:56
Alignment explanation
Indices: 4643234--4643353 Score: 188
Period size: 56 Copynumber: 2.1 Consensus size: 56
4643224 GGCTAAAGAT
*
4643234 ATAATTTCAGAATCATCAAGCGGATTATAATTT-AGTGACTGTAGCTCAAGATATAA
1 ATAATTTCAGAATCATCAAGCGGATTATAATTTCAAT-ACTGTAGCTCAAGATATAA
* *
4643290 ATAATTTCAGAATCATCAAGCGGATTATAATTTCGAATTCTGTAGTTCAAGATATAA
1 ATAATTTCAGAATCATCAAGCGGATTATAATTTC-AATACTGTAGCTCAAGATATAA
4643347 ATAATTT
1 ATAATTT
4643354 AGTGACTGTG
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
56 33 0.56
57 24 0.41
58 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (56 bp):
ATAATTTCAGAATCATCAAGCGGATTATAATTTCAATACTGTAGCTCAAGATATAA
Found at i:4643546 original size:21 final size:21
Alignment explanation
Indices: 4643520--4643565 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
4643510 TGATATTTGG
4643520 TTGTTATTTGGTTAAATTGAT
1 TTGTTATTTGGTTAAATTGAT
4643541 TTGTTATTTGGTTAAATTGAT
1 TTGTTATTTGGTTAAATTGAT
4643562 TTGT
1 TTGT
4643566 ATTACTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.59
Consensus pattern (21 bp):
TTGTTATTTGGTTAAATTGAT
Found at i:4643742 original size:18 final size:18
Alignment explanation
Indices: 4643719--4643755 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4643709 TTTGTGATCA
4643719 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
4643737 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
4643755 A
1 A
4643756 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:4648867 original size:23 final size:22
Alignment explanation
Indices: 4648836--4648879 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
4648826 TTTGTCTTTC
*
4648836 AAAAAAATTAATAAAACTTATTT
1 AAAAAAATTAA-AAAACATATTT
*
4648859 AAAATAATTAAAAAACATATT
1 AAAAAAATTAAAAAACATATT
4648880 AGAATGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAAAATTAAAAAACATATTT
Found at i:4648911 original size:27 final size:30
Alignment explanation
Indices: 4648857--4648911 Score: 80
Period size: 27 Copynumber: 1.9 Consensus size: 30
4648847 TAAAACTTAT
4648857 TTAAAATAATTAAAAAACATATTAGAATGC
1 TTAAAATAATTAAAAAACATATTAGAATGC
*
4648887 TTAAAATAA-T-AATAA-ATATTAGAAT
1 TTAAAATAATTAAAAAACATATTAGAAT
4648912 TGATAAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 4 0.17
29 1 0.04
30 9 0.38
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (30 bp):
TTAAAATAATTAAAAAACATATTAGAATGC
Found at i:4649988 original size:23 final size:23
Alignment explanation
Indices: 4649937--4649989 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
4649927 TCATTTAAAT
*
4649937 ATATATATAAATTATATAAATTA
1 ATATATATAAATAATATAAATTA
*
4649960 AAATATACT-AATAATATAGAA-TA
1 ATATATA-TAAATAATATA-AATTA
4649983 ATATATA
1 ATATATA
4649990 AATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
ATATATATAAATAATATAAATTA
Found at i:4650006 original size:21 final size:21
Alignment explanation
Indices: 4649939--4650007 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
4649929 ATTTAAATAT
*
4649939 ATATATAAATTATATAAATTAAA
1 ATATATAAA-TATATAAA-GAAA
*
4649962 ATATACT-AATA-ATATAGAATA
1 ATATA-TAAATATATAAAGAA-A
4649983 ATATATAAATATATAAAGAAA
1 ATATATAAATATATAAAGAAA
4650004 ATAT
1 ATAT
4650008 GCCGTTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.08
21 19 0.49
22 9 0.23
23 7 0.18
24 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (21 bp):
ATATATAAATATATAAAGAAA
Found at i:4650479 original size:30 final size:30
Alignment explanation
Indices: 4650439--4650500 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
4650429 ATCCTGAAAG
*
4650439 ATTTCGTTGAAATCATTATAGTAAATCAAT
1 ATTTCATTGAAATCATTATAGTAAATCAAT
4650469 ATTTCATTGAAATCATTATAGTAAATCAAT
1 ATTTCATTGAAATCATTATAGTAAATCAAT
4650499 AT
1 AT
4650501 AGATTTACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (30 bp):
ATTTCATTGAAATCATTATAGTAAATCAAT
Found at i:4653046 original size:138 final size:138
Alignment explanation
Indices: 4652798--4653074 Score: 545
Period size: 138 Copynumber: 2.0 Consensus size: 138
4652788 CTAATCTTGC
*
4652798 TATACTTTTTTATTATTAATAAATTAAAATATTTTTCGTAATTTTATTTAATTATTTTATTGTCT
1 TATACTTTTTTATTATTAATAAATTAAAATATTTTTCGTAATTTTATTTAATTATTTTATTGCCT
4652863 GTAATGATTGACTTGTTGAAAATAAATGGGGTACACTCACCAAACAAAAAATAAATAGGGTACTT
66 GTAATGATTGACTTGTTGAAAATAAATGGGGTACACTCACCAAACAAAAAATAAATAGGGTACTT
4652928 AGTCCCAG
131 AGTCCCAG
4652936 TATACTTTTTTATTATTAATAAATTAAAATATTTTTCGTAATTTTATTTAATTATTTTATTGCCT
1 TATACTTTTTTATTATTAATAAATTAAAATATTTTTCGTAATTTTATTTAATTATTTTATTGCCT
4653001 GTAATGATTGACTTGTTGAAAATAAATGGGGTACACTCACCAAACAAAAAATAAATAGGGTACTT
66 GTAATGATTGACTTGTTGAAAATAAATGGGGTACACTCACCAAACAAAAAATAAATAGGGTACTT
4653066 AGTCCCAG
131 AGTCCCAG
4653074 T
1 T
4653075 GTGGACGCTA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (138 bp):
TATACTTTTTTATTATTAATAAATTAAAATATTTTTCGTAATTTTATTTAATTATTTTATTGCCT
GTAATGATTGACTTGTTGAAAATAAATGGGGTACACTCACCAAACAAAAAATAAATAGGGTACTT
AGTCCCAG
Found at i:4653118 original size:39 final size:39
Alignment explanation
Indices: 4653064--4653141 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
4653054 AATAGGGTAC
4653064 TTAGTCCCAGTGTGGACGCTAGGCCAGTCATTTTAGTCT
1 TTAGTCCCAGTGTGGACGCTAGGCCAGTCATTTTAGTCT
*
4653103 TTAGTCCCAGTGTGGACGTTAGGCCAGTCATTTTAGTCT
1 TTAGTCCCAGTGTGGACGCTAGGCCAGTCATTTTAGTCT
4653142 CGGATAACCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.35
Consensus pattern (39 bp):
TTAGTCCCAGTGTGGACGCTAGGCCAGTCATTTTAGTCT
Found at i:4655281 original size:9 final size:9
Alignment explanation
Indices: 4655242--4655346 Score: 65
Period size: 9 Copynumber: 11.4 Consensus size: 9
4655232 TTTAATAAGA
4655242 TTTTATCAAT
1 TTTTAT-AAT
* *
4655252 TTTAAT-AC
1 TTTTATAAT
*
4655260 TTTTAGTATT
1 TTTTA-TAAT
4655270 TTTTATAAT
1 TTTTATAAT
*
4655279 TTTTTTAAAT
1 TTTTAT-AAT
4655289 ATTTTA-AAT
1 -TTTTATAAT
*
4655298 TTGTT-TTAT
1 TT-TTATAAT
4655307 TTTTATATAT
1 TTTTATA-AT
*
4655317 TTTTAAAAT
1 TTTTATAAT
*
4655326 TTATATAAT
1 TTTTATAAT
4655335 TTTT-TAAT
1 TTTTATAAT
4655343 TTTT
1 TTTT
4655347 TAGTATTTAA
Statistics
Matches: 73, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
8 17 0.23
9 31 0.42
10 21 0.29
11 4 0.05
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:4655298 original size:19 final size:20
Alignment explanation
Indices: 4655270--4655339 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
4655260 TTTTAGTATT
4655270 TTTTATAATTTTTTTAAATA
1 TTTTATAATTTTTTTAAATA
4655290 TTTTA-AATTTGTTTT--AT-
1 TTTTATAATTT-TTTTAAATA
*
4655307 TTTTAT-ATATTTTTAAA-A
1 TTTTATAATTTTTTTAAATA
4655325 TTTATATAATTTTTT
1 TTT-TATAATTTTTT
4655340 AATTTTTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
16 4 0.10
17 8 0.20
18 6 0.15
19 8 0.20
20 15 0.37
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (20 bp):
TTTTATAATTTTTTTAAATA
Found at i:4655320 original size:37 final size:37
Alignment explanation
Indices: 4655269--4655354 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 37
4655259 CTTTTAGTAT
*
4655269 TTTTTATA-ATTTTTTTAAATATTT-TA-AATTTGTTTTA
1 TTTTTATATA-TTTTTTAAA-ATTTATATAATTT-TTTAA
4655306 TTTTTATATA-TTTTTAAAATTTATATAATTTTTTAA
1 TTTTTATATATTTTTTAAAATTTATATAATTTTTTAA
4655342 TTTTT-TAGTATTT
1 TTTTTATA-TATTT
4655355 AATATTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
35 6 0.14
36 21 0.49
37 15 0.35
38 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (37 bp):
TTTTTATATATTTTTTAAAATTTATATAATTTTTTAA
Found at i:4655336 original size:28 final size:25
Alignment explanation
Indices: 4655273--4655346 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 25
4655263 TAGTATTTTT
*
4655273 TATAATTTTTTTAAATATTTTAAATTTG
1 TATAA-TTTTTT-AAT-TTTTAAATTTA
* *
4655301 TTTTATTTTTATATATTTTTAAAATTTA
1 TATAATTTTT-TA-ATTTTT-AAATTTA
4655329 TATAATTTTTTAATTTTT
1 TATAATTTTTTAATTTTT
4655347 TAGTATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
26 6 0.16
27 12 0.32
28 20 0.53
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (25 bp):
TATAATTTTTTAATTTTTAAATTTA
Found at i:4655340 original size:19 final size:19
Alignment explanation
Indices: 4655273--4655341 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
4655263 TAGTATTTTT
4655273 TATAATTTTTTTAAATATTT-
1 TATAA-TTTTTTAAA-ATTTA
* **
4655293 TA-AATTTGTTTTATTTTTA
1 TATAATTT-TTTAAAATTTA
4655312 TAT-A-TTTTTAAAATTTA
1 TATAATTTTTTAAAATTTA
4655329 TATAATTTTTTAA
1 TATAATTTTTTAA
4655342 TTTTTTAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
17 11 0.29
18 9 0.24
19 16 0.42
20 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (19 bp):
TATAATTTTTTAAAATTTA
Found at i:4655364 original size:9 final size:9
Alignment explanation
Indices: 4655251--4655414 Score: 56
Period size: 9 Copynumber: 17.6 Consensus size: 9
4655241 ATTTTATCAA
*
4655251 TTTTAATAC
1 TTTTAATAT
*
4655260 TTTTAGTATTT
1 TTTTA--ATAT
*
4655271 TTTATAATTT
1 TTT-TAATAT
4655281 TTTTAA-AT
1 TTTTAATAT
4655289 ATTTTAA-AT
1 -TTTTAATAT
*
4655298 TTGTT-TTAT
1 TT-TTAATAT
4655307 TTTTATATAT
1 TTTTA-ATAT
*
4655317 TTTTAAAAT
1 TTTTAATAT
4655326 TTATATAAT-T
1 TT-T-TAATAT
4655336 TTTTAAT-T
1 TTTTAATAT
*
4655344 TTTTAGTA-
1 TTTTAATAT
4655352 -TTTAATAT
1 TTTTAATAT
*
4655360 TTTT-ATTT
1 TTTTAATAT
4655368 TTTGATAATATT
1 TTT--TAATA-T
* *
4655380 TTTTATTTTT
1 TTTTA-ATAT
4655390 GTTTTAATGAT
1 -TTTTAAT-AT
*
4655401 ATTTAATAT
1 TTTTAATAT
4655410 TTTTA
1 TTTTA
4655415 TGAGAAAGAT
Statistics
Matches: 118, Mismatches: 17, Indels: 40
0.67 0.10 0.23
Matches are distributed among these distances:
7 6 0.05
8 22 0.19
9 37 0.31
10 30 0.25
11 17 0.14
12 6 0.05
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (9 bp):
TTTTAATAT
Found at i:4655369 original size:24 final size:24
Alignment explanation
Indices: 4655331--4655415 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
4655321 AAAATTTATA
*
4655331 TAAT-TTTTTAATTTTTTAGTATT
1 TAATATTTTTATTTTTTTAGTATT
*
4655354 TAATATTTTTATTTTTTGATAATATT
1 TAATATTTTTATTTTTT--TAGTATT
** * **
4655380 TTTTATTTTTGTTTTAAT-GATATT
1 TAATATTTTTATTTTTTTAG-TATT
4655404 TAATATTTTTAT
1 TAATATTTTTAT
4655416 GAGAAAGATT
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
23 4 0.09
24 25 0.53
26 18 0.38
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (24 bp):
TAATATTTTTATTTTTTTAGTATT
Found at i:4656834 original size:22 final size:22
Alignment explanation
Indices: 4656783--4656884 Score: 123
Period size: 22 Copynumber: 4.5 Consensus size: 22
4656773 GCTGAGGAAA
*
4656783 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
4656805 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
4656828 CAGTAGGCGCACATAATGCAAT
1 CAGTAGGCACACACAGTGCAAT
* * *
4656850 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
4656873 CAGTAGGCACAC
1 CAGTAGGCACAC
4656885 GAAGTGCGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
22 36 0.51
23 35 0.49
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:4656899 original size:23 final size:22
Alignment explanation
Indices: 4656780--4656900 Score: 109
Period size: 22 Copynumber: 5.4 Consensus size: 22
4656770 AATGCTGAGG
*
4656780 AAACAGTAAGCACACACAGTGC
1 AAACAGTAGGCACACACAGTGC
*
4656802 AATCCAGTAGGCACACACAGTGC
1 AA-ACAGTAGGCACACACAGTGC
* * * *
4656825 AATCAGTAGGCGCACATAATGC
1 AAACAGTAGGCACACACAGTGC
* * * *
4656847 AATCAGTAGGCGCACATAGCGC
1 AAACAGTAGGCACACACAGTGC
4656869 AAATCAGTAGGCACACGA-AGTGC
1 AAA-CAGTAGGCACAC-ACAGTGC
4656892 GAAACAGTA
1 -AAACAGTA
4656901 AGCGCGCTAG
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
22 40 0.48
23 40 0.48
24 4 0.05
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.13
Consensus pattern (22 bp):
AAACAGTAGGCACACACAGTGC
Found at i:4658594 original size:19 final size:19
Alignment explanation
Indices: 4658572--4658623 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
4658562 CTGCCTGCTA
4658572 CTGCTCCTGCCGAAGCTCC
1 CTGCTCCTGCCGAAGCTCC
4658591 CTGCTCCTGCCGAAGCTCC
1 CTGCTCCTGCCGAAGCTCC
*
4658610 CTGCTCCTGTCGAA
1 CTGCTCCTGCCGAA
4658624 AGGTGGGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.12, C:0.44, G:0.21, T:0.23
Consensus pattern (19 bp):
CTGCTCCTGCCGAAGCTCC
Found at i:4658884 original size:17 final size:17
Alignment explanation
Indices: 4658864--4658897 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4658854 AAAAAAATTT
*
4658864 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
4658881 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
4658898 TTATTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:4660086 original size:21 final size:21
Alignment explanation
Indices: 4660062--4660107 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
4660052 AAAATTGTAT
4660062 TAATTACTTCTGACAGATTGA
1 TAATTACTTCTGACAGATTGA
*
4660083 TAATTACTTTTGACAGATTGA
1 TAATTACTTCTGACAGATTGA
4660104 TAAT
1 TAAT
4660108 CTCAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (21 bp):
TAATTACTTCTGACAGATTGA
Found at i:4662298 original size:26 final size:26
Alignment explanation
Indices: 4662243--4662318 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
4662233 GCTAAACCTC
**
4662243 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
4662269 ATTAAATAAATTCAAATTTAAATAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
4662295 ATTAATTCAAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
4662319 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:4665674 original size:6 final size:6
Alignment explanation
Indices: 4665663--4665695 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4665653 TGATCAAAAT
*
4665663 TGAAAG TGAAAG TGAAAG TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
4665696 TATGAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.21
Consensus pattern (6 bp):
TGAAAG
Found at i:4665687 original size:24 final size:23
Alignment explanation
Indices: 4665659--4665716 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
4665649 TTTGTGATCA
4665659 AAATTGAAAGTGAAAGTGAAAGTG-
1 AAATTGAAAGTGAAA-TG-AAGTGT
* *
4665683 AAATTGAAAGTGATATGAATTGT
1 AAATTGAAAGTGAAATGAAGTGT
4665706 AAATTGAAAGT
1 AAATTGAAAGT
4665717 CCCTATTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 4 0.13
23 13 0.42
24 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (23 bp):
AAATTGAAAGTGAAATGAAGTGT
Found at i:4665845 original size:41 final size:40
Alignment explanation
Indices: 4665798--4665897 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 40
4665788 CGACCTTGAG
** *
4665798 TCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGA
1 TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGA
** *
4665838 TTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAGA
1 -TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGA
*
4665876 CCGATGAGACACTGGGTGTCAC
1 TCGATGAGACACTGGGTGTCAC
4665898 TTTATTGCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
37 10 0.21
38 18 0.38
39 4 0.09
40 4 0.09
41 11 0.23
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAGA
Found at i:4665890 original size:37 final size:38
Alignment explanation
Indices: 4665823--4665901 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
4665813 GTGTCATTAT
* **
4665823 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
* **
4665861 TTTACTTCGGCTAGA-CCGATGAGACACTGGGTGTCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
4665898 TTTA
1 TTTA
4665902 TTGCTTCGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 21 0.60
38 14 0.40
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (38 bp):
TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
Found at i:4668008 original size:10 final size:10
Alignment explanation
Indices: 4667993--4668029 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
4667983 CTTGTCAAAT
4667993 TTTAATTTTA
1 TTTAATTTTA
4668003 TTTAATTTTA
1 TTTAATTTTA
*
4668013 TTTTATTTT-
1 TTTAATTTTA
4668022 TTTAATTT
1 TTTAATTT
4668030 AAAAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTAATTTTA
Found at i:4668141 original size:13 final size:13
Alignment explanation
Indices: 4668093--4668143 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 13
4668083 GGGAATTTTT
4668093 TATAATAATAATATA
1 TATAA-AATAATA-A
4668108 TATAAAA-AATTTAA
1 TATAAAATAA--TAA
4668122 TACTAAAATAATAA
1 TA-TAAAATAATAA
4668136 TATAAAAT
1 TATAAAAT
4668144 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 8 0.25
14 10 0.31
15 12 0.38
16 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
TATAAAATAATAA
Found at i:4669362 original size:27 final size:27
Alignment explanation
Indices: 4669319--4669399 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
4669309 AAAATACGAG
* *
4669319 TTGGTGCCACCTGACAGGAAGGCACCA
1 TTGGTGCCGCCTGACAGGTAGGCACCA
* *
4669346 TTGGTGCCGCCTAACAGGTAGGCCCCA
1 TTGGTGCCGCCTGACAGGTAGGCACCA
* * *
4669373 CTAGTGCCGCCTGTCAGGTAGGCACCA
1 TTGGTGCCGCCTGACAGGTAGGCACCA
4669400 CCCCCTTATA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.21, C:0.32, G:0.30, T:0.17
Consensus pattern (27 bp):
TTGGTGCCGCCTGACAGGTAGGCACCA
Found at i:4670591 original size:17 final size:18
Alignment explanation
Indices: 4670555--4670592 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4670545 ATTGCTTCTC
* *
4670555 AAAAGTACTTTTGGGCCA
1 AAAAGCACTTTTGAGCCA
4670573 AAAAGCACTTTTGAG-CA
1 AAAAGCACTTTTGAGCCA
4670590 AAA
1 AAA
4670593 GCTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (18 bp):
AAAAGCACTTTTGAGCCA
Found at i:4672369 original size:13 final size:13
Alignment explanation
Indices: 4672351--4672376 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4672341 TCATGCGAAA
4672351 CGTAAATAGATGT
1 CGTAAATAGATGT
4672364 CGTAAATAGATGT
1 CGTAAATAGATGT
4672377 TGTTTCAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
CGTAAATAGATGT
Found at i:4679926 original size:17 final size:16
Alignment explanation
Indices: 4679900--4679931 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4679890 GTAAAAATTA
4679900 AGAAAAAATTTAATGC
1 AGAAAAAATTTAATGC
4679916 AGAAGAAAATTTAATG
1 AGAA-AAAATTTAATG
4679932 GACTTCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.16, T:0.25
Consensus pattern (16 bp):
AGAAAAAATTTAATGC
Found at i:4682336 original size:3 final size:3
Alignment explanation
Indices: 4682328--4682352 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4682318 AAAAATTTAA
4682328 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
4682353 CAGAAGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4693583 original size:30 final size:30
Alignment explanation
Indices: 4693547--4693611 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
4693537 ACTTATTTTA
4693547 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAGAGACAT
*
4693577 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAGAGACAT
4693607 TTGTT
1 TTGTT
4693612 TGTTAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.26, C:0.03, G:0.12, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAGAGACAT
Found at i:4694976 original size:20 final size:22
Alignment explanation
Indices: 4694951--4694990 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
4694941 TTTCTAAATT
4694951 TTTAAAAATA-AT-TAAAATAA
1 TTTAAAAATATATATAAAATAA
4694971 TTTAAAAATATATATAAAAT
1 TTTAAAAATATATATAAAAT
4694991 TATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAAATATATATAAAATAA
Found at i:4695268 original size:19 final size:19
Alignment explanation
Indices: 4695209--4695270 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
4695199 CTTGAATTTG
4695209 AATTAACATTTAATACTTA
1 AATTAACATTTAATACTTA
* *
4695228 AATT-CCATTTAA-A-TTG
1 AATTAACATTTAATACTTA
4695244 AATTAACATTTAATACTTA
1 AATTAACATTTAATACTTA
4695263 AATTAACA
1 AATTAACA
4695271 ATTAGACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 6 0.17
17 8 0.22
18 8 0.22
19 14 0.39
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTAACATTTAATACTTA
Found at i:4697883 original size:2 final size:2
Alignment explanation
Indices: 4697878--4697930 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
4697868 TATAATTTTA
4697878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4697920 AT AT AT AT AT A
1 AT AT AT AT AT A
4697931 ATGCATTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4712106 original size:33 final size:34
Alignment explanation
Indices: 4712041--4712117 Score: 140
Period size: 33 Copynumber: 2.3 Consensus size: 34
4712031 CCAACAGTTC
4712041 CTCT-TCTTCCTTAAATAATAAACCCCCCCTTAT
1 CTCTCTCTTCCTTAAATAATAAACCCCCCCTTAT
4712074 CTCTCTCTTCCTTAAATAATAAA-CCCCCCTTAT
1 CTCTCTCTTCCTTAAATAATAAACCCCCCCTTAT
4712107 CTCTCTCTTCC
1 CTCTCTCTTCC
4712118 ATTACTCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
33 25 0.58
34 18 0.42
ACGTcount: A:0.23, C:0.39, G:0.00, T:0.38
Consensus pattern (34 bp):
CTCTCTCTTCCTTAAATAATAAACCCCCCCTTAT
Found at i:4724352 original size:193 final size:192
Alignment explanation
Indices: 4724017--4724374 Score: 653
Period size: 193 Copynumber: 1.9 Consensus size: 192
4724007 TAATGTGGCA
4724017 ATATATATGTATATATAACTTTCCTGGTTACAATATCCCTAGCTCCGAGTTGCCTCATTGGGAAG
1 ATATATATGTATATATAACTTTCCTGGTTACAATATCCCTAGCTCCGAGTTGCCTCATTGGGAAG
*
4724082 CATTTTCTGTCAAATATGTGCATCAGTTTCCTTATCTGTTTCCTAGTGGCTTTTGGTTCTTTTCT
66 CATTTTCTGTCAAATATATGCATCAGTTTCCTTATCTGTTTCCTAGTGGCTTTTGGTTCTTTTCT
4724147 TCAATGGTCGGGTCTAAACGCACTTTAGTGCATGCTACTGCACAATATCAGTTTATACATGT
131 TCAATGGTCGGGTCTAAACGCACTTTAGTGCATGCTACTGCACAATATCAGTTTATACATGT
* *
4724209 ATATATAATGTATATATAACTTTCCTGGTTACTATATCCCTAGCTCTGAGTTGCCTCATTGGGAA
1 ATATAT-ATGTATATATAACTTTCCTGGTTACAATATCCCTAGCTCCGAGTTGCCTCATTGGGAA
* *
4724274 GCATTTTCTGTCAAATATATGCATCAGTTTTCTTATCTGTTTCCTGGTGGCTTTTGGTTCTTTTC
65 GCATTTTCTGTCAAATATATGCATCAGTTTCCTTATCTGTTTCCTAGTGGCTTTTGGTTCTTTTC
*
4724339 TTCAATGGTCGGGTCTAAAGGCACTTTAGTGCATGC
130 TTCAATGGTCGGGTCTAAACGCACTTTAGTGCATGC
4724375 CGCTGCAGAT
Statistics
Matches: 159, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
192 6 0.04
193 153 0.96
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (192 bp):
ATATATATGTATATATAACTTTCCTGGTTACAATATCCCTAGCTCCGAGTTGCCTCATTGGGAAG
CATTTTCTGTCAAATATATGCATCAGTTTCCTTATCTGTTTCCTAGTGGCTTTTGGTTCTTTTCT
TCAATGGTCGGGTCTAAACGCACTTTAGTGCATGCTACTGCACAATATCAGTTTATACATGT
Found at i:4726602 original size:23 final size:24
Alignment explanation
Indices: 4726562--4726607 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
4726552 GATGGGTTGT
4726562 GAAGGGGAGGAAGAGAGA-GAAGG
1 GAAGGGGAGGAAGAGAGATGAAGG
4726585 GAAGGGGAGGAA-AGGAGATGAAG
1 GAAGGGGAGGAAGA-GAGATGAAG
4726608 AGATGGAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.05
23 16 0.76
24 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.54, T:0.02
Consensus pattern (24 bp):
GAAGGGGAGGAAGAGAGATGAAGG
Found at i:4734090 original size:38 final size:38
Alignment explanation
Indices: 4734038--4734110 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
4734028 TTCAATCATG
* *
4734038 GGATTTGATTTGTTTTTGGTTCATCTTTCACGACACCA
1 GGATTAGATGTGTTTTTGGTTCATCTTTCACGACACCA
4734076 GGATTAGATGTGTTTTTGGTTCATCTTTCACGACA
1 GGATTAGATGTGTTTTTGGTTCATCTTTCACGACA
4734111 TTAGATGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (38 bp):
GGATTAGATGTGTTTTTGGTTCATCTTTCACGACACCA
Found at i:4734119 original size:32 final size:35
Alignment explanation
Indices: 4734039--4734127 Score: 112
Period size: 38 Copynumber: 2.5 Consensus size: 35
4734029 TCAATCATGG
* *
4734039 GATTTGATTTGTTTTTGGTTCATCTTTCACGACACC
1 GATTAGATGTGTTTTTGGTTCATCTTTCACGA-ACC
4734075 AGGATTAGATGTGTTTTTGGTTCATCTTTCACG-A-C
1 --GATTAGATGTGTTTTTGGTTCATCTTTCACGAACC
4734110 -ATTAGATGTGTTTTTGGT
1 GATTAGATGTGTTTTTGGT
4734128 GGCTCATCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
32 18 0.37
35 1 0.02
36 1 0.02
38 29 0.59
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.47
Consensus pattern (35 bp):
GATTAGATGTGTTTTTGGTTCATCTTTCACGAACC
Found at i:4735848 original size:29 final size:28
Alignment explanation
Indices: 4735816--4736004 Score: 103
Period size: 30 Copynumber: 6.4 Consensus size: 28
4735806 CCCGAGGGCA
* *
4735816 AAAATGTAATTTTGGGAAAATTTAGGGTT
1 AAAATGTAATTTT-AGAAAGTTTAGGGTT
* * * * *
4735845 AAAAATAG-GATTTTGGAAGGTTTGGGGGT
1 -AAAAT-GTAATTTTAGAAAGTTTAGGGTT
** * *
4735874 AAAATGGTAATTTT-GATAAAATCAGGGTC
1 AAAAT-GTAATTTTAGA-AAGTTTAGGGTT
* *
4735903 AAAATGTAAGTTTTAGAAAGTTTTGAGGTC
1 AAAATGTAA-TTTTAGAAAGTTTAG-GGTT
*
4735933 AAAATATAATTTTAGAGAAGTTTAGGGGTT
1 AAAATGTAATTTTAGA-AAGTTTA-GGGTT
* * *
4735963 AAAATGTAATTTTCAAAAAGTTTTGGGGTC
1 AAAATGTAATTTT-AGAAAG-TTTAGGGTT
*
4735993 AAAATATAATTT
1 AAAATGTAATTT
4736005 CTTGACAGTT
Statistics
Matches: 123, Mismatches: 26, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
28 12 0.10
29 41 0.33
30 63 0.51
31 7 0.06
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (28 bp):
AAAATGTAATTTTAGAAAGTTTAGGGTT
Found at i:4736015 original size:30 final size:29
Alignment explanation
Indices: 4735898--4736004 Score: 133
Period size: 30 Copynumber: 3.6 Consensus size: 29
4735888 GATAAAATCA
*
4735898 GGGTCAAAATGTAAGTTTTAGAAAGTTTTG
1 GGGTCAAAATATAA-TTTTAGAAAGTTTTG
* *
4735928 AGGTCAAAATATAATTTTAGAGAAGTTTAG
1 GGGTCAAAATATAATTTTAGA-AAGTTTTG
* * *
4735958 GGGTTAAAATGTAATTTTCAAAAAGTTTTG
1 GGGTCAAAATATAATTTT-AGAAAGTTTTG
4735988 GGGTCAAAATATAATTT
1 GGGTCAAAATATAATTT
4736005 CTTGACAGTT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 7 0.11
30 56 0.86
31 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.36
Consensus pattern (29 bp):
GGGTCAAAATATAATTTTAGAAAGTTTTG
Found at i:4737088 original size:15 final size:15
Alignment explanation
Indices: 4737049--4737095 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
4737039 TTTCTTCTTT
*
4737049 TATTAATATTATTAA
1 TATTATTATTATTAA
4737064 TTATTATTATTATTAA
1 -TATTATTATTATTAA
*
4737080 TATTGTTATTATTAA
1 TATTATTATTATTAA
4737095 T
1 T
4737096 GTCATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 15 0.52
16 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTATTATTATTAA
Found at i:4737110 original size:3 final size:3
Alignment explanation
Indices: 4737048--4737093 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
4737038 CTTTCTTCTT
* * *
4737048 TTA TTA ATA TTA TTAA TTA TTA TTA TTA TTA ATA TTG TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4737094 ATGTCATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:4737514 original size:26 final size:26
Alignment explanation
Indices: 4737429--4737517 Score: 117
Period size: 26 Copynumber: 3.4 Consensus size: 26
4737419 GATTTCGAAG
*
4737429 AGGGTTTGTATATT-AATTTTCAAGAAC
1 AGGGTTTGTAT-TTGGA-TTTCAAGAAC
* * *
4737456 TGGGTTCGTATTTGGATTTCAAGAAT
1 AGGGTTTGTATTTGGATTTCAAGAAC
4737482 AGGGTTTGTATTTGGATTTCAAGAAC
1 AGGGTTTGTATTTGGATTTCAAGAAC
4737508 AGGGTTTGTA
1 AGGGTTTGTA
4737518 ACCCCTTACA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 44 0.81
27 10 0.19
ACGTcount: A:0.27, C:0.07, G:0.26, T:0.40
Consensus pattern (26 bp):
AGGGTTTGTATTTGGATTTCAAGAAC
Found at i:4737894 original size:17 final size:17
Alignment explanation
Indices: 4737872--4737947 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
4737862 AATTTAATTT
*
4737872 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* **
4737889 TAAATTTAAATTTTATG
1 TAAATTTAAATTTAAAA
* *
4737906 CAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
4737923 TAAATCT-AATTTAAAA
1 TAAATTTAAATTTAAAA
4737939 CTAAATTTA
1 -TAAATTTA
4737948 TATCCCATTG
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 8 0.18
17 36 0.82
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:4737945 original size:34 final size:34
Alignment explanation
Indices: 4737858--4737947 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 34
4737848 GACATTGGAT
** * *
4737858 ATCTAATTTAATTTTAAATTTAAATTTATAATAA
1 ATCTAATTTAATACTAAATTTAAATTCAAAATAA
* * *
4737892 ATTTAAATTTTATGC-AAATTTAAATTCAAAATAA
1 ATCT-AATTTAATACTAAATTTAAATTCAAAATAA
*
4737926 ATCTAATTTAAAACTAAATTTA
1 ATCTAATTTAATACTAAATTTA
4737948 TATCCCATTG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
33 7 0.16
34 30 0.68
35 7 0.16
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (34 bp):
ATCTAATTTAATACTAAATTTAAATTCAAAATAA
Found at i:4738666 original size:201 final size:201
Alignment explanation
Indices: 4738316--4739126 Score: 1083
Period size: 201 Copynumber: 4.0 Consensus size: 201
4738306 TCGCAATTAC
* * *
4738316 TTGTTTTAATTCGCTTCTCTGGATCTCCTTAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTTA
1 TTGTTTTAATTCGCTTCTCTGAATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCA
* * *
4738381 TCAGAAAGCTAACCATTTTATTGCTTTGAT-CTGCTTCTCAGTATCTCATCAAGAAGCTGGGTTT
66 TCAGGAAGCTAACCATTTTATTGCTTTGATCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTC
** * *
4738445 GAGGATTTGCTCGCGTTTGAGCGTTGAGTTGGTATTCTTCTCTGCATTTCATCAGGAAGATGACC
131 GAAAATTTGCTCGCG-TTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACC
* *
4738510 GCTTCGG
195 GCCTCGA
* *
4738517 TTGTTTTAATTCGCTTCTCT-AGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCCGTATCTC
1 TTGTTTTAATTCGCTTCTCTGA-ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTC
* *
4738581 ATCAGGAAGCTAACCATTTTATTGCTTTG-TCCTGCTTCTCAGTGTCTCATCATGAAGCTGGGTT
65 ATCAGGAAGCTAACCATTTTATTGCTTTGATCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTT
* * *
4738645 CGAAAATTTACCCGTGTTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGAC
130 CGAAAATTTGCTCGCG-TTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGAC
4738710 CGCCTCGA
194 CGCCTCGA
* * *
4738718 TTGTTTTAATTCGCTTCTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCTGTGTCTCA
1 TTGTTTTAATTCGCTTCTCTGAATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCA
* *
4738783 TCAGGAAGCTAACCATTTTATTGCTTCGA-CCTGCTTCTCAGTATCTCCTCAGGAAGCTGGGTTC
66 TCAGGAAGCTAACCATTTTATTGCTTTGATCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTC
* ** * *
4738847 CACGATTTGCTCGCGTTGA--GTTGA-----TATTCTTCTCTGTATCTCATCAGAAAGATAACCG
131 GAAAATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCG
4738905 CCTCGA
196 CCTCGA
*
4738911 TCT-TTTTAATTCGCTTCTCTGAATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTT
1 T-TGTTTTAATTCGCTTCTCTGAATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTC
* * *
4738975 ATTAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGA
65 ATCAGGAAGCTAACCATTTTATTGCTT-----TG-AT---CCTGCTTCTCAGTATCTCATCAGGA
4739040 AGCTGGGTTC-AAAGATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAG
121 AGCTGGGTTCGAAA-ATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAG
* *
4739104 GAAGATGACTGCCTCTA
185 GAAGATGACCGCCTCGA
4739121 -TGTTTT
1 TTGTTTT
4739127 GTTGAACTAC
Statistics
Matches: 536, Mismatches: 50, Indels: 40
0.86 0.08 0.06
Matches are distributed among these distances:
193 122 0.23
194 1 0.00
198 6 0.01
200 5 0.01
201 307 0.57
202 1 0.00
203 48 0.09
205 5 0.01
208 1 0.00
209 4 0.01
210 36 0.07
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (201 bp):
TTGTTTTAATTCGCTTCTCTGAATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCA
TCAGGAAGCTAACCATTTTATTGCTTTGATCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTC
GAAAATTTGCTCGCGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCG
CCTCGA
Found at i:4739012 original size:10 final size:10
Alignment explanation
Indices: 4738997--4739022 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4738987 ACCATTTTAT
4738997 TGCTTCGACC
1 TGCTTCGACC
4739007 TGCTTCGACC
1 TGCTTCGACC
4739017 TGCTTC
1 TGCTTC
4739023 TCAGTGTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.38, G:0.19, T:0.35
Consensus pattern (10 bp):
TGCTTCGACC
Found at i:4746902 original size:26 final size:26
Alignment explanation
Indices: 4746854--4746904 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
4746844 CAAATATGTA
4746854 TTTTAAATAATGTTCAAATTTAATTT
1 TTTTAAATAATGTTCAAATTTAATTT
4746880 TTTTAAAATAATGTTCAAA-TTAATT
1 TTTT-AAATAATGTTCAAATTTAATT
4746905 AATATTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
TTTTAAATAATGTTCAAATTTAATTT
Found at i:4748522 original size:28 final size:27
Alignment explanation
Indices: 4748474--4748537 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
4748464 GATCTTGGAC
* * *
4748474 TCTGAACTTGGATTTTTGAATTTAGAT
1 TCTGAACTTGAATCTTGGAATTTAGAT
* *
4748501 CTTTGAACTTGAATCTTGGAATTTGGAT
1 -TCTGAACTTGAATCTTGGAATTTAGAT
4748529 TCTGAACTT
1 TCTGAACTT
4748538 TGGACCCTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (27 bp):
TCTGAACTTGAATCTTGGAATTTAGAT
Found at i:4751779 original size:28 final size:28
Alignment explanation
Indices: 4751739--4751792 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
4751729 GGTAACAGGT
*
4751739 ATGACCTTTGGGTCAACAAGGAGTAAGC
1 ATGACATTTGGGTCAACAAGGAGTAAGC
4751767 ATGACATTTGGGTCAACAAGGAGTAA
1 ATGACATTTGGGTCAACAAGGAGTAA
4751793 ATCGAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (28 bp):
ATGACATTTGGGTCAACAAGGAGTAAGC
Found at i:4754035 original size:51 final size:51
Alignment explanation
Indices: 4753976--4754315 Score: 409
Period size: 51 Copynumber: 6.7 Consensus size: 51
4753966 TGGAAGACAG
*
4753976 ATCATAAGGTCCGATGACTATGAGTCATCGTGAGAATATGAATCTTTGTGA
1 ATCATAAGGTCCGATGACTATGAGTCATCGTGAGAATATGAATCTTTGCGA
* * *
4754027 ATCATAAGGTCCAATGACTATGTGTCATCGTGAGAATATAAATCTTTGCGA
1 ATCATAAGGTCCGATGACTATGAGTCATCGTGAGAATATGAATCTTTGCGA
* * *
4754078 ATCATAAGGTCCGATGACTACGTGTCATCGTGAGAATATGAATCTATGCGA
1 ATCATAAGGTCCGATGACTATGAGTCATCGTGAGAATATGAATCTTTGCGA
* * * *
4754129 ATCATAAGGTCCGATGCCTACGTGTCATCATGAGAATATGAATCTTTGCGA
1 ATCATAAGGTCCGATGACTATGAGTCATCGTGAGAATATGAATCTTTGCGA
* * * * *
4754180 ATCATAAGGTCCGATGACTATTAGTCATCGTGAGAATATGAGTCTATACGG
1 ATCATAAGGTCCGATGACTATGAGTCATCGTGAGAATATGAATCTTTGCGA
* * * * *
4754231 ATTATAAAGTCCGATGACTA-CATGTCATCGTGAGAATATGAATTCTAT-AG-
1 ATCATAAGGTCCGATGACTATGA-GTCATCGTGAGAATATGAA-TCTTTGCGA
* * *
4754281 ATTATAGGGTCCGATGATTATGTA-TCATCGTGAGA
1 ATCATAAGGTCCGATGACTATG-AGTCATCGTGAGA
4754316 GTTAAACACA
Statistics
Matches: 256, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
50 29 0.11
51 221 0.86
52 6 0.02
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (51 bp):
ATCATAAGGTCCGATGACTATGAGTCATCGTGAGAATATGAATCTTTGCGA
Found at i:4754257 original size:153 final size:154
Alignment explanation
Indices: 4753976--4754278 Score: 457
Period size: 153 Copynumber: 2.0 Consensus size: 154
4753966 TGGAAGACAG
* * *
4753976 ATCATAAGGTCCGATGACTATGAGTCATCGTGAGAATATGAATCTTTGTGAATCATAAGGTCCAA
1 ATCATAAGGTCCGATGACTACGAGTCATCATGAGAATATGAATCTTTGCGAATCATAAGGTCCAA
* * * *
4754041 TGACTATGTGTCATCGTGAGAATATAAATCTTTGCGAATCATAAGGTCCGATGACTACGTGTCAT
66 TGACTATGTGTCATCGTGAGAATATAAATCTATACGAATCATAAAGTCCGATGACTACATGTCAT
4754106 CGTGAGAATATGAA-TCTATGCGA
131 CGTGAGAATATGAATTCTATGCGA
* * *
4754129 ATCATAAGGTCCGATGCCTACGTGTCATCATGAGAATATGAATCTTTGCGAATCATAAGGTCCGA
1 ATCATAAGGTCCGATGACTACGAGTCATCATGAGAATATGAATCTTTGCGAATCATAAGGTCCAA
* * * *
4754194 TGACTAT-TAGTCATCGTGAGAATATGAGTCTATACGGATTATAAAGTCCGATGACTACATGTCA
66 TGACTATGT-GTCATCGTGAGAATATAAATCTATACGAATCATAAAGTCCGATGACTACATGTCA
4754258 TCGTGAGAATATGAATTCTAT
130 TCGTGAGAATATGAATTCTAT
4754279 AGATTATAGG
Statistics
Matches: 134, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
152 1 0.01
153 128 0.96
154 5 0.04
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (154 bp):
ATCATAAGGTCCGATGACTACGAGTCATCATGAGAATATGAATCTTTGCGAATCATAAGGTCCAA
TGACTATGTGTCATCGTGAGAATATAAATCTATACGAATCATAAAGTCCGATGACTACATGTCAT
CGTGAGAATATGAATTCTATGCGA
Found at i:4754414 original size:37 final size:39
Alignment explanation
Indices: 4754373--4754489 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 39
4754363 AAAAGGTAGG
4754373 CTTCGTACCGA-TGTA-TTA-GGGCTTAGTGCCTAGCAGA
1 CTTCGTA-CGAGTGTATTTACGGGCTTAGTGCCTAGCAGA
* *
4754410 CTTCGTACTAGTGTATTTATCGGGCTTAGTGCCTAGCAGG
1 CTTCGTACGAGTGTATTTA-CGGGCTTAGTGCCTAGCAGA
* * * * *
4754450 CTTCGTGCTAGTGTATATTATCAGGCTTTGAGCCTAGCAG
1 CTTCGTACGAGTGTAT-TTA-CGGGCTTAGTGCCTAGCAG
4754490 GTTTCATGTC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
36 2 0.03
37 11 0.16
38 3 0.04
40 33 0.48
41 20 0.29
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (39 bp):
CTTCGTACGAGTGTATTTACGGGCTTAGTGCCTAGCAGA
Found at i:4754444 original size:40 final size:41
Alignment explanation
Indices: 4754391--4754489 Score: 146
Period size: 40 Copynumber: 2.4 Consensus size: 41
4754381 CGATGTATTA
4754391 GGGCTTAGTGCCTAGCAGACTTCGTACTAGTGTAT-TTATC
1 GGGCTTAGTGCCTAGCAGACTTCGTACTAGTGTATATTATC
* *
4754431 GGGCTTAGTGCCTAGCAGGCTTCGTGCTAGTGTATATTATC
1 GGGCTTAGTGCCTAGCAGACTTCGTACTAGTGTATATTATC
* * *
4754472 AGGCTTTGAGCCTAGCAG
1 GGGCTTAGTGCCTAGCAG
4754490 GTTTCATGTC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 33 0.62
41 20 0.38
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.32
Consensus pattern (41 bp):
GGGCTTAGTGCCTAGCAGACTTCGTACTAGTGTATATTATC
Found at i:4756141 original size:21 final size:22
Alignment explanation
Indices: 4756117--4756168 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
4756107 ATGATTTGTT
**
4756117 TCGGTAGAAGCT-TCACTCGTA
1 TCGGTAGAAGCTGTCACAAGTA
4756138 TCGGTAGAA-CTGTCACAAGTA
1 TCGGTAGAAGCTGTCACAAGTA
4756159 TCGGTAGAAG
1 TCGGTAGAAG
4756169 TCTGCACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (22 bp):
TCGGTAGAAGCTGTCACAAGTA
Found at i:4757413 original size:50 final size:50
Alignment explanation
Indices: 4757338--4757446 Score: 218
Period size: 50 Copynumber: 2.2 Consensus size: 50
4757328 TTAAAGTTAG
4757338 CAATTTATCTCATCATTTATTTCTATTTCACTTCTAGCTCCAAAATACAC
1 CAATTTATCTCATCATTTATTTCTATTTCACTTCTAGCTCCAAAATACAC
4757388 CAATTTATCTCATCATTTATTTCTATTTCACTTCTAGCTCCAAAATACAC
1 CAATTTATCTCATCATTTATTTCTATTTCACTTCTAGCTCCAAAATACAC
4757438 CAATTTATC
1 CAATTTATC
4757447 ATTAAAACTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.42
Consensus pattern (50 bp):
CAATTTATCTCATCATTTATTTCTATTTCACTTCTAGCTCCAAAATACAC
Found at i:4759045 original size:14 final size:14
Alignment explanation
Indices: 4759028--4759071 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
4759018 ACTCTGAACT
4759028 TTGGACCTTGGATC
1 TTGGACCTTGGATC
4759042 TTGGAACC-TGGATC
1 TTGG-ACCTTGGATC
* *
4759056 TTGAACTTTGGATC
1 TTGGACCTTGGATC
4759070 TT
1 TT
4759072 AGATCCCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 2 0.08
14 21 0.81
15 3 0.12
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (14 bp):
TTGGACCTTGGATC
Found at i:4759254 original size:14 final size:14
Alignment explanation
Indices: 4759231--4759270 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4759221 TCTAGGATTT
4759231 AGGATTCAAGGTCG
1 AGGATTCAAGGTCG
* * *
4759245 AGGGTTCAAGATCT
1 AGGATTCAAGGTCG
4759259 AGGATTCAAGGT
1 AGGATTCAAGGT
4759271 TTGGGGTTCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (14 bp):
AGGATTCAAGGTCG
Found at i:4759277 original size:28 final size:28
Alignment explanation
Indices: 4759213--4759280 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
4759203 AAGATTTAGA
* *
4759213 GTTTGGGG-TCTAGGATTTAGGATTCAAG
1 GTTTGGGGTTC-AAGATCTAGGATTCAAG
*
4759241 G-TCGAGGGTTCAAGATCTAGGATTCAAG
1 GTTTG-GGGTTCAAGATCTAGGATTCAAG
4759269 GTTTGGGGTTCA
1 GTTTGGGGTTCA
4759281 GGATTCAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 2 0.06
28 27 0.82
29 4 0.12
ACGTcount: A:0.22, C:0.10, G:0.35, T:0.32
Consensus pattern (28 bp):
GTTTGGGGTTCAAGATCTAGGATTCAAG
Found at i:4781560 original size:3 final size:3
Alignment explanation
Indices: 4781552--4781577 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4781542 TATCTATCTC
4781552 GTT GTT GTT GTT GTT GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GT
4781578 AGTTTAGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:4784100 original size:8 final size:8
Alignment explanation
Indices: 4784087--4784115 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4784077 ATAGTAGTAC
4784087 TTTTATTA
1 TTTTATTA
4784095 TTTTATTA
1 TTTTATTA
4784103 TTTTATTA
1 TTTTATTA
4784111 TTTTA
1 TTTTA
4784116 CATTTCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATTA
Found at i:4789011 original size:5 final size:5
Alignment explanation
Indices: 4789001--4789026 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4788991 TACTTATACA
4789001 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
4789027 TTACTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:4796093 original size:21 final size:21
Alignment explanation
Indices: 4796067--4796106 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4796057 ATTAAGCGAC
4796067 ACATTTTATTAATAATAAACT
1 ACATTTTATTAATAATAAACT
* *
4796088 ACATTTTGTTAATAGTAAA
1 ACATTTTATTAATAATAAA
4796107 AGTTATTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
ACATTTTATTAATAATAAACT
Found at i:4812533 original size:11 final size:11
Alignment explanation
Indices: 4812514--4812544 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4812504 TCACGTTATA
*
4812514 ATATTAACAAT
1 ATATAAACAAT
4812525 ATATAAACAAT
1 ATATAAACAAT
4812536 ATATAAACA
1 ATATAAACA
4812545 TAACGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATAAACAAT
Found at i:4812567 original size:33 final size:34
Alignment explanation
Indices: 4812524--4812589 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
4812514 ATATTAACAA
4812524 TATATAAACAATATATAAACATAACGTT-ATTTT
1 TATATAAACAATATATAAACATAACGTTCATTTT
*
4812557 TATATTAACAATATATAAACATAACGTTCATTT
1 TATATAAACAATATATAAACATAACGTTCATTT
4812590 AAACTCACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 27 0.87
34 4 0.13
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (34 bp):
TATATAAACAATATATAAACATAACGTTCATTTT
Found at i:4820776 original size:11 final size:12
Alignment explanation
Indices: 4820755--4820780 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4820745 TATCCACTCG
4820755 TTTATTTTTTTT
1 TTTATTTTTTTT
4820767 TTTATTTTTTTT
1 TTTATTTTTTTT
4820779 TT
1 TT
4820781 CATGATACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTATTTTTTTT
Found at i:4828005 original size:20 final size:20
Alignment explanation
Indices: 4827968--4828005 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4827958 CCCATCATAC
*
4827968 ATTAATATTTAATTATTATT
1 ATTAATATTTAATAATTATT
4827988 ATTAA-ATTTATATAATTA
1 ATTAATATTTA-ATAATTA
4828006 AAAATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTAATATTTAATAATTATT
Found at i:4828131 original size:16 final size:15
Alignment explanation
Indices: 4828109--4828146 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
4828099 TATAAACATT
4828109 AAATTTAAATATATG
1 AAATTTAAATATATG
4828124 ATAATTT--ATATATG
1 A-AATTTAAATATATG
4828138 AAATTTAAA
1 AAATTTAAA
4828147 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.25
14 8 0.40
15 2 0.10
16 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
AAATTTAAATATATG
Found at i:4828387 original size:59 final size:61
Alignment explanation
Indices: 4828292--4828405 Score: 171
Period size: 59 Copynumber: 1.9 Consensus size: 61
4828282 AAAATAATAT
*
4828292 TAATTTTATTTTATTATTTATCTATTTATTTATTATTGTATGAATATAAATAAATGTAAAA
1 TAATTTTATTTTATTATTTATCTAATTATTTATTATTGTATGAATATAAATAAATGTAAAA
* *
4828353 TAATATTTATTTTA-T-TTTAT-TAATTATTTATTATTTTATGAATATAGATAAAT
1 TAAT-TTTATTTTATTATTTATCTAATTATTTATTATTGTATGAATATAAATAAAT
4828406 AAATAACAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 30 0.61
60 5 0.10
61 5 0.10
62 9 0.18
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (61 bp):
TAATTTTATTTTATTATTTATCTAATTATTTATTATTGTATGAATATAAATAAATGTAAAA
Found at i:4828408 original size:67 final size:67
Alignment explanation
Indices: 4828281--4828411 Score: 167
Period size: 67 Copynumber: 2.0 Consensus size: 67
4828271 TTTATGAATA
* * * * *
4828281 TAAAATAATATTAATTTTATTTTATTATTTATCTATTTATTTATTATTGTATGAATATAAATAAA
1 TAAAATAATATTAATTTTATTTTATTAATTATCTATTTATTTATGAATATATGAAAATAAATAAA
4828346 TG
66 TG
* *
4828348 TAAAATAATATTTATTTTATTTTATTAATTATTTA-TTATTTTATGAATATA-GATAAATAAATA
1 TAAAATAATATTAATTTTATTTTATTAATTATCTATTTA-TTTATGAATATATGA-AAATAAATA
4828411 A
64 A
4828412 CAAACCCAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 5 0.09
67 50 0.91
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (67 bp):
TAAAATAATATTAATTTTATTTTATTAATTATCTATTTATTTATGAATATATGAAAATAAATAAA
TG
Found at i:4828491 original size:33 final size:32
Alignment explanation
Indices: 4828436--4828518 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 32
4828426 AAACCCAAAG
4828436 TCAAAGT-CCTCAAATCCTTGAAAATCAATCC
1 TCAAAGTCCCTCAAATCCTTGAAAATCAATCC
*
4828467 TCAAAGTCCTCTCAAAT-CTCTGAAAATCAATCT
1 TCAAAGTCC-CTCAAATCCT-TGAAAATCAATCC
4828500 TCAAAGTTCCCTCAAATCC
1 TCAAAG-TCCCTCAAATCC
4828519 CATTCAAACC
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 7 0.15
32 3 0.07
33 32 0.70
34 4 0.09
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.28
Consensus pattern (32 bp):
TCAAAGTCCCTCAAATCCTTGAAAATCAATCC
Found at i:4835387 original size:3 final size:3
Alignment explanation
Indices: 4835381--4835406 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4835371 TAACTTTTTT
4835381 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
4835407 TTATTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:4836006 original size:4 final size:4
Alignment explanation
Indices: 4835999--4836039 Score: 73
Period size: 4 Copynumber: 10.2 Consensus size: 4
4835989 TTTCTTTCCC
*
4835999 TATG TATG TATG TATG TATG TATG AATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
4836040 GCATTCTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:4848233 original size:15 final size:14
Alignment explanation
Indices: 4848208--4848245 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
4848198 GAGGAATTTT
4848208 AAAAA-AAAACTAA
1 AAAAATAAAACTAA
*
4848221 TAATAATAAAACTAA
1 -AAAAATAAAACTAA
4848236 AAAAATAAAA
1 AAAAATAAAA
4848246 AAAAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAAATAAAACTAA
Found at i:4859287 original size:12 final size:12
Alignment explanation
Indices: 4859270--4859299 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4859260 ATAATTATAT
4859270 TTTATTTATCAA
1 TTTATTTATCAA
4859282 TTTATTTATCAA
1 TTTATTTATCAA
*
4859294 TATATT
1 TTTATT
4859300 AATATGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATTTATCAA
Found at i:4861180 original size:23 final size:22
Alignment explanation
Indices: 4861148--4861190 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
4861138 TTTAGACTTG
4861148 AAAAAAAAT-GAAAAGAAAAAGA
1 AAAAAAAATGGAAAA-AAAAAGA
4861170 AAAACAAAATGGAAAAAAAAA
1 AAAA-AAAATGGAAAAAAAAA
4861191 TTCCCCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 10 0.53
24 5 0.26
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (22 bp):
AAAAAAAATGGAAAAAAAAAGA
Found at i:4861190 original size:12 final size:11
Alignment explanation
Indices: 4861148--4861191 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
4861138 TTTAGACTTG
4861148 AAAAAAAATGA
1 AAAAAAAATGA
4861159 AAAGAAAAA-GA
1 AAA-AAAAATGA
4861170 AAAACAAAATGGA
1 AAAA-AAAAT-GA
4861183 AAAAAAAAT
1 AAAAAAAAT
4861192 TCCCCTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 12 0.41
12 10 0.34
13 6 0.21
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:4869512 original size:15 final size:16
Alignment explanation
Indices: 4869492--4869521 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4869482 GCACCCTCTT
4869492 CTTCTTCTT-CTCCTC
1 CTTCTTCTTCCTCCTC
4869507 CTTCTTCTTCCTCCT
1 CTTCTTCTTCCTCCT
4869522 TGTCATTGTC
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:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (16 bp):
CTTCTTCTTCCTCCTC
Found at i:4872836 original size:46 final size:46
Alignment explanation
Indices: 4872769--4872862 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
4872759 TTATGATGAA
*
4872769 CAACATCTTCTTTATCACTGGAACCACTCGTTGGATTTCATTCAAT
1 CAACATCTTCTTTATCACTGGAACCACTCGTTGGATTCCATTCAAT
*
4872815 CAACATCTTCTTTATCACTGGAATCACTCGTTGGATTCCATTCAAT
1 CAACATCTTCTTTATCACTGGAACCACTCGTTGGATTCCATTCAAT
4872861 CA
1 CA
4872863 TTAATTTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.36
Consensus pattern (46 bp):
CAACATCTTCTTTATCACTGGAACCACTCGTTGGATTCCATTCAAT
Found at i:4875639 original size:14 final size:13
Alignment explanation
Indices: 4875608--4875669 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
4875598 TTTTTACCCA
*
4875608 GAACCCCAAATCT
1 GAACCCCAAACCT
4875621 CGAACCCCAAACCAT
1 -GAACCCCAAACC-T
*
4875636 GAACCTCAAACGCT
1 GAACCCCAAAC-CT
* *
4875650 AAACCTCAAACCAT
1 GAACCCCAAACC-T
4875664 GAACCC
1 GAACCC
4875670 TTCGAGGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 1 0.03
14 37 0.93
15 2 0.05
ACGTcount: A:0.40, C:0.40, G:0.08, T:0.11
Consensus pattern (13 bp):
GAACCCCAAACCT
Found at i:4884058 original size:23 final size:22
Alignment explanation
Indices: 4884015--4884066 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
4884005 TCTCTCTTCC
4884015 TTTATTTTTTTTCAACAATTTCA
1 TTTATTTTTTTTCAACAATTT-A
4884038 TTTATTTTTCTTTCAAC-ATTTA
1 TTTATTTTT-TTTCAACAATTTA
*
4884060 TTAATTT
1 TTTATTT
4884067 GTTGGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 7 0.26
23 13 0.48
24 7 0.26
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATTTTTTTTCAACAATTTA
Found at i:4890392 original size:24 final size:24
Alignment explanation
Indices: 4890359--4890404 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4890349 CCCGACCCGG
4890359 TTTTATAATAATAATTTTATTTTTA
1 TTTTATAATAATAATTTT-TTTTTA
*
4890384 TTTT-TAATACTAATTTTTTTT
1 TTTTATAATAATAATTTTTTTT
4890405 GCTTGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTATAATAATAATTTTTTTTTA
Found at i:4891827 original size:42 final size:43
Alignment explanation
Indices: 4891745--4891833 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 43
4891735 TAGTGATCCT
* *
4891745 GTGATATTTTAATTTTGCTTGAATTAGGTCTATCAAGAATCTC
1 GTGATATTTTAATTTTGCTTGAATTAGATCCATCAAGAATCTC
* * *
4891788 GTGATA-TTTAATTTTGTTTG-ATTTGAATCCATCAGGAATCTC
1 GTGATATTTTAATTTTGCTTGAATTAG-ATCCATCAAGAATCTC
4891830 GTGA
1 GTGA
4891834 GATATATGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
41 4 0.10
42 30 0.75
43 6 0.15
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (43 bp):
GTGATATTTTAATTTTGCTTGAATTAGATCCATCAAGAATCTC
Found at i:4892630 original size:28 final size:30
Alignment explanation
Indices: 4892568--4892632 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
4892558 AAATTTCAAA
* *
4892568 TCATTCTCGTACATAAATTTTTATTTGAGG
1 TCATTTTCGTAAATAAATTTTTATTTGAGG
4892598 T-ATTTTCGTAAAT-AATTTTT-TTT-AGAG
1 TCATTTTCGTAAATAAATTTTTATTTGAG-G
4892625 TCATTTTC
1 TCATTTTC
4892633 AAAACAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 5 0.16
28 13 0.42
29 10 0.32
30 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (30 bp):
TCATTTTCGTAAATAAATTTTTATTTGAGG
Found at i:4893345 original size:59 final size:60
Alignment explanation
Indices: 4893282--4893446 Score: 246
Period size: 59 Copynumber: 2.7 Consensus size: 60
4893272 TTTTAATAAG
*
4893282 ATTATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATTATATTTT-AACATA
1 ATTATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATTATATTTTAAACATA
*
4893341 ATTATTATTAAATATAATTTAAT--AAAATAATATATAATTTAATTATATTTTAAATATA
1 ATTATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATTATATTTTAAACATA
*
4893399 ATTATTATTAAAATATAAATTAATAAAAATCATAATATATAATATTAA
1 ATTATTATT-AAATATAATTTAATAAAAA--ATAATATATAAT-TTAA
4893447 AAAAAATATA
Statistics
Matches: 96, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
57 27 0.28
58 14 0.15
59 36 0.38
61 3 0.03
63 12 0.12
64 4 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (60 bp):
ATTATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATTATATTTTAAACATA
Found at i:4893402 original size:17 final size:17
Alignment explanation
Indices: 4893323--4893416 Score: 50
Period size: 17 Copynumber: 6.2 Consensus size: 17
4893313 ATAAATAATT
*
4893323 TAATTATATTTT-AACA
1 TAATTATATTTTAAATA
*
4893339 TAATTAT-TATTAAATA
1 TAATTATATTTTAAATA
*
4893355 TAATT-TA--ATAAA-A
1 TAATTATATTTTAAATA
*
4893368 TAA-TATA---T-AATT
1 TAATTATATTTTAAATA
4893380 TAATTATATTTTAAATA
1 TAATTATATTTTAAATA
*
4893397 TAATTAT-TATTAAAATA
1 TAATTATAT-TTTAAATA
4893414 TAA
1 TAA
4893417 ATTAATAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
11 2 0.03
12 5 0.08
13 10 0.16
14 4 0.06
15 4 0.06
16 17 0.27
17 20 0.32
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTATATTTTAAATA
Found at i:4893420 original size:15 final size:16
Alignment explanation
Indices: 4893392--4893442 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
4893382 ATTATATTTT
*
4893392 AAATATAATTATTATTA
1 AAATATAA-TATTAATA
4893409 AAATATAA-ATTAATAA
1 AAATATAATATTAAT-A
4893425 AAATCATAATATATAATA
1 AAAT-ATAATAT-TAATA
4893443 TTAAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.17
16 5 0.17
17 12 0.41
18 3 0.10
19 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATATAATATTAATA
Found at i:4893457 original size:24 final size:24
Alignment explanation
Indices: 4893411--4893458 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4893401 TATTATTAAA
*
4893411 ATATAAATTAATAAAAATCATAAT
1 ATATAAATTAAAAAAAATCATAAT
4893435 ATATAATATTAAAAAAAAT-ATAAT
1 ATATAA-ATTAAAAAAAATCATAAT
4893459 TCCTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
ATATAAATTAAAAAAAATCATAAT
Found at i:4894550 original size:48 final size:48
Alignment explanation
Indices: 4894479--4894576 Score: 187
Period size: 48 Copynumber: 2.0 Consensus size: 48
4894469 TGTTGATATG
*
4894479 AGAATGTGTAGTTGGTGAAGATGCACAGGTGGACCGTAATGGAGGACA
1 AGAATGTGTAGTTGGTGAAGATGCACAGGTGAACCGTAATGGAGGACA
4894527 AGAATGTGTAGTTGGTGAAGATGCACAGGTGAACCGTAATGGAGGACA
1 AGAATGTGTAGTTGGTGAAGATGCACAGGTGAACCGTAATGGAGGACA
4894575 AG
1 AG
4894577 GGGCCTTGCC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.33, C:0.10, G:0.37, T:0.20
Consensus pattern (48 bp):
AGAATGTGTAGTTGGTGAAGATGCACAGGTGAACCGTAATGGAGGACA
Found at i:4898037 original size:24 final size:23
Alignment explanation
Indices: 4898010--4898083 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 23
4898000 GAAGGATGAT
4898010 AAGGCTGAGACAAAAAAGGAAGTG
1 AAGGCTGAGA-AAAAAAGGAAGTG
* *
4898034 AAGGCT--GAAAAAGAGAAAGTG
1 AAGGCTGAGAAAAAAAGGAAGTG
4898055 AAGGCTGA-AAAAGAGAAGGAAGTG
1 AAGGCTGAGAAAA-A-AAGGAAGTG
4898079 AAGGC
1 AAGGC
4898084 CGAGTGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 17 0.40
22 6 0.14
23 1 0.02
24 18 0.43
ACGTcount: A:0.50, C:0.07, G:0.35, T:0.08
Consensus pattern (23 bp):
AAGGCTGAGAAAAAAAGGAAGTG
Found at i:4898046 original size:19 final size:20
Alignment explanation
Indices: 4898022--4898076 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
4898012 GGCTGAGACA
4898022 AAAAAG-GAAGTGAAGGCTG
1 AAAAAGAGAAGTGAAGGCTG
4898041 AAAAAGAGAAAGTGAAGGCTG
1 AAAAAGAG-AAGTGAAGGCTG
4898062 AAAAAGAGAAG-GAAG
1 AAAAAGAGAAGTGAAG
4898077 TGAAGGCCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.29
20 4 0.12
21 20 0.59
ACGTcount: A:0.55, C:0.04, G:0.35, T:0.07
Consensus pattern (20 bp):
AAAAAGAGAAGTGAAGGCTG
Found at i:4901625 original size:23 final size:23
Alignment explanation
Indices: 4901592--4901660 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
4901582 CACAAAACAC
*
4901592 GAGCACAAAAGTGCTAAATTTAG
1 GAGCACAAAAGTGCTAAATATAG
* *
4901615 GAGCACCAAAGTGCTAAACATAG
1 GAGCACAAAAGTGCTAAATATAG
* *
4901638 GAGCACTAGAGTGCTAAATATAG
1 GAGCACAAAAGTGCTAAATATAG
4901661 AAACACGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (23 bp):
GAGCACAAAAGTGCTAAATATAG
Found at i:4904925 original size:3 final size:3
Alignment explanation
Indices: 4904917--4904960 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
4904907 TCTCTCTCTC
* *
4904917 TCT TCT TCT TCT TCT TTT TCT TCT T-T TCT TCT TTT TC- TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
4904961 AAACCCTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TCT
Found at i:4905378 original size:25 final size:26
Alignment explanation
Indices: 4905290--4905376 Score: 165
Period size: 26 Copynumber: 3.3 Consensus size: 26
4905280 ATATGTAAAT
*
4905290 AAAATAAAAAGATATCATGAAATTGA
1 AAAAAAAAAAGATATCATGAAATTGA
4905316 AAAAAAAAAAGATATCATGAAATTGA
1 AAAAAAAAAAGATATCATGAAATTGA
4905342 AAAAAAAAAAGATATCATGAAATTGA
1 AAAAAAAAAAGATATCATGAAATTGA
4905368 AAAAAAAAA
1 AAAAAAAAA
4905377 GAAATCGAGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.18
Consensus pattern (26 bp):
AAAAAAAAAAGATATCATGAAATTGA
Found at i:4906726 original size:13 final size:13
Alignment explanation
Indices: 4906708--4906735 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4906698 TGATGTTTTC
4906708 ATTTATAACATTA
1 ATTTATAACATTA
4906721 ATTTATAACATTA
1 ATTTATAACATTA
4906734 AT
1 AT
4906736 GGTATACTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTATAACATTA
Found at i:4911622 original size:19 final size:20
Alignment explanation
Indices: 4911598--4911637 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4911588 ATTATAATTT
4911598 TTTATT-TTTTAAATTTAAA
1 TTTATTATTTTAAATTTAAA
* *
4911617 TTTATTATTTTTATTTTAAA
1 TTTATTATTTTAAATTTAAA
4911637 T
1 T
4911638 AAACTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTATTTTAAATTTAAA
Found at i:4917077 original size:18 final size:17
Alignment explanation
Indices: 4917042--4917088 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
4917032 AGAATTTTTA
*
4917042 AAAAATTGT-AAAAAAT
1 AAAAATTATAAAAAAAT
*
4917058 AAATATTATAAAAAATAT
1 AAAAATTATAAAAAA-AT
*
4917076 AAAAATTGTAAAA
1 AAAAATTATAAAA
4917089 GATTATAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 7 0.28
17 5 0.20
18 13 0.52
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (17 bp):
AAAAATTATAAAAAAAT
Found at i:4917088 original size:16 final size:16
Alignment explanation
Indices: 4917042--4917088 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
4917032 AGAATTTTTA
4917042 AAAAATTGTAAAAAAT
1 AAAAATTGTAAAAAAT
* *
4917058 AAATATTATAAAAAATAT
1 AAAAATTGT-AAAAA-AT
4917076 AAAAATTGTAAAA
1 AAAAATTGTAAAA
4917089 GATTATAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 7 0.28
17 9 0.36
18 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (16 bp):
AAAAATTGTAAAAAAT
Found at i:4917117 original size:9 final size:10
Alignment explanation
Indices: 4917057--4917123 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 10
4917047 TTGTAAAAAA
*
4917057 TAAATATTA-
1 TAAAAATTAT
*
4917066 TAAAAAATA-
1 TAAAAATTAT
*
4917075 TAAAAATT-G
1 TAAAAATTAT
4917084 TAAAAGATTAT
1 TAAAA-ATTAT
*
4917095 AGAAAAATTAT
1 -TAAAAATTAT
4917106 TAAAAATT-T
1 TAAAAATTAT
4917115 TAAAAATTA
1 TAAAAATTA
4917124 ATATATAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
9 28 0.60
10 10 0.21
11 5 0.11
12 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.34
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:4924333 original size:3 final size:3
Alignment explanation
Indices: 4924327--4924360 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4924317 TTTTTGAATA
4924327 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4924361 CTTTTGTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4924727 original size:12 final size:12
Alignment explanation
Indices: 4924710--4924734 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4924700 AAAACATAAA
4924710 TATTTTTTATTT
1 TATTTTTTATTT
4924722 TATTTTTTATTT
1 TATTTTTTATTT
4924734 T
1 T
4924735 CTGTATTTTC
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:4924892 original size:104 final size:105
Alignment explanation
Indices: 4924683--4924926 Score: 330
Period size: 104 Copynumber: 2.3 Consensus size: 105
4924673 GAAAGAATTG
* * * * *
4924683 AAATTTTAAAAATTATAAAAACATAAATATTTTTTATTTTATTTTTTATTTTCTGTATTTTCCAA
1 AAATATTAAAAATTTTAAAAATAT-AA-ATTTTTTATTTTATTTTATATTTTCTATATTTTCCAA
4924748 TTGTTTTGAAAATTTTTAATTTCAAATATTTATTGAATTTTT
64 TTGTTTTGAAAATTTTTAATTTCAAATATTTATTGAATTTTT
* * *
4924790 AAATATTAAAAATTTTAAAAATATAAATTTTTTA-TTTCTTTTAT-TTTTCTATGTTTTTCAATT
1 AAATATTAAAAATTTTAAAAATATAAATTTTTTATTTTATTTTATATTTTCTATATTTTCCAATT
*
4924853 GTTTTGAAAATTTTTAATTTTCAAATGTTTATTGAATTTTT
66 GTTTTGAAAATTTTTAA-TTTCAAATATTTATTGAATTTTT
* * * *
4924894 AAATATCAAAAATTTCAAATATATAAATATTTT
1 AAATATTAAAAATTTTAAAAATATAAATTTTTT
4924927 CAGTTCCATA
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
103 33 0.27
104 59 0.48
105 8 0.07
106 2 0.02
107 21 0.17
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.55
Consensus pattern (105 bp):
AAATATTAAAAATTTTAAAAATATAAATTTTTTATTTTATTTTATATTTTCTATATTTTCCAATT
GTTTTGAAAATTTTTAATTTCAAATATTTATTGAATTTTT
Found at i:4924939 original size:104 final size:103
Alignment explanation
Indices: 4924731--4924949 Score: 305
Period size: 104 Copynumber: 2.1 Consensus size: 103
4924721 TTATTTTTTA
* *
4924731 TTTTCTGTATTTTCCAATTGTTTTGAAAATTTTTAATTTCAAATATTTATTGAATTTTTAAATAT
1 TTTTCTATGTTTTCCAATTGTTTTGAAAATTTTTAATTTCAAATATTTATTGAATTTTTAAATAT
* * * * **
4924796 TAAAAATTTTAAAAATATAAATTTTTTATTTCTTTTAT
66 CAAAAATTTCAAAAATATAAATTTTTCAGTTCTCATAT
* *
4924834 TTTTCTATGTTTTTCAATTGTTTTGAAAATTTTTAATTTTCAAATGTTTATTGAATTTTTAAATA
1 TTTTCTATGTTTTCCAATTGTTTTGAAAATTTTTAA-TTTCAAATATTTATTGAATTTTTAAATA
*
4924899 TCAAAAATTTCAAATATATAAATATTTTCAGTTC-CATAT
65 TCAAAAATTTCAAAAATATAAAT-TTTTCAGTTCTCATAT
*
4924938 TTTTATATGTTT
1 TTTTCTATGTTT
4924950 ATAATTAATA
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
103 33 0.32
104 61 0.60
105 8 0.08
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (103 bp):
TTTTCTATGTTTTCCAATTGTTTTGAAAATTTTTAATTTCAAATATTTATTGAATTTTTAAATAT
CAAAAATTTCAAAAATATAAATTTTTCAGTTCTCATAT
Found at i:4946357 original size:2 final size:2
Alignment explanation
Indices: 4946350--4946380 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4946340 TAAAAAGGGA
4946350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4946381 AGAAGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4948061 original size:3 final size:3
Alignment explanation
Indices: 4948053--4948078 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4948043 TGGATCTTGT
4948053 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
4948079 TTGTGTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Done.