Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 78
Found at i:3289031 original size:2 final size:2
Alignment explanation
Indices: 3288923--3289016 Score: 52
Period size: 2 Copynumber: 47.0 Consensus size: 2
3288913 GTTTATAGCT
* * * * *
3288923 TA TA AA TA TA T- TG TA TA TA TA CA TA CTA TA TG T- TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
3288964 TA TA T- TA TA TA -A TA TA TA GTT TA TA TA CTA TA GA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA -TA TA
3289005 TA TA TA TA TA TA
1 TA TA TA TA TA TA
3289017 CATAAGTTAT
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
1 4 0.06
2 60 0.86
3 6 0.09
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3289236 original size:35 final size:35
Alignment explanation
Indices: 3289195--3289266 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
3289185 ATATATATAC
* *
3289195 ATAGTTTATACATACATGTACTATAAGTTACATAT
1 ATAGTTTACACATACATATACTATAAGTTACATAT
**
3289230 ATAGTTTACATGTACATATACTATAAGTTACATAT
1 ATAGTTTACACATACATATACTATAAGTTACATAT
3289265 AT
1 AT
3289267 TAACTTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.40
Consensus pattern (35 bp):
ATAGTTTACACATACATATACTATAAGTTACATAT
Found at i:3289263 original size:16 final size:16
Alignment explanation
Indices: 3289207--3289265 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
3289197 AGTTTATACA
*
3289207 TACATGTACTATAAGT
1 TACATATACTATAAGT
3289223 TACATATA-TAGTTTACA-T
1 TACATATACTA---TA-AGT
3289241 GTACATATACTATAAGT
1 -TACATATACTATAAGT
3289258 TACATATA
1 TACATATA
3289266 TTAACTTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 14
0.70 0.02 0.28
Matches are distributed among these distances:
15 2 0.06
16 16 0.46
17 3 0.09
18 3 0.09
19 9 0.26
20 2 0.06
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (16 bp):
TACATATACTATAAGT
Found at i:3289487 original size:2 final size:2
Alignment explanation
Indices: 3289475--3289602 Score: 78
Period size: 2 Copynumber: 66.5 Consensus size: 2
3289465 TGTTTCTTTA
3289475 AT AT AT A- AT AT AT AT AT AT AT AT AT A- 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
* *
3289515 AT -T ACT -T AT AT TT GT -T AT ACT ACT -T AT AT AT AT ACT AT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T A-T AT AT AT AT AT A-T AT AT
* * * *
3289555 A- AT AT AA AT -T AT A- AT AT AA AT AT AT -T TT AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
3289594 AC AT AT AT A
1 AT AT AT AT A
3289603 GTGTAATACC
Statistics
Matches: 101, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
1 10 0.10
2 83 0.82
3 8 0.08
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3289495 original size:15 final size:15
Alignment explanation
Indices: 3289475--3289602 Score: 76
Period size: 15 Copynumber: 8.9 Consensus size: 15
3289465 TGTTTCTTTA
3289475 ATATATA-ATAT-AT
1 ATATATATATATAAT
3289488 ATATATATATATAAT
1 ATATATATATATAAT
*
3289503 ATATATATATATATT
1 ATATATATATATAAT
* * *
3289518 ACT-TATATTTGTTAT
1 A-TATATATATATAAT
*
3289533 ACTACTTATATATATACT
1 A-TA--TATATATATAAT
3289551 ATATA-ATATA-AAT
1 ATATATATATATAAT
3289564 -TATA-ATATA-AAT
1 ATATATATATATAAT
* *
3289576 ATAT-TTTATATAGT
1 ATATATATATATAAT
* *
3289590 TTATACATATATA
1 ATATATATATATA
3289603 GTGTAATACC
Statistics
Matches: 90, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
12 12 0.13
13 16 0.18
14 14 0.16
15 36 0.40
16 1 0.01
17 2 0.02
18 9 0.10
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATATATATATAAT
Found at i:3289594 original size:52 final size:53
Alignment explanation
Indices: 3289476--3289602 Score: 127
Period size: 54 Copynumber: 2.4 Consensus size: 53
3289466 GTTTCTTTAA
* * **
3289476 TATATAATATATATATATATATATAATATATATATATATATTACTTATATTTGT
1 TATAT-ATTTATATATATATATATAATATAAATATATATATTAAATATATTTGT
*
3289530 TATACTACTTATATATATACTATATAATATAAAT-TATA-ATATAAATATA-TT-T
1 TATA-TATTTATATATATA-TATATAATATAAATATATATAT-TAAATATATTTGT
*
3289582 TATATAGTTTATACATATATA
1 TATATA-TTTATATATATATA
3289603 GTGTAATACC
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
51 4 0.06
52 15 0.24
53 4 0.06
54 25 0.40
55 14 0.23
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (53 bp):
TATATATTTATATATATATATATAATATAAATATATATATTAAATATATTTGT
Found at i:3299784 original size:13 final size:13
Alignment explanation
Indices: 3299752--3299867 Score: 62
Period size: 13 Copynumber: 8.7 Consensus size: 13
3299742 CTATATCTTT
3299752 TATAGTTTATACCTA
1 TATAGTTTATA--TA
3299767 TATAGTTTATATA
1 TATAGTTTATATA
* *
3299780 CATAGGTTATATA
1 TATAGTTTATATA
* *
3299793 TATAGTTCACATAAA
1 TATAGTT--TATATA
* *
3299808 CATAATTTAT-TA
1 TATAGTTTATATA
3299820 TACT--TATTAT-TA
1 TA-TAGT-TTATATA
*
3299832 TA-ACTTTATATAAA
1 TATAGTTTATAT--A
3299846 TATAGTTTATATA
1 TATAGTTTATATA
3299859 TATAGTTTA
1 TATAGTTTA
3299868 CATAAACATA
Statistics
Matches: 79, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
11 5 0.06
12 12 0.15
13 31 0.39
14 3 0.04
15 28 0.35
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:3299821 original size:66 final size:65
Alignment explanation
Indices: 3299751--3299893 Score: 166
Period size: 66 Copynumber: 2.2 Consensus size: 65
3299741 ACTATATCTT
* * *
3299751 TTATAGTTTATACCTATATAGTTTATAT-ACATAGGTTATATATATAGTTCACATAAACATAATT
1 TTATAGCTTATA-CTATA-ACTTTATATAACATAGGTTATATATATAGTTCACATAAACATAATA
3299815 TA
64 TA
* * * *
3299817 TTATA-CTTATTATTATAACTTTATATAAATATAGTTTATATATATAGTTTACATAAACATAATA
1 TTATAGCTTA-TACTATAACTTTATAT-AACATAGGTTATATATATAGTTCACATAAACATAATA
3299881 TA
64 TA
3299883 -TATAGCTTATA
1 TTATAGCTTATA
3299894 ATAATTATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
64 8 0.12
65 13 0.20
66 45 0.68
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (65 bp):
TTATAGCTTATACTATAACTTTATATAACATAGGTTATATATATAGTTCACATAAACATAATATA
Found at i:3299856 original size:15 final size:15
Alignment explanation
Indices: 3299836--3299931 Score: 55
Period size: 15 Copynumber: 6.5 Consensus size: 15
3299826 TTATTATAAC
3299836 TTTATATAAATATAG
1 TTTATATAAATATAG
3299851 TTTATAT--ATATAG
1 TTTATATAAATATAG
* *
3299864 TTTACATAAACATA-
1 TTTATATAAATATAG
3299878 ---ATAT--ATATAG
1 TTTATATAAATATAG
*
3299888 CTTATAATAATTATATAG
1 TTTAT-ATAA--ATATAG
3299906 TTAATAATATAAATATAG
1 TT--T-ATATAAATATAG
3299924 TTTATATA
1 TTTATATA
3299932 TAAAATATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 28
0.65 0.05 0.29
Matches are distributed among these distances:
9 4 0.06
11 3 0.05
13 14 0.23
14 2 0.03
15 16 0.26
16 1 0.02
18 15 0.24
20 5 0.08
21 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (15 bp):
TTTATATAAATATAG
Found at i:3299903 original size:22 final size:23
Alignment explanation
Indices: 3299852--3299904 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
3299842 TAAATATAGT
*
3299852 TTATATATATAGTTTACATAAACA
1 TTATATATATAGCTTA-ATAAACA
*
3299876 TAATATATATAGCTT-ATAATA-A
1 TTATATATATAGCTTAATAA-ACA
3299898 TTATATA
1 TTATATA
3299905 GTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 11 0.44
23 1 0.04
24 13 0.52
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (23 bp):
TTATATATATAGCTTAATAAACA
Found at i:3299904 original size:18 final size:19
Alignment explanation
Indices: 3299875--3299942 Score: 70
Period size: 18 Copynumber: 3.6 Consensus size: 19
3299865 TTACATAAAC
3299875 ATAATATATATAGCTT-ATA
1 ATAATATATATAG-TTAATA
3299894 ATAAT-TATATAGTTAATA
1 ATAATATATATAGTTAATA
* *
3299912 AT-ATAAATATAGTTTATA
1 ATAATATATATAGTTAATA
*
3299930 TATAAAATATATA
1 -ATAATATATATA
3299943 TATATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
17 4 0.10
18 23 0.56
19 7 0.17
20 7 0.17
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (19 bp):
ATAATATATATAGTTAATA
Found at i:3300293 original size:53 final size:56
Alignment explanation
Indices: 3300236--3300340 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
3300226 CCCTTACCTA
3300236 TGTGTGGTTTAA-TTATATTTT-AGA-TTTATTTGTAATTTTACATTTCTTCTATG
1 TGTGTGGTTTAATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTCTATG
*
3300289 TGTGTTGTTTAATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTC
1 TGTGTGGTTTAATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTC
3300341 AATTTTGTCA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
53 11 0.23
54 9 0.19
55 3 0.06
56 25 0.52
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (56 bp):
TGTGTGGTTTAATTTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTCTATG
Found at i:3300367 original size:55 final size:55
Alignment explanation
Indices: 3300248--3300364 Score: 159
Period size: 56 Copynumber: 2.2 Consensus size: 55
3300238 TGTGGTTTAA
* ** *
3300248 TTATATTTT-AGATTTATTTGTAATTTTACATTTCTTCTATGTGTGTTGTTTAAT
1 TTATATTTTAAGATTTATTTGTAATTTTACATTTCTTCAATGTGTGTCATTAAAT
*
3300302 TTATATTTTAAGATTTTATTTGTAATTTTACATTTCTTCAAT-TTTGTCATTAAAT
1 TTATATTTTAAGA-TTTATTTGTAATTTTACATTTCTTCAATGTGTGTCATTAAAT
3300357 TTA-ATTTT
1 TTATATTTT
3300365 TAAAAATTGA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 14 0.25
55 15 0.27
56 27 0.48
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.61
Consensus pattern (55 bp):
TTATATTTTAAGATTTATTTGTAATTTTACATTTCTTCAATGTGTGTCATTAAAT
Found at i:3303500 original size:16 final size:17
Alignment explanation
Indices: 3303462--3303500 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3303452 ACATATACCA
3303462 GTTTTTGTCTTAAAAAT
1 GTTTTTGTCTTAAAAAT
* *
3303479 GATTTT-TCTTAAAATT
1 GTTTTTGTCTTAAAAAT
3303495 GTTTTT
1 GTTTTT
3303501 AAAAGACGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (17 bp):
GTTTTTGTCTTAAAAAT
Found at i:3304853 original size:20 final size:21
Alignment explanation
Indices: 3304828--3304872 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
3304818 ATTTTGATAA
3304828 AAATATAATAATAAGTTAA-G
1 AAATATAATAATAAGTTAAGG
3304848 AAATATAATAATAAGTTAAGG
1 AAATATAATAATAAGTTAAGG
3304869 AAAT
1 AAAT
3304873 TTTATAAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (21 bp):
AAATATAATAATAAGTTAAGG
Found at i:3313139 original size:2 final size:2
Alignment explanation
Indices: 3313132--3313168 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3313122 TTATTTGTCA
3313132 AT AT AT 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 AT AT AT A
3313169 CGAAATACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3313297 original size:85 final size:85
Alignment explanation
Indices: 3313217--3313404 Score: 247
Period size: 84 Copynumber: 2.2 Consensus size: 85
3313207 AATGACATGT
* * * *
3313217 GCTTCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTATGGCA-CACAAATGTATG
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCATGTCATAAATTTATGGCACCACAAATATATG
3313281 TCAAGCAT-ATTTATGACGGGG
66 T-AAGCATAATTTATGAC-GGG
** * *
3313302 GCTTC-ATGACGCTTAATGTAAGTCATACATGCATGTCATAAATTTATGTCACCACAAATATGTG
1 GCTTCAATGACGCGCAATGTAAGTCATACATGCATGTCATAAATTTATGGCACCACAAATATATG
* *
3313366 TAATCTTAATTTATGACGGG
66 TAAGCATAATTTATGACGGG
3313386 GCTTCAATGACGCGCAATG
1 GCTTCAATGACGCGCAATG
3313405 CGCGTCATAA
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
84 52 0.59
85 36 0.41
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (85 bp):
GCTTCAATGACGCGCAATGTAAGTCATACATGCATGTCATAAATTTATGGCACCACAAATATATG
TAAGCATAATTTATGACGGG
Found at i:3313412 original size:85 final size:84
Alignment explanation
Indices: 3313217--3313427 Score: 241
Period size: 84 Copynumber: 2.5 Consensus size: 84
3313207 AATGACATGT
* * *
3313217 GCTTCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTATGGCACACAAATGTATGT
1 GCTTCAATGACGCGCAATGTAAGTCATAAATGC-TGTCATAAATTTATGGCACACAAATATATGT
3313282 CAAGCATATTTATGACGGGG
65 CAAGCATATTTATGACGGGG
** * * *
3313302 GCTTC-ATGACGCTTAATGTAAGTCATACATGCATGTCATAAATTTATGTCACCACAAATATGTG
1 GCTTCAATGACGCGCAATGTAAGTCATAAATGC-TGTCATAAATTTATGGCA-CACAAATATATG
* *
3313366 T-AATCTTAATTTATGAC-GGG
64 TCAAGCAT-ATTTATGACGGGG
***
3313386 GCTTCAATGACGCGCAATGCGCGTCATAAATGC-GTCATAAAT
1 GCTTCAATGACGCGCAATGTAAGTCATAAATGCTGTCATAAAT
3313428 GTGCGTCATA
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
83 9 0.08
84 52 0.49
85 46 0.43
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (84 bp):
GCTTCAATGACGCGCAATGTAAGTCATAAATGCTGTCATAAATTTATGGCACACAAATATATGTC
AAGCATATTTATGACGGGG
Found at i:3318792 original size:127 final size:126
Alignment explanation
Indices: 3318491--3318902 Score: 493
Period size: 127 Copynumber: 3.3 Consensus size: 126
3318481 AACAGAGCAA
* ** * *
3318491 GTCATCACCTGACCAGATCTCCTCAT-ATGTAGGAGTTGTGT-AA-CTCAGATAACCAGTTGTCC
1 GTCATCACCCGACCAGATCTCCTCATCATGTAGGAGCCGTGTCAACCTCTGATAACCAGTCGTCC
* * * * *
3318553 TTATCACATAGGAACC-TGTTATCACCTTAT-ATGACCAAGACTCATGAACAG-ATGAGTAGT
66 TTATCACATAGGAACCGTGTTATCACCTT-TGATGGCCAAGACTTAT-CATAGTATGAGCAGT
* * * *
3318613 GTCATCACCC-ACCTGATATCCTCATCATGTAGGAGCCATGTCAACCCCTGATAACCAGTCGTCC
1 GTCATCACCCGACCAGATCTCCTCATCATGTAGGAGCCGTGTCAACCTCTGATAACCAGTCGTCC
*
3318677 TTATCACTTAGGAACCGTGTTATCACCATTTGATGGCCAAGACTTATCATAGTATGAGCAGT
66 TTATCACATAGGAACCGTGTTATCACC-TTTGATGGCCAAGACTTATCATAGTATGAGCAGT
* * * *
3318739 TTCATCACCCGA-CATGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTTGATAACCA-TCCAT
1 GTCATCACCCGACCA-GATCTCCTCATCATGTAGGAGCCGTGTCAACCTCTGATAACCAGT-CGT
* * * *
3318802 CCTCATCACGTAGGAATCGTGTTATCACCCTTAGATGGCCAAGACTTATCATAGTATGAGCAGT
64 CCTTATCACATAGGAACCGTGTTATCA-CCTTTGATGGCCAAGACTTATCATAGTATGAGCAGT
3318866 GTCATCA-CCGACCAGATCTCCTCATCATGTAGGAGCC
1 GTCATCACCCGACCAGATCTCCTCATCATGTAGGAGCC
3318903 AAGTCAATCC
Statistics
Matches: 249, Mismatches: 29, Indels: 20
0.84 0.10 0.07
Matches are distributed among these distances:
121 13 0.05
122 21 0.08
123 2 0.01
124 31 0.12
125 14 0.06
126 60 0.24
127 106 0.43
128 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (126 bp):
GTCATCACCCGACCAGATCTCCTCATCATGTAGGAGCCGTGTCAACCTCTGATAACCAGTCGTCC
TTATCACATAGGAACCGTGTTATCACCTTTGATGGCCAAGACTTATCATAGTATGAGCAGT
Found at i:3319243 original size:17 final size:18
Alignment explanation
Indices: 3319215--3319261 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
3319205 CCAGGTCAAA
3319215 ATATATTAATTATATTATT
1 ATATA-TAATTATATTATT
*
3319234 AT-TATAATTA-ATTTTT
1 ATATATAATTATATTATT
*
3319250 ATATATATTTAT
1 ATATATAATTAT
3319262 GTTGTGCAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 7 0.29
17 13 0.54
18 2 0.08
19 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATATAATTATATTATT
Found at i:3320825 original size:29 final size:27
Alignment explanation
Indices: 3320763--3320826 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
3320753 TAACTTTTAT
* * *
3320763 TTATTTGTCTTATTATTGTACTAACTT
1 TTATTTTTCTTATTATTATACTAACTG
*
3320790 TTCATTTTTCTTATTGTTATCACTAACATG
1 TT-ATTTTTCTTATTATTAT-ACTAAC-TG
3320820 TTATTTT
1 TTATTTT
3320827 ATTGCACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 2 0.07
28 14 0.47
29 11 0.37
30 3 0.10
ACGTcount: A:0.22, C:0.12, G:0.06, T:0.59
Consensus pattern (27 bp):
TTATTTTTCTTATTATTATACTAACTG
Found at i:3322198 original size:29 final size:27
Alignment explanation
Indices: 3322159--3322228 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 27
3322149 ATTTTTGTTG
3322159 TTGAGATTTTTAGAAGTTTAAAGAGTTTTT
1 TTGAGATTTTTAGAA-TTT-AAGA-TTTTT
*
3322189 TTGAGATTTTCTGGAATTTAAGATTTTT
1 TTGAGATTTT-TAGAATTTAAGATTTTT
*
3322217 TTGAGAATTTTA
1 TTGAGATTTTTA
3322229 ATAATTCATG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.03
28 14 0.39
29 4 0.11
30 13 0.36
31 4 0.11
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGAGATTTTTAGAATTTAAGATTTTT
Found at i:3326099 original size:38 final size:38
Alignment explanation
Indices: 3326048--3326123 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
3326038 GTAAATGATG
*
3326048 ATTTGTTTGGAAAATAGATAATAAAATATTTCAGGTCT
1 ATTTGTTTAGAAAATAGATAATAAAATATTTCAGGTCT
3326086 ATTTGTTTAGAAAATAGATAATAAAATATTTCAGGTCT
1 ATTTGTTTAGAAAATAGATAATAAAATATTTCAGGTCT
3326124 TATGTTTCCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.39
Consensus pattern (38 bp):
ATTTGTTTAGAAAATAGATAATAAAATATTTCAGGTCT
Found at i:3333223 original size:28 final size:28
Alignment explanation
Indices: 3333183--3333238 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
3333173 CTCCGTTTAC
** *
3333183 ATTATACTTTCAAGTCAGTGCTTGAAAG
1 ATTATACAATCAAGTCACTGCTTGAAAG
* *
3333211 ATTATACAATCAATTTACTGCTTGAAAG
1 ATTATACAATCAAGTCACTGCTTGAAAG
3333239 CAACGGTGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (28 bp):
ATTATACAATCAAGTCACTGCTTGAAAG
Found at i:3333439 original size:60 final size:60
Alignment explanation
Indices: 3333373--3333485 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
3333363 TCAGGTGACT
*
3333373 ATTTTGTAACTTTTAATAGTTG-GAGGATTCAACAAAGCAAT-ATCCTATAGTCGTGAGATA
1 ATTTTGTAACTTTTAATAGTTGAGA-GACTCAACAAAGC-ATCATCCTATAGTCGTGAGATA
3333433 ATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAGCATCATCCTATAGTCG
1 ATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAGCATCATCCTATAGTCG
3333486 AGAACCATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
59 2 0.04
60 46 0.92
61 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTTGAGAGACTCAACAAAGCATCATCCTATAGTCGTGAGATA
Found at i:3337718 original size:21 final size:21
Alignment explanation
Indices: 3337694--3337745 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
3337684 TGATACAATG
3337694 CATCGATGCATTGTTACAGTA
1 CATCGATGCATTGTTACAGTA
*
3337715 CATCGATGCATTGTTACAGTG
1 CATCGATGCATTGTTACAGTA
3337736 CATCGATGCA
1 CATCGATGCA
3337746 CCAAAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (21 bp):
CATCGATGCATTGTTACAGTA
Found at i:3338509 original size:31 final size:31
Alignment explanation
Indices: 3338471--3338687 Score: 161
Period size: 31 Copynumber: 6.9 Consensus size: 31
3338461 CCTCGACAAC
* *
3338471 TGTCCATAGGTCCCGAAGAACCTAGGTAAAT
1 TGTCCATATGTCCCGAAGAACATAGGTAAAT
* *** * *
3338502 TGTCCATATGTTCTTTAGAACATAGGTATAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAT
** *
3338533 TGAACATATGTCCCGAA-AGACATAGGTAATTT
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA-AT
* * * * *
3338565 TGTCCATGTGTTCCGTAGAACATAGGTATAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAT
*
3338596 TGTCCATATGTCCCGAA-AGACATAGGTAATT
1 TGTCCATATGTCCCGAAGA-ACATAGGTAAAT
* * * *
3338627 CTGTCCATATGTTCCGTAGAACATAGGTATAC
1 -TGTCCATATGTCCCGAAGAACATAGGTAAAT
**
3338659 TGTTAATATGTCCCGAA-AGACATAGGTAA
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA
3338688 TTCTTCGACT
Statistics
Matches: 138, Mismatches: 41, Indels: 14
0.72 0.21 0.07
Matches are distributed among these distances:
30 3 0.02
31 88 0.64
32 45 0.33
33 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
TGTCCATATGTCCCGAAGAACATAGGTAAAT
Found at i:3338584 original size:63 final size:63
Alignment explanation
Indices: 3338469--3338689 Score: 313
Period size: 63 Copynumber: 3.5 Consensus size: 63
3338459 AACCTCGACA
* * * * **
3338469 ACTGTCCATAGGTCCCG-AAGAACCTAGGTAA-ATTGTCCATATGTTCTTTAGAACATAGGTAT
1 ACTGTACATATGTCCCGAAAG-ACATAGGTAATTTTGTCCATATGTTCCGTAGAACATAGGTAT
* *
3338531 ACTGAACATATGTCCCGAAAGACATAGGTAATTTTGTCCATGTGTTCCGTAGAACATAGGTAT
1 ACTGTACATATGTCCCGAAAGACATAGGTAATTTTGTCCATATGTTCCGTAGAACATAGGTAT
* *
3338594 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
1 ACTGTACATATGTCCCGAAAGACATAGGTAATTTTGTCCATATGTTCCGTAGAACATAGGTAT
3338657 ACTGTTA-ATATGTCCCGAAAGACATAGGTAATT
1 ACTG-TACATATGTCCCGAAAGACATAGGTAATT
3338690 CTTCGACTCT
Statistics
Matches: 143, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
62 23 0.16
63 119 0.83
64 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (63 bp):
ACTGTACATATGTCCCGAAAGACATAGGTAATTTTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:3338636 original size:32 final size:32
Alignment explanation
Indices: 3338537--3338691 Score: 174
Period size: 31 Copynumber: 4.9 Consensus size: 32
3338527 GTATACTGAA
*
3338537 CATATGTCCCGAAAGACATAGGTAATTTTGTC
1 CATATGTCCCGAAAGACATAGGTAATTCTGTC
* * * *
3338569 CATGTGTTCCG-TAGAACATAGGT-ATACTGTC
1 CATATGTCCCGAAAG-ACATAGGTAATTCTGTC
3338600 CATATGTCCCGAAAGACATAGGTAATTCTGTC
1 CATATGTCCCGAAAGACATAGGTAATTCTGTC
* * * *
3338632 CATATGTTCCG-TAGAACATAGGT-ATACTGTT
1 CATATGTCCCGAAAG-ACATAGGTAATTCTGTC
*
3338663 AATATGTCCCGAAAGACATAGGTAATTCT
1 CATATGTCCCGAAAGACATAGGTAATTCT
3338692 TCGACTCTTG
Statistics
Matches: 100, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
31 50 0.50
32 50 0.50
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (32 bp):
CATATGTCCCGAAAGACATAGGTAATTCTGTC
Found at i:3341715 original size:15 final size:15
Alignment explanation
Indices: 3341695--3341726 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3341685 AAAATCTTTC
*
3341695 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
3341710 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
3341725 TT
1 TT
3341727 CGATCTGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:3343365 original size:20 final size:20
Alignment explanation
Indices: 3343336--3343386 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3343326 TAACACATTT
* * *
3343336 TTTTTTGTCTTTTTGACACG
1 TTTTTCGTCTTTATGACACA
*
3343356 TTTTTCGTCTTTATGACATA
1 TTTTTCGTCTTTATGACACA
3343376 TTTTTCGTCTT
1 TTTTTCGTCTT
3343387 CTTTCTCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.61
Consensus pattern (20 bp):
TTTTTCGTCTTTATGACACA
Found at i:3352303 original size:14 final size:14
Alignment explanation
Indices: 3352281--3352335 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
3352271 CGTTCGTGAA
*
3352281 TGTTTGGTTATGTT
1 TGTTCGGTTATGTT
3352295 TGTTCGGTTA----
1 TGTTCGGTTATGTT
3352305 TGTTCGGTTATGTT
1 TGTTCGGTTATGTT
* *
3352319 CGTTCGGTTATGCT
1 TGTTCGGTTATGTT
3352333 TGT
1 TGT
3352336 ATGTTCATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 10 0.30
14 23 0.70
ACGTcount: A:0.07, C:0.09, G:0.29, T:0.55
Consensus pattern (14 bp):
TGTTCGGTTATGTT
Found at i:3352307 original size:24 final size:24
Alignment explanation
Indices: 3352280--3352330 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3352270 ACGTTCGTGA
* *
3352280 ATGTTTGGTTATGTTTGTTCGGTT
1 ATGTTCGGTTATGTTCGTTCGGTT
3352304 ATGTTCGGTTATGTTCGTTCGGTT
1 ATGTTCGGTTATGTTCGTTCGGTT
3352328 ATG
1 ATG
3352331 CTTGTATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.08, G:0.29, T:0.53
Consensus pattern (24 bp):
ATGTTCGGTTATGTTCGTTCGGTT
Found at i:3352308 original size:10 final size:10
Alignment explanation
Indices: 3352295--3352320 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3352285 TGGTTATGTT
3352295 TGTTCGGTTA
1 TGTTCGGTTA
3352305 TGTTCGGTTA
1 TGTTCGGTTA
3352315 TGTTCG
1 TGTTCG
3352321 TTCGGTTATG
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:0.12, G:0.31, T:0.50
Consensus pattern (10 bp):
TGTTCGGTTA
Found at i:3353446 original size:16 final size:16
Alignment explanation
Indices: 3353425--3353475 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
3353415 GTCTCCAACG
3353425 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
3353441 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
3353457 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
3353471 TTTAT
1 TTTAT
3353476 TAAATGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.15
15 2 0.06
16 26 0.79
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:3354896 original size:10 final size:10
Alignment explanation
Indices: 3354867--3354954 Score: 85
Period size: 10 Copynumber: 9.1 Consensus size: 10
3354857 GCTGCTGGAA
3354867 AACCGGTTTG
1 AACCGGTTTG
*
3354877 -ACCAGTTTTG
1 AACC-GGTTTG
3354887 AACCGGTTTG
1 AACCGGTTTG
*
3354897 -ACCGGTTCG
1 AACCGGTTTG
3354906 AACCGGTTTG
1 AACCGGTTTG
* *
3354916 -ATCGGTCTG
1 AACCGGTTTG
3354925 AACCGGTTTG
1 AACCGGTTTG
*
3354935 -ACCGGTCTG
1 AACCGGTTTG
*
3354944 AACCGGGTTG
1 AACCGGTTTG
3354954 A
1 A
3354955 CCCGACCCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 26 0.42
10 33 0.53
11 3 0.05
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:3354910 original size:19 final size:19
Alignment explanation
Indices: 3354867--3354956 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
3354857 GCTGCTGGAA
* *
3354867 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
3354887 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
*
3354906 AACCGGTTTGATCGGTCTG
1 AACCGGTTTGACCGGTCTG
3354925 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
3354944 AACCGGGTTGACC
1 AACCGGTTTGACC
3354957 CGACCCGACT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.02
19 49 0.77
20 14 0.22
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:3354972 original size:17 final size:17
Alignment explanation
Indices: 3354950--3355007 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
3354940 TCTGAACCGG
*
3354950 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
3354967 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
3354984 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
3355001 GTTGACC
1 GTTGACC
3355008 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:3355014 original size:6 final size:7
Alignment explanation
Indices: 3354997--3355026 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3354987 GACCCGACCC
3354997 GACCGTT
1 GACCGTT
3355004 GACCG-T
1 GACCGTT
3355010 GACCGTT
1 GACCGTT
3355017 GACCGTT
1 GACCGTT
3355024 GAC
1 GAC
3355027 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:3355015 original size:13 final size:13
Alignment explanation
Indices: 3354997--3355022 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3354987 GACCCGACCC
3354997 GACCGTTGACCGT
1 GACCGTTGACCGT
3355010 GACCGTTGACCGT
1 GACCGTTGACCGT
3355023 TGACTTTCTT
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:3362168 original size:10 final size:10
Alignment explanation
Indices: 3362139--3362207 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
3362129 GCTGCTGGAA
3362139 AACCGGTTTG
1 AACCGGTTTG
*
3362149 -ACCAGTTTTG
1 AACC-GGTTTG
3362159 AACCGGTTTG
1 AACCGGTTTG
*
3362169 -ACCGGTTCG
1 AACCGGTTTG
3362178 AACCGGTTTG
1 AACCGGTTTG
*
3362188 -ACCGGTCTG
1 AACCGGTTTG
*
3362197 AACCGGGTTG
1 AACCGGTTTG
3362207 A
1 A
3362208 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:3362182 original size:19 final size:19
Alignment explanation
Indices: 3362139--3362209 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
3362129 GCTGCTGGAA
* *
3362139 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
3362159 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
3362178 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
3362197 AACCGGGTTGACC
1 AACCGGTTTGACC
3362210 CGACCCGACT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 2 0.04
19 32 0.68
20 13 0.28
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:3362225 original size:17 final size:17
Alignment explanation
Indices: 3362203--3362260 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
3362193 TCTGAACCGG
*
3362203 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
3362220 GTTGACCCGACCCAACC
1 GTTGACCCGACCCGACC
3362237 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
3362254 GTTGACC
1 GTTGACC
3362261 GTGACCGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.19, C:0.43, G:0.22, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:3375227 original size:51 final size:51
Alignment explanation
Indices: 3375147--3375256 Score: 177
Period size: 51 Copynumber: 2.2 Consensus size: 51
3375137 CAGTAAGTAT
*
3375147 ATAC-AAGCATGTATATACAAGAGTTTGCATGCAGCTTTATACAGCTTACA
1 ATACTAAGCATGTATATACAAGAGTTTGCATGCAGCTTTATAAAGCTTACA
* * *
3375197 ATGCTAAGCATGTATTTACAAGAGTTTGCATGCAGCTTTATAAAGCTTACT
1 ATACTAAGCATGTATATACAAGAGTTTGCATGCAGCTTTATAAAGCTTACA
3375248 ATACTAAGC
1 ATACTAAGC
3375257 TAATTGCTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 3 0.06
51 51 0.94
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (51 bp):
ATACTAAGCATGTATATACAAGAGTTTGCATGCAGCTTTATAAAGCTTACA
Found at i:3384386 original size:60 final size:60
Alignment explanation
Indices: 3384267--3384444 Score: 168
Period size: 60 Copynumber: 3.0 Consensus size: 60
3384257 TATTTGGATG
* * * *
3384267 AATTTAGGGATGAAATTGGAA-GATTCAAAAGTTT-AGAAATCAATTTAGAAAGAA-TGTCAT
1 AATTTAGGGATGAAATTGGAATG-TTCAAAAGTTTAAGGACT-AATTTA-AAATAAGAGTCAT
*
3384327 AGTTTAGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAATAAGAGTCAT
1 AATTTAGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAATAAGAGTCAT
* * * * * *
3384387 AATTT-GAAGATAAAATTTAGAATATTCAAATGTTTAAGGAGC-AATTTAAAATGAGAGT
1 AATTTAG-GGATGAAA-TTGGAATGTTCAAAAGTTTAAGGA-CTAATTTAAAATAAGAGT
3384445 TACAGTCAAG
Statistics
Matches: 100, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
59 6 0.06
60 52 0.52
61 41 0.41
62 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.31
Consensus pattern (60 bp):
AATTTAGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAATAAGAGTCAT
Found at i:3387237 original size:16 final size:16
Alignment explanation
Indices: 3387216--3387259 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3387206 ATCATTAAAA
3387216 AATAATTTAAAATTTT
1 AATAATTTAAAATTTT
**
3387232 AATAATAAAAAATTTT
1 AATAATTTAAAATTTT
*
3387248 AA-ATTTTAAAAT
1 AATAATTTAAAAT
3387260 AAAAATCTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAATTTAAAATTTT
Found at i:3387251 original size:23 final size:22
Alignment explanation
Indices: 3387214--3387264 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 22
3387204 AAATCATTAA
3387214 AAAATAATTTAAAATTTTAATAAT
1 AAAA-AATTTAAAATTTTAA-AAT
*
3387238 AAAAAATTTTAAATTTTAAAAT
1 AAAAAATTTAAAATTTTAAAAT
3387260 AAAAA
1 AAAAA
3387265 TCTATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 8 0.31
23 14 0.54
24 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAAATTTAAAATTTTAAAAT
Found at i:3387331 original size:12 final size:12
Alignment explanation
Indices: 3387307--3387342 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
3387297 TTTGGGTATG
3387307 TTAAATA-AATT
1 TTAAATATAATT
*
3387318 TTAAATTTAATT
1 TTAAATATAATT
3387330 TTAAATATAATT
1 TTAAATATAATT
3387342 T
1 T
3387343 CATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAATATAATT
Found at i:3388599 original size:131 final size:131
Alignment explanation
Indices: 3388359--3388843 Score: 591
Period size: 131 Copynumber: 3.8 Consensus size: 131
3388349 TTTTAAGAAC
* * * * * *
3388359 GAAAACGATAAAATCTAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAACCAGTCA
1 GAAAACCATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAGTCA
* * * * * *
3388424 TTTATTTCTCCGATCGAAATGAAGAGATATAACTATTTCATCTTAAAAATTCAATATTGATTCGA
66 TTTATTACTCCAACCGAAATGAAAAGATATTACTATTTCTTCTT-AAAATTCAATATTGATTCGA
3388489 GA
130 GA
* * * * *
3388491 GAAAACGATAATATATGATTATTTCTAATCGAGTA-AAATGATCTCTCATACCTTAAAGCAGTCA
1 GAAAACCATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAGTCA
* * * *
3388555 TTTATTACTCCAATCGAAATGAATATATATCACTATTTCTTCTTAAAATTCAATATTGATTCGAG
66 TTTATTACTCCAACCGAAATGAAAAGATATTACTATTTCTTCTTAAAATTCAATATTGATTCGAG
3388620 A
131 A
* *
3388621 GAAAACCATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTTAAGCAGTCA
1 GAAAACCATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAGTCA
*
3388686 TTTATTACTCCAACCAAAATGAAAAGATATTACTA-TT-TTC----AA-T-AATA---ATTCGAG
66 TTTATTACTCCAACCGAAATGAAAAGATATTACTATTTCTTCTTAAAATTCAATATTGATTCGAG
3388740 A
131 A
* * * *
3388741 GAAAACCATAATATCTAATTATTTTCAATCGAGAAT-AATAGACCTCTCATACCTTTAAGCAATC
1 GAAAACCATAATATATAATTATTTCCAATCGAGAATAAAT-GACCTCTCATACCTTAAAGCAGTC
* *
3388805 ATTGATTTCTCCAACCGAAATGAAAAGATATTACTATTT
65 ATTTATTACTCCAACCGAAATGAAAAGATATTACTATTT
3388844 TCAATATTAA
Statistics
Matches: 316, Mismatches: 34, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
119 3 0.01
120 97 0.31
121 2 0.01
123 4 0.01
124 1 0.00
125 2 0.01
129 3 0.01
130 55 0.17
131 120 0.38
132 29 0.09
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (131 bp):
GAAAACCATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAGTCA
TTTATTACTCCAACCGAAATGAAAAGATATTACTATTTCTTCTTAAAATTCAATATTGATTCGAG
A
Found at i:3388817 original size:120 final size:120
Alignment explanation
Indices: 3388603--3388859 Score: 417
Period size: 120 Copynumber: 2.1 Consensus size: 120
3388593 CTTCTTAAAA
*
3388603 TTCAATATTGATTCGAGAGAAAACCATAATATATAATTATTTCCAATCGAGAATAAATGACCTCT
1 TTCAATATTAATTCGAGAGAAAACCATAATATATAATTATTTCCAATCGAGAATAAATGACCTCT
* * *
3388668 CATGCCTTTAAGCAGTCATTTATTACTCCAACCAAAATGAAAAGATATTACTATT
66 CATACCTTTAAGCAATCATTGATTACTCCAACCAAAATGAAAAGATATTACTATT
* * *
3388723 TTCAATAATAATTCGAGAGAAAACCATAATATCTAATTATTTTCAATCGAGAAT-AATAGACCTC
1 TTCAATATTAATTCGAGAGAAAACCATAATATATAATTATTTCCAATCGAGAATAAAT-GACCTC
* *
3388787 TCATACCTTTAAGCAATCATTGATTTCTCCAACCGAAATGAAAAGATATTACTATT
65 TCATACCTTTAAGCAATCATTGATTACTCCAACCAAAATGAAAAGATATTACTATT
3388843 TTCAATATTAATTCGAG
1 TTCAATATTAATTCGAG
3388860 TGTTATTTAT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
119 3 0.02
120 123 0.98
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (120 bp):
TTCAATATTAATTCGAGAGAAAACCATAATATATAATTATTTCCAATCGAGAATAAATGACCTCT
CATACCTTTAAGCAATCATTGATTACTCCAACCAAAATGAAAAGATATTACTATT
Found at i:3390905 original size:3 final size:3
Alignment explanation
Indices: 3390897--3390994 Score: 162
Period size: 3 Copynumber: 32.7 Consensus size: 3
3390887 TGAAAAACAA
3390897 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
3390945 AAT AAT AAT AAT -AT ATT AGT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
3390990 AAT AA
1 AAT AA
3390995 CAACAACAAT
Statistics
Matches: 90, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
2 2 0.02
3 86 0.96
4 2 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:3392186 original size:14 final size:14
Alignment explanation
Indices: 3392167--3392227 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
3392157 CTGTTATTTT
3392167 AATTTCAGCCTTTA
1 AATTTCAGCCTTTA
**
3392181 AATTTCAGTATTTA
1 AATTTCAGCCTTTA
* *
3392195 CATTCCAGTCCTTTA
1 AATTTCAG-CCTTTA
* *
3392210 AATTCCAG-TTTTA
1 AATTTCAGCCTTTA
3392223 AATTT
1 AATTT
3392228 TCTGTACTGT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
13 8 0.22
14 18 0.49
15 11 0.30
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.46
Consensus pattern (14 bp):
AATTTCAGCCTTTA
Found at i:3392214 original size:15 final size:14
Alignment explanation
Indices: 3392176--3392226 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
3392166 TAATTTCAGC
*
3392176 CTTTAAATTTCAGT
1 CTTTAAATTCCAGT
* *
3392190 ATTTACATTCCAGT
1 CTTTAAATTCCAGT
3392204 CCTTTAAATTCCAGT
1 -CTTTAAATTCCAGT
3392219 -TTTAAATT
1 CTTTAAATT
3392227 TTCTGTACTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 8 0.26
14 11 0.35
15 12 0.39
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (14 bp):
CTTTAAATTCCAGT
Found at i:3392586 original size:137 final size:138
Alignment explanation
Indices: 3392435--3392823 Score: 566
Period size: 138 Copynumber: 2.8 Consensus size: 138
3392425 AGATCCTTTT
* *
3392435 AATTTAGCCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCGCTTATACTCGAGGTTCCATTTT
1 AATTTAGCCCTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTTT
* ** * * *
3392500 AATTATTTGAATCAATAATCAATTAAAATTAATTAGGACTAATATTAG-GCATTCACTTTAGG-C
66 AATTATTCGAATCAATAATTGATTAAAATGAATTAGGATTAATATTAGAACATTCACTTTAGGTC
3392563 TTAATTTCA
131 -TAATTTCA
* * * * *
3392572 AATTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGTTTCTAGCTTCTGCTCGAGGTTCCATTTT
1 AATTTAGCCCTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTTT
* * * *
3392637 AATTATTCGAATCAATAATTGGTTAAAATGAATTACGATTAATGTTAGAACCTTCACTTTAGGTC
66 AATTATTCGAATCAATAATTGATTAAAATGAATTAGGATTAATATTAGAACATTCACTTTAGGTC
3392702 TAATTTCA
131 TAATTTCA
* * *
3392710 TATTTAACCCTTTAATTTAGGAGAATTTTTAATTCGGTCCTCGCTTATGCTCGAGGTTCCATTTT
1 AATTTAGCCCTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTTT
*
3392775 AATTATTCGAATCAATAATTGATTAAAATGAATTAGTATTAATATTAGA
66 AATTATTCGAATCAATAATTGATTAAAATGAATTAGGATTAATATTAGA
3392824 GCCTACATTT
Statistics
Matches: 221, Mismatches: 29, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
137 98 0.44
138 122 0.55
139 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (138 bp):
AATTTAGCCCTTTAATTTAGGAGAATTTTTAATTTGGTCCTCGCTTATGCTCGAGGTTCCATTTT
AATTATTCGAATCAATAATTGATTAAAATGAATTAGGATTAATATTAGAACATTCACTTTAGGTC
TAATTTCA
Found at i:3395592 original size:16 final size:16
Alignment explanation
Indices: 3395567--3395620 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
3395557 TAGTTAAAAT
*
3395567 TATTTTATATTTTTAA
1 TATTTAATATTTTTAA
*
3395583 TATTTAATA-TTTAATA
1 TATTTAATATTTTTA-A
3395599 TATTTAATATTTTATAA
1 TATTTAATATTTT-TAA
3395616 T-TTTA
1 TATTTA
3395621 TGAGTTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 4 0.12
16 22 0.69
17 5 0.16
18 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTAATATTTTTAA
Found at i:3395599 original size:23 final size:23
Alignment explanation
Indices: 3395567--3395610 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3395557 TAGTTAAAAT
* *
3395567 TATTTTATATTTTTAATATTTAA
1 TATTTAATATATTTAATATTTAA
3395590 TATTTAATATATTTAATATTT
1 TATTTAATATATTTAATATTT
3395611 TATAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTAATATATTTAATATTTAA
Found at i:3396931 original size:44 final size:44
Alignment explanation
Indices: 3396883--3397022 Score: 280
Period size: 44 Copynumber: 3.2 Consensus size: 44
3396873 TAATTAATTG
3396883 TTTATATCTTACACGTTTTAAATTATTTCCATCGTTTAGTTTGA
1 TTTATATCTTACACGTTTTAAATTATTTCCATCGTTTAGTTTGA
3396927 TTTATATCTTACACGTTTTAAATTATTTCCATCGTTTAGTTTGA
1 TTTATATCTTACACGTTTTAAATTATTTCCATCGTTTAGTTTGA
3396971 TTTATATCTTACACGTTTTAAATTATTTCCATCGTTTAGTTTGA
1 TTTATATCTTACACGTTTTAAATTATTTCCATCGTTTAGTTTGA
3397015 TTTATATC
1 TTTATATC
3397023 AATTGCTTAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 96 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.53
Consensus pattern (44 bp):
TTTATATCTTACACGTTTTAAATTATTTCCATCGTTTAGTTTGA
Found at i:3396943 original size:25 final size:25
Alignment explanation
Indices: 3396915--3396988 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
3396905 TTATTTCCAT
3396915 CGTTTAGTTTGATTTATATCTTACA
1 CGTTTAGTTTGATTTATATCTTACA
** *
3396940 CG--T--TTT-AAAT-TAT-TTCCA
1 CGTTTAGTTTGATTTATATCTTACA
3396958 TCGTTTAGTTTGATTTATATCTTACA
1 -CGTTTAGTTTGATTTATATCTTACA
3396984 CGTTT
1 CGTTT
3396989 TAAATTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 16
0.61 0.11 0.28
Matches are distributed among these distances:
18 4 0.11
19 5 0.14
20 2 0.06
21 4 0.11
23 4 0.11
24 2 0.06
25 10 0.29
26 4 0.11
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.53
Consensus pattern (25 bp):
CGTTTAGTTTGATTTATATCTTACA
Found at i:3402032 original size:14 final size:14
Alignment explanation
Indices: 3402013--3402043 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3402003 CCTTGTTGCA
3402013 TTTGCATCCCACAT
1 TTTGCATCCCACAT
*
3402027 TTTGCATTCCACAT
1 TTTGCATCCCACAT
3402041 TTT
1 TTT
3402044 ACACTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.45
Consensus pattern (14 bp):
TTTGCATCCCACAT
Found at i:3404806 original size:31 final size:31
Alignment explanation
Indices: 3404739--3404798 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
3404729 CAATTTAAGG
*
3404739 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATGATATTTGGACTTGAATTGAATTTA
3404770 CAAAATG-TATTTGGACTT-AATTGAATTTA
1 CAAAATGATATTTGGACTTGAATTGAATTTA
3404799 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATGATATTTGGACTTGAATTGAATTTA
Found at i:3405022 original size:21 final size:21
Alignment explanation
Indices: 3404996--3405037 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3404986 ATTTGAATAT
*
3404996 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3405017 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3405038 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3405363 original size:34 final size:32
Alignment explanation
Indices: 3405324--3405393 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
3405314 TTTTGTAAAG
*
3405324 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3405358 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3405390 GGGA
1 GGGA
3405394 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3405920 original size:17 final size:17
Alignment explanation
Indices: 3405900--3405934 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3405890 ATATTTATGC
*
3405900 ACACAAATATAAAATAA
1 ACACAAATAAAAAATAA
*
3405917 ACACGAATAAAAAATAA
1 ACACAAATAAAAAATAA
3405934 A
1 A
3405935 AATAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.14
Consensus pattern (17 bp):
ACACAAATAAAAAATAA
Found at i:3408720 original size:20 final size:20
Alignment explanation
Indices: 3408697--3408744 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3408687 CTTCGGAATG
* *
3408697 TTCTAGAAAATTCTACACTT
1 TTCTAGAAAACTCTACAATT
* *
3408717 TTCTAGAAAGCTCTAGAATT
1 TTCTAGAAAACTCTACAATT
3408737 TTCTAGAA
1 TTCTAGAA
3408745 CCTCTCCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
TTCTAGAAAACTCTACAATT
Found at i:3413990 original size:47 final size:47
Alignment explanation
Indices: 3413939--3414083 Score: 115
Period size: 47 Copynumber: 3.1 Consensus size: 47
3413929 TCATCTGTTT
3413939 GAGTAGTTAAATTTCTTGGCTACATGATCATCTTTGATCCTAAGCTG
1 GAGTAGTTAAATTTCTTGGCTACATGATCATCTTTGATCCTAAGCTG
** * ** * *
3413986 GAGTA--T--CCTACTTGG--A-ATGAGTCATATCCTTTGATCCTCTGTTT
1 GAGTAGTTAAATTTCTTGGCTACATGA-TC--AT-CTTTGATCCTAAGCTG
* * *
3414030 GAGTAGTTAAATTTCCTGGCTCCATGATCATCTTTGATCCTAAACTG
1 GAGTAGTTAAATTTCTTGGCTACATGATCATCTTTGATCCTAAGCTG
3414077 GAGTAGT
1 GAGTAGT
3414084 ATATTTTGAA
Statistics
Matches: 70, Mismatches: 17, Indels: 22
0.64 0.16 0.20
Matches are distributed among these distances:
40 4 0.06
41 3 0.04
43 8 0.11
44 17 0.24
45 1 0.01
46 1 0.01
47 23 0.33
48 7 0.10
50 2 0.03
51 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (47 bp):
GAGTAGTTAAATTTCTTGGCTACATGATCATCTTTGATCCTAAGCTG
Found at i:3414057 original size:91 final size:91
Alignment explanation
Indices: 3413902--3414081 Score: 315
Period size: 91 Copynumber: 2.0 Consensus size: 91
3413892 CAGATACTTG
* *
3413902 CTACTTGGAATGGGTCATATCCTTTGATCATCTGTTTGAGTAGTTAAATTTCTTGGCTACATGAT
1 CTACTTGGAATGAGTCATATCCTTTGATCATCTGTTTGAGTAGTTAAATTTCCTGGCTACATGAT
*
3413967 CATCTTTGATCCTAAGCTGGAGTATC
66 CATCTTTGATCCTAAACTGGAGTATC
* *
3413993 CTACTTGGAATGAGTCATATCCTTTGATCCTCTGTTTGAGTAGTTAAATTTCCTGGCTCCATGAT
1 CTACTTGGAATGAGTCATATCCTTTGATCATCTGTTTGAGTAGTTAAATTTCCTGGCTACATGAT
3414058 CATCTTTGATCCTAAACTGGAGTA
66 CATCTTTGATCCTAAACTGGAGTA
3414082 GTATATTTTG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (91 bp):
CTACTTGGAATGAGTCATATCCTTTGATCATCTGTTTGAGTAGTTAAATTTCCTGGCTACATGAT
CATCTTTGATCCTAAACTGGAGTATC
Found at i:3414385 original size:35 final size:35
Alignment explanation
Indices: 3414332--3414401 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
3414322 GTTAGACAAG
3414332 ATGATGTGTCGACATCGATCATATCATATAGAGAT
1 ATGATGTGTCGACATCGATCATATCATATAGAGAT
* **
3414367 ATGATGTGTTGATTTCGATCATATCATATAGAGAT
1 ATGATGTGTCGACATCGATCATATCATATAGAGAT
3414402 CTTAGCTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (35 bp):
ATGATGTGTCGACATCGATCATATCATATAGAGAT
Found at i:3424319 original size:23 final size:23
Alignment explanation
Indices: 3424287--3424339 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3424277 CATCCCGACT
3424287 TTATTATTATTAATTAATTA-ATG
1 TTATTATTATTAATT-ATTACATG
*
3424310 TTATTTTTATTAATTATTACATG
1 TTATTATTATTAATTATTACATG
*
3424333 TTTTTAT
1 TTATTAT
3424340 AATAAGCCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
TTATTATTATTAATTATTACATG
Found at i:3425368 original size:110 final size:108
Alignment explanation
Indices: 3425228--3425476 Score: 269
Period size: 109 Copynumber: 2.3 Consensus size: 108
3425218 GGAAAATCAC
* *
3425228 GTTTAGAT-CCCCTAACTTTGTGCGTGTTTTTTACAAAATAGTCACTTGTAG-GGAATAAAATTG
1 GTTTAG-TCCCCCTAACTTT-AGCGTGTTTTTTACAAAATAGTCACCTGTAGAGG-ATAAAATTG
*
3425291 ATATTTACCCAT-TTTTTGTGTATGCTTTATA-ATTTT-GGTATATTTGTT
63 ATATTTACCCATCTTTATGTGTA----TTATACATTTTAGGT-TATTTGTT
* *** *
3425339 GTTTAGTCCCCCTAACTTTAGCGTG-TTTTTGCATGTTAGTCACCTGTAGAGGCTAAAATTGATA
1 GTTTAGTCCCCCTAACTTTAGCGTGTTTTTTACAAAATAGTCACCTGTAGAGGATAAAATTGATA
3425403 TTTACCCATCTTTATGTGTATTATACATTTTAGGGTTATTTGTT
66 TTTACCCATCTTTATGTGTATTATACATTTTA-GGTTATTTGTT
**
3425447 GTTTAGTCCCTCC-ATGTTTAGCGTGTTTTT
1 GTTTAGTCCC-CCTAACTTTAGCGTGTTTTT
3425477 ATTTTGGTCA
Statistics
Matches: 120, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
106 5 0.04
107 5 0.04
108 28 0.23
109 48 0.40
110 17 0.14
111 17 0.14
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.46
Consensus pattern (108 bp):
GTTTAGTCCCCCTAACTTTAGCGTGTTTTTTACAAAATAGTCACCTGTAGAGGATAAAATTGATA
TTTACCCATCTTTATGTGTATTATACATTTTAGGTTATTTGTT
Found at i:3425396 original size:109 final size:107
Alignment explanation
Indices: 3425266--3425476 Score: 270
Period size: 109 Copynumber: 1.9 Consensus size: 107
3425256 TTTTACAAAA
* *
3425266 TAGTCACTTGTAGGGAATAAAATTGATATTTACCCAT-TTTTTGTGTATGCTTTATA-ATTTT-G
1 TAGTCACCTGTAGGGAATAAAATTGATATTTACCCATCTTTATGTGTA----TTATACATTTTAG
3425328 GTATATTTGTTGTTTAGTCCC-CCTAACTTTAGCGTGTTTTTGCATGT
62 GT-TATTTGTTGTTTAGTCCCTCC-AACTTTAGCGTGTTTTTGCATGT
*
3425375 TAGTCACCTGTAGAGG-CTAAAATTGATATTTACCCATCTTTATGTGTATTATACATTTTAGGGT
1 TAGTCACCTGTAG-GGAATAAAATTGATATTTACCCATCTTTATGTGTATTATACATTTTA-GGT
**
3425439 TATTTGTTGTTTAGTCCCTCCATGTTTAGCGTGTTTTT
64 TATTTGTTGTTTAGTCCCTCCAACTTTAGCGTGTTTTT
3425477 ATTTTGGTCA
Statistics
Matches: 91, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
106 5 0.05
107 5 0.05
108 33 0.36
109 37 0.41
110 11 0.12
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.47
Consensus pattern (107 bp):
TAGTCACCTGTAGGGAATAAAATTGATATTTACCCATCTTTATGTGTATTATACATTTTAGGTTA
TTTGTTGTTTAGTCCCTCCAACTTTAGCGTGTTTTTGCATGT
Found at i:3426534 original size:22 final size:23
Alignment explanation
Indices: 3426506--3426566 Score: 115
Period size: 22 Copynumber: 2.7 Consensus size: 23
3426496 TTCTCAATTG
3426506 AAAATCATTAGATATTTCCTT-A
1 AAAATCATTAGATATTTCCTTAA
3426528 AAAATCATTAGATATTTCCTTAA
1 AAAATCATTAGATATTTCCTTAA
3426551 AAAATCATTAGATATT
1 AAAATCATTAGATATT
3426567 ATCGTTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 21 0.55
23 17 0.45
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.39
Consensus pattern (23 bp):
AAAATCATTAGATATTTCCTTAA
Found at i:3426724 original size:131 final size:131
Alignment explanation
Indices: 3426552--3426837 Score: 457
Period size: 131 Copynumber: 2.2 Consensus size: 131
3426542 TTTCCTTAAA
* * *
3426552 AAATCATTAGATATTATCGTTTTCACTCGAATTGATATTGAATTTTAAGACGGAATAGTGATATC
1 AAATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAAGACGAAATAGTGATAAC
* * * *
3426617 TCTTCATTTCGATTGGAGTAATAAATG-TCTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATT
66 TCTTCATTTCGATTGGAATAATAAATGAT-TACTTTAAGGCATAAGAGGTCATTTATTCTCGATT
*
3426681 GG
130 AG
3426683 AAATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAAGACGAAATAGTGATAAC
1 AAATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAAGACGAAATAGTGATAAC
*
3426748 TCTTCATTTTGATTGGAATAATAAATGATTACTTTAAGGCATAAGAGGTCATTTATTCTCGATTA
66 TCTTCATTTCGATTGGAATAATAAATGATTACTTTAAGGCATAAGAGGTCATTTATTCTCGATTA
3426813 G
131 G
* *
3426814 AAATAATTAGATATTATCATTTTC
1 AAATCATTAGATATTATCGTTTTC
3426838 TCTCTTAAAA
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 142 0.99
132 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (131 bp):
AAATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAAGACGAAATAGTGATAAC
TCTTCATTTCGATTGGAATAATAAATGATTACTTTAAGGCATAAGAGGTCATTTATTCTCGATTA
G
Found at i:3427677 original size:31 final size:29
Alignment explanation
Indices: 3427629--3427687 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
3427619 GTTTCAAAAT
3427629 TATAATTATGAAAAAAATATATTAATTTATA
1 TATAATTATGAAAAAAATAT-TT-ATTTATA
*
3427660 TATATTTAT-AAATAAAATATTTATTTAT
1 TATAATTATGAAA-AAAATATTTATTTAT
3427688 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 5 0.19
31 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATGAAAAAAATATTTATTTATA
Found at i:3427866 original size:116 final size:113
Alignment explanation
Indices: 3427652--3427873 Score: 268
Period size: 116 Copynumber: 1.9 Consensus size: 113
3427642 AAAATATATT
* * * *
3427652 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGGT
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGT
* *
3427717 GCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAATTAAAAC
66 GCCTTAAGACAGCTCATTTCTTCAATATT-AAAAATAAATAATTAAAAC
**
3427766 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCA
* ** **
3427831 GTTGTTTTAAGACTTC-CATTTCTT-AATATTGAAAAATAAATAA
63 GGTGCCTTAAGACAGCTCATTTCTTCAATATT-AAAAATAAATAA
3427874 ATATATATTA
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
114 10 0.11
115 23 0.25
116 41 0.45
117 17 0.19
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.39
Consensus pattern (113 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGT
GCCTTAAGACAGCTCATTTCTTCAATATTAAAAATAAATAATTAAAAC
Found at i:3429301 original size:3 final size:3
Alignment explanation
Indices: 3429295--3429364 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
3429285 AATAATTATT
* *
3429295 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
3429338 TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3429365 ATTAAGTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:3429340 original size:18 final size:18
Alignment explanation
Indices: 3429284--3429364 Score: 94
Period size: 18 Copynumber: 4.3 Consensus size: 18
3429274 TTGGGCTTTG
3429284 TAATAATTATTTAATAATAA
1 TAATAA-TATTT-ATAATAA
*
3429304 T-ATAATATATATAATATAA
1 TAATAATATTTAT-A-ATAA
3429323 TAATAATATTTATAATAA
1 TAATAATATTTATAATAA
3429341 TAATAATAATTT-TAATAA
1 TAATAAT-ATTTATAATAA
3429359 TAATAA
1 TAATAA
3429365 ATTAAGTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.04
18 28 0.51
19 14 0.25
20 11 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATATTTATAATAA
Found at i:3429619 original size:76 final size:76
Alignment explanation
Indices: 3429517--3430381 Score: 1525
Period size: 76 Copynumber: 11.4 Consensus size: 76
3429507 GAGGTCATAA
** * * *
3429517 AAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
3429582 AGGCTTTTTGA
66 AGGCTTTTTGG
*
3429593 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
3429658 AGGCTTTTTGA
66 AGGCTTTTTGG
3429669 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
3429734 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
3429745 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAGAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
3429810 AGGCTTTTTGG
66 AGGCTTTTTGG
*
3429821 AAACATCATGCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
3429886 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
3429897 AAACATCAGGCACTATAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAGAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
3429962 AGGGTTTTTGG
66 AGGCTTTTTGG
* * *
3429973 AAACATCATGCACTATAGGACTTACAGATTA-CCTAAGGCTTTGAAAACATCAAAAACCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
3430037 AGGCTTTTTGG
66 AGGCTTTTTGG
3430048 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
3430113 AGGCTTTTTGG
66 AGGCTTTTTGG
3430124 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
3430189 AGGCTTTTTGG
66 AGGCTTTTTGG
3430200 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
3430265 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
3430276 AAAAATTATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
3430341 AGGCTTTTTGG
66 AGGCTTTTTGG
*
3430352 AAACATCATACACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
3430382 TGGTAAATAG
Statistics
Matches: 755, Mismatches: 33, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
75 69 0.09
76 686 0.91
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:3431502 original size:50 final size:50
Alignment explanation
Indices: 3431447--3431601 Score: 150
Period size: 54 Copynumber: 3.0 Consensus size: 50
3431437 ATAACTGGTT
* * *
3431447 TGTAAAACATTTGACAACACATTC-TTCATCTCATGTGGTTTCAGCTCAGA
1 TGTAAAACATTTGACAACACATTCATCCATCTC-CGTGGCTTCAGCTCAGA
** * * *
3431497 TGTAAAACACCTGACAACACATTCATCCTTTTCCGTGGCTTCTGCTCAGA
1 TGTAAAACATTTGACAACACATTCATCCATCTCCGTGGCTTCAGCTCAGA
* * * *
3431547 TGTTCATAAAGCATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA
1 TG-T-A-AAA-CATTTGACAACACATTCATCCATCTCCGTGGCTTCAGCTCAGA
3431601 T
1 T
3431602 TTCTCAATCA
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 38 0.43
51 6 0.07
52 1 0.01
53 3 0.03
54 41 0.46
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.34
Consensus pattern (50 bp):
TGTAAAACATTTGACAACACATTCATCCATCTCCGTGGCTTCAGCTCAGA
Found at i:3437960 original size:7 final size:7
Alignment explanation
Indices: 3437926--3437967 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
3437916 ATAAAAGTAT
3437926 AAATGCA
1 AAATGCA
* *
3437933 CAATGAA
1 AAATGCA
3437940 AAATGCA
1 AAATGCA
3437947 AAGATGCA
1 AA-ATGCA
3437955 AAATGC-
1 AAATGCA
3437961 AAATGCA
1 AAATGCA
3437968 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:3439478 original size:16 final size:16
Alignment explanation
Indices: 3439457--3439487 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3439447 AATACTTGAA
3439457 AATAAAATAAAATATT
1 AATAAAATAAAATATT
*
3439473 AATAAAATAATATAT
1 AATAAAATAAAATAT
3439488 ATAAATACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAAAATAAAATATT
Found at i:3439493 original size:24 final size:22
Alignment explanation
Indices: 3439433--3439509 Score: 79
Period size: 24 Copynumber: 3.4 Consensus size: 22
3439423 ACAGAAAAAT
3439433 AAATAATGAAATAAAATACT-TGA
1 AAATAAT--AATAAAATACTATGA
*
3439456 AAATAA-AATAAAATATTAAT-A
1 AAATAATAATAAAATACT-ATGA
3439477 AAATAATATATATAAATACTATGA
1 AAATAATA-ATA-AAATACTATGA
3439501 AAATAATAA
1 AAATAATAA
3439510 GTATATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
20 10 0.22
21 7 0.15
22 2 0.04
23 12 0.26
24 15 0.33
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.29
Consensus pattern (22 bp):
AAATAATAATAAAATACTATGA
Found at i:3439529 original size:28 final size:27
Alignment explanation
Indices: 3439478--3439531 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
3439468 ATATTAATAA
*
3439478 AATAATATATATAAATACTATGAAAAT
1 AATAATATATATAAAAACTATGAAAAT
* *
3439505 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAACTATGAAAA
3439532 GAAAGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (27 bp):
AATAATATATATAAAAACTATGAAAAT
Found at i:3440047 original size:31 final size:29
Alignment explanation
Indices: 3439999--3440057 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
3439989 GTTTCAAAAT
3439999 TATAATTATGAAAAAAATATATTAATTTATA
1 TATAATTATGAAAAAAATAT-TT-ATTTATA
*
3440030 TATATTTAT-AAATAAAATATTTATTTAT
1 TATAATTATGAAA-AAAATATTTATTTAT
3440058 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 5 0.19
31 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATAATTATGAAAAAAATATTTATTTATA
Found at i:3440372 original size:3 final size:3
Alignment explanation
Indices: 3440341--3440400 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
3440331 TATTTATATA
* * *
3440341 AAT AAT AAA AAT AAA AAT AAT GA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3440388 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
3440401 TTGCAAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3441699 original size:3 final size:3
Alignment explanation
Indices: 3441693--3441762 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
3441683 AATAATTATT
* *
3441693 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
3441736 TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3441763 ATTAAGTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:3441738 original size:18 final size:18
Alignment explanation
Indices: 3441682--3441762 Score: 94
Period size: 18 Copynumber: 4.3 Consensus size: 18
3441672 TTAGGCTTTG
3441682 TAATAATTATTTAATAATAA
1 TAATAA-TATTT-ATAATAA
*
3441702 T-ATAATATATATAATATAA
1 TAATAATATTTAT-A-ATAA
3441721 TAATAATATTTATAATAA
1 TAATAATATTTATAATAA
3441739 TAATAATAATTT-TAATAA
1 TAATAAT-ATTTATAATAA
3441757 TAATAA
1 TAATAA
3441763 ATTAAGTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.04
18 28 0.51
19 14 0.25
20 11 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATATTTATAATAA
Found at i:3445627 original size:23 final size:23
Alignment explanation
Indices: 3445597--3445655 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
3445587 CTCTTATAAA
3445597 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3445620 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3445643 TGCACCGTAGTGC
1 TGCACCGAAGTGC
3445656 TATATAAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3446159 original size:2 final size:2
Alignment explanation
Indices: 3446152--3446185 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3446142 AGTTTATCAC
3446152 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
3446186 CTCATAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3447482 original size:63 final size:62
Alignment explanation
Indices: 3447355--3447485 Score: 140
Period size: 63 Copynumber: 2.1 Consensus size: 62
3447345 ATAAAGTTTA
* * * * *
3447355 CATCGATGCACTACCTGTGCATCGGTACCCAAATCACCTTCGATGTTTAATCTTAAGGGGGTG
1 CATCGATGCACTAACTGTACATCGGTACCCAAAGCA-CTTCGATGTTTAATCTTAAGAGAGTG
* **
3447418 CATCGATGCACTAACTGTACATCGGTACACTCAAGGCA-TTCGATGTTTCTTCTTTAA-AGAGTG
1 CATCGATGCACTAACTGTACATCGGTAC-C-CAAAGCACTTCGATGTTTAATC-TTAAGAGAGTG
3447481 CATCG
1 CATCG
3447486 GTACACATTG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
63 47 0.82
64 5 0.09
65 5 0.09
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (62 bp):
CATCGATGCACTAACTGTACATCGGTACCCAAAGCACTTCGATGTTTAATCTTAAGAGAGTG
Found at i:3449475 original size:20 final size:20
Alignment explanation
Indices: 3449437--3449475 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3449427 GCATAAATTA
**
3449437 ATCCCTAACGACTCCAAATC
1 ATCCCTAACGACTAAAAATC
3449457 ATCCCTAACGACTAAAAAT
1 ATCCCTAACGACTAAAAAT
3449476 AGCCACAAAC
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:0.41, C:0.33, G:0.05, T:0.21
Consensus pattern (20 bp):
ATCCCTAACGACTAAAAATC
Found at i:3450753 original size:2 final size:2
Alignment explanation
Indices: 3450746--3450897 Score: 304
Period size: 2 Copynumber: 76.0 Consensus size: 2
3450736 ATATCCCCTA
3450746 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3450788 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3450830 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3450872 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
3450898 TTCATATATT
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 150 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3451372 original size:3 final size:3
Alignment explanation
Indices: 3451364--3451388 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3451354 ACTAATATAT
3451364 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
3451389 AACCCAATTC
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:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:3454299 original size:13 final size:13
Alignment explanation
Indices: 3454281--3454306 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3454271 AACCATCATG
3454281 AATTCATGTAATA
1 AATTCATGTAATA
3454294 AATTCATGTAATA
1 AATTCATGTAATA
3454307 CTGCTACAGT
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:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AATTCATGTAATA
Found at i:3454709 original size:465 final size:465
Alignment explanation
Indices: 3453838--3454764 Score: 1836
Period size: 465 Copynumber: 2.0 Consensus size: 465
3453828 GCACTGCTAC
3453838 AATACTGCTACAGTGACTTTCGTAAAATGTACATAAACTCATAAAAATTTAATCGTTCATTACTA
1 AATACTGCTACAGTGACTTTCGTAAAATGTACATAAACTCATAAAAATTTAATCGTTCATTACTA
*
3453903 TGCATTTATATTTACATAAATACGTTTAAAACATTACAAAACTCGATCACAGCATAAATACTTAA
66 TGCATTTATATTTACATAAATACGTTTAAAACATTACAAAACTAGATCACAGCATAAATACTTAA
3453968 TTTACCGACTTTGTTTACATGCCAACCTATTTTCACATAATAAGACATACTATTTAATCTACTTC
131 TTTACCGACTTTGTTTACATGCCAACCTATTTTCACATAATAAGACATACTATTTAATCTACTTC
3454033 TGATCTGACCTTCAAGTGGAGTTATGTTGTTTTGCTGAGCTTATTATAGGTCTCTCTGCTGTTCG
196 TGATCTGACCTTCAAGTGGAGTTATGTTGTTTTGCTGAGCTTATTATAGGTCTCTCTGCTGTTCG
3454098 GTACCTACGTGTAAAACACTTACACGCTAAGTCATCGACTTAGTGAGGCATAATAATAATAATAA
261 GTACCTACGTGTAAAACACTTACACGCTAAGTCATCGACTTAGTGAGGCATAATAATAATAATAA
3454163 TAATTAAATATAATAATGATGCCATAATAAGATGAAATGTAATGAAATCATCCATGCAATCCATG
326 TAATTAAATATAATAATGATGCCATAATAAGATGAAATGTAATGAAATCATCCATGCAATCCATG
3454228 TAATATGCATAACAATGTATCTTACCAATAATTTCTTCAAATTAACCATCATGAATTCATGTAAT
391 TAATATGCATAACAATGTATCTTACCAATAATTTCTTCAAATTAACCATCATGAATTCATGTAAT
3454293 AAATTCATGT
456 AAATTCATGT
3454303 AATACTGCTACAGTGACTTTCGTAAAATGTACATAAACTCATAAAAATTTAATCGTTCATTACTA
1 AATACTGCTACAGTGACTTTCGTAAAATGTACATAAACTCATAAAAATTTAATCGTTCATTACTA
3454368 TGCATTTATATTTACATAAATACGTTTAAAACATTACAAAACTAGATCACAGCATAAATACTTAA
66 TGCATTTATATTTACATAAATACGTTTAAAACATTACAAAACTAGATCACAGCATAAATACTTAA
3454433 TTTACCGACTTTGTTTACATGCCAACCTATTTTCACATAATAAGACATACTATTTAATCTACTTC
131 TTTACCGACTTTGTTTACATGCCAACCTATTTTCACATAATAAGACATACTATTTAATCTACTTC
3454498 TGATCTGACCTTCAAGTGGAGTTATGTTGTTTTGCTGAGCTTATTATAGGTCTCTCTGCTGTTCG
196 TGATCTGACCTTCAAGTGGAGTTATGTTGTTTTGCTGAGCTTATTATAGGTCTCTCTGCTGTTCG
3454563 GTACCTACGTGTAAAACACTTACACGCTAAGTCATCGACTTAGTGAGGCATAATAATAATAATAA
261 GTACCTACGTGTAAAACACTTACACGCTAAGTCATCGACTTAGTGAGGCATAATAATAATAATAA
3454628 TAATTAAATATAATAATGATGCCATAATAAGATGAAATGTAATGAAATCATCCATGCAATCCATG
326 TAATTAAATATAATAATGATGCCATAATAAGATGAAATGTAATGAAATCATCCATGCAATCCATG
3454693 TAATATGCATAACAATGTATCTTACCAATAATTTCTTCAAATTAACCATCATGAATTCATGTAAT
391 TAATATGCATAACAATGTATCTTACCAATAATTTCTTCAAATTAACCATCATGAATTCATGTAAT
*
3454758 AAGTTCA
456 AAATTCA
3454765 AAAGGTTTAA
Statistics
Matches: 460, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
465 460 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (465 bp):
AATACTGCTACAGTGACTTTCGTAAAATGTACATAAACTCATAAAAATTTAATCGTTCATTACTA
TGCATTTATATTTACATAAATACGTTTAAAACATTACAAAACTAGATCACAGCATAAATACTTAA
TTTACCGACTTTGTTTACATGCCAACCTATTTTCACATAATAAGACATACTATTTAATCTACTTC
TGATCTGACCTTCAAGTGGAGTTATGTTGTTTTGCTGAGCTTATTATAGGTCTCTCTGCTGTTCG
GTACCTACGTGTAAAACACTTACACGCTAAGTCATCGACTTAGTGAGGCATAATAATAATAATAA
TAATTAAATATAATAATGATGCCATAATAAGATGAAATGTAATGAAATCATCCATGCAATCCATG
TAATATGCATAACAATGTATCTTACCAATAATTTCTTCAAATTAACCATCATGAATTCATGTAAT
AAATTCATGT
Found at i:3457509 original size:30 final size:30
Alignment explanation
Indices: 3457474--3457780 Score: 177
Period size: 30 Copynumber: 10.2 Consensus size: 30
3457464 AATTAAGATA
*
3457474 AAAATATATTTTTATAGTTAAGATAAAAAT
1 AAAATATATTTTTATAGTTAAGATAAGAAT
* * *
3457504 AAAATATATTTCTA-AATTAAAATAAGAAT
1 AAAATATATTTTTATAGTTAAGATAAGAAT
* ** *
3457533 AAAATATATTAATATATTTTTTAAAATTAA-AAT
1 AAAATATATT--TTTA-TAGTTAAGA-TAAGAAT
3457566 AAAATATAGTTTTTCA-AGTTAAGATAAGAAT
1 AAAATATA-TTTTT-ATAGTTAAGATAAGAAT
* * * *
3457597 -AAATA-ATATTTAATAATTAAAGGTAATAAT
1 AAAATATAT-TTTTATAGTT-AAGATAAGAAT
* * * *
3457627 ATAATATATTTATTAT--TTTAGTTAATAAT
1 AAAATATATTT-TTATAGTTAAGATAAGAAT
* * * * *
3457656 ATAATATA-TGTAACAAGTTAAGATAAAAAT
1 AAAATATATTTTTA-TAGTTAAGATAAGAAT
* *
3457686 AAAATATATATTTTA-AGTTAAGGTAGGAAT
1 AAAATATAT-TTTTATAGTTAAGATAAGAAT
* * *
3457716 AAAATATA-ATTTATAATTTAAGATAAGATT
1 AAAATATATTTTTAT-AGTTAAGATAAGAAT
* *
3457746 AAAATATATATTT-TAGTTAATATAAGAAT
1 AAAATATATTTTTATAGTTAAGATAAGAAT
3457775 AAAATA
1 AAAATA
3457781 AATTCAATAA
Statistics
Matches: 216, Mismatches: 39, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
27 2 0.01
28 7 0.03
29 64 0.30
30 89 0.41
31 21 0.10
32 10 0.05
33 18 0.08
34 5 0.02
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (30 bp):
AAAATATATTTTTATAGTTAAGATAAGAAT
Found at i:3457542 original size:59 final size:59
Alignment explanation
Indices: 3457474--3457826 Score: 213
Period size: 59 Copynumber: 5.9 Consensus size: 59
3457464 AATTAAGATA
* * *
3457474 AAAATATATTTTTATAGTTAAGATAAAAATAAAATATATTTCTAAATTAAAATAAGAAT
1 AAAATATATTTTTATAGTTAAGATAAAAATAAAATATATTTTTAAGTTAAGATAAGAAT
* ** * *
3457533 AAAATATATTAATATATTTTTTAAAATTAAAATAAAATATAGTTTTTCAAGTTAAGATAAGAAT
1 AAAATATATT--TTTA-TAGTTAAGATAAAAATAAAATATA-TTTTT-AAGTTAAGATAAGAAT
* * * * * * * * *
3457597 -AAATA-ATATTTAATAATTAAAGGTAATAATATAATATATTTATT-ATTTTAGTTAATAAT
1 AAAATATAT-TTTTATAGTT-AAGATAAAAATAAAATATATTT-TTAAGTTAAGATAAGAAT
* * * * * *
3457656 ATAATATA-TGTAACAAGTTAAGATAAAAATAAAATATATATTTTAAGTTAAGGTAGGAAT
1 AAAATATATTTTTA-TAGTTAAGATAAAAATAAAATATAT-TTTTAAGTTAAGATAAGAAT
* * * * *
3457716 AAAATATA-ATTTATAATTTAAGATAAGATTAAAATATATATTTT-AGTTAATATAAGAAT
1 AAAATATATTTTTAT-AGTTAAGATAAAAATAAAATATAT-TTTTAAGTTAAGATAAGAAT
* ** *
3457775 AAAATA-AATTCAATAAGTT-A-A-AAAAACAAAATATATTTTTTAATGTTAAGAT
1 AAAATATATTTTTAT-AGTTAAGATAAAAATAAAATATA-TTTTTAA-GTTAAGAT
3457827 GTGATTTTAA
Statistics
Matches: 224, Mismatches: 52, Indels: 37
0.72 0.17 0.12
Matches are distributed among these distances:
56 15 0.07
57 3 0.01
58 9 0.04
59 69 0.31
60 60 0.27
61 22 0.10
62 22 0.10
63 10 0.04
64 14 0.06
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (59 bp):
AAAATATATTTTTATAGTTAAGATAAAAATAAAATATATTTTTAAGTTAAGATAAGAAT
Found at i:3457578 original size:25 final size:26
Alignment explanation
Indices: 3457543--3457597 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
3457533 AAAATATATT
*
3457543 AATATATTTTTTAAAATTAAAATAA-
1 AATATAGTTTTTAAAATTAAAATAAG
* * *
3457568 AATATAGTTTTTCAAGTTAAGATAAG
1 AATATAGTTTTTAAAATTAAAATAAG
3457594 AATA
1 AATA
3457598 AATAATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (26 bp):
AATATAGTTTTTAAAATTAAAATAAG
Found at i:3457615 original size:93 final size:94
Alignment explanation
Indices: 3457450--3457645 Score: 235
Period size: 93 Copynumber: 2.1 Consensus size: 94
3457440 CTTTTTATTC
* *
3457450 TAATA-ATATTTTAAAATTAAGATAAAAATATATTTTTATAGTTAAGATAAAAATAAAATATATT
1 TAATATATTTTTTAAAATTAAAATAAAAATATATTTTTATAGTTAAGATAAAAATAAAATATATT
*
3457514 TCTAAATTAAA-ATAAGAATAAAATATAT
66 TATAAATTAAAGATAAGAATAAAATATAT
*
3457542 TAATATATTTTTTAAAATTAAAAT-AAAATATAGTTTTTCA-AGTTAAGATAAGAAT-AAATAAT
1 TAATATATTTTTTAAAATTAAAATAAAAATATA-TTTTT-ATAGTTAAGATAAAAATAAAAT-AT
* * *
3457604 ATTTA-ATAATTAAAGGTAATAATATAATATAT
63 ATTTATA-AATTAAAGATAAGAATAAAATATAT
*
3457636 TTAT-TATTTT
1 TAATATATTTT
3457646 AGTTAATAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
92 18 0.20
93 54 0.60
94 18 0.20
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (94 bp):
TAATATATTTTTTAAAATTAAAATAAAAATATATTTTTATAGTTAAGATAAAAATAAAATATATT
TATAAATTAAAGATAAGAATAAAATATAT
Found at i:3457764 original size:89 final size:86
Alignment explanation
Indices: 3457474--3457780 Score: 235
Period size: 89 Copynumber: 3.4 Consensus size: 86
3457464 AATTAAGATA
* **
3457474 AAAATATATTTTTATAGTTAAGATAAAAATAAAATATAT-TTCTAAATTAAAATAAGAATAAAAT
1 AAAATATA-TTTT-TAGTTAAGATAAAAATAAAATATATATT-TTAATTAAGGTAAGAATAAAAT
* *
3457538 ATATTAATATATTTTTTAAAATTAA-AAT
63 ATATT--TATA--ATTTAAGA-TAAGAAT
* * *
3457566 AAAATATAGTTTTTCAAGTTAAGATAAGAAT-AAATA-ATATTTAATAATTAAAGGTAATAATAT
1 AAAATATA-TTTTT--AGTTAAGATAAAAATAAAATATATATTT--TAATT-AAGGTAAGAATAA
* * * *
3457629 AATATATTTATTATTTTAGTTAATAAT
60 AATATATTTATAATTTAAGATAAGAAT
* *** *
3457656 ATAATATATGTAACAAGTTAAGATAAAAATAAAATATATATTTTAAGTTAAGGTAGGAATAAAAT
1 AAAATATAT-T-TTTAGTTAAGATAAAAATAAAATATATATTTTAA-TTAAGGTAAGAATAAAAT
*
3457721 ATAATTTATAATTTAAGATAAGATT
63 AT-ATTTATAATTTAAGATAAGAAT
* *
3457746 AAAATATATATTTTAGTTAATATAAGAATAAAATA
1 AAAATATAT-TTTTAGTTAAGATAAAAATAAAATA
3457781 AATTCAATAA
Statistics
Matches: 170, Mismatches: 32, Indels: 29
0.74 0.14 0.13
Matches are distributed among these distances:
89 55 0.32
90 48 0.28
91 10 0.06
92 22 0.13
93 18 0.11
94 17 0.10
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (86 bp):
AAAATATATTTTTAGTTAAGATAAAAATAAAATATATATTTTAATTAAGGTAAGAATAAAATATA
TTTATAATTTAAGATAAGAAT
Found at i:3462564 original size:16 final size:16
Alignment explanation
Indices: 3462545--3462605 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
3462535 AAAAATAATT
3462545 TATAAAATTAATATAA
1 TATAAAATTAATATAA
*
3462561 TATAAAA-TAATTTAA
1 TATAAAATTAATATAA
* * *
3462576 GATTATATTAATATAA
1 TATAAAATTAATATAA
*
3462592 TATACAATTAATAT
1 TATAAAATTAATAT
3462606 TCTTATAATA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 11 0.31
16 24 0.69
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
TATAAAATTAATATAA
Found at i:3462594 original size:11 final size:11
Alignment explanation
Indices: 3462545--3462617 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 11
3462535 AAAAATAATT
*
3462545 TATAAAATTAA
1 TATAATATTAA
3462556 TATAATA-TAA
1 TATAATATTAA
*
3462566 AATAAT-TTAA
1 TATAATATTAA
* *
3462576 GATTATATTAA
1 TATAATATTAA
*
3462587 TATAATATACAA
1 TATAATAT-TAA
**
3462599 T-TAATATTCT
1 TATAATATTAA
3462609 TATAATATT
1 TATAATATT
3462618 TTATAATTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
10 16 0.33
11 29 0.60
12 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (11 bp):
TATAATATTAA
Found at i:3462953 original size:7 final size:7
Alignment explanation
Indices: 3462943--3462977 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
3462933 TAAAAATAAT
3462943 TTTTTAA
1 TTTTTAA
3462950 TTTTTAA
1 TTTTTAA
3462957 TTTTTAA
1 TTTTTAA
*
3462964 TTTTAAA
1 TTTTTAA
*
3462971 GTTTTAA
1 TTTTTAA
3462978 ATTAATGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (7 bp):
TTTTTAA
Found at i:3472290 original size:20 final size:20
Alignment explanation
Indices: 3472253--3472295 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3472243 ATTCCACCAC
*
3472253 ATGCAACTATATGCTCCTAA
1 ATGCAACTACATGCTCCTAA
* *
3472273 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
3472293 ATG
1 ATG
3472296 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:3476143 original size:23 final size:21
Alignment explanation
Indices: 3476115--3476173 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 21
3476105 ACCTTCAGAG
3476115 GGGTATCGATACCACTATATAGA
1 GGGTATCGATACC-CTATAT-GA
*
3476138 GGGTATCGGTA-CC-ATATGA
1 GGGTATCGATACCCTATATGA
3476157 GGGTATCGATACCCTAT
1 GGGTATCGATACCCTAT
3476174 TTCGATTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 12 0.38
20 6 0.19
21 3 0.09
22 1 0.03
23 10 0.31
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (21 bp):
GGGTATCGATACCCTATATGA
Found at i:3479272 original size:18 final size:19
Alignment explanation
Indices: 3479249--3479287 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3479239 TTTAAATAGT
3479249 AATAAAAACTATTAAA-TA
1 AATAAAAACTATTAAAGTA
*
3479267 AATAAAAGCTATTAAAGTA
1 AATAAAAACTATTAAAGTA
3479286 AA
1 AA
3479288 AATAAGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AATAAAAACTATTAAAGTA
Found at i:3485868 original size:264 final size:264
Alignment explanation
Indices: 3485391--3485909 Score: 700
Period size: 264 Copynumber: 2.0 Consensus size: 264
3485381 TTAAGGGCGT
* *
3485391 CTTTGGTCGAGAATAAAATTGGTATGAAGAGTAACGCTCTTAAAAGGAAGAAGAAGAGCACGAGA
1 CTTTGGTCGAGAATAAAATTGGTATGAAGAGCAACACTCTTAAAAGGAAGAAGAAGAGCACGAGA
* * *
3485456 ATGCGAGTTTTATTGCAAAATGGCATAAGGGATGAGGCTATTCGAGGTTCTTCTGAGGGTGAGTT
66 ATGCGAGTTTTATTGCAAAATGGAAGAAGGGATGAGGCTATTCGAGGTTCTTCTGAGGGTGAGAT
* * * *
3485521 CTGTGTTGATCGGTCGGAGACACAAAATGAAGCGGTGGAATCGTTGGGTATCGGCTAGGCATTGG
131 CCGTGCTGATCGGTCGGAGACACAAAATGAAGCGGTGGAAACGTTGGGTATCGGCTAAGCATTGG
* * *
3485586 ATGTAATTATCACTGCGTCAAAAGAGGTTGCGATTCAAAGATTGGAGAAGAATGAGCTTTTGGGG
196 ACGTAATTATCACTGCGTCAAAAGAGGTTGCGATTCAAAGATTGAAGAAGAACGAGCTTTTGGGG
3485651 GTTC
261 GTTC
* * * ** *
3485655 CTTTGGTTGAGAATAAATTTTGTATGAAGAGCAACACTCTTAAAAGGAAGAAGAAGAGCGTGATA
1 CTTTGGTCGAGAATAAAATTGGTATGAAGAGCAACACTCTTAAAAGGAAGAAGAAGAGCACGAGA
* * * *
3485720 ATGCTAGTTTTATTGCAAAATGGAAGAAGGGATGAGGTTGTTCGAGG-TCTTTCTGGGGGTGAGA
66 ATGCGAGTTTTATTGCAAAATGGAAGAAGGGATGAGGCTATTCGAGGTTC-TTCTGAGGGTGAGA
* * *
3485784 TCCGTGCTGATCGGTTGGAGACACAAAATGAAGCGGTGGAAACGTTGGGTGTTGG-TGAAGCATT
130 TCCGTGCTGATCGGTCGGAGACACAAAATGAAGCGGTGGAAACGTTGGGTATCGGCT-AAGCATT
* * * * ** * * *
3485848 GGGCGTAGTTTTCGCTGCGTCGGAAGGGGTTGTGATTCAAAGGTTGAAGAAGAACGAGCTTT
194 GGACGTAATTATCACTGCGTCAAAAGAGGTTGCGATTCAAAGATTGAAGAAGAACGAGCTTT
3485910 CGAGTAAGCT
Statistics
Matches: 219, Mismatches: 34, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
263 3 0.01
264 216 0.99
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.27
Consensus pattern (264 bp):
CTTTGGTCGAGAATAAAATTGGTATGAAGAGCAACACTCTTAAAAGGAAGAAGAAGAGCACGAGA
ATGCGAGTTTTATTGCAAAATGGAAGAAGGGATGAGGCTATTCGAGGTTCTTCTGAGGGTGAGAT
CCGTGCTGATCGGTCGGAGACACAAAATGAAGCGGTGGAAACGTTGGGTATCGGCTAAGCATTGG
ACGTAATTATCACTGCGTCAAAAGAGGTTGCGATTCAAAGATTGAAGAAGAACGAGCTTTTGGGG
GTTC
Found at i:3492006 original size:32 final size:32
Alignment explanation
Indices: 3491965--3492031 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
3491955 CCACTGGTGC
3491965 CGCTCCCTTCTTTGCTTCCCTCTGATTACATG
1 CGCTCCCTTCTTTGCTTCCCTCTGATTACATG
3491997 CGCTCCCTTCTTTGCTTCCCTCTGATTACATG
1 CGCTCCCTTCTTTGCTTCCCTCTGATTACATG
3492029 CGC
1 CGC
3492032 ATGTGATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.09, C:0.39, G:0.13, T:0.39
Consensus pattern (32 bp):
CGCTCCCTTCTTTGCTTCCCTCTGATTACATG
Found at i:3492460 original size:23 final size:23
Alignment explanation
Indices: 3492425--3492472 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
3492415 ATCAAGTACA
*
3492425 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
3492448 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
3492471 AT
1 AT
3492473 TGACCTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:3492837 original size:198 final size:199
Alignment explanation
Indices: 3492494--3493190 Score: 819
Period size: 198 Copynumber: 3.5 Consensus size: 199
3492484 ATAAGTAAAT
* *
3492494 CGGTATATTTATATC-GGTAACATTGCAAATTTACCCATTACATTATAATTATCGGTTTCGATGT
1 CGGTATATTTATATCGGGT-ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
* * * * *
3492558 TTTTTGGATCGATACAATTT--GAAATGTATCGACACTTTATGCGTGCACCTCGTTAGGCATTCA
65 TTTTGGGATCAATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCA
* * *
3492621 TTCTGGAAATAAGTATCGACACAAACTTACA-AAGTGTAAATACATTATTCAGGCCTTTTTTCTC
129 TTCTGGAAATAAGTATCGACACAAA-TTACACAAGTGTAAATACATTATTCAGACATATTTTCTC
*
3492685 ATAAAAT
193 ATAAAAC
* * * *
3492692 CGGTATATTTCTATCGGGTACATTGTAAATTTACCTATCACATTGTAATTATCGGTTTCAATGTT
1 CGGTATATTTATATCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
*
3492757 TTTGGGATCTATACTTTTAATAAATGTATCGACACTTTATGCGTGCACC-CGTTTGGCATTCATT
66 TTTGGGATCAATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATT
* * * * *
3492821 ATGGAAA-AATGTATCGACACAAATTTA-ACAAGTGTTAATACTTTATGCTA-ACATACTTTCTC
131 CTGGAAATAA-GTATCGACACAAA-TTACACAAGTGTAAATACATTATTC-AGACATATTTTCTC
3492883 ATAAAAC
193 ATAAAAC
* * * * *** *
3492890 CGGTATATTTATATCGGTTACATTGTAAATTTACATATTATA-TACAAATTTAAAAGTATCGAT-
1 CGGTATATTTATATCGGGTACATTGTAAATTTACCTATTACATTA-TAA-TTATCGGTTTCGATG
3492953 TTTATTGGGATCAATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGGCATT
64 TTT-TTGGGATCAATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GGCATT
** * *
3493018 CATTCTGGACAATAAGTATCGACACAAATTACACAAGTGTCGATACATTATGT-TGACATGTTTT
127 CATTCTGGA-AATAAGTATCGACACAAATTACACAAGTGTAAATACATTAT-TCAGACATATTTT
* *
3493082 CTAAT-TAAC
190 CTCATAAAAC
* * * *
3493091 CGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGATGTT
1 CGGTATATTTATATCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-T
3493156 TTTTGGG-TCAATACTTTTAGA-AAATGTATCGACAC
65 TTTTGGGATCAATACTTTTA-ATAAATGTATCGACAC
3493191 ATATTTAGGT
Statistics
Matches: 426, Mismatches: 53, Indels: 38
0.82 0.10 0.07
Matches are distributed among these distances:
197 7 0.02
198 175 0.41
199 88 0.21
200 41 0.10
201 66 0.15
202 47 0.11
203 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (199 bp):
CGGTATATTTATATCGGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
TTTGGGATCAATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATT
CTGGAAATAAGTATCGACACAAATTACACAAGTGTAAATACATTATTCAGACATATTTTCTCATA
AAAC
Found at i:3495293 original size:18 final size:18
Alignment explanation
Indices: 3495266--3495339 Score: 114
Period size: 18 Copynumber: 4.1 Consensus size: 18
3495256 TCCTCCTCAT
3495266 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
3495284 TTCC-CTCATCTTTTCTTC
1 TTCCTC-CATCTTTTCTTC
*
3495302 TTCCTCCATCTTTTATTC
1 TTCCTCCATCTTTTCTTC
*
3495320 TTCCTCCAGCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
3495338 TT
1 TT
3495340 TATATTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
17 1 0.02
18 49 0.96
19 1 0.02
ACGTcount: A:0.07, C:0.36, G:0.01, T:0.55
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:3495561 original size:33 final size:33
Alignment explanation
Indices: 3495524--3495623 Score: 182
Period size: 33 Copynumber: 3.0 Consensus size: 33
3495514 CTATCTTAAG
*
3495524 TTCACCCCTCAACACCTCAACTTCTTCCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
*
3495557 TTCACCCCTCAACACCTCAACTTCTTTCACCAA
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
3495590 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
3495623 T
1 T
3495624 CTATCTATTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.25, C:0.48, G:0.00, T:0.27
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:3495684 original size:21 final size:21
Alignment explanation
Indices: 3495660--3495701 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3495650 CTTATGCCTC
3495660 TCAAGTGTCTCTTCGACTCTT
1 TCAAGTGTCTCTTCGACTCTT
* *
3495681 TCAAGTTTTTCTTCGACTCTT
1 TCAAGTGTCTCTTCGACTCTT
3495702 GATTTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.26, G:0.12, T:0.48
Consensus pattern (21 bp):
TCAAGTGTCTCTTCGACTCTT
Found at i:3495802 original size:15 final size:15
Alignment explanation
Indices: 3495782--3495813 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3495772 CTCTGTTTTT
3495782 CCTCACTGGCATCCC
1 CCTCACTGGCATCCC
*
3495797 CCTCACTGTCATCCC
1 CCTCACTGGCATCCC
3495812 CC
1 CC
3495814 AATACAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.56, G:0.09, T:0.22
Consensus pattern (15 bp):
CCTCACTGGCATCCC
Found at i:3498444 original size:182 final size:182
Alignment explanation
Indices: 3498108--3498960 Score: 1288
Period size: 182 Copynumber: 4.7 Consensus size: 182
3498098 TACTCGTACT
* * * * * * * *
3498108 TATTAAAATATCAACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
*
3498173 GTTTTGTCATATTTTTAC-TGTTATATCGTTGTGGACCGATACATTGTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
3498237 TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAATTTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATACTTA
* *
3498289 TATTAAAGTATCGACACTTTAAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAAAGACCG
1 TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
*
3498354 GTTTTGTCATATTTTTACATGTTATATCGTTTTGGATCGATACATTGTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
3498419 TTATGGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATACTTA
* *
3498471 TATTAAAGTATCAACACTTTCAATATATTCGGTCGCTCTATATCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* * *
3498536 GCTTTGTCATATTTTTACATGTTATATCGTTTTGGATTGATACATTGTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
3498601 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTTACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATACTTA
* *
3498653 TATTAAAGTATCGACACTTTCAATATATTTGGTCGCTC-ATACCGGTTTTATCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* *
3498717 ATTTTGTCATATTTTTACATGTTATATCATTGTGGATCTG-TACATTGTTATAAAGTATCGACAC
66 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATC-GATACATTGTTATAAAGTATCGACAC
* * * *
3498781 TTTGTAGGCTCTAAAACTGCTTCTCTTTTAAATTCAC-AAAGGTAGATACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATACTTA
* * *
3498833 TATTAAAGTATCGACACTTTCAATATATTCGGTACCGCT-T-TACCGGTTTTGTCTTTTCGAGAT
1 TATTAAAGTATCGACACTTTCAATATATTCGGT--CGCTCTATACCGGTTTTGTCCTTTAGAGAC
* * *
3498896 CGATTTTGTCATATTTTTACATGTTATATTGATGTGGATCGATACAGTT-TTATAAAGTATCGAC
64 CGGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACA-TTGTTATAAAGTATCGAC
3498960 A
128 A
3498961 TAAACTGACA
Statistics
Matches: 618, Mismatches: 47, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
180 45 0.07
181 264 0.43
182 309 0.50
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATACTTA
Found at i:3498773 original size:363 final size:362
Alignment explanation
Indices: 3498108--3498960 Score: 1322
Period size: 363 Copynumber: 2.4 Consensus size: 362
3498098 TACTCGTACT
* *
3498108 TATTAAAATATCAACACTTTCAATATATCCGGTAGCGCT-TTACCGGTTTTGTCATTTCGAGACC
1 TATTAAAGTATCAACACTTTCAATATATTCGGT--CGCTCTTACCGGTTTTGTCATTTCGAGACC
*
3498172 GGTTTTGTCATATTTTTAC-TGTTATATCGTTGTGGACCGATACATTGTTATAAAGTATCGACAC
64 GGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACAC
* *
3498236 TTTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAATTTCGATACTTATATTAAAGTATC
129 TTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATACTTATATTAAAGTATC
* *
3498301 GACACTTTAAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAAAGACCGGTTTTGTCATAT
194 GACACTTTAAATATATTCGGTCGCTCTATACCGGTTTTATCCTTTAAAGACCGATTTTGTCATAT
* * *
3498366 TTTTACATGTTATATCGTTTTGGATCGATACATTGTTATAAAGTATCGACACTTTATGGGCGCTA
259 TTTTACATGTTATATCATTGTGGATCGATACATTGTTATAAAGTATCGACACTTTATAGGCGCTA
*
3498431 AAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
324 AAACTGCTTCTCTTTTAAATTCACAAAG-GTAGATACTTA
* * *
3498471 TATTAAAGTATCAACACTTTCAATATATTCGGTCGCTCTATATCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCAACACTTTCAATATATTCGGTCGCTCT-TACCGGTTTTGTCATTTCGAGACCG
* * *
3498536 GCTTTGTCATATTTTTACATGTTATATCGTTTTGGATTGATACATTGTTATAAAGTATCGACACT
65 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
3498601 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTTACAAAGTGTCGATACTTATATTAAAGTATCG
130 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATACTTATATTAAAGTATCG
* * *
3498666 ACACTTTCAATATATTTGGTCGCTC-ATACCGGTTTTATCCTTTAGAGACCGATTTTGTCATATT
195 ACACTTTAAATATATTCGGTCGCTCTATACCGGTTTTATCCTTTAAAGACCGATTTTGTCATATT
* *
3498730 TTTACATGTTATATCATTGTGGATCTG-TACATTGTTATAAAGTATCGACACTTTGTAGGCTCTA
260 TTTACATGTTATATCATTGTGGATC-GATACATTGTTATAAAGTATCGACACTTTATAGGCGCTA
3498794 AAACTGCTTCTCTTTTAAATTCACAAAGGTAGATACTTA
324 AAACTGCTTCTCTTTTAAATTCACAAAGGTAGATACTTA
* * *
3498833 TATTAAAGTATCGACACTTTCAATATATTCGGTACCGCT-TTACCGGTTTTGTCTTTTCGAGATC
1 TATTAAAGTATCAACACTTTCAATATATTCGGT--CGCTCTTACCGGTTTTGTCATTTCGAGACC
* * *
3498897 GATTTTGTCATATTTTTACATGTTATATTGATGTGGATCGATACAGTT-TTATAAAGTATCGACA
64 GGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACA-TTGTTATAAAGTATCGACA
3498961 TAAACTGACA
Statistics
Matches: 448, Mismatches: 35, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
361 4 0.01
362 118 0.26
363 194 0.43
364 132 0.29
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (362 bp):
TATTAAAGTATCAACACTTTCAATATATTCGGTCGCTCTTACCGGTTTTGTCATTTCGAGACCGG
TTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACTT
TATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATACTTATATTAAAGTATCGA
CACTTTAAATATATTCGGTCGCTCTATACCGGTTTTATCCTTTAAAGACCGATTTTGTCATATTT
TTACATGTTATATCATTGTGGATCGATACATTGTTATAAAGTATCGACACTTTATAGGCGCTAAA
ACTGCTTCTCTTTTAAATTCACAAAGGTAGATACTTA
Found at i:3501613 original size:18 final size:18
Alignment explanation
Indices: 3501583--3501619 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3501573 CAAAAATATC
3501583 AATTTTTTATATAATTTG
1 AATTTTTTATATAATTTG
3501601 AATTTCTTT-TATAATTTG
1 AATTT-TTTATATAATTTG
3501619 A
1 A
3501620 TTGATGATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (18 bp):
AATTTTTTATATAATTTG
Found at i:3504754 original size:56 final size:55
Alignment explanation
Indices: 3504626--3504821 Score: 209
Period size: 55 Copynumber: 3.5 Consensus size: 55
3504616 TGACGAGCCT
* * * *
3504626 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATC-TTCATAAAACGTGTCT
1 GCTCTCTATTCCTTCAGAG-AGTAT-AGACTCGAACAATCTTTAATAAAACGGGTCC
* * *
3504681 ACTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCTCTATTCCTTCAGAGAGTAT-AGACTCGAACAATCTTTAATAAAACGGGTCC
* * * *
3504737 GCTCTCTCTTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAAT-AAACAGGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAG-ACTCGAACAATCTTTAATAAAACGGGTCC
* * *
3504792 GCTCCCTATTCTTTCAGGGAGTATAGACTC
1 GCTCTCTATTCCTTCAGAGAGTATAGACTC
3504822 AATCTTCAAC
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
54 4 0.03
55 66 0.55
56 50 0.42
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (55 bp):
GCTCTCTATTCCTTCAGAGAGTATAGACTCGAACAATCTTTAATAAAACGGGTCC
Found at i:3505022 original size:51 final size:51
Alignment explanation
Indices: 3504733--3505129 Score: 553
Period size: 51 Copynumber: 7.9 Consensus size: 51
3504723 AATAAAACGG
* * * ** **
3504733 GTCCGCTCTCTCTTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* * *
3504788 GTCCGCTCCCTATTCTTTCAGGGAGTATA-GACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
3504838 GTCCCGCTCCCTA-TCCTTCAGAGAGTATA-GACTCAATCTTC-ACGAACTT
1 GT-CCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
3504887 GTCC-CTCCCTATTCATTCAGAGAGTATAGGACTC--TC-TCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
3504934 GTCCGCTCCCTA-T-CTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
3504983 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
3505034 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
3505085 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
3505130 AAACGAATTT
Statistics
Matches: 313, Mismatches: 19, Indels: 24
0.88 0.05 0.07
Matches are distributed among these distances:
46 21 0.07
47 22 0.07
48 26 0.08
49 37 0.12
50 41 0.13
51 137 0.44
54 4 0.01
55 25 0.08
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:3506473 original size:16 final size:16
Alignment explanation
Indices: 3506452--3506575 Score: 86
Period size: 16 Copynumber: 7.8 Consensus size: 16
3506442 CCTCCTTTTA
3506452 TTTCTCTTTTTTCATT
1 TTTCTCTTTTTTCATT
3506468 TTTCTCTTTTTTCATT
1 TTTCTCTTTTTTCATT
*
3506484 TTTC-ATTTTTTC---
1 TTTCTCTTTTTTCATT
*
3506496 -TTCCCTTTTTTCATTT
1 TTTCTCTTTTTTCA-TT
*
3506512 TTTCTTCTTTTTTC-CT
1 TTTC-TCTTTTTTCATT
3506528 TTTCGT-TTTTTCCATCATT
1 TTTC-TCTTTTT---TCATT
3506547 TTTCT-TTTTTCTCA-T
1 TTTCTCTTTTT-TCATT
3506562 TTTCTCATTTTTTC
1 TTTCTC-TTTTTTC
3506576 CTCTTTTATT
Statistics
Matches: 88, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
11 3 0.03
12 7 0.08
15 18 0.20
16 31 0.35
17 8 0.09
18 16 0.18
19 5 0.06
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (16 bp):
TTTCTCTTTTTTCATT
Found at i:3506477 original size:8 final size:8
Alignment explanation
Indices: 3506452--3506573 Score: 51
Period size: 8 Copynumber: 14.4 Consensus size: 8
3506442 CCTCCTTTTA
3506452 TTTCTCTT
1 TTTCTCTT
3506460 TTT-TCATT
1 TTTCTC-TT
3506468 TTTCTCTT
1 TTTCTCTT
3506476 TTT-TCATT
1 TTTCTC-TT
3506484 TTTCAT-TT
1 TTTC-TCTT
3506492 TTTCTTCCCTT
1 TTTC-T--CTT
3506503 TTT-TCATTT
1 TTTCTC--TT
3506512 TTTCTTCTT
1 TTTC-TCTT
*
3506521 TTT-TCCT
1 TTTCTCTT
3506528 TTTCGT-TT
1 TTTC-TCTT
3506536 TTTCCATCATT
1 TTT-C-TC-TT
3506547 TTTCT-TT
1 TTTCTCTT
*
3506554 TTTCTCAT
1 TTTCTCTT
3506562 TTTCTCATT
1 TTTCTC-TT
3506571 TTT
1 TTT
3506574 TCCTCTTTTA
Statistics
Matches: 89, Mismatches: 6, Indels: 37
0.67 0.05 0.28
Matches are distributed among these distances:
7 18 0.20
8 36 0.40
9 21 0.24
10 2 0.02
11 12 0.13
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.72
Consensus pattern (8 bp):
TTTCTCTT
Done.