Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008694.1 Hibiscus syriacus cultivar Beakdansim tig00111723_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: 1352611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:3160 original size:17 final size:16
Alignment explanation
Indices: 3130--3170 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
3120 CTGATGAGTG
3130 TTTTT-TTTTTCTTGA
1 TTTTTCTTTTTCTTGA
3145 TTTTTCTTTGTTCTTGA
1 TTTTTCTTT-TTCTTGA
*
3162 TTTTCCTTT
1 TTTTTCTTT
3171 CCCTTTGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.22
16 3 0.13
17 15 0.65
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTTTCTTTTTCTTGA
Found at i:6935 original size:341 final size:340
Alignment explanation
Indices: 6312--7005 Score: 1025
Period size: 341 Copynumber: 2.0 Consensus size: 340
6302 ATGATACTAT
*
6312 AAATATATTATTTTCTTCATCTCTTGGAACCCTAATTTTCTATAGCCTCCATTTATTTTTCTATT
1 AAATATAATATTTTCTTCATCTCTTGGAACCCTAATTTTCTATAGCCTCCATTTATTTTTCTATT
** * ** * *
6377 TTACCGTCAACCATGGCTCCTAAACCCACCACTGGGAGTGCAGCAGCAGCTGGGGAGCAATGCCG
66 TTACCACCAACCATGACTCCTAAACCCACCACAAGGAATGCAGCAACAGCTGGGGAGCAATGCCG
* * * ** * * *
6442 TGTAGCAGCGGTGACTGATCGGGATTCAATCGTGTTTTGTAGCTCTTTACTTGAGAAGGGAAGAT
131 TGTAGCAGCGGTAACCGATCAGGAAACAATCGTGTTTTATAGCTCCTTACTTGAGAAAGGAAGAT
6507 ACTATTTGATACGATTGGATGTTTAAATTTATTATTGCTATTTGGATTTGAACACAAGATGTTTG
196 ACTATTTGATACGATTGGATGTTTAAATTTATTATTGCTATTTGGATTTGAACACAAGATGTTTG
*
6572 ATGAAATGCTTTTCAATTTGATTTTGCTTTTATTATATGGTTATGTTGCTAGGATTTTTTGGAAA
261 ATGAAATGCTTTTCAATTTGATTTTGCTTTTATGATATGGTTATGTTGCTAGGATTTTTTGGAAA
6637 CCATTTTTAGAAATTA
326 CCATTTTTAGAAA-TA
* * * ** *
6653 AAATATAATATTTTCTTCATTTCTTGGAACCTTAATTTT-TGTATTCTCCTTTTATTTTTCTATT
1 AAATATAATATTTTCTTCATCTCTTGGAACCCTAATTTTCTATAGCCTCCATTTATTTTTCTATT
* * * * *
6717 TTACCACCGACCATGAC-CGCTAAACCCACCGTCAATGAATGCAGCAACATCTGGGGAGCAATGT
66 TTACCACCAACCATGACTC-CTAAACCCACC-ACAAGGAATGCAGCAACAGCTGGGGAGCAATGC
* *
6781 CGTGTAGCAGCGGTAACCGATCAGGAAACAATCGTGTTTTATAGTTCCTTACTTGAGAAATGAAG
129 CGTGTAGCAGCGGTAACCGATCAGGAAACAATCGTGTTTTATAGCTCCTTACTTGAGAAAGGAAG
* *
6846 ATACTATTTGATACGATTGGATGTTTGAATTTATTATTGCTATTTGGATTTGAACACAATATGTT
194 ATACTATTTGATACGATTGGATGTTTAAATTTATTATTGCTATTTGGATTTGAACACAAGATGTT
*
6911 TGATGAAATGCTTTTCAATTTGATTTTGCTTTTATGATATGGTTATGTTTCTAGGATTTTTTGGA
259 TGATGAAATGCTTTTCAATTTGATTTTGCTTTTATGATATGGTTATGTTGCTAGGATTTTTTGGA
*
6976 AACTATTTTTAGAAATA
324 AACCATTTTTAGAAATA
*
6993 AAA-ATAGTATTTT
1 AAATATAATATTTT
7006 GCATATTTAA
Statistics
Matches: 316, Mismatches: 35, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
339 10 0.03
340 50 0.16
341 256 0.81
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (340 bp):
AAATATAATATTTTCTTCATCTCTTGGAACCCTAATTTTCTATAGCCTCCATTTATTTTTCTATT
TTACCACCAACCATGACTCCTAAACCCACCACAAGGAATGCAGCAACAGCTGGGGAGCAATGCCG
TGTAGCAGCGGTAACCGATCAGGAAACAATCGTGTTTTATAGCTCCTTACTTGAGAAAGGAAGAT
ACTATTTGATACGATTGGATGTTTAAATTTATTATTGCTATTTGGATTTGAACACAAGATGTTTG
ATGAAATGCTTTTCAATTTGATTTTGCTTTTATGATATGGTTATGTTGCTAGGATTTTTTGGAAA
CCATTTTTAGAAATA
Found at i:8883 original size:3 final size:3
Alignment explanation
Indices: 8868--8901 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
8858 TCTACAAAAA
*
8868 TAT TAT T-T AAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
8902 ATACAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:11274 original size:12 final size:12
Alignment explanation
Indices: 11257--11294 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
11247 TGTTTCTTAC
11257 TCTTGTTGTGTT
1 TCTTGTTGTGTT
11269 TCTTGTTGTG--
1 TCTTGTTGTGTT
11279 TCTTGTTGTGTT
1 TCTTGTTGTGTT
11291 TCTT
1 TCTT
11295 TCTGTGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.00, C:0.11, G:0.24, T:0.66
Consensus pattern (12 bp):
TCTTGTTGTGTT
Found at i:11285 original size:22 final size:22
Alignment explanation
Indices: 11257--11319 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
11247 TGTTTCTTAC
11257 TCTTGTTGTGTTTCTTGT-TGTG
1 TCTTGTTGTGTTTCTT-TCTGTG
11279 TCTTGTTGTGTTTCTTTCTGTG
1 TCTTGTTGTGTTTCTTTCTGTG
*
11301 TCTTGCTGCTGTTT-TTTCT
1 TCTTGTTG-TGTTTCTTTCT
11320 TTGCAGGTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.84
23 5 0.13
ACGTcount: A:0.00, C:0.14, G:0.22, T:0.63
Consensus pattern (22 bp):
TCTTGTTGTGTTTCTTTCTGTG
Found at i:11831 original size:14 final size:13
Alignment explanation
Indices: 11808--11863 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 13
11798 GGGCTTTGTA
11808 AATAATA-ATATT
1 AATAATATATATT
11820 AATAATATAATATT
1 AATAATAT-ATATT
*
11834 -ATTATATATA-T
1 AATAATATATATT
*
11845 AATAATGTATATAT
1 AATAATATATAT-T
11859 AATAA
1 AATAA
11864 ACGTCCCTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.03
12 18 0.50
13 6 0.17
14 11 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
AATAATATATATT
Found at i:11831 original size:17 final size:17
Alignment explanation
Indices: 11809--11859 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
11799 GGCTTTGTAA
11809 ATAATAATATTA-ATAAT
1 ATAATAATATTATAT-AT
*
11826 ATAATATTATTATATAT
1 ATAATAATATTATATAT
*
11843 ATAATAAT-GTATATAT
1 ATAATAATATTATATAT
11859 A
1 A
11860 ATAAACGTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.27
17 20 0.67
18 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATAATAATATTATATAT
Found at i:12547 original size:20 final size:20
Alignment explanation
Indices: 12524--12568 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
12514 ACCCAAAAGA
12524 TTTACAAATTACCCGAAGGC
1 TTTACAAATTACCCGAAGGC
*
12544 TTTACAAATTACCCGGAGGC
1 TTTACAAATTACCCGAAGGC
12564 TTTAC
1 TTTAC
12569 TTTTCTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (20 bp):
TTTACAAATTACCCGAAGGC
Found at i:16328 original size:18 final size:18
Alignment explanation
Indices: 16286--16328 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
16276 TTGTTTACTA
*
16286 TTGCTTCCCTAAAAATGT
1 TTGCTTTCCTAAAAATGT
16304 TTGCTTTCCTAAAAATGT
1 TTGCTTTCCTAAAAATGT
16322 TTGCTTT
1 TTGCTTT
16329 GAATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.47
Consensus pattern (18 bp):
TTGCTTTCCTAAAAATGT
Found at i:20176 original size:22 final size:22
Alignment explanation
Indices: 20148--20204 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
20138 TGTTTCTTGC
*
20148 TCTTGTTGTGTTTCTTGCTGTG
1 TCTTGTTGTGTTTCTCGCTGTG
20170 TCTTGTTGTGTTTCTCGCTGTG
1 TCTTGTTGTGTTTCTCGCTGTG
* *
20192 TTTTGCTGTGTTT
1 TCTTGTTGTGTTT
20205 TTTTTTATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.00, C:0.14, G:0.26, T:0.60
Consensus pattern (22 bp):
TCTTGTTGTGTTTCTCGCTGTG
Found at i:20199 original size:10 final size:10
Alignment explanation
Indices: 20162--20205 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
20152 GTTGTGTTTC
*
20162 TTGCTGTGTC
1 TTGCTGTGTT
*
20172 TTGTTGTGTT
1 TTGCTGTGTT
20182 TCTCGCTGTGTT
1 T-T-GCTGTGTT
20194 TTGCTGTGTT
1 TTGCTGTGTT
20204 TT
1 TT
20206 TTTTTATAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.66
11 2 0.07
12 8 0.28
ACGTcount: A:0.00, C:0.14, G:0.27, T:0.59
Consensus pattern (10 bp):
TTGCTGTGTT
Found at i:20207 original size:12 final size:12
Alignment explanation
Indices: 20148--20204 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
20138 TGTTTCTTGC
*
20148 TCTTGTTGTGTT
1 TCTTGCTGTGTT
20160 TCTTGCTGTG--
1 TCTTGCTGTGTT
*
20170 TCTTGTTGTGTT
1 TCTTGCTGTGTT
*
20182 TCTCGCTGTG-T
1 TCTTGCTGTGTT
20193 T-TTGCTGTGTT
1 TCTTGCTGTGTT
20204 T
1 T
20205 TTTTTTATAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 16 0.43
11 4 0.11
12 17 0.46
ACGTcount: A:0.00, C:0.14, G:0.26, T:0.60
Consensus pattern (12 bp):
TCTTGCTGTGTT
Found at i:20694 original size:14 final size:16
Alignment explanation
Indices: 20675--20725 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 16
20665 TTTGTAAATA
20675 ATAATATTA-ATAT-T
1 ATAATATTATATATAT
20689 ATAATATTATTATATAT
1 ATAATATTA-TATATAT
*
20706 ATAATA--ATGTATAT
1 ATAATATTATATATAT
20720 ATAATA
1 ATAATA
20726 AACGTCACTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 21 0.64
15 1 0.03
16 4 0.12
17 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATAATATTATATATAT
Found at i:20694 original size:17 final size:17
Alignment explanation
Indices: 20672--20722 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
20662 GGTTTTGTAA
20672 ATAATAATATTA-ATATT
1 ATAATAATATTATATA-T
*
20689 ATAATATTATTATATAT
1 ATAATAATATTATATAT
*
20706 ATAATAAT-GTATATAT
1 ATAATAATATTATATAT
20722 A
1 A
20723 ATAAACGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.27
17 19 0.63
18 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATAATAATATTATATAT
Found at i:27508 original size:33 final size:37
Alignment explanation
Indices: 27469--27544 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 37
27459 AAAATAATAA
*
27469 AATAAAACAAT-AAATATAAA-AAT-T-GAA-GAAAAT
1 AATAAAA-AATAAAATATAAATAATATAAAAGGAAAAT
*
27502 AATAAAAACTAAAATATAAATAATATAAAAGGAAAAT
1 AATAAAAAATAAAATATAAATAATATAAAAGGAAAAT
27539 AATAAA
1 AATAAA
27545 TGATGATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 2 0.06
33 16 0.44
34 3 0.08
35 1 0.03
36 2 0.06
37 12 0.33
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (37 bp):
AATAAAAAATAAAATATAAATAATATAAAAGGAAAAT
Found at i:27521 original size:39 final size:38
Alignment explanation
Indices: 27437--27523 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 38
27427 ATGTAAAAAT
* *
27437 ATATAAATATCAAAATTACAATAAAATAATAAAATAAA
1 ATATAAATATAAAAATTACAAGAAAATAATAAAATAAA
* *
27475 ACAATAAATATAAAAATT-GAAGAAAATAATAAAAACTAAA
1 A-TATAAATATAAAAATTACAAGAAAATAAT-AAAA-TAAA
27515 ATATAAATA
1 ATATAAATA
27524 ATATAAAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
38 11 0.27
39 25 0.61
40 5 0.12
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (38 bp):
ATATAAATATAAAAATTACAAGAAAATAATAAAATAAA
Found at i:27543 original size:23 final size:22
Alignment explanation
Indices: 27498--27554 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
27488 AAATTGAAGA
*
27498 AAATAATA-AAAACTAAAATAT
1 AAATAATATAAAACGAAAATAT
*
27519 AAATAATATAAAAGGAAAATAAT
1 AAATAATATAAAACGAAAAT-AT
*
27542 AAATGATGATAAA
1 AAATAAT-ATAAA
27555 TAAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.27
22 9 0.30
23 8 0.27
24 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (22 bp):
AAATAATATAAAACGAAAATAT
Found at i:27593 original size:20 final size:20
Alignment explanation
Indices: 27497--27594 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 20
27487 AAAATTGAAG
*
27497 AAAATAATAAAAACTAAAATATA
1 AAAAT-ATATAAA-TAAAA-ATA
**
27520 AATAATATA-AAAGGAAAATA
1 AA-AATATATAAATAAAAATA
27540 ATAAATGATGATAAATAAAAATA
1 A-AAAT-AT-ATAAATAAAAATA
* * *
27563 AACAGACATAAATAAAAATA
1 AAAATATATAAATAAAAATA
27583 AAAATATATAAA
1 AAAATATATAAA
27595 ATTATGCATA
Statistics
Matches: 60, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
20 29 0.48
21 7 0.12
22 6 0.10
23 15 0.25
24 3 0.05
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATATATAAATAAAAATA
Found at i:31041 original size:72 final size:71
Alignment explanation
Indices: 30923--31061 Score: 174
Period size: 72 Copynumber: 1.9 Consensus size: 71
30913 AATGCATCCT
* * * * * *
30923 TTGGCTGAATTCATCCCACCTTGTGTGAACTTGTTGATTTGTCTTCTATGGATGAATGTTCATGA
1 TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCT-TGCATGAATATGCATGA
30988 ATGTATC
65 ATGTATC
*
30995 TTGGCTGAAATTCTTCCC-CCTTGTGTGAACATGACT-ATTTGGCTTCTTGCATGAATATGCATG
1 TTGGCTG-AATTCATCCCACCTTGTGTGAACATG-CTGATTTGGCTTCTTGCATGAATATGCATG
31058 AATG
64 AATG
31062 GATTAACTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
71 17 0.29
72 31 0.53
73 10 0.17
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (71 bp):
TTGGCTGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCTTGCATGAATATGCATGAA
TGTATC
Found at i:37251 original size:20 final size:21
Alignment explanation
Indices: 37214--37274 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
37204 TTTTGGTGCA
*
37214 GAGGGAATCGA-TCACCCC-TT
1 GAGGGAACCGATTC-CCCCTTT
37234 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTTT
*
37255 GAAGGGGAACCAATTCCCCC
1 G-A-GGGAACCGATTCCCCC
37275 CACAAGGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 14 0.40
21 5 0.14
22 1 0.03
23 15 0.43
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTTT
Found at i:39566 original size:34 final size:34
Alignment explanation
Indices: 39528--39612 Score: 170
Period size: 34 Copynumber: 2.5 Consensus size: 34
39518 AACAAAAAGG
39528 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
39562 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
39596 GGGAGAAGTGTTAAAGT
1 GGGAGAAGTGTTAAAGT
39613 AAGGGGAAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.33
Consensus pattern (34 bp):
GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
Found at i:44829 original size:5 final size:5
Alignment explanation
Indices: 44821--44865 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
44811 ATACAATACG
* * *
44821 ATATA ATATG ATATG ATATA ATATA ATATA ATATA ACATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
44866 TGCACATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:44840 original size:15 final size:15
Alignment explanation
Indices: 44815--44864 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
44805 TAATACATAC
*
44815 AATACGATATAATAT
1 AATATGATATAATAT
*
44830 GATATGATATAATAT
1 AATATGATATAATAT
* *
44845 AATATAATATAACAT
1 AATATGATATAATAT
44860 AATAT
1 AATAT
44865 ATGCACATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (15 bp):
AATATGATATAATAT
Found at i:44865 original size:15 final size:15
Alignment explanation
Indices: 44784--44865 Score: 55
Period size: 15 Copynumber: 5.5 Consensus size: 15
44774 TTTGGAGAGT
44784 TAAT-TAATATAACA
1 TAATATAATATAACA
*
44798 TAACAT-ATA-ATACA
1 TAATATAATATA-ACA
*
44812 TACA-ATACGATATAATA
1 TA-ATATA--ATATAACA
* * *
44829 TGATATGATATAATA
1 TAATATAATATAACA
44844 TAATATAATATAACA
1 TAATATAATATAACA
44859 TAATATA
1 TAATATA
44866 TGCACATTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
13 1 0.02
14 13 0.25
15 29 0.55
16 1 0.02
17 8 0.15
18 1 0.02
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (15 bp):
TAATATAATATAACA
Found at i:48004 original size:10 final size:10
Alignment explanation
Indices: 47989--48013 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
47979 TGGACTAATT
47989 TGTTTGCTAA
1 TGTTTGCTAA
47999 TGTTTGCTAA
1 TGTTTGCTAA
48009 TGTTT
1 TGTTT
48014 TTAGATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (10 bp):
TGTTTGCTAA
Found at i:55394 original size:18 final size:18
Alignment explanation
Indices: 55371--55407 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55361 AAAAAATAAA
* *
55371 AAATTTCCAAATTAATCT
1 AAATTTCAAAACTAATCT
55389 AAATTTCAAAACTAATCT
1 AAATTTCAAAACTAATCT
55407 A
1 A
55408 TTAAAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTTCAAAACTAATCT
Found at i:55768 original size:12 final size:12
Alignment explanation
Indices: 55748--55779 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
55738 AAAGGAGTCC
55748 TAAATATACATA
1 TAAATATACATA
*
55760 TACATATACATA
1 TAAATATACATA
55772 TAAATATA
1 TAAATATA
55780 TAGAACACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATATACATA
Found at i:63141 original size:2 final size:2
Alignment explanation
Indices: 63134--63165 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
63124 ATATGTTTCC
*
63134 CA CA CA CA CA AA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
63166 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:68249 original size:6 final size:6
Alignment explanation
Indices: 68169--68247 Score: 131
Period size: 6 Copynumber: 13.2 Consensus size: 6
68159 AATGTACATA
68169 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * *
68217 TACATA TATATG TATATG TATATG TGTATG T
1 TATATG TATATG TATATG TATATG TATATG T
68248 GTGTGTGTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.49
Consensus pattern (6 bp):
TATATG
Found at i:68273 original size:6 final size:6
Alignment explanation
Indices: 68248--68308 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
68238 ATGTGTATGT
* * * * *
68248 GTGTGT GTGTGT GTGCGC GTGTGC GTGCGC GTGCGC GTGTGC GTGTGC
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC
*
68296 GTGTGC GCGTGC G
1 GTGTGC GTGTGC G
68309 CGCAAGCGCG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.00, C:0.20, G:0.51, T:0.30
Consensus pattern (6 bp):
GTGTGC
Found at i:68398 original size:12 final size:12
Alignment explanation
Indices: 68381--68405 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68371 AATTTATTCA
68381 TTGTGGGACCTT
1 TTGTGGGACCTT
68393 TTGTGGGACCTT
1 TTGTGGGACCTT
68405 T
1 T
68406 GTATGTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.32, T:0.44
Consensus pattern (12 bp):
TTGTGGGACCTT
Found at i:69251 original size:31 final size:31
Alignment explanation
Indices: 69213--69281 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
69203 CAAGTATACC
69213 TTAAGTGACCAAATGTTGTTATGTGCATCAA
1 TTAAGTGACCAAATGTTGTTATGTGCATCAA
* *
69244 TTAAGTGACCAAATGTTGTTATGTGCCTTAA
1 TTAAGTGACCAAATGTTGTTATGTGCATCAA
69275 TTAAGTG
1 TTAAGTG
69282 TTTTGATCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (31 bp):
TTAAGTGACCAAATGTTGTTATGTGCATCAA
Found at i:72165 original size:16 final size:17
Alignment explanation
Indices: 72144--72192 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
72134 ATGTAACATG
72144 ATGAC-ATGCAAATGC-A
1 ATGACAATG-AAATGCAA
*
72160 ATGACAATGACATGCAA
1 ATGACAATGAAATGCAA
72177 ATG-CAATGAAATGCAA
1 ATGACAATGAAATGCAA
72193 CGACATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 22 0.76
17 7 0.24
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.18
Consensus pattern (17 bp):
ATGACAATGAAATGCAA
Found at i:72169 original size:22 final size:21
Alignment explanation
Indices: 72144--72189 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 21
72134 ATGTAACATG
72144 ATGACATGCAAATGCAATGACA
1 ATGACATGCAAATGCAATGA-A
72166 ATGACATGCAAATGCAATGAA
1 ATGACATGCAAATGCAATGAA
72187 ATG
1 ATG
72190 CAACGACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
ATGACATGCAAATGCAATGAA
Found at i:78214 original size:17 final size:17
Alignment explanation
Indices: 78192--78254 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
78182 TTAGGGAAAG
78192 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
78209 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
78226 TAGTTCATTTATTAAAT
1 TAGTTCATTAATTAAAC
*
78243 TAATTC-TTAATT
1 TAGTTCATTAATT
78255 GTTTCATGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
16 5 0.13
17 34 0.87
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.46
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:94274 original size:16 final size:16
Alignment explanation
Indices: 94253--94294 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
94243 GTAAGTTATC
94253 TTCATTTTTTTA-TCAT
1 TTCATTTTTTTATTC-T
*
94269 TTCATTTCTTTATTCT
1 TTCATTTTTTTATTCT
94285 TTCATCTTTT
1 TTCAT-TTTT
94295 CTTAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCATTTTTTTATTCT
Found at i:97271 original size:58 final size:59
Alignment explanation
Indices: 97194--97814 Score: 213
Period size: 57 Copynumber: 10.8 Consensus size: 59
97184 CCCTTCTGTT
* * * * * * *
97194 TCCAATATAGAAACTCATACACATAGTATGAATTTCTTGTCCT-TTAGCACCCAAAATG
1 TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
*
97252 TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAGTG
1 TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
* * * * * * ** * *
97311 CCCTAT-CTGAAAATTCATACACTTAGAATG-ATTTCTTAACATTTTAGCGTACTAAACG
1 TCCAATAC-AAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
* * ** * * * ** * *
97369 CCCTAT-CTGAAATTCATACACATAGTATG-ATTTCTTAACATTTTAGCGTACGAAACG
1 TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
* * ** * * * ** * *
97426 CCCTAT-CTGAAATACATACACTTAGTAT-AATTTCTTAACATTTTAGCGTACGAAACG
1 TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
* * * ** * *
97483 -CTCTAT-CTAAAATTCATACACTTAGTATG-ATTTCTTATCATTTTAGCGTACGAAACG
1 TC-CAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
* * ** * * * * ** *
97540 CCCTAT-CTGAAA-TCGATACACTTAGTGTG-ATTTCTTAACATTTTAACGTACGAAATG
1 TCCAATACAAAAATTC-ATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
* * ** * * ***** *
97597 CCCTAT-CTGAAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTGTGAAACG
1 TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
* * * * * ** * *
97654 CCCTATAC-GAAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAACG
1 TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
* * ** * * ** * *
97711 CCCTAT-CTGAAATTCATACACTTAGTAT-AATTTCTTAACATTTTAGCGTACGAAACG
1 TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
* * ** * *
97768 CCCTAT-CTGAAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGC
1 TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGC
97815 GTATGAAATG
Statistics
Matches: 510, Mismatches: 41, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
56 4 0.01
57 399 0.78
58 70 0.14
59 37 0.07
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (59 bp):
TCCAATACAAAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACACAAAATG
Found at i:97406 original size:57 final size:57
Alignment explanation
Indices: 97262--98032 Score: 1215
Period size: 57 Copynumber: 13.5 Consensus size: 57
97252 TCCAATACAA
* * ** *
97262 AAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACAC-AAAGTGCCCTATCTG
1 AAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAA-CGCCCTATCTG
* *
97320 AAAATTCATACACTTAGAATGATTTCTTAACATTTTAGCGTACTAAACGCCCTATCTG
1 -AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
97378 AAATTCATACACATAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * *
97435 AAATACATACACTTAGTATAATTTCTTAACATTTTAGCGTACGAAACGCTCTATCTA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
97492 AAATTCATACACTTAGTATGATTTCTTATCATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
97549 AAA-TCGATACACTTAGTGTGATTTCTTAACATTTTAACGTACGAAATGCCCTATCTG
1 AAATTC-ATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
**
97606 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTGTGAAACGCCCTATAC-G
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTAT-CTG
97663 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
97720 AAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
97777 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAATGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
97834 AAATCCATACACTTAGTATGATTTCTTAACATTTTAACGTATGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
97891 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAACGCCCTATATG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
97948 AAATTCATACACTTAGTATAATTTCTTAACATTTTAGCGTATGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
98005 AAATTCATACACTTACTATGATTTCTTA
1 AAATTCATACACTTAGTATGATTTCTTA
98033 TATTTTGCAC
Statistics
Matches: 663, Mismatches: 44, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
56 3 0.00
57 607 0.92
58 31 0.05
59 22 0.03
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
Found at i:98497 original size:19 final size:22
Alignment explanation
Indices: 98445--98499 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
98435 CGATATAGAC
*
98445 TGGTATCGATACCCCTATGCTA
1 TGGTACCGATACCCCTATGCTA
* *
98467 TGATACCAATACCCC-AT-CTA
1 TGGTACCGATACCCCTATGCTA
98487 -GGTACCGATACCC
1 TGGTACCGATACCC
98500 AAATTAGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 11 0.39
20 3 0.11
21 2 0.07
22 12 0.43
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (22 bp):
TGGTACCGATACCCCTATGCTA
Found at i:102988 original size:57 final size:57
Alignment explanation
Indices: 102844--103271 Score: 642
Period size: 57 Copynumber: 7.5 Consensus size: 57
102834 TCTAATACAA
** * ** ** *
102844 AAATTCATACACTTAGTATGAATTTCTTATTATGTTAGCACACGAAGTGCCCAATCTG
1 AAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
102902 AAAATTCATACACTTAGTATGATTT-TTAACATTTTAGCATACGAAACGCCCTATCTG
1 -AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
102959 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCACTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * *
103016 AAATTTATACACTTAGTATGATTTCTTGACATTTTAGCGTATGAAACGCCCTACCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
103073 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACAAAATGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * *
103130 AAATTCATACCCTTAGTATGATTTCTTAATATTTTAGCGTACGAAATGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
103187 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTACCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
103244 AAATTCATACACTTACTATGATTTCTTA
1 AAATTCATACACTTAGTATGATTTCTTA
103272 TATTTTGCAC
Statistics
Matches: 340, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
56 24 0.07
57 292 0.86
58 4 0.01
59 20 0.06
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
Found at i:103713 original size:22 final size:20
Alignment explanation
Indices: 103662--103736 Score: 82
Period size: 20 Copynumber: 3.7 Consensus size: 20
103652 CGATATAGAC
* *
103662 TGGTATCGATACCCTCA-CCA
1 TGGTACCGATACCC-CATCTA
*
103682 TGGTATCGATACCCCTATGCTA
1 TGGTACCGATACCCC-AT-CTA
103704 TGGTACCGATACCCCATCTA
1 TGGTACCGATACCCCATCTA
103724 -GGTACCGATACCC
1 TGGTACCGATACCC
103737 AAATTAGATT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.28
20 18 0.36
21 2 0.04
22 16 0.32
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.25
Consensus pattern (20 bp):
TGGTACCGATACCCCATCTA
Found at i:103729 original size:19 final size:22
Alignment explanation
Indices: 103681--103736 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
103671 TACCCTCACC
*
103681 ATGGTATCGATACCCCTATGCT
1 ATGGTACCGATACCCCTATGCT
103703 ATGGTACCGATACCCC-AT-CT
1 ATGGTACCGATACCCCTATGCT
103723 A-GGTACCGATACCC
1 ATGGTACCGATACCC
103737 AAATTAGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 13 0.39
20 3 0.09
21 2 0.06
22 15 0.45
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (22 bp):
ATGGTACCGATACCCCTATGCT
Found at i:108163 original size:2 final size:2
Alignment explanation
Indices: 108158--108189 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
108148 TTTTTAAAGG
108158 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
108190 TTGTTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112561 original size:28 final size:28
Alignment explanation
Indices: 112516--112577 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
112506 GATCATTGAT
112516 ATAATGCTTCAAGAACTAGCTCAATGAC
1 ATAATGCTTCAAGAACTAGCTCAATGAC
* * *
112544 GTAATGCTTCAAGGACTAGCTCGATGAC
1 ATAATGCTTCAAGAACTAGCTCAATGAC
112572 ATAATG
1 ATAATG
112578 TAAAAGGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (28 bp):
ATAATGCTTCAAGAACTAGCTCAATGAC
Found at i:114528 original size:65 final size:64
Alignment explanation
Indices: 114459--114618 Score: 225
Period size: 65 Copynumber: 2.5 Consensus size: 64
114449 GAATAAATTG
* * * *
114459 AACATCGAATGCATTTTATGCATAGATGCACATA-CCATGCATCGATGCACTCAGGGT-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-TG
114522 AA
64 -A
*
114524 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
*
114588 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
114619 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 31 0.36
65 53 0.61
66 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
Found at i:114618 original size:17 final size:19
Alignment explanation
Indices: 114590--114638 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
114580 TATTTTGAAA
114590 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
114608 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
114627 CACCGATGCACT
1 CATCGATGCACT
114639 AAGGTTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:114634 original size:64 final size:63
Alignment explanation
Indices: 114459--114638 Score: 202
Period size: 65 Copynumber: 2.8 Consensus size: 63
114449 GAATAAATTG
* * *
114459 AACATCGAATGCATTTTATGCATAGATGCACATACCATGCATCGATGCACTCAGGGTTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCAC-T-CCATGCATCGATGCACTCAGGCTTTTATGAA
* **
114524 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTT-TG-
1 AACATCGAATGCATTTCATGCATCGATGCAC--TCCATGCATCGATGCACTCAGGCT-TTTATGA
114587 A
63 A
* * *
114588 AACATCGAATGCACTTCATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTC-CA-TGCATCGATGCACT
114639 AAGGTTCCAA
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
63 1 0.01
64 43 0.43
65 52 0.52
66 4 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCCATGCATCGATGCACTCAGGCTTTTATGAA
Found at i:117554 original size:12 final size:12
Alignment explanation
Indices: 117537--117561 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
117527 TTATAAATAT
117537 ACATGACGTTGG
1 ACATGACGTTGG
117549 ACATGACGTTGG
1 ACATGACGTTGG
117561 A
1 A
117562 GAACCATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (12 bp):
ACATGACGTTGG
Found at i:120380 original size:64 final size:61
Alignment explanation
Indices: 120310--120488 Score: 186
Period size: 64 Copynumber: 2.8 Consensus size: 61
120300 TTGGAACCTT
120310 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATCAAGTGCATTCGATGTT-TTA-AAATAGCC-
1 AGTGCATCGGTGCACT--G-GTGCATCGATGCATCAA-TGCATTCGATGTTCTTATAAA-AGCCT
120372 C
61 C
* *
120373 GAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAAATCCT
1 -AGTGCATCGGTGCA---CTGGTGCATCGATGCATC-AATGCATTCGATGTTCTTATAAAAGCCT
120438 C
61 C
*
120439 AGTGCATCGGTGCA-TGGTGTGCATCGATGCATGGAATGCATTCGATGTTC
1 AGTGCATCGGTGCACT-G-GTGCATCGATGCAT-CAATGCATTCGATGTTC
120489 AATTTAATTC
Statistics
Matches: 101, Mismatches: 4, Indels: 21
0.80 0.03 0.17
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 30 0.30
64 41 0.41
65 22 0.22
66 4 0.04
67 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (61 bp):
AGTGCATCGGTGCACTGGTGCATCGATGCATCAATGCATTCGATGTTCTTATAAAAGCCTC
Found at i:120462 original size:17 final size:17
Alignment explanation
Indices: 120440--120472 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
120430 AAAATCCTCA
*
120440 GTGCATCGGTGCATGGT
1 GTGCATCGATGCATGGT
120457 GTGCATCGATGCATGG
1 GTGCATCGATGCATGG
120473 AATGCATTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.18, G:0.39, T:0.27
Consensus pattern (17 bp):
GTGCATCGATGCATGGT
Found at i:120478 original size:17 final size:17
Alignment explanation
Indices: 120441--120485 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
120431 AAATCCTCAG
* **
120441 TGCATCGGTGCATGGTG
1 TGCATCGATGCATGGAA
120458 TGCATCGATGCATGGAA
1 TGCATCGATGCATGGAA
120475 TGCATTCGATG
1 TGCA-TCGATG
120486 TTCAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:121525 original size:28 final size:28
Alignment explanation
Indices: 121493--121552 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
121483 GAGAAGAAGA
121493 AAAACATTGGAGTTGCTCTCAAATTCAC
1 AAAACATTGGAGTTGCTCTCAAATTCAC
121521 AAAACATTGGAGTTGCTCTCAAATTCAC
1 AAAACATTGGAGTTGCTCTCAAATTCAC
121549 AAAA
1 AAAA
121553 GATGGCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (28 bp):
AAAACATTGGAGTTGCTCTCAAATTCAC
Found at i:123676 original size:19 final size:19
Alignment explanation
Indices: 123643--123680 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
123633 TTTAAAAAAC
123643 ATTTCAACACTTAACATTT
1 ATTTCAACACTTAACATTT
123662 ATTTCAACACTTAACATTT
1 ATTTCAACACTTAACATTT
123681 CTCCCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTCAACACTTAACATTT
Found at i:124395 original size:21 final size:21
Alignment explanation
Indices: 124371--124414 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
124361 AAGGAGGAGG
* *
124371 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
*
124392 AGGAGCAGCTCGAGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
124413 AG
1 AG
124415 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.43, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:131538 original size:56 final size:55
Alignment explanation
Indices: 131469--131585 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 55
131459 AGTGCATCAA
* *
131469 TGCATCAAGTGCATTCGATATT-TTA-AAATAGCCCGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATATTCTTATAAA-AGCCCCAGTGCATCGATGCATGG-T-G
* * * *
131525 TGCATCAAATGCATTCGATGTTCTTATAAAATCCCCAGTGCATTGGTGCATGGTG
1 TGCATCAAATGCATTCGATATTCTTATAAAAGCCCCAGTGCATCGATGCATGGTG
131580 TGCATC
1 TGCATC
131586 GATGCATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
55 7 0.13
56 21 0.40
57 22 0.42
58 3 0.06
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (55 bp):
TGCATCAAATGCATTCGATATTCTTATAAAAGCCCCAGTGCATCGATGCATGGTG
Found at i:133686 original size:20 final size:20
Alignment explanation
Indices: 133657--133694 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
133647 TTTCGAAGGA
133657 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
133677 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
133695 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:133863 original size:17 final size:19
Alignment explanation
Indices: 133836--133884 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
133826 TATTTTGAAA
133836 CATCGAATGCACT-TCA-TG
1 CATC-AATGCACTCTCAGTG
*
133854 CATCAATGCACTCTTAGTG
1 CATCAATGCACTCTCAGTG
*
133873 CATCGATGCACT
1 CATCAATGCACT
133885 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 8 0.30
18 6 0.22
19 13 0.48
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (19 bp):
CATCAATGCACTCTCAGTG
Found at i:133863 original size:64 final size:65
Alignment explanation
Indices: 133744--133864 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 65
133734 ACATACCTTT
* * * * * * *
133744 CATCGATGCACTCAGGGTTTTATGAAAACATTGAATGTATTTGATGCATCGATGCACAAGACATG
1 CATCGACGCACTCAGGCTTTTATGAAAACATCGAATGCACTTCATGCATCAATGCACAAGACATG
133809 CATCGACGCACTCAGGCTATTT-TG-AAACATCGAATGCACTTCATGCATCAATGCAC
1 CATCGACGCACTCAGGCT-TTTATGAAAACATCGAATGCACTTCATGCATCAATGCAC
133865 TCTTAGTGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
64 27 0.56
65 18 0.38
66 3 0.06
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (65 bp):
CATCGACGCACTCAGGCTTTTATGAAAACATCGAATGCACTTCATGCATCAATGCACAAGACATG
Found at i:137402 original size:2 final size:2
Alignment explanation
Indices: 137395--137461 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
137385 ATAGTTATTT
137395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
137437 TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
137462 GTTATTATGA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:139069 original size:9 final size:8
Alignment explanation
Indices: 139053--139106 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 8
139043 ATTGGAGTAC
139053 AAAAAAGA
1 AAAAAAGA
139061 AATAAAAGA
1 AA-AAAAGA
*
139070 CAAAAAGA
1 AAAAAAGA
139078 AGAAAAAGA
1 A-AAAAAGA
139087 AAAAGAAGA
1 AAAA-AAGA
139096 AAAAGAAGA
1 AAAA-AAGA
139105 AA
1 AA
139107 TTCAAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
8 11 0.27
9 30 0.73
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:139091 original size:15 final size:15
Alignment explanation
Indices: 139071--139102 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
139061 AATAAAAGAC
139071 AAAAAGAAGAAAAAG
1 AAAAAGAAGAAAAAG
139086 AAAAAGAAGAAAAAG
1 AAAAAGAAGAAAAAG
139101 AA
1 AA
139103 GAAATTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAAAAG
Found at i:139113 original size:24 final size:24
Alignment explanation
Indices: 139071--139117 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
139061 AATAAAAGAC
*
139071 AAAAAGAAGAAAAAGAAAAAGAAG
1 AAAAAGAAGAAAAACAAAAAGAAG
**
139095 AAAAAGAAGAAATTCAAAAAGAA
1 AAAAAGAAGAAAAACAAAAAGAA
139118 AGCAAAGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAAAGAAGAAAAACAAAAAGAAG
Found at i:141961 original size:2 final size:2
Alignment explanation
Indices: 141954--142003 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
141944 AGTTATTTTC
141954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
141995 AT AT CT AT A
1 AT AT AT AT A
142004 ATTCATTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151235 original size:19 final size:20
Alignment explanation
Indices: 151206--151244 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
151196 GCTTCCAACA
151206 TTTCTTTCTTTTCTTTTCTT
1 TTTCTTTCTTTTCTTTTCTT
*
151226 TTTC-TTCTTTTTTTTTCTT
1 TTTCTTTCTTTTCTTTTCTT
151245 CTTTTGAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTCTTTCTTTTCTTTTCTT
Found at i:151242 original size:13 final size:14
Alignment explanation
Indices: 151206--151249 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
151196 GCTTCCAACA
151206 TTTCTTTCTT-TTCT
1 TTTCTTT-TTCTTCT
151220 TTTCTTTTTCTTCT
1 TTTCTTTTTCTTCT
151234 TTT-TTTTTCTTCT
1 TTTCTTTTTCTTCT
151247 TTT
1 TTT
151250 GAGTGCTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 15 0.52
14 14 0.48
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTCTTCT
Found at i:151928 original size:20 final size:19
Alignment explanation
Indices: 151903--151953 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
151893 GAAATCCCTT
*
151903 TGAAAATACATGATTTTTAA
1 TGAAAATACATGA-CTTTAA
* *
151923 TGAAAAAACAAGACTTTAA
1 TGAAAATACATGACTTTAA
*
151942 TGAAGATACATG
1 TGAAAATACATG
151954 CTCTTGGCCG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (19 bp):
TGAAAATACATGACTTTAA
Found at i:155093 original size:13 final size:13
Alignment explanation
Indices: 155060--155096 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
155050 TCTTAAATTG
*
155060 TTATTGTACTCAT
1 TTATTGTTCTCAT
155073 TTATTGTTCTCAT
1 TTATTGTTCTCAT
155086 TTATTGTTCTC
1 TTATTGTTCTC
155097 TCTTGTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.59
Consensus pattern (13 bp):
TTATTGTTCTCAT
Found at i:155342 original size:22 final size:21
Alignment explanation
Indices: 155285--155346 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
155275 TCTGGGATAA
*
155285 ACTTATAGTATCGATACCTCT
1 ACTTAGAGTATCGATACCTCT
*
155306 ACTTTGAGTAT-GATACTCTTCT
1 ACTTAGAGTATCGATAC-C-TCT
*
155328 AC-TAGGGTATCGATACCTC
1 ACTTAGAGTATCGATACCTC
155347 CCCAGGGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 7 0.21
21 17 0.50
22 10 0.29
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (21 bp):
ACTTAGAGTATCGATACCTCT
Found at i:162300 original size:17 final size:17
Alignment explanation
Indices: 162280--162397 Score: 85
Period size: 17 Copynumber: 6.9 Consensus size: 17
162270 ACTAAGTAAC
* *
162280 TCATTGATTAAACTATT
1 TCATTCATTAAACTAGT
*
162297 TCATTCATCAAACTAGT
1 TCATTCATTAAACTAGT
* * * *
162314 TCACTCAATATTACAAGT
1 TCATTCATTA-AACTAGT
* * *
162332 TCATTGAATAAAGTTAGT
1 TCATTCATTAAA-CTAGT
*
162350 TCATTAATTAAACTAGT
1 TCATTCATTAAACTAGT
* *
162367 TCATT-ATCAAAATAGT
1 TCATTCATTAAACTAGT
*
162383 TCATTTATTAAACTA
1 TCATTCATTAAACTA
162398 ACTCTTAATT
Statistics
Matches: 78, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
16 14 0.18
17 38 0.49
18 26 0.33
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (17 bp):
TCATTCATTAAACTAGT
Found at i:162384 original size:16 final size:17
Alignment explanation
Indices: 162346--162387 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
162336 TGAATAAAGT
* *
162346 TAGTTCATTAATTAAAC
1 TAGTTCATTAATCAAAA
162363 TAGTTCATT-ATCAAAA
1 TAGTTCATTAATCAAAA
162379 TAGTTCATT
1 TAGTTCATT
162388 TATTAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (17 bp):
TAGTTCATTAATCAAAA
Found at i:164443 original size:17 final size:17
Alignment explanation
Indices: 164421--164526 Score: 81
Period size: 17 Copynumber: 6.1 Consensus size: 17
164411 TGCACTTAAG
164421 TAGTTCATTGATTAAAC
1 TAGTTCATTGATTAAAC
* *
164438 TAGTTCATTCATCAAAC
1 TAGTTCATTGATTAAAC
*
164455 TAATTCATTCAAGATT--AC
1 TAGTTCATT---GATTAAAC
* * * *
164473 AAGCTCATTGAATAAAGT
1 TAGTTCATTGATTAAA-C
*
164491 TAGTTCATTAATTAAAC
1 TAGTTCATTGATTAAAC
*
164508 TAGTTCATTTATTAAAC
1 TAGTTCATTGATTAAAC
164525 TA
1 TA
164527 ACTCCTAATT
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
15 3 0.04
17 42 0.63
18 20 0.30
20 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (17 bp):
TAGTTCATTGATTAAAC
Found at i:166378 original size:20 final size:20
Alignment explanation
Indices: 166340--166379 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
166330 GGAGTGTTTG
166340 GTGAGGTTTTTCCTTTTATTT
1 GTGAGGTTTTT-CTTTTATTT
166361 GTGAGGTTATTT-TTTTATT
1 GTGAGGTT-TTTCTTTTATT
166380 ACTAATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 8 0.44
22 3 0.17
ACGTcount: A:0.12, C:0.05, G:0.20, T:0.62
Consensus pattern (20 bp):
GTGAGGTTTTTCTTTTATTT
Found at i:171528 original size:17 final size:17
Alignment explanation
Indices: 171487--171530 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
171477 ATTTAAACAT
* *
171487 GTAGTTCATTTAGCTAT
1 GTAGTTCATTTAACTAA
* *
171504 GCACTTCATTTAACTAA
1 GTAGTTCATTTAACTAA
171521 GTAGTTCATT
1 GTAGTTCATT
171531 GATTAAACTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (17 bp):
GTAGTTCATTTAACTAA
Found at i:171622 original size:17 final size:17
Alignment explanation
Indices: 171600--171635 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
171590 TGAATAAAGT
171600 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
171617 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
171634 TA
1 TA
171636 ACTCCTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:172908 original size:14 final size:14
Alignment explanation
Indices: 172889--172940 Score: 104
Period size: 14 Copynumber: 3.7 Consensus size: 14
172879 TTAATTTCAT
172889 ATACATATTTATGC
1 ATACATATTTATGC
172903 ATACATATTTATGC
1 ATACATATTTATGC
172917 ATACATATTTATGC
1 ATACATATTTATGC
172931 ATACATATTT
1 ATACATATTT
172941 CCCTTCTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (14 bp):
ATACATATTTATGC
Found at i:174091 original size:3 final size:3
Alignment explanation
Indices: 174083--174158 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
174073 GTCTATGCAT
174083 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
174131 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
174159 ATACGCCATG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:180341 original size:30 final size:30
Alignment explanation
Indices: 180290--180347 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
180280 ATTGGCATTG
*
180290 ACTTCACTTTGCATACATTCATTCTCTTTC
1 ACTTCACTTTGCACACATTCATTCTCTTTC
* *
180320 ACTTCACTTTGGACACTTTCATTCTCTT
1 ACTTCACTTTGCACACATTCATTCTCTT
180348 CCAATGGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.29, G:0.05, T:0.47
Consensus pattern (30 bp):
ACTTCACTTTGCACACATTCATTCTCTTTC
Found at i:181396 original size:20 final size:21
Alignment explanation
Indices: 181371--181413 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
181361 ATCAAAGGAG
181371 AAACCCT-AAA-TTAGGGATAT
1 AAACCCTAAAATTTAGGGA-AT
181391 AAACCCTAAAATTTAGGGAAT
1 AAACCCTAAAATTTAGGGAAT
181412 AA
1 AA
181414 TCGGGGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (21 bp):
AAACCCTAAAATTTAGGGAAT
Found at i:182581 original size:60 final size:60
Alignment explanation
Indices: 182476--182634 Score: 173
Period size: 60 Copynumber: 2.6 Consensus size: 60
182466 GAGGATATTA
* * *
182476 TTGGAATGTACAAAAGTTTGGGGACTAATTTAGAATAAGGTTCATAGTTTGAGGG-TGAAT
1 TTGGAATGTACAAAAGTTTGGGGACCAATTTAGAATAAGGGTCATAATTT-AGGGATGAAT
*
182536 TTGGAATGT-CAAAAAGTTTGGGGACCGATTTAGAAT-AGGAGTCATAATTTAGGGATGAAAT
1 TTGGAATGTAC-AAAAGTTTGGGGACCAATTTAGAATAAGG-GTCATAATTTAGGGATG-AAT
* * * **
182597 TT-AAATATTCAAAAGTTTAAGGACCAATTTAGAATAAG
1 TTGGAATGTACAAAAGTTTGGGGACCAATTTAGAATAAG
182635 ATGGGAATGT
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
59 8 0.10
60 68 0.81
61 8 0.10
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (60 bp):
TTGGAATGTACAAAAGTTTGGGGACCAATTTAGAATAAGGGTCATAATTTAGGGATGAAT
Found at i:190625 original size:35 final size:35
Alignment explanation
Indices: 190571--190694 Score: 184
Period size: 35 Copynumber: 3.6 Consensus size: 35
190561 TTAAAAATTG
190571 ATTTTTG-AAAATATA-TATATAGTTTTGAAAACA
1 ATTTTTGAAAAATATATTATATAGTTTTGAAAACA
*
190604 ATTTTTGAAAAATGTATTATATAGTTTTGAAAACA
1 ATTTTTGAAAAATATATTATATAGTTTTGAAAACA
*
190639 ATTTTTGAAAAATATATTTTATAGTTTTGAAAAC-
1 ATTTTTGAAAAATATATTATATAGTTTTGAAAACA
*
190673 ATTTTTG-AATATATATATATAT
1 ATTTTTGAAAAATATAT-TATAT
190695 TATATAGTTG
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
33 15 0.18
34 18 0.22
35 50 0.60
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (35 bp):
ATTTTTGAAAAATATATTATATAGTTTTGAAAACA
Found at i:191065 original size:14 final size:14
Alignment explanation
Indices: 191048--191204 Score: 83
Period size: 14 Copynumber: 11.3 Consensus size: 14
191038 AAATGTAATG
191048 AAAATAAAGAAAAT
1 AAAATAAAGAAAAT
* *
191062 AAAAAAAAAAACAAAT
1 -AAAATAAAGA-AAAT
* *
191078 GAATTAAAGAAAAT
1 AAAATAAAGAAAAT
* *
191092 GAGATAAAGAAAAT
1 AAAATAAAGAAAAT
*
191106 -AAA-AAAG-AGA-
1 AAAATAAAGAAAAT
191116 AAAATAAAGTAAAAAT
1 AAAATAAAG--AAAAT
*
191132 AGAAA-AAAGTAAAT
1 A-AAATAAAGAAAAT
*
191146 AAAATAAATAAAAT
1 AAAATAAAGAAAAT
* *
191160 AAGATAAATAAAAT
1 AAAATAAAGAAAAT
* *
191174 AAAAGAAATAAAA-
1 AAAATAAAGAAAAT
* * *
191187 AGAAGAAAAAAAAT
1 AAAATAAAGAAAAT
191201 AAAA
1 AAAA
191205 AATAAAAATA
Statistics
Matches: 112, Mismatches: 20, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
11 5 0.04
12 8 0.07
13 16 0.14
14 55 0.49
15 16 0.14
16 9 0.08
17 3 0.03
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAATAAAGAAAAT
Found at i:191069 original size:9 final size:9
Alignment explanation
Indices: 191048--191206 Score: 70
Period size: 9 Copynumber: 16.2 Consensus size: 9
191038 AAATGTAATG
*
191048 AAAATAAAG
1 AAAATAAAA
191057 AAAATAAAA
1 AAAATAAAA
191066 AAAA-AAACA
1 AAAATAAA-A
*
191075 AATGAATTAAAG
1 AA--AA-TAAAA
191087 AAAATGAGATAA
1 AAAAT-A-A-AA
191099 AGAAAATAAAA
1 A--AAATAAAA
* *
191110 AAGAGAAAA
1 AAAATAAAA
191119 ATAAAGTAAAA
1 A-AAA-TAAAA
191130 ATAGAA-AAAA
1 A-A-AATAAAA
*
191140 GTAAATAAAA
1 -AAAATAAAA
*
191150 TAAATAAAA
1 AAAATAAAA
* *
191159 TAAGATAAAT
1 -AAAATAAAA
191169 AAAATAAAA
1 AAAATAAAA
*
191178 GAAATAAAA
1 AAAATAAAA
* *
191187 AGAAGAAAA
1 AAAATAAAA
191196 AAAATAAAA
1 AAAATAAAA
191205 AA
1 AA
191207 TAAAAATATA
Statistics
Matches: 115, Mismatches: 19, Indels: 32
0.69 0.11 0.19
Matches are distributed among these distances:
8 3 0.03
9 64 0.56
10 20 0.17
11 13 0.11
12 7 0.06
13 4 0.03
14 4 0.03
ACGTcount: A:0.77, C:0.01, G:0.09, T:0.13
Consensus pattern (9 bp):
AAAATAAAA
Found at i:191211 original size:5 final size:5
Alignment explanation
Indices: 191116--191204 Score: 57
Period size: 5 Copynumber: 18.8 Consensus size: 5
191106 AAAAAAGAGA
* * *
191116 AAAAT AAAGT AAAAAT AGAAA- AAAGT -AAAT AAAAT -AAAT AAAAT AAGAT
1 AAAAT AAAAT -AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * *
191165 -AAAT AAAAT AAAA- GAAAT AAAA- AGAAG AAAA- AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
191205 AATAAAAATA
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
4 22 0.34
5 36 0.55
6 7 0.11
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:191588 original size:7 final size:7
Alignment explanation
Indices: 191576--191660 Score: 59
Period size: 7 Copynumber: 11.6 Consensus size: 7
191566 GGAAAAACAT
191576 AATAAAA
1 AATAAAA
191583 AAT--AA
1 AATAAAA
*
191588 AATAAAC
1 AATAAAA
191595 AATAATAA
1 AATAA-AA
191603 TAATAAAA
1 -AATAAAA
191611 CAA-AAAA
1 -AATAAAA
*
191618 TAATAAAT
1 -AATAAAA
*
191626 AATAATA
1 AATAAAA
191633 AATAATAA
1 AATAA-AA
191641 ATATAAAA
1 A-ATAAAA
191649 ACATAAAA
1 A-ATAAAA
191657 AATA
1 AATA
191661 TATGTATAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
5 5 0.08
7 28 0.45
8 20 0.32
9 9 0.15
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (7 bp):
AATAAAA
Found at i:191607 original size:21 final size:22
Alignment explanation
Indices: 191570--191630 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 22
191560 ACATTAGGAA
* *
191570 AAAC-ATAATAAAAAATAAAAT
1 AAACAATAATAAATAATAAAAC
191591 AAACAATAAT-AATAATAAAAC
1 AAACAATAATAAATAATAAAAC
*
191612 AAAAAATAATAAATAATAA
1 AAACAATAATAAATAATAA
191631 TAAATAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (22 bp):
AAACAATAATAAATAATAAAAC
Found at i:191608 original size:28 final size:28
Alignment explanation
Indices: 191574--191648 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 28
191564 TAGGAAAAAC
191574 ATAATAAAAAATAAAATAA-ACAATAATA
1 ATAATAAAAAATAAAATAATA-AATAATA
191602 ATAATAAAACAA-AAAATAATAAATAATA
1 ATAATAAAA-AATAAAATAATAAATAATA
191630 ATAAATAATAAATATAAAA
1 AT-AATAA-AAA-ATAAAA
191649 ACATAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
28 25 0.61
29 9 0.22
30 3 0.07
31 4 0.10
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (28 bp):
ATAATAAAAAATAAAATAATAAATAATA
Found at i:191654 original size:17 final size:16
Alignment explanation
Indices: 191601--191662 Score: 72
Period size: 17 Copynumber: 3.8 Consensus size: 16
191591 AAACAATAAT
*
191601 AATAATAAA-ACAAAA
1 AATAATAAATATAAAA
*
191616 AATAATAAATAATAATA
1 AATAATAAAT-ATAAAA
191633 AATAATAAATATAAAA
1 AATAATAAATATAAAA
*
191649 ACATAAAAAATATA
1 A-ATAATAAATATA
191663 TGTATAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.22
16 6 0.15
17 25 0.62
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAATAAATATAAAA
Found at i:191675 original size:21 final size:21
Alignment explanation
Indices: 191612--191681 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
191602 ATAATAAAAC
*
191612 AAAAAAT-AATAAATAATAAT
1 AAAAAATAAATATATAATAAT
* *
191632 AAATAATAAATATA-AAAACAT
1 AAAAAATAAATATATAATA-AT
* *
191653 AAAAAATATATGTATAATAAT
1 AAAAAATAAATATATAATAAT
191674 AATAAAAT
1 AA-AAAAT
191682 GGCTAATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
20 9 0.23
21 22 0.56
22 8 0.21
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (21 bp):
AAAAAATAAATATATAATAAT
Found at i:192639 original size:18 final size:18
Alignment explanation
Indices: 192613--192651 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
192603 ACCAAATAAA
192613 ATAAATAATA-ATATATAT
1 ATAAATAATATA-ATATAT
*
192631 ATAATTAATATAATATAT
1 ATAAATAATATAATATAT
192649 ATA
1 ATA
192652 TTATAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAATAATATAATATAT
Found at i:192646 original size:14 final size:13
Alignment explanation
Indices: 192607--192657 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
192597 CCTGTAACCA
*
192607 AATAAAATAA-AT
1 AATAATATAATAT
192619 AATAATATATATAT
1 AATAATATA-ATAT
192633 AATTAATATAATAT
1 AA-TAATATAATAT
*
192647 ATATATTATAA
1 A-ATAATATAA
192658 ATGTGTAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 8 0.24
13 1 0.03
14 16 0.48
15 8 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATAATATAATAT
Found at i:193518 original size:85 final size:85
Alignment explanation
Indices: 193403--193784 Score: 478
Period size: 85 Copynumber: 4.5 Consensus size: 85
193393 AAGTCTATAG
* * * *
193403 TTTGTTGACAGATAGCCCTTCTCATCTTGAGCTGTGCTGTAAATTTGATGTGCCTTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATGTGCCTTTGAGCTGAA
* * *
193468 TATAATC-AGACTCGAATGTG
66 TGTAATCGA-ACTCGAAGGTC
** ** * * *
193488 TTTACTGACAGATAACCCTTCTGGCCTTGAGTTATGCTGTAAGTTTGATATGCCTTTGAGCTTAA
1 TTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATGTGCCTTTGAGCTGAA
193553 TGTAATCGAACTCGAAGGTC
66 TGTAATCGAACTCGAAGGTC
* *
193573 TTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTTTAAATTTGATGTGCCTTTGACCTGAA
1 TTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATGTGCCTTTGAGCTGAA
*
193638 TGTAATCGAACTCGAAGGTT
66 TGTAATCGAACTCGAAGGTC
* * * * * *
193658 TTTGTTAACAGATAACCATTATCGCCTTGAGTTATGCTATAAATTTGATGTGACTTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATGTGCCTTTGAGCTGAA
*
193723 TGTAATCGAACTCTAAGGTC
66 TGTAATCGAACTCGAAGGTC
* * * * *
193743 TTGGTTGACATATAACTCTTCTCCCCTTTGAGTTATGTTGTA
1 TTTGTTGACAGATAACCCTTCTCACC-TTGAGTTATGCTGTA
193785 CTTGGCTGGG
Statistics
Matches: 253, Mismatches: 42, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
85 239 0.94
86 14 0.06
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (85 bp):
TTTGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGTAAATTTGATGTGCCTTTGAGCTGAA
TGTAATCGAACTCGAAGGTC
Found at i:194048 original size:25 final size:25
Alignment explanation
Indices: 194020--194071 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
194010 CCAACCTTGT
* *
194020 GTAAATTTCACCAAATTTGCTTTGA
1 GTAAATTTCACCAAATTGGATTTGA
**
194045 GTAAATTTCGTCAAATTGGATTTGA
1 GTAAATTTCACCAAATTGGATTTGA
194070 GT
1 GT
194072 TGGATATCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (25 bp):
GTAAATTTCACCAAATTGGATTTGA
Found at i:194055 original size:60 final size:58
Alignment explanation
Indices: 193930--194046 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 58
193920 ATTGGATATC
** *
193930 CTTCGTTGTGAAGTTGAAATCCAAGTGTTGTTTCACCAAATTGGCTTTGAGTTGGATAT
1 CTTCGTTGTGAAGTTGAAATCCAAGTGTAATTTCACCAAATTGGCTTTGAGTT-GAAAT
*
193989 CCTTCGTTGTGAAGTTGAAATCCAACCTTGTGTAAATTTCACCAAATTTGCTTTGAGT
1 -CTTCGTTGTGAAGTTGAAATCCAA----GTGT-AATTTCACCAAATTGGCTTTGAGT
194047 AAATTTCGTC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
60 24 0.49
64 4 0.08
65 21 0.43
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (58 bp):
CTTCGTTGTGAAGTTGAAATCCAAGTGTAATTTCACCAAATTGGCTTTGAGTTGAAAT
Found at i:195672 original size:95 final size:94
Alignment explanation
Indices: 195477--195739 Score: 321
Period size: 95 Copynumber: 2.7 Consensus size: 94
195467 GGCTAGCTGG
* * * * *
195477 ATCCATAAAGCCCGGGCGTTTAACAAATTTCTCTAGAGGGACAACTCGATATCATTGTATAG-AT
1 ATCCATAAA-ACCGGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTAT
195541 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
61 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
195575 ATCCATAAAACCGGAGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAACCGG-GCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* * * *
195640 TAATCGCCTTTATTAGGCTAGTTGAATCTT
65 TAATCACCTTTATCAGGCTAGCTGAATATT
* * * **
195670 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGAGACAGTTCAAGCTTTATTGTATATAT
1 ATCCATAAA-ACCGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
195735 ATAAT
64 ATAAT
195740 ATTATAATAT
Statistics
Matches: 147, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
94 4 0.03
95 88 0.60
96 11 0.07
97 5 0.03
98 39 0.27
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (94 bp):
ATCCATAAAACCGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTAT
AATCACCTTTATCAGGCTAGCTGAATATT
Found at i:196942 original size:150 final size:150
Alignment explanation
Indices: 196671--196967 Score: 323
Period size: 150 Copynumber: 2.0 Consensus size: 150
196661 TGATATAGGT
* * * *
196671 GTTTGAGGTGTCTTCAAAGCTACGTCTGTCCCACTGATTCTTAAACCCACATGCCCGTCTCGGAC
1 GTTTGAGGTGTCTTCAAAGCTACATCTGCCCCACTGATTCTCAAACCCACATGCCAGTCTCGGAC
* * ** * *
196736 TACATTCATAGAAGCCCTTTTACTTGGATTTCCTTTCCGATCCTCTTGCGCCTTATGTTTTTCGC
66 TACATTCATAGAAGCCATTCTACTTAAATTTCCTTTCCGATCCTCTTGCGCCTTATGTTCTTCAC
*
196801 TGGAATCCTCTGTTGAAGTA
131 AGGAATCCTCTGTTGAAGTA
***
196821 GTTTGAGGTGTCTTCTTGGCTACATCTGCCCCATCT-ATTCTCAAACCCAC-TGGCCAGTCTCGG
1 GTTTGAGGTGTCTTCAAAGCTACATCTGCCCCA-CTGATTCTCAAACCCACAT-GCCAGTCTCGG
* * * * * * *
196884 ATTACATTTATGGAGGCCATTCTGCTTAAATTTCCTTTTTC-ATCCTTTTGC-CTCTTATGTTCT
64 ACTACATTCATAGAAGCCATTCTACTTAAATTTCC-TTTCCGATCCTCTTGCGC-CTTATGTTCT
* *
196947 TCACAGGCATTCTCTGTTGAA
127 TCACAGGAATCCTCTGTTGAA
196968 TCGACGACTT
Statistics
Matches: 120, Mismatches: 23, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
149 2 0.02
150 112 0.93
151 6 0.05
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (150 bp):
GTTTGAGGTGTCTTCAAAGCTACATCTGCCCCACTGATTCTCAAACCCACATGCCAGTCTCGGAC
TACATTCATAGAAGCCATTCTACTTAAATTTCCTTTCCGATCCTCTTGCGCCTTATGTTCTTCAC
AGGAATCCTCTGTTGAAGTA
Found at i:199676 original size:9 final size:9
Alignment explanation
Indices: 199662--199794 Score: 100
Period size: 9 Copynumber: 14.7 Consensus size: 9
199652 AAAGGTAATG
199662 AAAATAAAT
1 AAAATAAAT
199671 AAAAT-AA-
1 AAAATAAAT
*
199678 AAAACAAAT
1 AAAATAAAT
* *
199687 AAATTAAAG
1 AAAATAAAT
199696 AAAATAAA-
1 AAAATAAAT
199704 AAAATAAAGT
1 AAAATAAA-T
199714 AAAGATAGAA-
1 AAA-ATA-AAT
199724 AAAAGTAAAT
1 AAAA-TAAAT
199734 AAAATAAGAT
1 AAAATAA-AT
199744 -AAATAAA-
1 AAAATAAAT
* *
199751 AAAAGAAAA
1 AAAATAAAT
199760 AACAATAAAT
1 AA-AATAAAT
199770 AATAAT-AAT
1 AA-AATAAAT
199779 AAAATAAAAT
1 AAAAT-AAAT
199789 AAAATA
1 AAAATA
199795 TATCTAACTA
Statistics
Matches: 101, Mismatches: 9, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
7 4 0.04
8 22 0.22
9 38 0.38
10 32 0.32
11 3 0.03
12 2 0.02
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (9 bp):
AAAATAAAT
Found at i:199677 original size:5 final size:5
Alignment explanation
Indices: 199662--199794 Score: 70
Period size: 5 Copynumber: 27.2 Consensus size: 5
199652 AAAGGTAATG
* * *
199662 AAAAT -AAAT AAAAT AAAAA ACAAAT -AAAT TAAAG AAAAT -AAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * *
199709 AAAGT AAAGAT AGAAA- AAAGT -AAAT AAAAT AAGAT -AAAT AAAA- AAAGA-
1 AAAAT AAA-AT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT
*
199757 AAAA- ACAAT AAATAAT AATAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT -AA-AAT AA-AAT AAAAT AAAAT AAAAT A
199795 TATCTAACTA
Statistics
Matches: 101, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
4 29 0.29
5 52 0.51
6 15 0.15
7 5 0.05
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:199751 original size:25 final size:24
Alignment explanation
Indices: 199662--199791 Score: 89
Period size: 22 Copynumber: 5.6 Consensus size: 24
199652 AAAGGTAATG
*
199662 AAAATAAATA-AAATAAAAAACAAAT
1 AAAATAAAGATAAAT-AAAAA-AAAT
*
199687 AAATTAAAGA-AAAT-AAAAAAAT
1 AAAATAAAGATAAATAAAAAAAAT
* *
199709 AAAGTAAAGATAGAA-AAAAGTAAAT
1 AAAATAAAGATA-AATAAAA-AAAAT
199734 AAAAT-AAGATAAATAAAAAAAGA-
1 AAAATAAAGATAAATAAAAAAA-AT
* * *
199757 AAAA-ACA-ATAAATAATAATAAT
1 AAAATAAAGATAAATAAAAAAAAT
199779 AAAATAAA-ATAAA
1 AAAATAAAGATAAA
199792 ATATATCTAA
Statistics
Matches: 86, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
21 1 0.01
22 28 0.33
23 21 0.24
24 16 0.19
25 20 0.23
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (24 bp):
AAAATAAAGATAAATAAAAAAAAT
Found at i:200182 original size:35 final size:35
Alignment explanation
Indices: 200143--200238 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 35
200133 AACATTAGGA
*
200143 AAAACATAATAAAATAAATAAATAAT-AATAATAAT
1 AAAACATAATAAAATAAA-AAATAATAAAAAATAAT
* *
200178 AAAAC--CA-AAAATAAAAAATAGTAAAAAATAAT
1 AAAACATAATAAAATAAAAAATAATAAAAAATAAT
200210 AAAA-ATAATAAAAATAAAAACATAA-AAAA
1 AAAACATAAT-AAAATAAAAA-ATAATAAAA
200239 CTATATGTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
31 6 0.12
32 20 0.40
33 2 0.04
35 19 0.38
36 3 0.06
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.19
Consensus pattern (35 bp):
AAAACATAATAAAATAAAAAATAATAAAAAATAAT
Found at i:200223 original size:9 final size:9
Alignment explanation
Indices: 200143--200238 Score: 67
Period size: 9 Copynumber: 10.4 Consensus size: 9
200133 AACATTAGGA
200143 AAAACATAAT
1 AAAA-ATAAT
200153 -AAAATAAAT
1 AAAAAT-AAT
200162 AAATAATAAT
1 AAA-AATAAT
*
200172 AATAATAA-
1 AAAAATAAT
200180 AACCAAA-AAT
1 AA--AAATAAT
*
200190 AAAAAATAGT
1 -AAAAATAAT
200200 AAAAAATAAT
1 -AAAAATAAT
200210 AAAAATAAT
1 AAAAATAAT
200219 AAAAATAA-
1 AAAAATAAT
*
200227 AAACATAA-
1 AAAAATAAT
200235 AAAA
1 AAAA
200239 CTATATGTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
8 14 0.19
9 33 0.46
10 20 0.28
11 5 0.07
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.19
Consensus pattern (9 bp):
AAAAATAAT
Found at i:200239 original size:9 final size:8
Alignment explanation
Indices: 200142--200238 Score: 63
Period size: 8 Copynumber: 11.8 Consensus size: 8
200132 AAACATTAGG
*
200142 AAAAACAT
1 AAAAAAAT
*
200150 AATAAAAT
1 AAAAAAAT
*
200158 AAATAAAT
1 AAAAAAAT
*
200166 AATAATAAT
1 AA-AAAAAT
*
200175 AATAAAA-
1 AAAAAAAT
**
200182 CCAAAAAT
1 AAAAAAAT
200190 -AAAAAAT
1 AAAAAAAT
200197 AGTAAAAAAT
1 A--AAAAAAT
200207 AATAAAAAT
1 AA-AAAAAT
200216 AATAAAAAT
1 AA-AAAAAT
*
200225 AAAAACAT
1 AAAAAAAT
200233 AAAAAA
1 AAAAAA
200239 CTATATGTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
7 10 0.14
8 28 0.41
9 23 0.33
10 8 0.12
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.19
Consensus pattern (8 bp):
AAAAAAAT
Found at i:201327 original size:13 final size:14
Alignment explanation
Indices: 201295--201344 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
201285 CCTGTAACCA
201295 AATAAA-ATAA-AT
1 AATAAATATAATAT
201307 AATAAATAT-ATAT
1 AATAAATATAATAT
*
201320 AATTAATATAATAT
1 AATAAATATAATAT
*
201334 ATATAGATATA
1 A-ATAAATATA
201345 TAAATGTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 7 0.23
13 12 0.39
14 5 0.16
15 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AATAAATATAATAT
Found at i:201476 original size:35 final size:36
Alignment explanation
Indices: 201400--201503 Score: 138
Period size: 35 Copynumber: 2.9 Consensus size: 36
201390 TGTGTCTACA
*
201400 ATAGTTTTGAAAACGAATTTTGAAAATATTTATAATAT
1 ATAGTTTTGAAAAC-ATTTTTGAAAATA-TTATAATAT
201438 ATAGTTTTGAAAACATTTTTGAAAATA-TATAATAT
1 ATAGTTTTGAAAACATTTTTGAAAATATTATAATAT
* * * *
201473 ATAGTTTGGAAATCGTTTTTGAAAATGTTAT
1 ATAGTTTTGAAAACATTTTTGAAAATATTAT
201504 TTCTTTAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
35 31 0.52
36 3 0.05
37 12 0.20
38 14 0.23
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.43
Consensus pattern (36 bp):
ATAGTTTTGAAAACATTTTTGAAAATATTATAATAT
Found at i:201565 original size:4 final size:4
Alignment explanation
Indices: 201556--201596 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
201546 AGTTATATAT
201556 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
201597 ATTATTCCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:201585 original size:15 final size:15
Alignment explanation
Indices: 201556--201599 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
201546 AGTTATATAT
201556 TTTATTTATTTATTTA
1 TTTATTTA-TTATTTA
201572 TTTATTTATTATTTA
1 TTTATTTATTATTTA
201587 TTTATTTATTATT
1 TTTATTTATTATT
201600 ATTCCCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 20 0.71
16 8 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTATTATTTA
Found at i:203264 original size:64 final size:65
Alignment explanation
Indices: 203123--203284 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 65
203113 TTGTTTAGGG
* * * * **
203123 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTTAAATAGAAAAAATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATAGAAAAAATCGAATAGGATTTA
** * *
203188 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATAGAAAAAATCGAATAGGATTTA
*
203252 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
203285 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 32 0.38
65 51 0.61
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATAGAAAAAATCGAATAGGATTTA
Found at i:204753 original size:22 final size:21
Alignment explanation
Indices: 204699--204762 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
204689 AGTCGAGGGT
204699 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
204720 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
204742 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
204763 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:208077 original size:65 final size:64
Alignment explanation
Indices: 207991--208132 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 64
207981 TAGTTTAGGG
* * **
207991 TGCATCGATGCACATACAGTGCATCGATACATGAATTTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATATACAGTGCATCGATACATCAACATTAAATA-AAAACATCGAATAGGATTTA
* ** ** *
208056 TGCATCGATGCATA-AGGAGTGCATCGATGTATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATATA-CAGTGCATCGATACATCAACATTAAATAAAAACATCGAATAGGATTTA
208120 TGCATCGATGCAT
1 TGCATCGATGCAT
208133 GGTGTAGTGC
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
64 33 0.50
65 33 0.50
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATATACAGTGCATCGATACATCAACATTAAATAAAAACATCGAATAGGATTTA
Found at i:208130 original size:64 final size:66
Alignment explanation
Indices: 208028--208149 Score: 196
Period size: 64 Copynumber: 1.9 Consensus size: 66
208018 TACATGAATT
208028 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G-AGTGCATCGATGTATCCC
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCAT-AGTGTAGTGCATCGATGTATCCC
208091 CA
65 CA
* *
208093 TTAAATA-CAAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCGATG
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATG
208150 CATACCTTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
63 1 0.02
64 33 0.62
65 19 0.36
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (66 bp):
TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGTATCCCC
A
Found at i:209619 original size:22 final size:21
Alignment explanation
Indices: 209565--209628 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
209555 AGTCGAGGGT
209565 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
209586 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
209608 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
209629 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:211181 original size:20 final size:20
Alignment explanation
Indices: 211145--211183 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
211135 AATGATAAAA
*
211145 TATAAAATATATGATTTATT
1 TATAAAATATATCATTTATT
211165 TATAAAATA-ATACATTTAT
1 TATAAAATATAT-CATTTAT
211184 ATACGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
TATAAAATATATCATTTATT
Found at i:211536 original size:23 final size:23
Alignment explanation
Indices: 211502--211548 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
211492 AGTCTACATG
*
211502 TATGACATATTTTCATCTGTCTT
1 TATGACACATTTTCATCTGTCTT
*
211525 TATGACACATTTTCTTCTGTCTT
1 TATGACACATTTTCATCTGTCTT
211548 T
1 T
211549 CGACATGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (23 bp):
TATGACACATTTTCATCTGTCTT
Found at i:211559 original size:22 final size:23
Alignment explanation
Indices: 211505--211559 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
211495 CTACATGTAT
*
211505 GACATATTTTCATCTGTCTTTAT
1 GACATATTTTCATCTGTCTTTAC
* *
211528 GACACATTTTCTTCTGTCTTT-C
1 GACATATTTTCATCTGTCTTTAC
*
211550 GACATGTTTT
1 GACATATTTT
211560 TCGGTTGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (23 bp):
GACATATTTTCATCTGTCTTTAC
Found at i:215673 original size:23 final size:24
Alignment explanation
Indices: 215647--215698 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
215637 TAATTATGAA
* *
215647 AAATATATA-ATTTATATATTTAT
1 AAATATAAATATTTATATATTTAG
*
215670 AAATA-AAATATTTATTTATTTAG
1 AAATATAAATATTTATATATTTAG
215693 AAATAT
1 AAATAT
215699 CAGAAAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AAATATAAATATTTATATATTTAG
Found at i:215842 original size:104 final size:102
Alignment explanation
Indices: 215645--215862 Score: 258
Period size: 104 Copynumber: 2.1 Consensus size: 102
215635 TATAATTATG
* * *
215645 AAAAATATATAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGAC
1 AAAAATAAATAATTTATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGAAC
* * * * * *
215710 TTCTAGGTGCCTTAAGACAGCTCTTTTCTTTGATATTA
66 ATCCAAGTACCTTAAGACAGCTCCTTTC-TTAATATTA
**
215748 AAAAATAAATAATTTATATAATTTATAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGA
1 AAAAATAAATAATTTATAT-ATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GA
* ** * *
215813 ACATCCAATTATTTTAAGACTGC-CCTTTCTTAATATTG
64 ACATCCAAGTACCTTAAGACAGCTCCTTTCTTAATATTA
215851 AAAAATAAATAA
1 AAAAATAAATAA
215863 ATATTAAAAC
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
103 37 0.38
104 44 0.45
105 16 0.16
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (102 bp):
AAAAATAAATAATTTATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGAAC
ATCCAAGTACCTTAAGACAGCTCCTTTCTTAATATTA
Found at i:215933 original size:24 final size:23
Alignment explanation
Indices: 215906--216003 Score: 58
Period size: 25 Copynumber: 4.1 Consensus size: 23
215896 ATTAAATAAG
215906 ATTTTAATAAATAAAATAAATAT
1 ATTTTAATAAATAAAATAAATAT
* * *
215929 -TATTTATTATAT-AAATATATAT
1 AT-TTTAATAAATAAAATAAATAT
215951 ATTTATAACTAAATAATAAT-AATAAT
1 ATTT-TAA-TAAATAA-AATAAAT-AT
** *
215977 AGTAATAATAATTAAAAGTAAATAT
1 A-TTTTAATAAATAAAA-TAAATAT
216002 AT
1 AT
216004 AAAATTAACA
Statistics
Matches: 56, Mismatches: 9, Indels: 19
0.67 0.11 0.23
Matches are distributed among these distances:
22 12 0.21
23 11 0.20
24 7 0.12
25 13 0.23
26 12 0.21
27 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (23 bp):
ATTTTAATAAATAAAATAAATAT
Found at i:217123 original size:3 final size:3
Alignment explanation
Indices: 217115--217167 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
217105 ATATTGTTTG
* *
217115 TAA TAA TAA TATA TAA TAA TAAA TAA -AA TTA TAA TAA T-A TAT TAA
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
217160 TAA TAA TA
1 TAA TAA TA
217168 TTAAAAACAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:217132 original size:10 final size:10
Alignment explanation
Indices: 217117--217164 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
217107 ATTGTTTGTA
217117 ATAATAATAT
1 ATAATAATAT
*
217127 ATAATAATAA
1 ATAATAATAT
217137 ATAA-AAT-T
1 ATAATAATAT
217145 ATAATAATAT
1 ATAATAATAT
217155 ATTAATAATA
1 A-TAATAATA
217165 ATATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 15 0.45
11 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATAATAT
Found at i:217148 original size:25 final size:25
Alignment explanation
Indices: 217120--217170 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
217110 GTTTGTAATA
217120 ATAAT-ATATAATAATAAATAAAATT
1 ATAATAATATAATAAT-AATAAAATT
* *
217145 ATAATAATATATTAATAATAATATT
1 ATAATAATATAATAATAATAAAATT
217170 A
1 A
217171 AAAACAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATAATATAATAATAATAAAATT
Found at i:218009 original size:101 final size:101
Alignment explanation
Indices: 217721--218018 Score: 406
Period size: 101 Copynumber: 3.0 Consensus size: 101
217711 TGTGATAGAG
* * *
217721 TCAAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAATTCTTCTTCC-TCTTCAGATAAGTTCT
1 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *** *
217785 TCTCATTATGAACCTTCT-T-TCCATCGAATGATGAAT
66 TCTCATTATGAACTTTCTCTGGAAAT-G-CTGATGAAT
* *
217821 TCGAGCAAAAGGTTGAACAAGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
**
217886 TCTCATTATGAACTCGAC-CTGGAAATGCTGATGAAT
66 TCTCATTATGAACT-TTCTCTGGAAATGCTGATGAAT
* *
217922 TCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCT
1 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
217987 TCTCATTATGAACTTTCTCTGGAAAAGCTGAT
66 TCTCATTATGAACTTTCTCTGGAAATGCTGAT
218019 CCATCAAGTG
Statistics
Matches: 174, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
100 45 0.26
101 124 0.71
102 3 0.02
103 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (101 bp):
TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTTTCTCTGGAAATGCTGATGAAT
Done.