Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 183 of 226
Found at i:55517992 original size:23 final size:23
Alignment explanation
Indices: 55517966--55518040 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
55517956 TAAACCATAA
55517966 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAACCCTTAAACTACAT
*
55517989 ACTATAGTAAA--CATAAACCTTA-A-
1 ACTATA--AAACCCTTAAA-C-TACAT
55518012 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAACCCTTAAACTACAT
55518035 ACTATA
1 ACTATA
55518041 GCCCTTAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
21 5 0.12
22 2 0.05
23 28 0.67
24 2 0.05
25 5 0.12
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.27
Consensus pattern (23 bp):
ACTATAAAACCCTTAAACTACAT
Found at i:55518493 original size:41 final size:41
Alignment explanation
Indices: 55518442--55518625 Score: 239
Period size: 41 Copynumber: 4.5 Consensus size: 41
55518432 GCGTTTTTTA
* * *
55518442 AAAAAGCGCCGCTAAAGGCCTGAGA-ATTAGCGGCGCAT-CAAT
1 AAAAA-CGCCGCTAAAGCCCAGA-ACATTAGCGGCGCTTAC-AT
55518484 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTA-ATT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACA-T
* *
55518525 AAAAACGCCACTAAATCCCAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* * *
55518566 ACAAACGCCACTAAATCCCAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
55518607 AAAAACGCCGCTAAAGCCC
1 AAAAACGCCGCTAAAGCCC
55518626 CCGAAAAGTC
Statistics
Matches: 129, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
40 2 0.02
41 121 0.94
42 6 0.05
ACGTcount: A:0.38, C:0.29, G:0.18, T:0.15
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
Found at i:55521586 original size:25 final size:25
Alignment explanation
Indices: 55521558--55521616 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
55521548 CATAGCTTGC
55521558 GTGAGCATTTATAGTCACAGCTCAT
1 GTGAGCATTTATAGTCACAGCTCAT
* * **
55521583 GTGAGCATTTATCGTCAGAGCTTGT
1 GTGAGCATTTATAGTCACAGCTCAT
55521608 GTGAGCATT
1 GTGAGCATT
55521617 GTTCTCGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (25 bp):
GTGAGCATTTATAGTCACAGCTCAT
Found at i:55523048 original size:25 final size:25
Alignment explanation
Indices: 55523002--55523081 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
55522992 TCCAGCTCTT
*
55523002 ATGAGCTTCCCGATACTCAGCTCGC
1 ATGAGCTTCCCGTTACTCAGCTCGC
* * * *
55523027 ATGAGCTTCCCGTTATTTAGCTTGG
1 ATGAGCTTCCCGTTACTCAGCTCGC
* *
55523052 ATGAGCTTACCGTT--TACAGCTCGT
1 ATGAGCTTCCCGTTACT-CAGCTCGC
55523076 ATGAGC
1 ATGAGC
55523082 AAACATGTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 1 0.02
24 11 0.24
25 33 0.73
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACTCAGCTCGC
Found at i:55535634 original size:18 final size:17
Alignment explanation
Indices: 55535601--55535639 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
55535591 TTTTATAAAT
55535601 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
55535619 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
55535636 TGTG
1 TGTG
55535640 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:55535891 original size:23 final size:23
Alignment explanation
Indices: 55535865--55535986 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
55535855 AGTGTTATTG
55535865 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
55535888 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
55535911 ATTAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
55535934 TTCAGTGATAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
55535957 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
55535980 ATCAGTG
1 ATCAGTG
55535987 TGGCACTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 86 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:55553022 original size:15 final size:16
Alignment explanation
Indices: 55553002--55553033 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
55552992 AGGCCCACTA
55553002 TCTCAGCCC-AACTGG
1 TCTCAGCCCAAACTGG
55553017 TCTCAGCCCAAACTGG
1 TCTCAGCCCAAACTGG
55553033 T
1 T
55553034 TCATGGGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.22
Consensus pattern (16 bp):
TCTCAGCCCAAACTGG
Found at i:55560737 original size:56 final size:50
Alignment explanation
Indices: 55560670--55560812 Score: 169
Period size: 50 Copynumber: 2.7 Consensus size: 50
55560660 AGGAATGAGA
* * * *
55560670 TCCCATATAAGAACATATCTGGGATATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA-C--CGAGA-TA--AGAGG
* *
55560726 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATAAGAGG
*
55560776 TCCCATGTAAGACCATGTATGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA
55560813 GTATAGGAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 39 0.50
52 2 0.03
53 4 0.05
55 1 0.01
56 32 0.41
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATAAGAGG
Found at i:55561081 original size:12 final size:12
Alignment explanation
Indices: 55561064--55561114 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
55561054 ATGAGTTATT
55561064 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
55561076 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
55561088 TAAGTGAGTAAG
1 TAAGTAAGCAAG
55561100 TAAAG-AAGCAAG
1 T-AAGTAAGCAAG
55561112 TAA
1 TAA
55561115 AGATTCTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.06
12 27 0.84
13 3 0.09
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:55561112 original size:20 final size:20
Alignment explanation
Indices: 55561074--55561112 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55561064 TAAGTAAGCA
*
55561074 AGTAAGTAAACAAGTAAGTG
1 AGTAAGTAAACAAGCAAGTG
*
55561094 AGTAAGTAAAGAAGCAAGT
1 AGTAAGTAAACAAGCAAGT
55561113 AAAGATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.18
Consensus pattern (20 bp):
AGTAAGTAAACAAGCAAGTG
Found at i:55563414 original size:36 final size:36
Alignment explanation
Indices: 55563351--55563421 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
55563341 GAGGAGTGCC
* *
55563351 TCAGTCAGAATAGATTCGAAATGCTGCTGAACTGAG
1 TCAGTCAGAATAGATTCGAAAAGCTGCTAAACTGAG
* *
55563387 TCAGTTAGAATAGA-TCTAAAAGACTGCTAAACTGA
1 TCAGTCAGAATAGATTCGAAAAG-CTGCTAAACTGA
55563422 ATAGAGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 6 0.20
36 24 0.80
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (36 bp):
TCAGTCAGAATAGATTCGAAAAGCTGCTAAACTGAG
Found at i:55565983 original size:25 final size:25
Alignment explanation
Indices: 55565956--55566167 Score: 119
Period size: 25 Copynumber: 8.5 Consensus size: 25
55565946 AAGCTCTTTT
*
55565956 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGA
* * * **
55565981 GAGCTATGTAACGGGAAGATCCGGA
1 GAGCCATATAACGGGAAGCTCATGA
*
55566006 GAGCCAT-TAACGGGAAGCTCATAA
1 GAGCCATATAACGGGAAGCTCATGA
* ** *
55566030 GAGCCATTTATTGGGAAGCTC-CGAA
1 GAGCCATATAACGGGAAGCTCATG-A
* *
55566055 GAGCAATA-AACGGGAAGCTCAAAAGA
1 GAGCCATATAACGGGAAGCTC--ATGA
* * ***
55566081 GAGCCAT-TAATCAGGAAACTCGCAA
1 GAGCCATATAA-CGGGAAGCTCATGA
* * * *
55566106 GAACCATTTAACGGGAAGCTCGTAA
1 GAGCCATATAACGGGAAGCTCATGA
* * *
55566131 GAGCCAAATATCAGGAAGCTCATGA
1 GAGCCATATAACGGGAAGCTCATGA
*
55566156 GAGCTA-ATAACG
1 GAGCCATATAACG
55566168 AGACACTCTT
Statistics
Matches: 139, Mismatches: 40, Indels: 17
0.71 0.20 0.09
Matches are distributed among these distances:
24 34 0.24
25 84 0.60
26 12 0.09
27 9 0.06
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.17
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGA
Found at i:55566019 original size:49 final size:49
Alignment explanation
Indices: 55565956--55566136 Score: 152
Period size: 49 Copynumber: 3.6 Consensus size: 49
55565946 AAGCTCTTTT
** * *
55565956 GAGCCATATAACGGGAAGCTCATGTGAGCTATGTAACGGGAAGATCCGGA
1 GAGCCAT-TAACGGGAAGCTCATAAGAGCCATGTAACGGGAAGATCCGAA
* ** *
55566006 GAGCCATTAACGGGAAGCTCATAAGAGCCATTTATTGGGAAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCATAAGAGCCATGTAACGGGAAGATCCGAA
* * * *
55566055 GAGCAATAAACGGGAAGCTCAAAAGAGAGCCAT-TAATCAGGAA-A-CTCGCAA
1 GAGCCATTAACGGGAAGCTC-ATA-AGAGCCATGTAA-CGGGAAGATC-CG-AA
* *
55566106 GAACCATTTAACGGGAAGCTCGTAAGAGCCA
1 GAGCCA-TTAACGGGAAGCTCATAAGAGCCA
55566137 AATATCAGGA
Statistics
Matches: 105, Mismatches: 20, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
49 53 0.50
50 20 0.19
51 19 0.18
52 13 0.12
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (49 bp):
GAGCCATTAACGGGAAGCTCATAAGAGCCATGTAACGGGAAGATCCGAA
Found at i:55566074 original size:24 final size:24
Alignment explanation
Indices: 55565989--55566074 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
55565979 GTGAGCTATG
* * *
55565989 TAACGGGAAGATCCGGAGAGCCAT
1 TAACGGGAAGCTCCGAAGAGCAAT
** *
55566013 TAACGGGAAGCTCATAAGAGCCATT
1 TAACGGGAAGCTCCGAAGAG-CAAT
**
55566038 TATTGGGAAGCTCCGAAGAGCAAT
1 TAACGGGAAGCTCCGAAGAGCAAT
*
55566062 AAACGGGAAGCTC
1 TAACGGGAAGCTC
55566075 AAAAGAGAGC
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
24 29 0.62
25 18 0.38
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (24 bp):
TAACGGGAAGCTCCGAAGAGCAAT
Found at i:55571332 original size:18 final size:19
Alignment explanation
Indices: 55571292--55571335 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
55571282 TATTGAAATT
55571292 TATATTATATAAATTTAGAA
1 TATATTATATAAATTTA-AA
55571312 TAT-TTATAT--ATTTAAA
1 TATATTATATAAATTTAAA
55571328 TATATTAT
1 TATATTAT
55571336 TATCGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
19 6 0.26
20 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATTATATAAATTTAAA
Found at i:55572543 original size:23 final size:23
Alignment explanation
Indices: 55572515--55572564 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
55572505 TAAGAATGTT
55572515 TTTGATGTTTTAAATTATGATCC
1 TTTGATGTTTTAAATTATGATCC
55572538 TTTGATGTTTTAAATTATGATCC
1 TTTGATGTTTTAAATTATGATCC
55572561 TTTG
1 TTTG
55572565 CCCTCTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.54
Consensus pattern (23 bp):
TTTGATGTTTTAAATTATGATCC
Found at i:55578947 original size:3 final size:3
Alignment explanation
Indices: 55578939--55578964 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55578929 ATTTTGTGTC
55578939 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
55578965 TGTTAGGTGT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55587206 original size:3 final size:3
Alignment explanation
Indices: 55587198--55587230 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
55587188 CAGCCATAGC
55587198 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
55587231 TTGAATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:55590304 original size:13 final size:13
Alignment explanation
Indices: 55590286--55590314 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
55590276 GTTAAGAGTA
55590286 AAACTTTATTTGT
1 AAACTTTATTTGT
55590299 AAACTTTATTTGT
1 AAACTTTATTTGT
55590312 AAA
1 AAA
55590315 AAAGTCCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
AAACTTTATTTGT
Found at i:55592234 original size:33 final size:33
Alignment explanation
Indices: 55592191--55592257 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
55592181 TTGGACCTTC
55592191 AGCGTATCATAGAACTAATGTTTTGTACTGTTA
1 AGCGTATCATAGAACTAATGTTTTGTACTGTTA
*
55592224 AGCGTGTCATAGAACTAATGTTTTGTACTGTTA
1 AGCGTATCATAGAACTAATGTTTTGTACTGTTA
55592257 A
1 A
55592258 TTTATGTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
AGCGTATCATAGAACTAATGTTTTGTACTGTTA
Found at i:55594979 original size:27 final size:27
Alignment explanation
Indices: 55594941--55594996 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
55594931 TTCTTTCCTT
55594941 TCATTTTCTGTTTTTGTTTAGCAGCAA
1 TCATTTTCTGTTTTTGTTTAGCAGCAA
55594968 TCATTTTCTGTTTTTGTTTAGCAGCAA
1 TCATTTTCTGTTTTTGTTTAGCAGCAA
55594995 TC
1 TC
55594997 TTTGGCCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (27 bp):
TCATTTTCTGTTTTTGTTTAGCAGCAA
Found at i:55601903 original size:6 final size:7
Alignment explanation
Indices: 55601876--55601901 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55601866 ATAAATATAT
55601876 ATTTTTA
1 ATTTTTA
55601883 ATTTTTA
1 ATTTTTA
55601890 ATTTTTA
1 ATTTTTA
55601897 ATTTT
1 ATTTT
55601902 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTA
Found at i:55601925 original size:29 final size:29
Alignment explanation
Indices: 55601891--55601955 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
55601881 TAATTTTTAA
*
55601891 TTTTTAATTTTAAAATACTTTTAAAATAT
1 TTTTTAATTTTAAAATAATTTTAAAATAT
* **
55601920 TTTTTATTTTTAAAATAATTTTTTAATAT
1 TTTTTAATTTTAAAATAATTTTAAAATAT
*
55601949 TTATTAA
1 TTTTTAA
55601956 AAAATGGGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTTAATTTTAAAATAATTTTAAAATAT
Found at i:55601930 original size:18 final size:19
Alignment explanation
Indices: 55601909--55601944 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
55601899 TTTAAAATAC
55601909 TTTTAAAAT-ATTTTTTAT
1 TTTTAAAATAATTTTTTAT
55601927 TTTTAAAATAATTTTTTA
1 TTTTAAAATAATTTTTTA
55601945 ATATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAAAATAATTTTTTAT
Found at i:55624239 original size:38 final size:40
Alignment explanation
Indices: 55624173--55624262 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 40
55624163 ATATTAAAAA
* * *
55624173 TATATCATATTAAAAAAACTACCATAAATATAATAAATCT
1 TATATTATATTAAAAAAACTAACATAAATATAATAAATAT
* *
55624213 TTTATTATATTAAAAACAC-AAC-TAAATATAATAAATAT
1 TATATTATATTAAAAAAACTAACATAAATATAATAAATAT
*
55624251 TATATTGTATTA
1 TATATTATATTA
55624263 GATATAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 25 0.58
39 2 0.05
40 16 0.37
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (40 bp):
TATATTATATTAAAAAAACTAACATAAATATAATAAATAT
Found at i:55624989 original size:18 final size:20
Alignment explanation
Indices: 55624959--55624999 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
55624949 TATTATTAAA
55624959 TAAAATATTAAAAATATT-T
1 TAAAATATTAAAAATATTAT
*
55624978 TAAAAT-TTAAAATTATTAT
1 TAAAATATTAAAAATATTAT
55624997 TAA
1 TAA
55625000 TGCTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAATATTAAAAATATTAT
Found at i:55625243 original size:80 final size:80
Alignment explanation
Indices: 55625094--55625244 Score: 207
Period size: 81 Copynumber: 1.9 Consensus size: 80
55625084 TATAAATATA
* * *
55625094 TATGTTTAATAATATAAACTTATGAGAAAATATTTGGTGCACCATCGGTGGCAAGTTTTAGACTC
1 TATGATTAATAATATAAAATTATGAGAAAATATTTGGTGCACCATCAGTGGCAAGTTTTAGACTC
55625159 CACAAGCTAATCATG
66 CACAAGCTAATCATG
* * * *
55625174 TATGATTAATGATATTAAAATTATGAGAAAATATTTGGTGTACTATCAGT-G-AAGGTTTTATAC
1 TATGATTAATAATA-TAAAATTATGAGAAAATATTTGGTGCACCATCAGTGGCAA-GTTTTAGAC
55625237 TCCACAAG
64 TCCACAAG
55625245 TAAGTTTAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
79 2 0.03
80 29 0.47
81 31 0.50
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (80 bp):
TATGATTAATAATATAAAATTATGAGAAAATATTTGGTGCACCATCAGTGGCAAGTTTTAGACTC
CACAAGCTAATCATG
Found at i:55628744 original size:6 final size:6
Alignment explanation
Indices: 55628733--55628795 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
55628723 AGGTAAATTG
** * * *
55628733 ATAAAA ATAAAA ATAAAA ATAAAA ATACTA ATAATA ATAATA ATAATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
55628781 ATAATAA ACTAAAA A
1 ATAA-AA A-TAAAA A
55628796 ATGCAAAAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
6 43 0.84
7 5 0.10
8 3 0.06
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (6 bp):
ATAAAA
Found at i:55628756 original size:18 final size:18
Alignment explanation
Indices: 55628733--55628795 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
55628723 AGGTAAATTG
*
55628733 ATAAAAATAAAAATAAAA
1 ATAAAAATAATAATAAAA
* *
55628751 ATAAAAATACTAATAATA
1 ATAAAAATAATAATAAAA
*
55628769 ATAATAATAATAATAATAA
1 ATAAAAATAATAATAA-AA
55628788 ACTAAAAA
1 A-TAAAAA
55628796 ATGCAAAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 29 0.81
19 2 0.06
20 5 0.14
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAATAATAATAAAA
Found at i:55630289 original size:89 final size:89
Alignment explanation
Indices: 55630138--55630608 Score: 567
Period size: 89 Copynumber: 5.3 Consensus size: 89
55630128 TTTCACTTTT
* *
55630138 CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCAAATCAGATCGAAGACACCAGCTT
1 CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAGCTT
*
55630203 GGCCTCTCTGAGTTTGCAGCGGAG
66 GGCCTCTCTGAGTTTGCAGTGGAG
* * * *
55630227 CAGACTGAAGATAACAGATCTTGTCTTCCTTTATTGGCAGCAAAGTAGATCGAAGACACCAGCCT
1 CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAGCTT
* * *
55630292 GACCT-TATTGAGTTTGCAGTGAAG
66 GGCCTCT-CTGAGTTTGCAGTGGAG
* * * *
55630316 TAGACTAAAGATAGCAGATCTTGTCTTTCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGTCT
1 CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAG-CT
* *
55630381 T-GCCTC-CTTGAGTTTGTAGCGGAG
65 TGGCCTCTC-TGAGTTTGCAGTGGAG
* * *
55630405 CAGACTAGAA-ATAGCAGATCTTGTCTTCCTATATTGGCAGCAAAGCAGATCGAAGGCACCAGCC
1 CAGACT-GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAGCT
* *
55630469 TGACCTCCCTGAGTTTGCAGTGGAG
65 TGGCCTCTCTGAGTTTGCAGTGGAG
* * * * *
55630494 CATAGTAAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAA-CAGATCGAAAACACCAGCC
1 CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGC-AAAGCAGATCGAAGACACCAG-C
55630558 TT-GCCTCTCTGAGTTTGCAGTGGAG
64 TTGGCCTCTCTGAGTTTGCAGTGGAG
* ** * *
55630583 TAGGTTGAAGATTGTAGATCTTGTCT
1 CAGACTGAAGATAGCAGATCTTGTCT
55630609 CCCTAAGTAG
Statistics
Matches: 323, Mismatches: 49, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
88 5 0.02
89 308 0.95
90 10 0.03
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (89 bp):
CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAGCTT
GGCCTCTCTGAGTTTGCAGTGGAG
Found at i:55630457 original size:178 final size:177
Alignment explanation
Indices: 55630138--55630582 Score: 644
Period size: 178 Copynumber: 2.5 Consensus size: 177
55630128 TTTCACTTTT
* *
55630138 CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGC-AAATCAGATCGAAGACACCAGCT
1 CAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAA-CAGATCGAAGACACCAGCT
*
55630202 TGGCCTCTCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTTTATTGGCAG
65 T-GCCTCTCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTATATTGGCAG
* * *
55630267 CAAAGTAGATCGAAGACACCAGCCTGACCTTATTGAGTTTGCAGTGAAG
129 CAAAGCAGATCGAAGACACCAGCCTGACCTCACTGAGTTTGCAGTGAAG
* * *
55630316 TAGACTAAAGATAGCAGATCTTGTCTTTCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGTCT
1 CAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAACAGATCGAAGACACCAG-CT
* *
55630381 TGCCTC-CTTGAGTTTGTAGCGGAGCAGACTAGAA-ATAGCAGATCTTGTCTTCCTATATTGGCA
65 TGCCTCTC-TGAGTTTGCAGCGGAGCAGACT-GAAGATAACAGATCTTGTCTTCCTATATTGGCA
* * *
55630444 GCAAAGCAGATCGAAGGCACCAGCCTGACCTCCCTGAGTTTGCAGTGGAG
128 GCAAAGCAGATCGAAGACACCAGCCTGACCTCACTGAGTTTGCAGTGAAG
* * * *
55630494 CATAGTAAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAACAGATCGAAAACACCAGCCT
1 CAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAACAGATCGAAGACACCAG-CT
*
55630559 TGCCTCTCTGAGTTTGCAGTGGAG
65 TGCCTCTCTGAGTTTGCAGCGGAG
55630583 TAGGTTGAAG
Statistics
Matches: 238, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
177 1 0.00
178 228 0.96
179 9 0.04
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (177 bp):
CAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAACAGATCGAAGACACCAGCTT
GCCTCTCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTATATTGGCAGCA
AAGCAGATCGAAGACACCAGCCTGACCTCACTGAGTTTGCAGTGAAG
Found at i:55630899 original size:97 final size:97
Alignment explanation
Indices: 55630783--55631124 Score: 463
Period size: 97 Copynumber: 3.5 Consensus size: 97
55630773 CGAATCTTAT
* * * * * * *
55630783 TTTCC-TGGCGTTGCAGTGGAACAGATTAAATCTGAAGGTAGCGAGTCTTATTTCCCTGGCGTCA
1 TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGTGTCG
*
55630847 CAGCAGATTAAAGCTGAAGGCAGCAAGTCTCA
66 CAGTAGATTAAAGCTGAAGGCAGCAAGTCTCA
* * *
55630879 TTTCCTTGGCGTTGGAGTGGAGCAGATTAAAGCTAAAGGCAGCAAATCTTATCTT-TCTGGTGTC
1 TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTAT-TTCCCTGGTGTC
* * * *
55630943 GTAGTAGATTAAAGCTAAAGGCAGCAAATTTCA
65 GCAGTAGATTAAAGCTGAAGGCAGCAAGTCTCA
* * * *
55630976 TTTCCTTAGTGTTGCAGTGGAGCAGATTAAAGCTTAAGGCAGCAAATCTTATCTCCCTGGTGTCG
1 TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGTGTCG
*
55631041 CAATAGATTAAAGCTGAAGGCAGCAAGTCTCA
66 CAGTAGATTAAAGCTGAAGGCAGCAAGTCTCA
* *
55631073 TTTCCTTGGCATTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCAAATCTTAT
1 TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTAT
55631125 ATCCTTGGAG
Statistics
Matches: 212, Mismatches: 31, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
96 6 0.03
97 204 0.96
98 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (97 bp):
TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGTGTCG
CAGTAGATTAAAGCTGAAGGCAGCAAGTCTCA
Found at i:55631130 original size:51 final size:51
Alignment explanation
Indices: 55630775--55631132 Score: 302
Period size: 51 Copynumber: 7.3 Consensus size: 51
55630765 GAAGACAACG
** * * *
55630775 AATCTTATTTTCC-TGGCGTTGCAGTGGAACAGATTAAATCTGAAGGTAGCG
1 AATCTTA-TTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * * *
55630826 AGTCTTATTTCCCTGGCG-T-CA---CAGCAGATTAAAGCTGAAGGCAGCA
1 AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * * * *
55630872 AGTCTCATTTCCTTGGCGTTGGAGTGGAGCAGATTAAAGCTAAAGGCAGCA
1 AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * *
55630923 AATCTTATCTTTC-TGGTG-T-C-GT--AGTAGATTAAAGCTAAAGGCAGCA
1 AATCTTAT-TTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * * *
55630969 AAT-TTCATTTCCTTAGTGTTGCAGTGGAGCAGATTAAAGCTTAAGGCAGCA
1 AATCTT-ATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * * *
55631020 AATCTTATCTCCCTGGTGTCGCA----A-TAGATTAAAGCTGAAGGCAGCA
1 AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * *
55631066 AGTCTCATTTCCTTGGCATTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
1 AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
*
55631117 AATCTTATATCCTTGG
1 AATCTTATTTCCTTGG
55631133 AGTTAAGATT
Statistics
Matches: 250, Mismatches: 37, Indels: 40
0.76 0.11 0.12
Matches are distributed among these distances:
45 5 0.02
46 104 0.42
47 3 0.01
48 4 0.02
49 4 0.02
50 8 0.03
51 117 0.47
52 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (51 bp):
AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
Found at i:55633272 original size:22 final size:23
Alignment explanation
Indices: 55633203--55633284 Score: 89
Period size: 22 Copynumber: 3.7 Consensus size: 23
55633193 CTTAACTATG
**
55633203 TTTTAAATTTATCATTAGCATTA
1 TTTTAAATTTATCATTAATATTA
* * *
55633226 TTTT-AATATATAATATACTATTA
1 TTTTAAATTTATCAT-TAATATTA
55633249 TTTTAAA-TTATCATTAATATTA
1 TTTTAAATTTATCATTAATATTA
55633271 -TTTAAATTTATCAT
1 TTTTAAATTTATCAT
55633285 ACATCATAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 6 0.12
22 22 0.45
23 19 0.39
24 2 0.04
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (23 bp):
TTTTAAATTTATCATTAATATTA
Found at i:55633302 original size:45 final size:45
Alignment explanation
Indices: 55633204--55633303 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
55633194 TTAACTATGT
* * * * *
55633204 TTTAAATTTATCATTAGCATTATTTTAATATATAATATACTATTA
1 TTTAAAATTATCATTAACATTATTTAAATATATAATACACTATAA
* * * *
55633249 TTTTAAATTATCATTAATATTATTTAAATTTATCATACA-TCATAA
1 TTTAAAATTATCATTAACATTATTTAAATATATAATACACT-ATAA
55633294 TTTAAAATTA
1 TTTAAAATTA
55633304 ATATATTTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (45 bp):
TTTAAAATTATCATTAACATTATTTAAATATATAATACACTATAA
Found at i:55634951 original size:40 final size:39
Alignment explanation
Indices: 55634853--55634970 Score: 166
Period size: 40 Copynumber: 3.0 Consensus size: 39
55634843 ATTGTTAGAT
*
55634853 GTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGC-TTT
1 GTGCGAGTT-TTAATTCCGGGTTAAGTCCCGAAGGCATTC
**
55634892 GTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTC
1 GTGCGAG-TTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
*
55634932 GTGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATT
1 GTGCGAGTTTT-AATTCCGGGTTAAGTCCCGAAGGCATT
55634971 GTATGAGTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
39 34 0.49
40 36 0.51
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (39 bp):
GTGCGAGTTTTAATTCCGGGTTAAGTCCCGAAGGCATTC
Found at i:55634991 original size:39 final size:38
Alignment explanation
Indices: 55634852--55635007 Score: 161
Period size: 39 Copynumber: 4.0 Consensus size: 38
55634842 TATTGTTAGA
* * *
55634852 TGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCTT
1 TGTGCGAGTTACTAA-ACCGGGTTAAGTCCCGAAGGCAT
* *
55634891 TGTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCAT
1 TGTGCGAGTTACTAA-ACCGGGTTAAGTCCCGAAGGCAT
*
55634930 TCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGGCAT
1 T-GTGCGAGTTACT-AAA-CCGGGTTAAGTCCCGAAGGCAT
** * *
55634970 TGTATGAGTTACTATAACCGGGCTATGTCCCGAAGGCA
1 TGTGCGAGTTACTA-AACCGGGTTAAGTCCCGAAGGCA
55635008 CTTGAACGAG
Statistics
Matches: 101, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
39 65 0.64
40 36 0.36
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (38 bp):
TGTGCGAGTTACTAAACCGGGTTAAGTCCCGAAGGCAT
Found at i:55634991 original size:79 final size:79
Alignment explanation
Indices: 55634853--55635007 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 79
55634843 ATTGTTAGAT
* * * * *
55634853 GTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGATACTAATTCCGGGTTAAG
1 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTGTACGAGATACTAATACCGGGCTAAG
55634918 TCCCGAAGGCATTC
66 TCCCGAAGGCATTC
* *
55634932 GTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGGCATTGTATGAGTTACT-ATAACCGGGCTA
1 GTGCGAGTTATT-AAATCCGGGTTAAGTCCCGAAGGCATTGTACGAGATACTAAT-ACCGGGCTA
*
55634995 TGTCCCGAAGGCA
64 AGTCCCGAAGGCA
55635008 CTTGAACGAG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 4 0.06
79 62 0.94
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (79 bp):
GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTGTACGAGATACTAATACCGGGCTAAG
TCCCGAAGGCATTC
Found at i:55642695 original size:40 final size:39
Alignment explanation
Indices: 55642639--55642758 Score: 168
Period size: 40 Copynumber: 3.0 Consensus size: 39
55642629 TATTGTTAGA
*
55642639 TGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTT
1 TGTGCGAG-TATTAATTCCGGGTTAAGTCCCGAAGGCATT
*
55642679 TGTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAG-TATTAATTCCGGGTTAAGTCCCGAAGGCATT
* * *
55642719 CGTGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTATT-AATTCCGGGTTAAGTCCCGAAGGCATT
55642759 GTATGAGTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 2 0.03
40 70 0.97
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
TGTGCGAGTATTAATTCCGGGTTAAGTCCCGAAGGCATT
Found at i:55642779 original size:39 final size:38
Alignment explanation
Indices: 55642639--55642795 Score: 154
Period size: 40 Copynumber: 4.0 Consensus size: 38
55642629 TATTGTTAGA
* * *
55642639 TGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTT
1 TGTGCGAGTTACTAA-ACCGGGTTAAGTCCCGAAGG-CAT
* *
55642679 TGTGCGAGATACTAATTCCGGGTTAAGTCCCGAAGGCAT
1 TGTGCGAGTTACTAA-ACCGGGTTAAGTCCCGAAGGCAT
*
55642718 TCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGGCAT
1 T-GTGCGAGTTACT-AAA-CCGGGTTAAGTCCCGAAGGCAT
** * *
55642758 TGTATGAGTTACTATAACCGGGCTATGTCCCGAAGGCA
1 TGTGCGAGTTACTA-AACCGGGTTAAGTCCCGAAGGCA
55642796 CTTGAACGAG
Statistics
Matches: 101, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
39 31 0.31
40 70 0.69
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (38 bp):
TGTGCGAGTTACTAAACCGGGTTAAGTCCCGAAGGCAT
Found at i:55655909 original size:24 final size:24
Alignment explanation
Indices: 55655882--55655929 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
55655872 GTTCATGAAC
*
55655882 AAGCTCGTCCATTGGCTCATTTAT
1 AAGCTCGTCCATTGACTCATTTAT
* **
55655906 AAGCTCTTTTATTGACTCATTTAT
1 AAGCTCGTCCATTGACTCATTTAT
55655930 TTATTAATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (24 bp):
AAGCTCGTCCATTGACTCATTTAT
Found at i:55656072 original size:24 final size:24
Alignment explanation
Indices: 55656045--55656090 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
55656035 TTATTAACAT
*
55656045 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAAAATGTTCAATTATA
* *
55656069 TGTTCGTTAAAATGTTCGATTA
1 TGTTCGTGAAAATGTTCAATTA
55656091 AGTTAAATGA
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:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (24 bp):
TGTTCGTGAAAATGTTCAATTATA
Found at i:55656174 original size:26 final size:27
Alignment explanation
Indices: 55656112--55656176 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 27
55656102 CATGTTCGTG
55656112 AAAA-TTAAATAAACGAACAGGAACAC
1 AAAATTTAAATAAACGAACAGGAACAC
*
55656138 ACATAATTTTAAATAAACGAACATGAACA-
1 A-A-AA-TTTAAATAAACGAACAGGAACAC
55656167 AAAATTTAAA
1 AAAATTTAAA
55656177 ATTCTTAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
26 7 0.21
27 3 0.09
28 3 0.09
29 1 0.03
30 20 0.59
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.20
Consensus pattern (27 bp):
AAAATTTAAATAAACGAACAGGAACAC
Found at i:55660661 original size:61 final size:62
Alignment explanation
Indices: 55660483--55660661 Score: 152
Period size: 61 Copynumber: 2.9 Consensus size: 62
55660473 TTAGTCTAGT
* ** * *
55660483 AACAAAATTAGCCCTCTAATGTTTAC-ATATTCTATCAATTT-GATCTTAAATATAAAAAAAATT
1 AACAAATTTAGCCCTC-AACATTTACAAAATT-TATCAATTTAG-TCTTAAATCT-AAAAAAATT
55660546 C
62 C
* * * * * *
55660547 AACAAATTTAGCTCTCAATATTTACAAAATTTTTCATTTTAAT-TCTAATTCTAAAAAAATT-
1 AACAAATTTAGCCCTCAACATTTACAAAATTTATCAATTTAGTCT-TAAATCTAAAAAAATTC
* *
55660608 AATAAATTT-GACCCTCAACATTTACAAAATTTATCAATTTAGTCTTAACTCTAA
1 AACAAATTTAG-CCCTCAACATTTACAAAATTTATCAATTTAGTCTTAAATCTAA
55660662 TTTAAAAAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
60 1 0.01
61 43 0.46
62 11 0.12
63 21 0.22
64 18 0.19
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (62 bp):
AACAAATTTAGCCCTCAACATTTACAAAATTTATCAATTTAGTCTTAAATCTAAAAAAATTC
Found at i:55661143 original size:61 final size:62
Alignment explanation
Indices: 55661078--55661206 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 62
55661068 AAGGGGAAAG
*
55661078 TTTATTGAATTTTTTAGAATTAGAACTAAAA-TGA-AAAATTTTGTAAACAAT-GAGGGCTAAA
1 TTTATTGAATTTTTTAGAATTAGAA-TAAAATTGATAAAA-TATGTAAACAATAGAGGGCTAAA
* * * * * *
55661139 TTTATTGAATTTTTTATATTTAGGATAAAATTGATAGAATATGTAAACATTAGAGGGCTAAT
1 TTTATTGAATTTTTTAGAATTAGAATAAAATTGATAAAATATGTAAACAATAGAGGGCTAAA
55661201 TTTATT
1 TTTATT
55661207 ACTAGACCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
60 5 0.09
61 35 0.60
62 18 0.31
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (62 bp):
TTTATTGAATTTTTTAGAATTAGAATAAAATTGATAAAATATGTAAACAATAGAGGGCTAAA
Found at i:55669154 original size:40 final size:40
Alignment explanation
Indices: 55669099--55669189 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
55669089 TTCAAATTAT
*
55669099 TGAAAAGGTTGAAAAGGATACATCTAAAACGAATATCTAA
1 TGAAAAGGTTGAAAAGGATACATCCAAAACGAATATCTAA
* * * *
55669139 TGAAAATGTTGAAAAGGATATATCCGAAAGGAATATCT-A
1 TGAAAAGGTTGAAAAGGATACATCCAAAACGAATATCTAA
55669178 TCGAAAAGGTTG
1 T-GAAAAGGTTG
55669190 TTACCCTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
39 2 0.05
40 42 0.95
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (40 bp):
TGAAAAGGTTGAAAAGGATACATCCAAAACGAATATCTAA
Found at i:55669829 original size:22 final size:23
Alignment explanation
Indices: 55669801--55669845 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55669791 ATGCAATTTT
55669801 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
55669823 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
55669846 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:55677809 original size:7 final size:7
Alignment explanation
Indices: 55677797--55677821 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55677787 TTTAATTAAA
55677797 TTACCTT
1 TTACCTT
55677804 TTACCTT
1 TTACCTT
55677811 TTACCTT
1 TTACCTT
55677818 TTAC
1 TTAC
55677822 TAAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (7 bp):
TTACCTT
Found at i:55687234 original size:38 final size:38
Alignment explanation
Indices: 55687182--55687260 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
55687172 AAATTTTATT
*
55687182 ACACCAACAATAAGCATGCTCGGCACAAAGCCT-AAATA
1 ACACCAACAATAAGCATGCTAGGCACAAAGCCTGAAA-A
* * *
55687220 ACACCAGCACTAAGCCTGCTAGGCACAAAGCCTGAAAA
1 ACACCAACAATAAGCATGCTAGGCACAAAGCCTGAAAA
55687258 ACA
1 ACA
55687261 ATATACTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 33 0.92
39 3 0.08
ACGTcount: A:0.43, C:0.30, G:0.15, T:0.11
Consensus pattern (38 bp):
ACACCAACAATAAGCATGCTAGGCACAAAGCCTGAAAA
Found at i:55688936 original size:3 final size:3
Alignment explanation
Indices: 55688928--55688954 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55688918 TCCCATTAAT
55688928 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
55688955 CGTTCTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:55691102 original size:17 final size:18
Alignment explanation
Indices: 55691069--55691102 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55691059 TATGACTTGA
*
55691069 TAAATGATAATATAATTT
1 TAAATGATAATAAAATTT
55691087 TAAATGA-AATAAAATT
1 TAAATGATAATAAAATT
55691103 AAATAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAATGATAATAAAATTT
Found at i:55691104 original size:15 final size:15
Alignment explanation
Indices: 55691086--55691119 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
55691076 TAATATAATT
55691086 TTAAAT-GAAATAAAA
1 TTAAATAGAAA-AAAA
55691101 TTAAATAGAAAAAAA
1 TTAAATAGAAAAAAA
55691116 TTAA
1 TTAA
55691120 TTTTATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
TTAAATAGAAAAAAA
Found at i:55696880 original size:19 final size:20
Alignment explanation
Indices: 55696836--55696882 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
55696826 TATAGATTTT
55696836 AAATTTTATTTATTAATATA
1 AAATTTTATTTATTAATATA
**
55696856 TTATTTTATTT-TTAA-ATAA
1 AAATTTTATTTATTAATAT-A
55696875 AAATTTTA
1 AAATTTTA
55696883 AAAAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.09
19 11 0.50
20 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATTTTATTTATTAATATA
Found at i:55697686 original size:33 final size:33
Alignment explanation
Indices: 55697644--55697709 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
55697634 CGTTCCTTTG
55697644 GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
1 GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
55697677 GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
1 GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
55697710 CTTAGGTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.12, C:0.06, G:0.39, T:0.42
Consensus pattern (33 bp):
GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
Found at i:55712261 original size:42 final size:42
Alignment explanation
Indices: 55712176--55712261 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
55712166 AAAGAGGATC
* * * *
55712176 AAGGTGAAAACTCACAAAGGGCGCTTTGAGTTCTAAACAAAT
1 AAGGTGAAAACCCACAAAGGGCGCTTGGAGTTCCAAAAAAAT
*
55712218 AAGGTGAAAACCCGCAAAGGGCGCTTGGAG-TCCAAAAATAAT
1 AAGGTGAAAACCCACAAAGGGCGCTTGGAGTTCCAAAAA-AAT
55712260 AA
1 AA
55712262 TAAAATGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 6 0.16
42 32 0.84
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (42 bp):
AAGGTGAAAACCCACAAAGGGCGCTTGGAGTTCCAAAAAAAT
Found at i:55713690 original size:89 final size:89
Alignment explanation
Indices: 55713525--55713709 Score: 282
Period size: 89 Copynumber: 2.1 Consensus size: 89
55713515 ATGGATTGAA
*
55713525 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
1 GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
*
55713590 CCTAAGTTTGCAGCGGAAC-AGACT
66 CCTAAGCTTGCAGCGGAACTA-ACT
* *
55713614 GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGTGAAGTAGATCGAAGACACCAGCCTCGCCTC
1 GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
* * * *
55713679 CTTGAGCTTGCAGTGGAGCTAACT
66 CCTAAGCTTGCAGCGGAACTAACT
55713703 GAAGATA
1 GAAGATA
55713710 ACCAACCTTA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 86 0.99
90 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (89 bp):
GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
CCTAAGCTTGCAGCGGAACTAACT
Found at i:55713773 original size:44 final size:44
Alignment explanation
Indices: 55713702--55714192 Score: 245
Period size: 44 Copynumber: 10.9 Consensus size: 44
55713692 TGGAGCTAAC
*
55713702 TGAAGATAACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
1 TGAAGAT-ACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
*
55713747 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* ** * * * * *
55713791 TGAAGCTATTAATCATATCTCCCTAAAGTTGTAATGGAG-TGGAT
1 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-T
* * *
55713835 TAGAACGAT--CAATCCTATAC-CCCTAAAGTTCCAGTGG-G-ATGGAT
1 T-GAA-GATACCAATCTTAT-CTCCCTGAAGTTGCAGTGGAGCA-GG-T
* **
55713879 TGAAG-TCATCGTGGCAAATCTTATCTCCCTGAAGTTGCAGCGGAGCAGAC
1 TGAAGAT-A-C----C-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* * * * *
55713929 TGAAGATAGCGAATCTTATTTCCCTGAAGTTGTAGGGGAGCAGAT
1 TGAAGATA-CCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* * * *
55713974 TGAAGCTATACACTACAGATCTTATCTCTCTAAAGTTGCAGTAGAACA---
1 TGAAG--AT--AC--CA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
** * * * * * *
55714022 -GATCATATCAAACTTATCCCCCCTAAAGTTGCAGTAGG-GTATGT
1 TGAAGATACCAATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGGT
* * * * *
55714066 TGAA-ATTGCAAACCTTATCTTCCTGAAGTTGCAATGGAGCAGGT
1 TGAAGA-TACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* * *
55714110 TGAAGATA-CAATCTTACCTCCCTGAAGTTGCAGTGGAGTAGAT
1 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* ** * *
55714153 TGAAGCTATTAATCCTATCTCCCTGAAGTTACAGTGGAGC
1 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGC
55714193 GGACTAAAAC
Statistics
Matches: 339, Mismatches: 72, Indels: 71
0.70 0.15 0.15
Matches are distributed among these distances:
40 6 0.02
41 19 0.06
42 2 0.01
43 43 0.13
44 144 0.42
45 59 0.17
46 2 0.01
47 4 0.01
48 1 0.00
49 3 0.01
50 29 0.09
51 26 0.08
52 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
Found at i:55714156 original size:43 final size:44
Alignment explanation
Indices: 55714087--55714192 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 44
55714077 ACCTTATCTT
* * *
55714087 CCTGAAGTTGCAATGGAGCAGGTTGAAGATA-CAATCTTACCTC
1 CCTGAAGTTGCAGTGGAGCAGATTGAAGATATCAATCCTACCTC
* * * *
55714130 CCTGAAGTTGCAGTGGAGTAGATTGAAGCTATTAATCCTATCTC
1 CCTGAAGTTGCAGTGGAGCAGATTGAAGATATCAATCCTACCTC
*
55714174 CCTGAAGTTACAGTGGAGC
1 CCTGAAGTTGCAGTGGAGC
55714193 GGACTAAAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 27 0.51
44 26 0.49
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (44 bp):
CCTGAAGTTGCAGTGGAGCAGATTGAAGATATCAATCCTACCTC
Found at i:55714211 original size:44 final size:44
Alignment explanation
Indices: 55714127--55714214 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
55714117 ACAATCTTAC
* * * * * * *
55714127 CTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTATTAATCCTAT
1 CTCCCTGAAGTTACAGTGGAGCAGACTAAAACGATGAATCCTAT
*
55714171 CTCCCTGAAGTTACAGTGGAGCGGACTAAAACGATGAATCCTAT
1 CTCCCTGAAGTTACAGTGGAGCAGACTAAAACGATGAATCCTAT
55714215 ACCTCTAAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
CTCCCTGAAGTTACAGTGGAGCAGACTAAAACGATGAATCCTAT
Found at i:55714581 original size:27 final size:27
Alignment explanation
Indices: 55714550--55714606 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
55714540 AAGTCAAGAA
55714550 TCTGTGAGACCGGGCAAGATTGGTCTT
1 TCTGTGAGACCGGGCAAGATTGGTCTT
55714577 TCTGTGAGACCGGGCAAGATTGGTCTT
1 TCTGTGAGACCGGGCAAGATTGGTCTT
55714604 TCT
1 TCT
55714607 TAGTTTCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (27 bp):
TCTGTGAGACCGGGCAAGATTGGTCTT
Found at i:55716003 original size:3 final size:3
Alignment explanation
Indices: 55715995--55716033 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
55715985 ATAGGTTTGA
* * *
55715995 TAT TAT TAT TAT TAC TAT TGT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55716034 ATTTCTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:55716045 original size:15 final size:15
Alignment explanation
Indices: 55715995--55716042 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
55715985 ATAGGTTTGA
55715995 TATTATTATTATTAC
1 TATTATTATTATTAC
*
55716010 TATTGTTATTATTAC
1 TATTATTATTATTAC
*
55716025 TATTATTA-TATTTC
1 TATTATTATTATTAC
55716039 TATT
1 TATT
55716043 TATATTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 9 0.30
15 21 0.70
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:55721757 original size:22 final size:22
Alignment explanation
Indices: 55721713--55721757 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
55721703 AATTTATAAA
**
55721713 ATATGAAATTTTGTGATTTATT
1 ATATGAAATTTTGTGATAAATT
55721735 ATATG-AATTTTGTGCATAAATT
1 ATATGAAATTTTGTG-ATAAATT
55721757 A
1 A
55721758 AATTAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
ATATGAAATTTTGTGATAAATT
Found at i:55724506 original size:25 final size:24
Alignment explanation
Indices: 55724438--55724519 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 24
55724428 CGGACTCACC
*
55724438 ACAGCTCGTATGAGCTTACCTATTT
1 ACAGCTCGTATGAGATTA-CTATTT
55724463 ACAGCTC--ATGAGAGCTTACTGATTCT
1 ACAGCTCGTATGAGA--TTACT-ATT-T
55724489 -CAGCTCGTATGAGATTACCATATTT
1 ACAGCTCGTATGAGATTA-C-TATTT
55724514 -CAGCTC
1 ACAGCTC
55724520 AGAAAATACC
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
23 5 0.10
24 2 0.04
25 29 0.60
26 5 0.10
27 7 0.15
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (24 bp):
ACAGCTCGTATGAGATTACTATTT
Found at i:55733891 original size:19 final size:15
Alignment explanation
Indices: 55733850--55733886 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
55733840 TTGTTAAATA
55733850 TTAAATATTTTCATG
1 TTAAATATTTTCATG
55733865 TTAAATATTTTCATG
1 TTAAATATTTTCATG
55733880 TTAAATA
1 TTAAATA
55733887 AATATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (15 bp):
TTAAATATTTTCATG
Found at i:55740800 original size:29 final size:26
Alignment explanation
Indices: 55740763--55740820 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
55740753 TTTGTAAGTT
*
55740763 TTTATAATATTTTGAATTTTTATTATAA
1 TTTATAATATTTT-AACTTTT-TTATAA
*
55740791 TTTAGTAATATTTTTACTTTTTTATAA
1 TTTA-TAATATTTTAACTTTTTTATAA
55740818 TTT
1 TTT
55740821 TTAAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 9 0.33
29 9 0.33
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTATAATATTTTAACTTTTTTATAA
Found at i:55747626 original size:39 final size:41
Alignment explanation
Indices: 55747572--55747693 Score: 131
Period size: 39 Copynumber: 3.0 Consensus size: 41
55747562 ATGGTCTTTG
* * *
55747572 GCGTTTGTGGGGAAAGCGTCGCTAAAGGTCATGTCTTTAGCT
1 GCGTTTGT-GAGAAAGCGCCGCTAAAGGTCATGTCTTTAGCA
* *
55747614 GTG-TT-TGAGAAAGTGCCGCTAAAGGTCATGTTCTTTAGCA
1 GCGTTTGTGAGAAAGCGCCGCTAAAGGTCATG-TCTTTAGCA
* * *
55747654 GCGTTTGTGAGAAAAGCACCACTAAAGGTCATGTTTTTAG
1 GCGTTTGTGAG-AAAGCGCCGCTAAAGGTCATGTCTTTAG
55747694 TGGCATTTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
39 21 0.32
40 11 0.17
41 4 0.06
42 12 0.18
43 18 0.27
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (41 bp):
GCGTTTGTGAGAAAGCGCCGCTAAAGGTCATGTCTTTAGCA
Found at i:55747687 original size:43 final size:40
Alignment explanation
Indices: 55747593--55747693 Score: 116
Period size: 43 Copynumber: 2.5 Consensus size: 40
55747583 GAAAGCGTCG
* * ** *
55747593 CTAAAGGTCATG-TCTTTAGCTGTGTTTGAGAAAGTGCCG
1 CTAAAGGTCATGTTCTTTAGCAGCGTTTGAGAAAGCACCA
55747632 CTAAAGGTCATGTTCTTTAGCAGCGTTTGTGAGAAAAGCACCA
1 CTAAAGGTCATGTTCTTTAGCAGCG-TT-TGAG-AAAGCACCA
55747675 CTAAAGGTCATGTT-TTTAG
1 CTAAAGGTCATGTTCTTTAG
55747694 TGGCATTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
39 12 0.23
40 10 0.19
41 2 0.04
42 9 0.17
43 20 0.38
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
CTAAAGGTCATGTTCTTTAGCAGCGTTTGAGAAAGCACCA
Found at i:55748612 original size:20 final size:21
Alignment explanation
Indices: 55748546--55748614 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 21
55748536 AAATTACAAA
55748546 AAAAAATTCAAAATAATTT-T
1 AAAAAATTCAAAATAATTTAT
** * *
55748566 ATGAGATTAAAAATAATTGTA-
1 AAAAAATTCAAAATAATT-TAT
55748587 AAAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTTAT
55748607 AAAAAATT
1 AAAAAATT
55748615 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.05
20 25 0.66
21 11 0.29
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTAT
Found at i:55748620 original size:21 final size:21
Alignment explanation
Indices: 55748545--55748612 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
55748535 AAAATTACAA
55748545 AAAAAAATTCAAAATAATT-T
1 AAAAAAATTCAAAATAATTAT
* ** * * *
55748565 TATGAGATTAAAAATAATTGT
1 AAAAAAATTCAAAATAATTAT
*
55748586 AAAAAAATTCAAAATATTTAT
1 AAAAAAATTCAAAATAATTAT
55748607 AAAAAA
1 AAAAAA
55748613 TTTTAAAAAT
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAAAATTCAAAATAATTAT
Found at i:55748627 original size:28 final size:28
Alignment explanation
Indices: 55748596--55748666 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
55748586 AAAAAAATTC
*
55748596 AAAATATTTATAAAAAATTTTAAAA-ATA
1 AAAATATTTATAAAAAA-GTTAAAATATA
* * *
55748624 AAAAAATATATAAAAAAGTTAAAATTTA
1 AAAATATTTATAAAAAAGTTAAAATATA
* *
55748652 AAAATTTTTGTAAAA
1 AAAATATTTATAAAA
55748667 CAATAATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 6 0.18
28 28 0.82
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATATTTATAAAAAAGTTAAAATATA
Found at i:55748654 original size:27 final size:28
Alignment explanation
Indices: 55748589--55748655 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
55748579 TAATTGTAAA
* * * *
55748589 AAAATTCAAAATATTTATAAAAAATTTT
1 AAAATTAAAAAAATATATAAAAAATGTT
*
55748617 AAAAATAAAAAAATATATAAAAAA-GTT
1 AAAATTAAAAAAATATATAAAAAATGTT
*
55748644 AAAATTTAAAAA
1 AAAATTAAAAAA
55748656 TTTTTGTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 12 0.38
28 20 0.62
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (28 bp):
AAAATTAAAAAAATATATAAAAAATGTT
Found at i:55750424 original size:11 final size:11
Alignment explanation
Indices: 55750404--55750446 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
55750394 AGATAAATGT
*
55750404 TATTTAATTAA
1 TATTTTATTAA
55750415 TATTTTATTAA
1 TATTTTATTAA
* * *
55750426 GATTTTAGTAT
1 TATTTTATTAA
55750437 TATTTTATTA
1 TATTTTATTA
55750447 TTAAATGATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:55756203 original size:9 final size:9
Alignment explanation
Indices: 55756165--55756201 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
55756155 CTATTTTTTG
55756165 ATATTATTA
1 ATATTATTA
55756174 ATATTATTTA
1 ATATTA-TTA
55756184 ATATTATTA
1 ATATTATTA
*
55756193 TTATTATTA
1 ATATTATTA
55756202 TTTCATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTATTA
Found at i:55756526 original size:16 final size:16
Alignment explanation
Indices: 55756505--55756538 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55756495 CGTTTTATAA
* *
55756505 TACATATGCATTTTTT
1 TACATATACATGTTTT
55756521 TACATATACATGTTTT
1 TACATATACATGTTTT
55756537 TA
1 TA
55756539 GAAATTATTA
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:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (16 bp):
TACATATACATGTTTT
Found at i:55768616 original size:132 final size:132
Alignment explanation
Indices: 55768317--55768776 Score: 735
Period size: 132 Copynumber: 3.5 Consensus size: 132
55768307 ATCATAAAGC
*
55768317 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCT-AAGGTTATA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAA-GTTACA
55768381 GTGGAGTACATTGAAGCCAGTAATTCTATCT-CCTGGGCAGCAGTGGAATAGATTGAAGATTACA
65 GTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACA
55768445 GAT
130 GAT
* * * * *
55768448 CTTATCTCCCTAAACAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACCTCCCTGAAGTTACAA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
* * * * *
55768513 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGTAGCAGTGGAATATATTGAAGTTTACGG
66 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
55768578 AT
131 AT
* * *
55768580 CTTATCCCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTATCTCCCTGAGGTTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
*
55768645 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTACAG
66 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
55768710 AT
131 AT
* * *
55768712 CTTATCTCCCTAAGCAATAGTGGAACAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
55768777 CTATTATACC
Statistics
Matches: 298, Mismatches: 29, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
131 86 0.29
132 212 0.71
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
AT
Found at i:55768718 original size:44 final size:44
Alignment explanation
Indices: 55768407--55768748 Score: 137
Period size: 44 Copynumber: 7.8 Consensus size: 44
55768397 CCAGTAATTC
* *
55768407 TATCT-CCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
** * ** **** *
55768450 TATCTCCCTAAACAGTAGTGGAGTAGATCAAAGATGGTGGATTT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
* * * * * * *
55768494 TACCTCCCT--GAAGTTACAATGGAGTACATTGAAGCCAGTA-A-TTC-
1 TATCTCCCTAGGCAG-T--AGTGGAATAGATTGAAG--ATTACAGATCT
* * * * *
55768538 TATCTCCCTAGGTAGCAGTGGAATATATTGAAGTTTACGGATCT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
* * ** * ** * *
55768582 TATCCCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
* * * * * *
55768626 TATCTCCCTGAGGTTA-CAGTGGAGTACATTGAAGCCAGTA-A-TTC-
1 TATCTCCCT-AGG-CAGTAGTGGAATAGATTGAAG--ATTACAGATCT
*
55768670 TATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
* * * *
55768714 TATCTCCCTAAGCAATAGTGGAACAGATCGAAGAT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGAT
55768749 GGCGGATTTT
Statistics
Matches: 208, Mismatches: 72, Indels: 37
0.66 0.23 0.12
Matches are distributed among these distances:
41 5 0.02
42 4 0.02
43 41 0.20
44 121 0.58
45 31 0.15
46 4 0.02
47 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
Found at i:55773721 original size:18 final size:18
Alignment explanation
Indices: 55773679--55773714 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55773669 ATACCATTAA
55773679 CACCCCTTGTTGGGCAAC
1 CACCCCTTGTTGGGCAAC
55773697 CACCCCTTGTTGGGCAAC
1 CACCCCTTGTTGGGCAAC
55773715 GGCCCCTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (18 bp):
CACCCCTTGTTGGGCAAC
Found at i:55774127 original size:101 final size:101
Alignment explanation
Indices: 55773955--55774151 Score: 286
Period size: 101 Copynumber: 2.0 Consensus size: 101
55773945 AACCTGACTT
* * * * *
55773955 GTTTCTTAGGCCTTTGAATAGAACTAGAGGGCTCTAAATCCCTCTTGCTCTTACCCCTCTCAAGG
1 GTTTCTTAGGCCTCTAAACAGAACTAGAGGGCTCCAAATCCCTCTTACTCTTACCCCTCTCAAGG
*
55774020 TCCCTATTTTCGCATTGAGAGCGTTTAACCTAGCTC
66 TCCCTATTTTCGCATTGAGAGCGCTTAACCTAGCTC
* * *
55774056 GTTTCTTAGGCCTCTAAACAGAACTAGAGGGCTCCAAATCCCTCTTACTCTTACCCTTTTCATGG
1 GTTTCTTAGGCCTCTAAACAGAACTAGAGGGCTCCAAATCCCTCTTACTCTTACCCCTCTCAAGG
* * *
55774121 TTCCTATTTTTGCATTGAGAGTGCTTAACCT
66 TCCCTATTTTCGCATTGAGAGCGCTTAACCT
55774152 CATCGGTAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 84 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (101 bp):
GTTTCTTAGGCCTCTAAACAGAACTAGAGGGCTCCAAATCCCTCTTACTCTTACCCCTCTCAAGG
TCCCTATTTTCGCATTGAGAGCGCTTAACCTAGCTC
Found at i:55778041 original size:22 final size:22
Alignment explanation
Indices: 55778013--55778060 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
55778003 CTTGAATTTT
*
55778013 TAAATTC-AAAAAATATAAATA
1 TAAATTCTAAAAAATAAAAATA
*
55778034 CTAAATTCTTAAAAATAAAAATA
1 -TAAATTCTAAAAAATAAAAATA
55778057 TAAA
1 TAAA
55778061 AATTAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAATTCTAAAAAATAAAAATA
Found at i:55778367 original size:76 final size:76
Alignment explanation
Indices: 55778280--55778431 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
55778270 CACATATGTT
55778280 GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
1 GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
55778345 TTTAAATAAAC
66 TTTAAATAAAC
55778356 GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
1 GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
55778421 TTTAAATAAAC
66 TTTAAATAAAC
55778432 ACTACTATTA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (76 bp):
GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
TTTAAATAAAC
Found at i:55780711 original size:3 final size:3
Alignment explanation
Indices: 55780698--55780733 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
55780688 TTTTAAATAT
*
55780698 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55780734 CTATACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:55784533 original size:18 final size:18
Alignment explanation
Indices: 55784510--55784571 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
55784500 AAGTTAATTC
55784510 TAAAATTATAAAAAAAAT
1 TAAAATTATAAAAAAAAT
55784528 TAAAATTTATAAAAAAATCAT
1 TAAAA-TTATAAAAAAA--AT
*
55784549 TAAAATTAT-AAAAATAT
1 TAAAATTATAAAAAAAAT
55784566 TAAAAT
1 TAAAAT
55784572 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 8 0.20
18 5 0.12
19 16 0.40
20 4 0.10
21 7 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAATTATAAAAAAAAT
Found at i:55784579 original size:17 final size:18
Alignment explanation
Indices: 55784510--55784590 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 18
55784500 AAGTTAATTC
*
55784510 TAAAAT-TATAAAAAAAAT
1 TAAAATATAT-AAAAATAT
*
55784528 TAAAATTTATAAAAAAATCAT
1 TAAAA--TATATAAAAAT-AT
55784549 TAAAAT-TATAAAAATAT
1 TAAAATATATAAAAATAT
* *
55784566 TAAAATATTTAAAATTA-
1 TAAAATATATAAAAATAT
55784583 TAAAATAT
1 TAAAATAT
55784591 CAAAGAAGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
17 16 0.30
18 21 0.40
19 1 0.02
20 6 0.11
21 9 0.17
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATATAAAAATAT
Found at i:55784903 original size:19 final size:18
Alignment explanation
Indices: 55784878--55784919 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
55784868 TGAACTTGAA
*
55784878 TTTTTTAAAAAATATATT
1 TTTTTTAAAAAAAATATT
55784896 TATTTTTAAAAAAAATATT
1 T-TTTTTAAAAAAAATATT
55784915 TTTTT
1 TTTTT
55784920 CTGATGTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTTAAAAAAAATATT
Found at i:55785354 original size:45 final size:45
Alignment explanation
Indices: 55785248--55785441 Score: 173
Period size: 45 Copynumber: 4.3 Consensus size: 45
55785238 AATTTTTCTA
* * *
55785248 TATTGGCAGCGAAGTAGATTAAAGAACACCAGCCTTGCCTCCCTG
1 TATTGGCAGCGAAGCAGACTGAAGAACACCAGCCTTGCCTCCCTG
* * * * * *
55785293 -AGTTTGCAGTGGAGCAGACTGAA-AACAGCAGATCTTGCCTTCCTG
1 TA-TTGGCAGCGAAGCAGACTGAAGAACACCAG-CCTTGCCTCCCTG
55785338 TATTGGCAGCGAAGCAGA-TCGAAGAACACCAGCCTTGCCTCCCTG
1 TATTGGCAGCGAAGCAGACT-GAAGAACACCAGCCTTGCCTCCCTG
* * ** * *
55785383 -AGTTTGCAGCGGAGCAGACTGAA-AACAATAGATCTTGCCTTCCTG
1 TA-TTGGCAGCGAAGCAGACTGAAGAACACCAG-CCTTGCCTCCCTG
55785428 TATTGGCAGCGAAG
1 TATTGGCAGCGAAG
55785442 TAGATCGAAG
Statistics
Matches: 117, Mismatches: 23, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
44 16 0.14
45 91 0.78
46 10 0.09
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (45 bp):
TATTGGCAGCGAAGCAGACTGAAGAACACCAGCCTTGCCTCCCTG
Found at i:55785401 original size:90 final size:90
Alignment explanation
Indices: 55785248--55785752 Score: 518
Period size: 90 Copynumber: 5.7 Consensus size: 90
55785238 AATTTTTCTA
* **
55785248 TATTGGCAGCGAAGTAGATTAAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
*
55785313 GAAAACAGCAGATCTTGCCTTCCTG
66 GAAAATAGCAGATCTTGCCTTCCTG
*
55785338 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGCGGAGCAGACT
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
* **
55785403 GAAAACAATAGATCTTGCCTTCCTG
66 GAAAATAGCAGATCTTGCCTTCCTG
* ** * ** * ** *
55785428 TATTGGCAGCGAAGTAGATCGAAGATAGCA--AGCCTTATCTCTCTGAG-CAGCGGTGGAATAGG
1 TATTGGCAGCGAAGCAGATCGAAGA-A-CACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGA
* **
55785490 TTGAAAATAGCAGATCTTATCTTCCTG
64 CTGAAAATAGCAGATCTTGCCTTCCTG
* * * * * ** ** * * **
55785517 TATTAGCAGCGAAGTAGATTGAAG-ACCCCAACCTTATCTCCCTGAG-CAGCAGTGGTGTAGGTT
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
**
55785580 GAAAATAGCAGATCTTGCCTTATTG
66 GAAAATAGCAGATCTTGCCTTCCTG
* *
55785605 TATTAGCAGCGAAGCAGATCGAAGAACACTAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
* * * *
55785670 AAAAATAGCATATCTTGTCTTTCTG
66 GAAAATAGCAGATCTTGCCTTCCTG
* * * * **
55785695 TACTGGCAACGAAGCAGATC-AACAACACTAGCCTTGCCTCTTTGAGTTTGCAGTGGAG
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAG
55785753 TAGGTTGAAG
Statistics
Matches: 350, Mismatches: 59, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
86 1 0.00
87 1 0.00
88 72 0.21
89 103 0.29
90 170 0.49
91 1 0.00
92 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (90 bp):
TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
GAAAATAGCAGATCTTGCCTTCCTG
Found at i:55785957 original size:50 final size:50
Alignment explanation
Indices: 55785812--55785975 Score: 179
Period size: 50 Copynumber: 3.3 Consensus size: 50
55785802 CAAAGAAAGG
* * *
55785812 AAATCTTACTTCCCCGACATTGCAATTAAATAGATTGAAGCTACAATAGC
1 AAATCTTACTCCCCCGACATTGCAGTTAAACAGATTGAAGCTACAATAGC
** * * ** *
55785862 AAATCTTACTTCCCTGGAGA-TGTAGTGGAACAGATTGAAGCTACAATGGC
1 AAATCTTAC-TCCCCCGACATTGCAGTTAAACAGATTGAAGCTACAATAGC
*
55785912 AAATCTTACTCCCCCGACATTGCAGTTAAAACAGATTGAAG-TACAACAGC
1 AAATCTTACTCCCCCGACATTGCAGTT-AAACAGATTGAAGCTACAATAGC
*
55785962 AAATCCTATCTCCC
1 AAATCTTA-CTCCC
55785976 TGACGTTGTA
Statistics
Matches: 91, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
49 7 0.08
50 61 0.67
51 23 0.25
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (50 bp):
AAATCTTACTCCCCCGACATTGCAGTTAAACAGATTGAAGCTACAATAGC
Found at i:55786201 original size:15 final size:15
Alignment explanation
Indices: 55786181--55786210 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55786171 CTCGGCCCAT
*
55786181 AACCAAATTAATAAA
1 AACCAAAATAATAAA
55786196 AACCAAAATAATAAA
1 AACCAAAATAATAAA
55786211 TTAAATGTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (15 bp):
AACCAAAATAATAAA
Found at i:55787396 original size:3 final size:3
Alignment explanation
Indices: 55787390--55787423 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
55787380 AAAAAATTAA
55787390 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
55787424 GCGTAAGTAC
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:55790457 original size:18 final size:18
Alignment explanation
Indices: 55790434--55790495 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
55790424 AAGTTAATTC
55790434 TAAAATTATAAAAAAAAT
1 TAAAATTATAAAAAAAAT
55790452 TAAAATTTATAAAAAAATCAT
1 TAAAA-TTATAAAAAAA--AT
*
55790473 TAAAATTAT-AAAAATAT
1 TAAAATTATAAAAAAAAT
55790490 TAAAAT
1 TAAAAT
55790496 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 8 0.20
18 5 0.12
19 16 0.40
20 4 0.10
21 7 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAATTATAAAAAAAAT
Found at i:55790503 original size:17 final size:18
Alignment explanation
Indices: 55790434--55790514 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 18
55790424 AAGTTAATTC
*
55790434 TAAAAT-TATAAAAAAAAT
1 TAAAATATAT-AAAAATAT
*
55790452 TAAAATTTATAAAAAAATCAT
1 TAAAA--TATATAAAAAT-AT
55790473 TAAAAT-TATAAAAATAT
1 TAAAATATATAAAAATAT
* *
55790490 TAAAATATTTAAAATTA-
1 TAAAATATATAAAAATAT
55790507 TAAAATAT
1 TAAAATAT
55790515 CAAAGAAGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
17 16 0.30
18 21 0.40
19 1 0.02
20 6 0.11
21 9 0.17
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATATAAAAATAT
Found at i:55793157 original size:3 final size:3
Alignment explanation
Indices: 55793149--55793173 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55793139 AAATATTGTT
55793149 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
55793174 TTGGTATCAA
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:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:55799243 original size:15 final size:15
Alignment explanation
Indices: 55799223--55799252 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55799213 CATGCCACAC
55799223 ACTTCAACTTATTTA
1 ACTTCAACTTATTTA
55799238 ACTTCAACTTATTTA
1 ACTTCAACTTATTTA
55799253 TCGTCCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (15 bp):
ACTTCAACTTATTTA
Found at i:55805110 original size:31 final size:31
Alignment explanation
Indices: 55805068--55805126 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
55805058 TTGTCATCAC
*
55805068 TGGTTTTAAAGATATAAGAAAATTTTGTCAA
1 TGGTTTGAAAGATATAAGAAAATTTTGTCAA
* *
55805099 TGGTTTGAAAGATATGAGAAACTTTTGT
1 TGGTTTGAAAGATATAAGAAAATTTTGT
55805127 TTCCATACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.39
Consensus pattern (31 bp):
TGGTTTGAAAGATATAAGAAAATTTTGTCAA
Found at i:55806256 original size:12 final size:12
Alignment explanation
Indices: 55806241--55806279 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
55806231 TTACATAATT
55806241 ATATACATAAAA
1 ATATACATAAAA
*
55806253 ATATCCATAAAA
1 ATATACATAAAA
*
55806265 ATGTACATAAAA
1 ATATACATAAAA
55806277 ATA
1 ATA
55806280 CATGTGTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.26
Consensus pattern (12 bp):
ATATACATAAAA
Found at i:55813494 original size:18 final size:18
Alignment explanation
Indices: 55813471--55813512 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
55813461 TTCTATTCTA
55813471 AATAAA-AACAACAATAAT
1 AATAAAGAA-AACAATAAT
* *
55813489 ATTAAAGAAACCAATAAT
1 AATAAAGAAAACAATAAT
55813507 AATAAA
1 AATAAA
55813513 TATATAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (18 bp):
AATAAAGAAAACAATAAT
Found at i:55814727 original size:34 final size:34
Alignment explanation
Indices: 55814689--55814821 Score: 115
Period size: 29 Copynumber: 4.2 Consensus size: 34
55814679 TGCACAATCT
* *
55814689 TAGGGTTCACATGGGATATATGTTCGCATGTTCC
1 TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
* * *
55814723 TAGGGTT--C--GTG-TATAGGCTCGTATGATCC
1 TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
* * *
55814752 TAGGGTACGCATGGCATATAGGCTCGCATGTTCC
1 TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
*
55814786 TAGGGTTCACA---G--ATAGGCTCGCAAGTTCC
1 TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
55814815 TAGGGTT
1 TAGGGTT
55814822 TGCATGAGCC
Statistics
Matches: 80, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
29 43 0.54
30 2 0.03
31 1 0.01
32 1 0.01
33 1 0.01
34 32 0.40
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (34 bp):
TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
Found at i:55814728 original size:63 final size:63
Alignment explanation
Indices: 55814646--55814808 Score: 191
Period size: 63 Copynumber: 2.6 Consensus size: 63
55814636 TGATCACATG
* * * * *
55814646 GGCTCGCATGTACCTAGGGTTCGCATATAGGCTTGCACAATCTTAGGGTTCACATGGGATATA
1 GGCTCGCATGTTCCTAGGGTTCGCATATAGGCTCGCACAATCCTAGGGTACACATGGCATATA
* * ** * ** *
55814709 TGTTCGCATGTTCCTAGGGTTCGTGTATAGGCTCGTATGATCCTAGGGTACGCATGGCATATA
1 GGCTCGCATGTTCCTAGGGTTCGCATATAGGCTCGCACAATCCTAGGGTACACATGGCATATA
* *
55814772 GGCTCGCATGTTCCTAGGGTTCACAGATAGGCTCGCA
1 GGCTCGCATGTTCCTAGGGTTCGCATATAGGCTCGCA
55814809 AGTTCCTAGG
Statistics
Matches: 80, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
63 80 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (63 bp):
GGCTCGCATGTTCCTAGGGTTCGCATATAGGCTCGCACAATCCTAGGGTACACATGGCATATA
Found at i:55814827 original size:63 final size:62
Alignment explanation
Indices: 55814628--55814827 Score: 186
Period size: 63 Copynumber: 3.2 Consensus size: 62
55814618 CACGTTTGAA
* * * * * * *
55814628 GGTTCGCATGATCACATGGGCTCGCATGTACCTAGGGTTCGCATATAGGCTTGCACA-ATCTTAG
1 GGTTCGCATG-GCATATAGGCTCGCATGTTCCTAGGGTTC-CAGATAGGCTCGCA-AGATCCTAG
* * * * ** * *
55814692 GGTTCACATGGGATATATGTTCGCATGTTCCTAGGGTTCGTGTATAGGCTCGTATGATCCTAG
1 GGTTCGCATGGCATATAGGCTCGCATGTTCCTAGGGTTCCAG-ATAGGCTCGCAAGATCCTAG
* *
55814755 GGTACGCATGGCATATAGGCTCGCATGTTCCTAGGGTTCACAGATAGGCTCGCAAGTTCCTAG
1 GGTTCGCATGGCATATAGGCTCGCATGTTCCTAGGGTTC-CAGATAGGCTCGCAAGATCCTAG
*
55814818 GGTTTGCATG
1 GGTTCGCATG
55814828 AGCCTAGGGT
Statistics
Matches: 106, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
63 96 0.91
64 10 0.09
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.30
Consensus pattern (62 bp):
GGTTCGCATGGCATATAGGCTCGCATGTTCCTAGGGTTCCAGATAGGCTCGCAAGATCCTAG
Found at i:55815330 original size:21 final size:20
Alignment explanation
Indices: 55815306--55815348 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
55815296 TATGGGGTAT
55815306 GCACATAATAACCTAGGGTTC
1 GCACAT-ATAACCTAGGGTTC
* * *
55815327 GCACGTATAATCTAGGTTTC
1 GCACATATAACCTAGGGTTC
55815347 GC
1 GC
55815349 TTAGTTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (20 bp):
GCACATATAACCTAGGGTTC
Found at i:55817513 original size:20 final size:20
Alignment explanation
Indices: 55817488--55817527 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55817478 AATATTTTCC
*
55817488 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55817508 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55817528 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55817533 original size:34 final size:35
Alignment explanation
Indices: 55817476--55817542 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
55817466 CAAACACCAG
*
55817476 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
55817511 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
55817543 TATTACGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:55817550 original size:12 final size:12
Alignment explanation
Indices: 55817533--55817558 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55817523 AGAAATCATT
55817533 TTACGGAAAATA
1 TTACGGAAAATA
55817545 TTACGGAAAATA
1 TTACGGAAAATA
55817557 TT
1 TT
55817559 TTACTGGCAA
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (12 bp):
TTACGGAAAATA
Found at i:55818789 original size:42 final size:42
Alignment explanation
Indices: 55818742--55818857 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 42
55818732 ACATTTTTAA
*
55818742 ATAAACTACCACTTGGTTCGTG-ATCGAACCACATATTTGTAG
1 ATAAACTACCACTTGGTTCGTGAAT-GAACCACATAATTGTAG
* * *
55818784 ATAAACTGCCACTT-GTT-GTGAATGCACAACATAATTGTAG
1 ATAAACTACCACTTGGTTCGTGAATGAACCACATAATTGTAG
* *
55818824 ATAAAAACTATCACTTGGTTCATGAATGAACCAC
1 AT--AAACTACCACTTGGTTCGTGAATGAACCAC
55818858 GTTGTTTGCA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
40 19 0.32
41 5 0.08
42 23 0.38
43 3 0.05
44 10 0.17
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (42 bp):
ATAAACTACCACTTGGTTCGTGAATGAACCACATAATTGTAG
Found at i:55822334 original size:6 final size:6
Alignment explanation
Indices: 55822323--55822375 Score: 74
Period size: 6 Copynumber: 8.8 Consensus size: 6
55822313 AAATATTTAA
55822323 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAAG AAAAA- AGAAAAG -AAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG A-AAAAG AAAAAG
55822371 AAAAA
1 AAAAA
55822376 AAGGGAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 6 0.14
6 31 0.72
7 6 0.14
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:55822350 original size:25 final size:24
Alignment explanation
Indices: 55822322--55822376 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 24
55822312 AAAATATTTA
55822322 AAAAAAG-AAAAAGAAAAAGAAAAAG
1 AAAAAAGAAAAAAG-AAAAG-AAAAG
55822347 AAAAAAGAAAAAAGAAAAGAAAAG
1 AAAAAAGAAAAAAGAAAAGAAAAG
55822371 AAAAAA
1 AAAAAA
55822377 AGGGAGAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 11 0.38
25 12 0.41
26 6 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAAGAAAAAAGAAAAGAAAAG
Found at i:55823048 original size:15 final size:15
Alignment explanation
Indices: 55823028--55823068 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
55823018 TAAACCCGAA
*
55823028 TAGCCCAATTACATC-
1 TAGCCCAACTACA-CG
55823043 TAGCCCAACTACACG
1 TAGCCCAACTACACG
55823058 TAGCCCAACTA
1 TAGCCCAACTA
55823069 TCATACAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.34, C:0.37, G:0.10, T:0.20
Consensus pattern (15 bp):
TAGCCCAACTACACG
Found at i:55829351 original size:12 final size:13
Alignment explanation
Indices: 55829329--55829358 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
55829319 GATTCAATAA
55829329 AAAAAAGAAAAAC
1 AAAAAAGAAAAAC
55829342 AAAAAA-AAAAAC
1 AAAAAAGAAAAAC
55829354 AAAAA
1 AAAAA
55829359 CCTCTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAC
Found at i:55830492 original size:9 final size:9
Alignment explanation
Indices: 55830476--55830536 Score: 104
Period size: 9 Copynumber: 6.8 Consensus size: 9
55830466 GGTATTTTTC
55830476 GGTAATTCG
1 GGTAATTCG
*
55830485 GTTAATTCG
1 GGTAATTCG
*
55830494 GTTAATTCG
1 GGTAATTCG
55830503 GGTAATTCG
1 GGTAATTCG
55830512 GGTAATTCG
1 GGTAATTCG
55830521 GGTAATTCG
1 GGTAATTCG
55830530 GGTAATT
1 GGTAATT
55830537 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.38
Consensus pattern (9 bp):
GGTAATTCG
Found at i:55830713 original size:12 final size:12
Alignment explanation
Indices: 55830696--55830720 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55830686 AGTAATTTCG
55830696 GGTCGGTTAACC
1 GGTCGGTTAACC
55830708 GGTCGGTTAACC
1 GGTCGGTTAACC
55830720 G
1 G
55830721 AATGAACACC
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:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:55831931 original size:44 final size:44
Alignment explanation
Indices: 55831790--55831919 Score: 233
Period size: 44 Copynumber: 3.0 Consensus size: 44
55831780 AAGTTATAAA
55831790 TCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAG
1 TCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAG
*
55831834 TCCTATCTCCCTAGACAACAGTGGAATAGGTTGAAGATTGTAAG
1 TCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAG
**
55831878 TCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTA
1 TCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTA
55831920 GATCATGTCT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 82 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
TCCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAG
Found at i:55832180 original size:50 final size:50
Alignment explanation
Indices: 55832126--55832396 Score: 173
Period size: 50 Copynumber: 5.5 Consensus size: 50
55832116 ACAGTGGAAC
*
55832126 AGATTGAAACTACAACAGCGAATCTTACTTTCCCGACGTTGCAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTTCCCGACGTTGCAGTTAAAT
* * * * *
55832176 AGATTGAAGCTATAACAGTGAATCTTAC-TTCCCTGATAG-TGTAG-AAGAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTTCCC-GA-CGTTGCAGTTA-AAT
* * * * **
55832226 AGATTGAAGCTACAATAGCAAATCTTACTTCCCCGACATTGCAGTTAAGC
1 AGATTGAAGCTACAACAGCGAATCTTACTTTCCCGACGTTGCAGTTAAAT
* * ** * ** * * *** *
55832276 AGACTG-AG-GACATTA---AATCTTAC-TTCCTTGGTGGTGTAGTGGGAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTTCC-CGACGTTGCAGTTAAAT
* * * *
55832321 AGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTTCCCGACGTTGCAGTTAAAT
*
55832371 AGATTGAAGCTACAACAGTGAATCTT
1 AGATTGAAGCTACAACAGCGAATCTT
55832397 CCCCGACATT
Statistics
Matches: 161, Mismatches: 47, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
44 3 0.02
45 20 0.12
46 2 0.01
47 4 0.02
48 5 0.03
49 8 0.05
50 110 0.68
51 9 0.06
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGAATCTTACTTTCCCGACGTTGCAGTTAAAT
Found at i:55832345 original size:95 final size:97
Alignment explanation
Indices: 55832096--55832379 Score: 329
Period size: 95 Copynumber: 2.9 Consensus size: 97
55832086 AAGGACAGCG
** * *
55832096 AATCTTACTTCCTTGGTGGTACAGTGGAACAGATTGAAACTACAACAGCGAATCTTACTTTCCCG
1 AATCTTACTTCCTTGGTGGTGTAGTGGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCG
* * * *
55832161 ACGTTGCAGTTAAATAGATTGAAGCTATAACAGTG
66 ACATTGCAGTTAAACAGACTGAAG---TAACAGTA
* * * ** * * *
55832196 AATCTTACTTCCCTGATAGTGTAGAAGAATAGATTGAAGCTACAATAGCAAATCTTACTTCCCCG
1 AATCTTACTTCCTTGGTGGTGTAGTGGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCG
* * *
55832261 ACATTGCAGTTAAGCAGACTG-AG-GACATTA
66 ACATTGCAGTTAAACAGACTGAAGTAACAGTA
* *
55832291 AATCTTACTTCCTTGGTGGTGTAGTGGGACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCG
1 AATCTTACTTCCTTGGTGGTGTAGTGGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCG
*
55832356 ACATTGCAGTTAAACAGATTGAAG
66 ACATTGCAGTTAAACAGACTGAAG
55832380 CTACAACAGT
Statistics
Matches: 152, Mismatches: 31, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
95 78 0.51
96 2 0.01
99 2 0.01
100 70 0.46
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (97 bp):
AATCTTACTTCCTTGGTGGTGTAGTGGAACAGATTGAAGCTACAACAGCGAATCTTACTTCCCCG
ACATTGCAGTTAAACAGACTGAAGTAACAGTA
Found at i:55832415 original size:46 final size:48
Alignment explanation
Indices: 55832319--55832421 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 48
55832309 GTGTAGTGGG
55832319 ACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAA
1 ACAGATTGAAGCTACAACAGCGAA--TTGCTTCCCCGACATTGCAGTTAA
* *
55832369 ACAGATTGAAGCTACAACAGTGAA-T-CTTCCCCGACATTGTAGTTAA
1 ACAGATTGAAGCTACAACAGCGAATTGCTTCCCCGACATTGCAGTTAA
55832415 ACAGATT
1 ACAGATT
55832422 AAGGTTACGA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
46 27 0.53
47 1 0.02
50 23 0.45
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (48 bp):
ACAGATTGAAGCTACAACAGCGAATTGCTTCCCCGACATTGCAGTTAA
Found at i:55832810 original size:15 final size:15
Alignment explanation
Indices: 55832789--55832830 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
55832779 CTAAACCCAA
*
55832789 ATAGCCCAATTACAC
1 ATAGCCCAACTACAC
*
55832804 CTAGCCCAACTACAC
1 ATAGCCCAACTACAC
*
55832819 ATAGCCTAACTA
1 ATAGCCCAACTA
55832831 TCATACAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.38, C:0.36, G:0.07, T:0.19
Consensus pattern (15 bp):
ATAGCCCAACTACAC
Found at i:55833047 original size:20 final size:20
Alignment explanation
Indices: 55833009--55833045 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55832999 AAAAAACACT
55833009 ACAGCAAATAAGAGAAAATA
1 ACAGCAAATAAGAGAAAATA
*
55833029 ACAGTAAATAAG-GAAAA
1 ACAGCAAATAAGAGAAAA
55833046 ATGTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.65, C:0.08, G:0.16, T:0.11
Consensus pattern (20 bp):
ACAGCAAATAAGAGAAAATA
Found at i:55833887 original size:11 final size:11
Alignment explanation
Indices: 55833842--55833888 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
55833832 CTTTTTTTAC
55833842 ATTTT-TTATT
1 ATTTTATTATT
*
55833852 AATTTATTAATT
1 ATTTTATT-ATT
55833864 ATTTTATTATT
1 ATTTTATTATT
55833875 ATTTTATTATT
1 ATTTTATTATT
55833886 ATT
1 ATT
55833889 GGTACATCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 4 0.12
11 19 0.58
12 10 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:55834218 original size:28 final size:27
Alignment explanation
Indices: 55834177--55834272 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 27
55834167 CTATATAGAT
*
55834177 ATTTT-ATTTCTTTCAAATATTTTAAC
1 ATTTTAATTTATTTCAAATATTTTAAC
* ** *
55834203 ATCTTTAATTTATTTCAACTTATTTCGAT
1 AT-TTTAATTTATTTCAA-ATATTTTAAC
55834232 ATTGTTAATTTA-TTCAAATTTATTTTAAC
1 ATT-TTAATTTATTTCAAA--TATTTTAAC
*
55834261 TTTTTAATTTAT
1 ATTTTAATTTAT
55834273 ATATATTATA
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 24 0.45
29 24 0.45
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTTTAATTTATTTCAAATATTTTAAC
Found at i:55836085 original size:142 final size:142
Alignment explanation
Indices: 55835708--55836130 Score: 508
Period size: 142 Copynumber: 3.0 Consensus size: 142
55835698 CATTATGATA
* * * * *
55835708 GATCTTATCTTCCTAAAGTTGCAGTGAATCAGATTGAAGCCACTAGCCTTATCTTCCTGAAGTTG
1 GATCTTATCTTCCTGAAGTTACAGTGAGT-AGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTG
* * *
55835773 CAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTAGCATGGCAGTGGAACAAGATTAAAGC
65 CAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAAC-AGATTAAAGC
* *
55835838 TTCAAGTTATGGCG
129 TACAAATTATGGCG
* * * * * **
55835852 GATCTTATCTTCTTGAAATTTCAGTAGAGCAAATTGAAGTTACCAGCCTTATCTCCCTGAAGTTG
1 GATCTTATCTTCCTGAAGTTACAGT-GAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTG
* * * *
55835917 CAGCAGAGCAGACTAAAGACAACGAATCTTATTTCTCTGGCGTTGCAGTGGAACAGATTAAAGCT
65 CAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCT
55835982 ACAAATTATGGCG
130 ACAAATTATGGCG
* * *
55835995 GAT-TTATCTTCCTGAAGTTACAGTGGAGTAGATTGAAGCCACCAACTTTATCACCCTGAAGTAT
1 GATCTTATCTTCCTGAAGTTACAGT-GAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGT-T
* * * ** *
55836059 -TAGCGGAACAGACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGC
64 GCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGC
*
55836123 TATAAATT
129 TACAAATT
55836131 GTAGATCTTA
Statistics
Matches: 235, Mismatches: 42, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
142 109 0.46
143 26 0.11
144 98 0.42
145 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (142 bp):
GATCTTATCTTCCTGAAGTTACAGTGAGTAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGC
AGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTA
CAAATTATGGCG
Done.