Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003055.1 Hibiscus syriacus cultivar Beakdansim tig00006371_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: 306309
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5761 original size:19 final size:20
Alignment explanation
Indices: 5737--5787 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5727 CGGCCAAGAG
**
5737 CATGTATTTTCAT-TTAAAT
1 CATGTATTTTCATCAAAAAT
5756 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
5776 CATGTATTTTCA
1 CATGTATTTTCA
5788 AAAGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:12856 original size:27 final size:27
Alignment explanation
Indices: 12808--12859 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
12798 TTCTTTCTTT
*
12808 TTTTTCTTCTTTTTTCGGAGTGCTTGA
1 TTTTTCTTCTTTTTTCGCAGTGCTTGA
12835 TTTTTCTTCTTCTTTT-GCAGTGCTT
1 TTTTTCTTCTT-TTTTCGCAGTGCTT
12860 CAATTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.06, C:0.17, G:0.15, T:0.62
Consensus pattern (27 bp):
TTTTTCTTCTTTTTTCGCAGTGCTTGA
Found at i:14797 original size:19 final size:20
Alignment explanation
Indices: 14770--14809 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
14760 GTATAATAAT
14770 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
14790 ATAA-TAATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
14809 A
1 A
14810 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:15272 original size:19 final size:20
Alignment explanation
Indices: 15222--15264 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
15212 GAAACCCCTT
*
15222 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
15242 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
15261 TGAA
1 TGAA
15265 GATGCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:18972 original size:19 final size:20
Alignment explanation
Indices: 18944--18983 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
18934 GTATAATAAT
18944 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
18964 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
18983 A
1 A
18984 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:19438 original size:19 final size:20
Alignment explanation
Indices: 19396--19447 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
19386 GAAACCCCTT
*
19396 TGAAAATACATGATTTTTTTA
1 TGAAAATACATGA-TTTTTAA
19417 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
19436 TGAAGATACATG
1 TGAAAATACATG
19448 CTCTTGGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:20376 original size:30 final size:31
Alignment explanation
Indices: 20337--20396 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
20327 ACATGCTGCC
**
20337 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
20368 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
20397 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:24833 original size:36 final size:36
Alignment explanation
Indices: 24793--24865 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
24783 TCAGACTATT
24793 TTGATTAATATAACTGAGATTATTCTCTTCCTTAAG
1 TTGATTAATATAACTGAGATTATTCTCTTCCTTAAG
*
24829 TTGATTAATATAAGTGAGATTATTCTCTTCCTTAAG
1 TTGATTAATATAACTGAGATTATTCTCTTCCTTAAG
24865 T
1 T
24866 CCTGGTGACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (36 bp):
TTGATTAATATAACTGAGATTATTCTCTTCCTTAAG
Found at i:25404 original size:23 final size:25
Alignment explanation
Indices: 25369--25423 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
25359 AAATCCAGCA
25369 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGCACTCAAAAATG
* *
25392 AAGAAATTGAAAGCACTCAAAAATG
1 AAGAAAATCAAAGCACTCAAAAATG
25417 AAGAAAA
1 AAGAAAA
25424 AGAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 16 0.59
24 4 0.15
25 7 0.26
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.11
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAAATG
Found at i:31973 original size:59 final size:57
Alignment explanation
Indices: 31910--32029 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 57
31900 GGAGGGTTTG
* *
31910 TTAGAGCCATATTATCTTG-TTTTCCTTTTTATTATGACTAGGAGGATTCGATAGGACAC
1 TTAGAGCCATATTA--TTGATTTTAC-TTTTATTACGACTAGGAGGATTCGATAGGACAC
* * *
31969 TTAGAGCCATATTATTGACTTTTACTTTTCTTGCGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATTGA-TTTTACTTTTATTACGACTAGGAGGATTCGATAGGACAC
32027 TTA
1 TTA
32030 TCCATCTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
57 3 0.06
58 32 0.59
59 19 0.35
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (57 bp):
TTAGAGCCATATTATTGATTTTACTTTTATTACGACTAGGAGGATTCGATAGGACAC
Found at i:36320 original size:24 final size:24
Alignment explanation
Indices: 36266--36320 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
36256 GAAAAATTAG
*
36266 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
36289 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
36313 AAAAGAAA
1 AAAAGAAA
36321 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:40623 original size:25 final size:26
Alignment explanation
Indices: 40576--40625 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
40566 AAGAAAGTGA
40576 AGCACTCAAAAGAAAGAAAAAAATCC
1 AGCACTCAAAAGAAAGAAAAAAATCC
40602 AGCACTCAAAAG-AAGAAAAAAATC
1 AGCACTCAAAAGAAAGAAAAAAATC
40626 AAAGAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.62, C:0.18, G:0.12, T:0.08
Consensus pattern (26 bp):
AGCACTCAAAAGAAAGAAAAAAATCC
Found at i:43392 original size:13 final size:13
Alignment explanation
Indices: 43352--43426 Score: 102
Period size: 13 Copynumber: 6.0 Consensus size: 13
43342 TTGGTCAAAT
43352 AGGTATGTTG-AA
1 AGGTATGTTGAAA
43364 AGGTATGTTG-AA
1 AGGTATGTTGAAA
43376 AGGTATGTTGAAA
1 AGGTATGTTGAAA
43389 AGGTATGTTGAAA
1 AGGTATGTTGAAA
***
43402 AGGTAAAATGAAA
1 AGGTATGTTGAAA
43415 AGGTATG-TGAAA
1 AGGTATGTTGAAA
43427 GGTGTTTAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
12 27 0.47
13 30 0.53
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (13 bp):
AGGTATGTTGAAA
Found at i:46510 original size:20 final size:21
Alignment explanation
Indices: 46469--46517 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
46459 GCAAAGCTAT
*
46469 TGAGCTAATGTAAACATAACA
1 TGAGCTAAAGTAAACATAACA
*
46490 TGAGCTAAAGT-AACATGACA
1 TGAGCTAAAGTAAACATAACA
46510 TGAGCTAA
1 TGAGCTAA
46518 TGAATGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.22
Consensus pattern (21 bp):
TGAGCTAAAGTAAACATAACA
Found at i:46664 original size:20 final size:20
Alignment explanation
Indices: 46621--46663 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
46611 TAAAGATGTG
*
46621 AAAA-CATATATTATGCAAT
1 AAAATCATATAATATGCAAT
46640 AAAATCATATAATATGCAAGT
1 AAAATCATATAATATGCAA-T
46661 AAA
1 AAA
46664 TGATAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAATCATATAATATGCAAT
Found at i:46673 original size:25 final size:22
Alignment explanation
Indices: 46623--46674 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 22
46613 AAGATGTGAA
*
46623 AACATATATTATGCAATAAAAT
1 AACATATAATATGCAATAAAAT
46645 --CATATAATATGCAAGTAAATGAT
1 AACATATAATATGCAA-TAAA--AT
46668 AACATAT
1 AACATAT
46675 GATTATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 13 0.54
21 4 0.17
23 2 0.08
25 5 0.21
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.31
Consensus pattern (22 bp):
AACATATAATATGCAATAAAAT
Found at i:59492 original size:20 final size:21
Alignment explanation
Indices: 59468--59516 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
59458 AAATTTTGGC
59468 TTTTTTTGGCTCTTTTTT-TTG
1 TTTTTTTGGC-CTTTTTTGTTG
*
59489 TTTTTTTTGCCTTTTTTGTT-
1 TTTTTTTGGCCTTTTTTGTTG
59509 TTTTTTTG
1 TTTTTTTG
59517 TTTTTTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (21 bp):
TTTTTTTGGCCTTTTTTGTTG
Found at i:59513 original size:10 final size:9
Alignment explanation
Indices: 59480--59523 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
59470 TTTTTGGCTC
59480 TTTTTTTTG
1 TTTTTTTTG
59489 TTTTTTTTG
1 TTTTTTTTG
**
59498 CCTTTTTTG
1 TTTTTTTTG
59507 TTTTTTTTTG
1 -TTTTTTTTG
59517 TTTTTTT
1 TTTTTTT
59524 GAAAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:61260 original size:24 final size:25
Alignment explanation
Indices: 61224--61273 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
61214 TTAACTTTTC
*
61224 TTTTCTTCTTTTTGAGTGCTTGAAT
1 TTTTCTTCTTTTTGAGTGCTTCAAT
61249 TTTTCTTC-TTTTGAGTGCTTCAAT
1 TTTTCTTCTTTTTGAGTGCTTCAAT
61273 T
1 T
61274 ACTTTGCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (25 bp):
TTTTCTTCTTTTTGAGTGCTTCAAT
Found at i:63779 original size:11 final size:11
Alignment explanation
Indices: 63763--63807 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
63753 CACTCTATGG
63763 CAGCTCACAAT
1 CAGCTCACAAT
*
63774 CAGCTCACAGT
1 CAGCTCACAAT
* *
63785 TAGCTCACAGT
1 CAGCTCACAAT
*
63796 CAGCTCTCAAT
1 CAGCTCACAAT
63807 C
1 C
63808 TCCATGGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.29, C:0.36, G:0.13, T:0.22
Consensus pattern (11 bp):
CAGCTCACAAT
Found at i:66847 original size:95 final size:96
Alignment explanation
Indices: 66720--66944 Score: 267
Period size: 95 Copynumber: 2.4 Consensus size: 96
66710 AGGACCGACG
* *
66720 TAGTGGTATCGATACCATAGTAAGGGTATCGATACCAGGT-AACATCGAACCTAATTTTGGTATC
1 TAGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTCAACATCGAACCTAATTTTGGTATC
* * * *
66784 GATACCATAAGGGGGTATTGGTACTATAACA
66 GATACCAGAAGGGAGTATCGATACTATAACA
* ** * * *
66815 TAGTAGTATCGATACAATGGTAAGGGTATCGATA-TTGGTCCACATCGAATCTAATTTTGGTATT
1 TAGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTCAACATCGAACCTAATTTTGGTATC
* **
66879 GATACCAGAAGGGAGTATCGATATTATAGTA
66 GATACCAGAAGGGAGTATCGATACTATAACA
* *
66910 TGGTAGTATCGATACCATGGT-GGGAGTATCGATAC
1 TAGTAGTATCGATACCATGGTAAGG-GTATCGATAC
66945 TAAGGAACCA
Statistics
Matches: 109, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
94 5 0.05
95 104 0.95
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (96 bp):
TAGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGTCAACATCGAACCTAATTTTGGTATC
GATACCAGAAGGGAGTATCGATACTATAACA
Found at i:67382 original size:59 final size:59
Alignment explanation
Indices: 67291--67536 Score: 377
Period size: 59 Copynumber: 4.1 Consensus size: 59
67281 TAAAATGATA
*
67291 GTATGAATTTCAATATATTGGGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGT
1 GTATGAATTTCAGTATA--GGGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGT
* * *
67352 GTATGAATTTTAGTATAGGGCACTTTGTGTGCTAAAATGATAATAAATTCATACTAAGT
1 GTATGAATTTCAGTATAGGGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGT
* *
67411 GTATGAATTTCCA-TATAGGGCACTTCGTGTGCTAACATGATAAGAAATTCATGCTAAGT
1 GTATGAATTT-CAGTATAGGGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGT
* * *
67470 GTATGAATTTCAGTATAGGGCAATTTGTGTGCTAAAATGTTAAGAAATTCATACTAAGT
1 GTATGAATTTCAGTATAGGGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGT
67529 GTATGAAT
1 GTATGAAT
67537 GGTTGATAAA
Statistics
Matches: 169, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
58 2 0.01
59 151 0.89
60 1 0.01
61 15 0.09
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (59 bp):
GTATGAATTTCAGTATAGGGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGT
Found at i:78164 original size:19 final size:20
Alignment explanation
Indices: 78140--78190 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
78130 CGGCCAAGAG
**
78140 CATGTATTTTCAT-TTAAAT
1 CATGTATTTTCATCAAAAAT
78159 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
78179 CATGTATTTTCA
1 CATGTATTTTCA
78191 AAAGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:85112 original size:19 final size:20
Alignment explanation
Indices: 85071--85121 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
85061 GAAACCCCTT
*
85071 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
85091 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
85110 TGAAGATACATG
1 TGAAAATACATG
85122 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:88815 original size:19 final size:19
Alignment explanation
Indices: 88793--88835 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
88783 AATGAATAAT
*
88793 AATATAAGTAAT-GGAATGA
1 AATATAAG-AATAGAAATGA
88812 AATAATAAGAATAGAAATGA
1 AAT-ATAAGAATAGAAATGA
88832 AATA
1 AATA
88836 AATAAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.23
Consensus pattern (19 bp):
AATATAAGAATAGAAATGA
Found at i:88845 original size:24 final size:24
Alignment explanation
Indices: 88802--88849 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
88792 TAATATAAGT
* *
88802 AATGGAATGAAATAATAAGAATAGA
1 AATGAAATGAAATAAAAAG-ATAGA
88827 AATGAAAT-AAATAAAAAGATAGA
1 AATGAAATGAAATAAAAAGATAGA
88850 GATGGCTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 7 0.33
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.19
Consensus pattern (24 bp):
AATGAAATGAAATAAAAAGATAGA
Found at i:89290 original size:19 final size:20
Alignment explanation
Indices: 89249--89299 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
89239 GAAACCCCTT
*
89249 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
89269 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
89288 TGAAGATACATG
1 TGAAAATACATG
89300 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:91286 original size:11 final size:11
Alignment explanation
Indices: 91270--91330 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
91260 AAATTTTAGC
*
91270 TTTTTTGGCTT
1 TTTTTTGCCTT
***
91281 TTTTTTTTGTT
1 TTTTTTGCCTT
91292 -TTTTTGCCTT
1 TTTTTTGCCTT
91302 TTTTTTGCCTT
1 TTTTTTGCCTT
* **
91313 ATTTTTGTTTT
1 TTTTTTGCCTT
91324 TTTTTTG
1 TTTTTTG
91331 AAAAAAATAG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
10 7 0.18
11 32 0.82
ACGTcount: A:0.02, C:0.08, G:0.11, T:0.79
Consensus pattern (11 bp):
TTTTTTGCCTT
Found at i:91324 original size:21 final size:19
Alignment explanation
Indices: 91270--91330 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 19
91260 AAATTTTAGC
*
91270 TTTTTTGGCTTTTTTTTTTG
1 TTTTTTTGC-TTTTTTTTTG
*
91290 TTTTTTTGCCTTTTTTTTG
1 TTTTTTTGCTTTTTTTTTG
*
91309 CCTTATTTTTGTTTTTTTTTTG
1 --TT-TTTTTGCTTTTTTTTTG
91331 AAAAAAATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.26
20 8 0.24
21 2 0.06
22 15 0.44
ACGTcount: A:0.02, C:0.08, G:0.11, T:0.79
Consensus pattern (19 bp):
TTTTTTTGCTTTTTTTTTG
Found at i:99990 original size:5 final size:5
Alignment explanation
Indices: 99980--100010 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
99970 CTTCAACTTC
*
99980 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
100011 CTTTTTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:104013 original size:16 final size:16
Alignment explanation
Indices: 103980--104028 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
103970 TAAGGTAATG
103980 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
103998 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
104014 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
104029 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:105474 original size:201 final size:201
Alignment explanation
Indices: 105129--105528 Score: 782
Period size: 201 Copynumber: 2.0 Consensus size: 201
105119 GTAGGCTGCA
105129 ATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCCAAAACACCAAGGGATG
1 ATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCCAAAACACCAAGGGATG
105194 CTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGCATTC
66 CTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGCATTC
105259 AAATCATCCTTAGGGCCAAACCAACACATAACCATTCGGCCAAGAGCATGTATCTTCATTAAAAT
131 AAATCATCCTTAGGGCCAAACCAACACATAACCATTCGGCCAAGAGCATGTATCTTCATTAAAAT
105324 CATGCC
196 CATGCC
105330 ATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCCAAAACACCAAGGGATG
1 ATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCCAAAACACCAAGGGATG
105395 CTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGCATTC
66 CTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGCATTC
* *
105460 AAATCATCCTTAGGGCCGAACCAACACATAACTATTCGGCCAAGAGCATGTATCTTCATTAAAAT
131 AAATCATCCTTAGGGCCAAACCAACACATAACCATTCGGCCAAGAGCATGTATCTTCATTAAAAT
105525 CATG
196 CATG
105529 TATTTTCATC
Statistics
Matches: 197, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
201 197 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (201 bp):
ATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATAGGCGCCAAAACACCAAGGGATG
CTTCCTATTCGGCCAAAGACTCCTTCCTCTCCATTTTGGCGCCCAAATAACTTCCAAATGCATTC
AAATCATCCTTAGGGCCAAACCAACACATAACCATTCGGCCAAGAGCATGTATCTTCATTAAAAT
CATGCC
Found at i:105530 original size:19 final size:20
Alignment explanation
Indices: 105506--105556 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
105496 CGGCCAAGAG
* *
105506 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
105525 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
*
105545 AATGTATTTTCA
1 CATGTATTTTCA
105557 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:106327 original size:6 final size:6
Alignment explanation
Indices: 106316--106359 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
106306 GATGTATGAG
*
106316 TCTTTT TC-TTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
106360 TGTTACTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:106339 original size:12 final size:12
Alignment explanation
Indices: 106316--106359 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
106306 GATGTATGAG
106316 TCTTTTTC-TTT
1 TCTTTTTCTTTT
*
106327 TCTTTTTGTTTT
1 TCTTTTTCTTTT
106339 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
106352 TCTCTTTT
1 TCT-TTTT
106360 TGTTACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 13 0.46
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:108336 original size:14 final size:13
Alignment explanation
Indices: 108319--108368 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
108309 GTGCAAAAAG
108319 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
108333 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
108346 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
108357 AAAGAAAAAGAA
1 AAAGAAAAAGAA
108369 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:108365 original size:19 final size:18
Alignment explanation
Indices: 108313--108368 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
108303 ATTGGAGTGC
108313 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
108330 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
108349 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
108368 A
1 A
108369 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:108366 original size:11 final size:11
Alignment explanation
Indices: 108313--108368 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
108303 ATTGGAGTGC
108313 AAAAAG-AAAG
1 AAAAAGAAAAG
108323 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
108337 AAGAAGAAAAG
1 AAAAAGAAAAG
108348 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
108361 AAAAAGAA
1 AAAAAGAA
108369 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:118520 original size:22 final size:21
Alignment explanation
Indices: 118489--118529 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
118479 CATCTCCATT
*
118489 TCATCATCAATACCATCAACA
1 TCATCATCAAGACCATCAACA
*
118510 TCATCCATCAAGACTATCAA
1 TCAT-CATCAAGACCATCAA
118530 TTCCACAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.24
Consensus pattern (21 bp):
TCATCATCAAGACCATCAACA
Found at i:119475 original size:169 final size:169
Alignment explanation
Indices: 119196--119517 Score: 635
Period size: 169 Copynumber: 1.9 Consensus size: 169
119186 AAAAACAACA
119196 CTTTAATGAGAATACATGCTCTTGGCCAAATGGTTATGTGTTGGTTCGGCCCTAAGGATGATTTG
1 CTTTAATGAGAATACATGCTCTTGGCCAAATGGTTATGTGTTGGTTCGGCCCTAAGGATGATTTG
119261 AATGCATTTGGAAGTTATTTGGGCGCCAAAATGAAGAGGAAAGTGTCTTTGGTCGAATAGGAAGC
66 AATGCATTTGGAAGTTATTTGGGCGCCAAAATGAAGAGGAAAGTGTCTTTGGTCGAATAGGAAGC
119326 ATCACTTGATGTTTTGGCGCCAAATGAAGAGGAAAATGT
131 ATCACTTGATGTTTTGGCGCCAAATGAAGAGGAAAATGT
*
119365 CTTTAATGAGAATACATGCTCTTGGCCGAATGGTTATGTGTTGGTTCGGCCCTAAGGATGATTTG
1 CTTTAATGAGAATACATGCTCTTGGCCAAATGGTTATGTGTTGGTTCGGCCCTAAGGATGATTTG
119430 AATGCATTTGGAAGTTATTTGGGCGCCAAAATGAAGAGGAAAGTGTCTTTGGTCGAATAGGAAGC
66 AATGCATTTGGAAGTTATTTGGGCGCCAAAATGAAGAGGAAAGTGTCTTTGGTCGAATAGGAAGC
119495 ATCACTTGATGTTTTGGCGCCAA
131 ATCACTTGATGTTTTGGCGCCAA
119518 TTTGTTGTCA
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 152 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (169 bp):
CTTTAATGAGAATACATGCTCTTGGCCAAATGGTTATGTGTTGGTTCGGCCCTAAGGATGATTTG
AATGCATTTGGAAGTTATTTGGGCGCCAAAATGAAGAGGAAAGTGTCTTTGGTCGAATAGGAAGC
ATCACTTGATGTTTTGGCGCCAAATGAAGAGGAAAATGT
Found at i:120389 original size:30 final size:30
Alignment explanation
Indices: 120353--120413 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
120343 AAGGCTAACC
120353 AGGCTTCTTTAATAATAGAGAAGTTGGCAA
1 AGGCTTCTTTAATAATAGAGAAGTTGGCAA
120383 AGGCTTCTTTAATAATAGAGAAGTTGGCAA
1 AGGCTTCTTTAATAATAGAGAAGTTGGCAA
120413 A
1 A
120414 CATGTTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (30 bp):
AGGCTTCTTTAATAATAGAGAAGTTGGCAA
Found at i:121149 original size:19 final size:20
Alignment explanation
Indices: 121102--121152 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
121092 GAAACCCCTT
**
121102 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
121122 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
121141 TGAAGATACATG
1 TGAAAATACATG
121153 CTCTTGGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:124391 original size:11 final size:11
Alignment explanation
Indices: 124375--124417 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
124365 TGTAAATTGC
124375 TTCTTTTCGTT
1 TTCTTTTCGTT
124386 TTCTTTTCGTT
1 TTCTTTTCGTT
*
124397 TTC--TTCTTT
1 TTCTTTTCGTT
124406 TTCTTTTC-TT
1 TTCTTTTCGTT
124416 TT
1 TT
124418 GCACTCCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 8 0.28
10 4 0.14
11 17 0.59
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (11 bp):
TTCTTTTCGTT
Found at i:124412 original size:5 final size:5
Alignment explanation
Indices: 124375--124417 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
124365 TGTAAATTGC
*
124375 TTCTT TTCGTT TTCTT TTCGTT TTCTT CT-TT TTCTT TTCTT TT
1 TTCTT TTC-TT TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT TT
124418 GCACTCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 20 0.61
6 10 0.30
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.77
Consensus pattern (5 bp):
TTCTT
Found at i:124464 original size:6 final size:6
Alignment explanation
Indices: 124441--124484 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
124431 GTTGTAGGAG
* *
124441 TCTTTT TCTTTC TCTTTT TGTTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
124485 GTTGCTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:124474 original size:25 final size:24
Alignment explanation
Indices: 124441--124487 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
124431 GTTGTAGGAG
124441 TCTTTTTCTTTCTCTTTTTGTTTT
1 TCTTTTTCTTTCTCTTTTTGTTTT
*
124465 TCTTCTTTCTTTTTCTTTTTGTT
1 TCTT-TTTCTTTCTCTTTTTGTT
124488 GCTTTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (24 bp):
TCTTTTTCTTTCTCTTTTTGTTTT
Found at i:124475 original size:19 final size:18
Alignment explanation
Indices: 124441--124484 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
124431 GTTGTAGGAG
124441 TCTTTTTCTTTCTCTTTT
1 TCTTTTTCTTTCTCTTTT
* *
124459 TGTTTTTCTTCTTTCTTTT
1 TCTTTTTCTT-TCTCTTTT
124478 TCTTTTT
1 TCTTTTT
124485 GTTGCTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (18 bp):
TCTTTTTCTTTCTCTTTT
Found at i:127097 original size:9 final size:9
Alignment explanation
Indices: 127083--127122 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
127073 TTAGAGTACA
127083 AAAAGAAAG
1 AAAAGAAAG
*
127092 AAAAGACA-
1 AAAAGAAAG
*
127100 AAAGGAAAG
1 AAAAGAAAG
127109 AAAAGAAAG
1 AAAAGAAAG
127118 AAAAG
1 AAAAG
127123 GAATAGAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 6 0.23
9 20 0.77
ACGTcount: A:0.75, C:0.03, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:127102 original size:17 final size:17
Alignment explanation
Indices: 127080--127114 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
127070 AAATTAGAGT
127080 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
*
127097 ACAAAAGGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
127114 A
1 A
127115 AAGAAAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.74, C:0.06, G:0.20, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:127370 original size:12 final size:14
Alignment explanation
Indices: 127340--127371 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
127330 TTAATCTTTC
127340 TTCTACTTTTCCAT
1 TTCTACTTTTCCAT
127354 TTCTA-TTTTCC-T
1 TTCTACTTTTCCAT
127366 TTCTAC
1 TTCTAC
127372 CCTACCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 6 0.35
14 5 0.29
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCTACTTTTCCAT
Found at i:132655 original size:21 final size:20
Alignment explanation
Indices: 132631--132669 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
132621 ATGTTTGTTT
132631 ATGGTAATGGAGCTAAGTATG
1 ATGGTAAT-GAGCTAAGTATG
*
132652 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
132670 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:133675 original size:19 final size:21
Alignment explanation
Indices: 133651--133702 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
133641 CGGCCAAGAG
*
133651 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
133670 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
133691 CATGTATTTTCA
1 CATGTATTTTCA
133703 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:136016 original size:22 final size:22
Alignment explanation
Indices: 135991--136032 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
135981 CAATTCATTT
135991 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
136013 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
136033 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:136368 original size:11 final size:10
Alignment explanation
Indices: 136352--136378 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
136342 ATTTTTTTTC
136352 AAAAAAACAA
1 AAAAAAACAA
136362 AAAAAAACAA
1 AAAAAAACAA
136372 AAAAAAA
1 AAAAAAA
136379 GCCTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:140590 original size:22 final size:21
Alignment explanation
Indices: 140561--140605 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
140551 TTGCAATTCA
140561 TTTATCTT-TTCTTTATCTTGT
1 TTTATCTTATT-TTTATCTTGT
140582 TTTAGTCTTATTTTTATCTTGT
1 TTTA-TCTTATTTTTATCTTGT
140604 TT
1 TT
140606 CCAGCACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.18
22 16 0.73
23 2 0.09
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (21 bp):
TTTATCTTATTTTTATCTTGT
Found at i:145149 original size:22 final size:22
Alignment explanation
Indices: 145124--145165 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
145114 CAATTCATTT
145124 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
145146 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
145166 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:148408 original size:912 final size:912
Alignment explanation
Indices: 146755--148580 Score: 3418
Period size: 912 Copynumber: 2.0 Consensus size: 912
146745 GAAGGGGAGG
*
146755 ATGATGTGATCCTGTTTAGCACCAACTTTCTGCATGACATACTCACATCATTGAAGAACCATCAA
1 ATGAAGTGATCCTGTTTAGCACCAACTTTCTGCATGACATACTCACATCATTGAAGAACCATCAA
* *
146820 ACTCAATATAAGGGAGTTCTACCATACTTTATATTATATTTACTTATTTATACACTATATATATT
66 ACTCAATATAAGGGAGTTCTACCATACTTTATATTATATTTACTGATTTACACACTATATATATT
*
146885 ATTATGAGCATACATTTGCATATTTGACTATACTTGAATTATCATAGTATGTGCATTCATTCATT
131 ATTATGAGCATACATTTGCATATTAGACTATACTTGAATTATCATAGTATGTGCATTCATTCATT
146950 ATATCCTATGGTTTGCATCATTGATTGATATTCATGTATATAATCTATAGTTATAATATTAATAT
196 ATATCCTATGGTTTGCATCATTGATTGATATTCATGTATATAATCTATAGTTATAATATTAATAT
*
147015 TCATTCATTATCATATGATGCATGAATTATTATTATAACCTATAGTTCACATCTTTATAATATGC
261 TCATTCATTATCATATGATGCATAAATTATTATTATAACCTATAGTTCACATCTTTATAATATGC
* *
147080 ACATCATTATATTATATGCATTATATAGTTTATATACTTAGTTTATTTCTTTATGTTATGCATGT
326 ACATCATTATATTATATGCATTATATAGTCTATATACTTAGTTTATTTCTTCATGTTATGCATGT
147145 AGGCATATTCGGCCAACACTTGGAAACTACATTTGAGCTTAAATAATGATAAGGAGCTAGGAAAA
391 AGGCATATTCGGCCAACACTTGGAAACTACATTTGAGCTTAAATAATGATAAGGAGCTAGGAAAA
147210 CTTTCATAGGATGACTCGGGAGATCATGAAGAACAAATGATGAAAAGTTGTCAGCTGACCCCCGA
456 CTTTCATAGGATGACTCGGGAGATCATGAAGAACAAATGATGAAAAGTTGTCAGCTGACCCCCGA
*
147275 GCTCATAGCTCACTTGAGCTGGACTTTTGAGCTAGCTAGAGACCTCATTTCAGCTGGAGAGTTGC
521 GCTCATAGCTCACTTGAGCTGGACTTTTGAGCTAGATAGAGACCTCATTTCAGCTGGAGAGTTGC
*
147340 ACCATCATCACCACAACACAGAGTACTTCAAATATAGTCTAAGTCAATTTTTGTGGATTCGTACC
586 ACCATCATCACCACAACACAGAGTACTTCAAATATAGTATAAGTCAATTTTTGTGGATTCGTACC
147405 TTTTCGCGAAGAGTTGCCATTCCAAGAGGTGCCTTTTCACAAGGAGCTGGCCAAAGACTCATCTT
651 TTTTCGCGAAGAGTTGCCATTCCAAGAGGTGCCTTTTCACAAGGAGCTGGCCAAAGACTCATCTT
* *
147470 CATGTAATTCACCTATGACCAGCTCATCTTCATCTCATACACATGGGAAGTAGCTCAAATGATGA
716 CATGTAATTCACCTATGACCAGCTCATCTTCAGCTCATACACATGGGAACTAGCTCAAATGATGA
* *
147535 AAGGTTACCTTCCACAAATGTGACCTTTCATGACAAGTTGCTGCCCATTGAATACCATGACACCT
781 AAGGTTACCTTCCACAAATGTGACCTTTCATGACAAGCTGCTGCCCATTGAAGACCATGACACCT
147600 AGATGCATGTTGGAAGCCAAGTCACGCCTAGTTGCTGCAATCTTCATTCCATGGACTTCAAGACA
846 AGATGCATGTTGGAAGCCAAGTCACGCCTAGTTGCTGCAATCTTCATTCCATGGACTTCAAGACA
147665 TT
911 TT
* *
147667 ATGAAGTGATCCTGTTTAGCACCAACTTTCTGCATGGCATACTTACATCATTGAAGAACCATCAA
1 ATGAAGTGATCCTGTTTAGCACCAACTTTCTGCATGACATACTCACATCATTGAAGAACCATCAA
*
147732 ACTCAATATAAGGGAGTTCTACCATACTTTATATTATATTTACTGATTTACGCACTATATATATT
66 ACTCAATATAAGGGAGTTCTACCATACTTTATATTATATTTACTGATTTACACACTATATATATT
147797 ATTATGAGCATACATTTGCATATTAGACTATACTTGAATTATCATAGTATGTGCATTCATTCATT
131 ATTATGAGCATACATTTGCATATTAGACTATACTTGAATTATCATAGTATGTGCATTCATTCATT
147862 ATATCCTATGGTTTGCATCATTGATTGATATTCATGTATATAATCTATAGTTATAATATTAATAT
196 ATATCCTATGGTTTGCATCATTGATTGATATTCATGTATATAATCTATAGTTATAATATTAATAT
*
147927 TCATTCATTATCATATGATGCATAAATTATTATTATAACGTATAGTTCACATCTTTATAATATGC
261 TCATTCATTATCATATGATGCATAAATTATTATTATAACCTATAGTTCACATCTTTATAATATGC
147992 ACATCATTATATTATATGCATTATATAGTCTATATACTTAGTTTATTTCTTCATGTTATGCATGT
326 ACATCATTATATTATATGCATTATATAGTCTATATACTTAGTTTATTTCTTCATGTTATGCATGT
* * *
148057 AGGCATATTCGGCCAACACTTGGGAGCTACATTTGAGCTTAACTAATGATAAGGAGCTAGGAAAA
391 AGGCATATTCGGCCAACACTTGGAAACTACATTTGAGCTTAAATAATGATAAGGAGCTAGGAAAA
*
148122 CTTTCATAGGATGACTCGGGAGATCATGAAGAACAAATGATGAAAAGTTGTCAGCTGACCCCTGA
456 CTTTCATAGGATGACTCGGGAGATCATGAAGAACAAATGATGAAAAGTTGTCAGCTGACCCCCGA
148187 GCTCATAGCTCACTTGAGCTGGACTTTTGAGCTAGATAGAGACCTCATTTCAGCTGGAGAGTTGC
521 GCTCATAGCTCACTTGAGCTGGACTTTTGAGCTAGATAGAGACCTCATTTCAGCTGGAGAGTTGC
* * *
148252 ACCATCATCACCACCACATAGAGTACTTCAAATATGGTATAAGTCAATTTTTGTGGATTCGTACC
586 ACCATCATCACCACAACACAGAGTACTTCAAATATAGTATAAGTCAATTTTTGTGGATTCGTACC
148317 TTTTCGCGAAGAGTTGCCATTCCAAGAGGTGCCTTTTCACAAGGAGCTGGCCAAAGACTCATCTT
651 TTTTCGCGAAGAGTTGCCATTCCAAGAGGTGCCTTTTCACAAGGAGCTGGCCAAAGACTCATCTT
148382 CATGTAATTCACCTATGACCAGCTCATCTTCAGCTCATACACATGGGAACTAGCTCAAATGATGA
716 CATGTAATTCACCTATGACCAGCTCATCTTCAGCTCATACACATGGGAACTAGCTCAAATGATGA
*
148447 AAGGTTACCTTCCACAAATGTGACCTTTCATGACAAGCTGCTGCCCATTGAAGCCCATGACACCT
781 AAGGTTACCTTCCACAAATGTGACCTTTCATGACAAGCTGCTGCCCATTGAAGACCATGACACCT
*
148512 AGATGCATGTTGGAAGCCAAGTCACGCCTAGTTGCTGCCATCTTCATTCCATGGACTTCAAGACA
846 AGATGCATGTTGGAAGCCAAGTCACGCCTAGTTGCTGCAATCTTCATTCCATGGACTTCAAGACA
148577 TT
911 TT
148579 AT
1 AT
148581 CCTATGGTTG
Statistics
Matches: 888, Mismatches: 26, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
912 888 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (912 bp):
ATGAAGTGATCCTGTTTAGCACCAACTTTCTGCATGACATACTCACATCATTGAAGAACCATCAA
ACTCAATATAAGGGAGTTCTACCATACTTTATATTATATTTACTGATTTACACACTATATATATT
ATTATGAGCATACATTTGCATATTAGACTATACTTGAATTATCATAGTATGTGCATTCATTCATT
ATATCCTATGGTTTGCATCATTGATTGATATTCATGTATATAATCTATAGTTATAATATTAATAT
TCATTCATTATCATATGATGCATAAATTATTATTATAACCTATAGTTCACATCTTTATAATATGC
ACATCATTATATTATATGCATTATATAGTCTATATACTTAGTTTATTTCTTCATGTTATGCATGT
AGGCATATTCGGCCAACACTTGGAAACTACATTTGAGCTTAAATAATGATAAGGAGCTAGGAAAA
CTTTCATAGGATGACTCGGGAGATCATGAAGAACAAATGATGAAAAGTTGTCAGCTGACCCCCGA
GCTCATAGCTCACTTGAGCTGGACTTTTGAGCTAGATAGAGACCTCATTTCAGCTGGAGAGTTGC
ACCATCATCACCACAACACAGAGTACTTCAAATATAGTATAAGTCAATTTTTGTGGATTCGTACC
TTTTCGCGAAGAGTTGCCATTCCAAGAGGTGCCTTTTCACAAGGAGCTGGCCAAAGACTCATCTT
CATGTAATTCACCTATGACCAGCTCATCTTCAGCTCATACACATGGGAACTAGCTCAAATGATGA
AAGGTTACCTTCCACAAATGTGACCTTTCATGACAAGCTGCTGCCCATTGAAGACCATGACACCT
AGATGCATGTTGGAAGCCAAGTCACGCCTAGTTGCTGCAATCTTCATTCCATGGACTTCAAGACA
TT
Found at i:148842 original size:19 final size:21
Alignment explanation
Indices: 148818--148864 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
148808 CGGCCAAGAG
148818 CATGTATCTTCA-TTAAAA-T
1 CATGTATCTTCATTTAAAAGT
*
148837 CATGTATTTTCATTTAAAAGT
1 CATGTATCTTCATTTAAAAGT
148858 CATGTAT
1 CATGTAT
148865 TTTCCAAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.44
20 6 0.24
21 8 0.32
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.45
Consensus pattern (21 bp):
CATGTATCTTCATTTAAAAGT
Found at i:148862 original size:21 final size:19
Alignment explanation
Indices: 148818--148868 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 19
148808 CGGCCAAGAG
*
148818 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
148837 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCA-TTAAAA-T
148858 CATGTATTTTC
1 CATGTATTTTC
148869 CAAGGGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.38
20 6 0.21
21 12 0.41
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:149889 original size:19 final size:19
Alignment explanation
Indices: 149827--149882 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
149817 ATTTTTTTCA
* *
149827 AAAAAAAAACAAAAACAAAC
1 AAAAAAAAGCCAAAA-AAAC
* *
149847 ATAAAAAAGGCAAAAAAAC
1 AAAAAAAAGCCAAAAAAAC
149866 AAAAAAAAGCCAAAAAA
1 AAAAAAAAGCCAAAAAA
149883 TCCAAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.80, C:0.12, G:0.05, T:0.02
Consensus pattern (19 bp):
AAAAAAAAGCCAAAAAAAC
Found at i:164125 original size:19 final size:21
Alignment explanation
Indices: 164082--164133 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
164072 GAAACCCCTT
164082 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
164103 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
164122 TGAAGATACATG
1 TGAAAATACATG
164134 CTCTTCGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:165044 original size:30 final size:31
Alignment explanation
Indices: 165005--165063 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
164995 ACATGCTGCC
165005 ATGATATCTAAATA-ATATGCAAACATAATAA
1 ATGATATCTAAA-ACATATGCAAACATAATAA
* *
165036 ATGA-ATCTAAAACGTATGTAAACATAAT
1 ATGATATCTAAAACATATGCAAACATAAT
165064 TTAAAGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 20 0.80
31 4 0.16
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:167933 original size:5 final size:5
Alignment explanation
Indices: 167925--167980 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
167915 ATTCTATTCT
167925 TTTTC TTTTC --TTC TTTTC -TTTC TTTTC TTTTC TTCTT- TTTGTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTT-TC TTTTC
167973 -TTTC TTTT
1 TTTTC TTTT
167981 TTTACTCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
3 3 0.07
4 9 0.20
5 27 0.61
6 5 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:167946 original size:17 final size:16
Alignment explanation
Indices: 167926--167982 Score: 75
Period size: 17 Copynumber: 3.6 Consensus size: 16
167916 TTCTATTCTT
167926 TTTCTTTTCTTCTTTTC
1 TTTCTTTT-TTCTTTTC
167943 TTTC--TTTTCTTTTC
1 TTTCTTTTTTCTTTTC
167957 -TTCTTTTTGTCTTTTC
1 TTTCTTTTT-TCTTTTC
167973 TTTCTTTTTT
1 TTTCTTTTTT
167983 TACTCCAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.08
14 8 0.22
15 5 0.14
16 8 0.22
17 12 0.33
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTTCTTTTC
Found at i:169270 original size:26 final size:26
Alignment explanation
Indices: 169240--169306 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
169230 CCTAGAACAG
* *
169240 CCATGTACTTTGCATATGATCAGCCC
1 CCATGTGCCTTGCATATGATCAGCCC
169266 CCATGTGCCTTGCATATGATCAGCCC
1 CCATGTGCCTTGCATATGATCAGCCC
169292 CCATGTGCCTTGCAT
1 CCATGTGCCTTGCAT
169307 GTGGTTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.19, C:0.33, G:0.18, T:0.30
Consensus pattern (26 bp):
CCATGTGCCTTGCATATGATCAGCCC
Found at i:170188 original size:27 final size:28
Alignment explanation
Indices: 170127--170188 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
170117 AAAGAAAATC
*
170127 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
170155 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
170182 AGAAAAG
1 AGAAAAG
170189 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.60, C:0.11, G:0.18, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:177215 original size:12 final size:12
Alignment explanation
Indices: 177200--177225 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
177190 TTTTTGTTTA
177200 TTTTGCCTTTTT
1 TTTTGCCTTTTT
177212 TTTTGCCTTTTT
1 TTTTGCCTTTTT
177224 TT
1 TT
177226 GGTTTTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTGCCTTTTT
Found at i:177232 original size:22 final size:21
Alignment explanation
Indices: 177169--177232 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
177159 TTTTTTGAAA
* *
177169 TTTTGGCTTTTTTAGCTTTTT
1 TTTTTGCTTTTTTTGCTTTTT
*
177190 TTTTTG-TTTATTTTGCCTTTT
1 TTTTTGCTTT-TTTTGCTTTTT
*
177211 TTTTTGCCTTTTTTTGGTTTTT
1 TTTTTG-CTTTTTTTGCTTTTT
177233 GAAAAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.09
21 20 0.57
22 9 0.26
23 3 0.09
ACGTcount: A:0.03, C:0.09, G:0.12, T:0.75
Consensus pattern (21 bp):
TTTTTGCTTTTTTTGCTTTTT
Found at i:185841 original size:26 final size:26
Alignment explanation
Indices: 185789--185853 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
185779 CCCTAGAACA
* ***
185789 CCCATGTGCTTTGCATATGATTGGCC
1 CCCATGTGCCTTGCATATGACCAGCC
*
185815 CCCATGTGCCTTGCATATTACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
*
185841 CCCATGAGCCTTG
1 CCCATGTGCCTTG
185854 TATGTGGTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.17, C:0.34, G:0.20, T:0.29
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:190714 original size:15 final size:15
Alignment explanation
Indices: 190646--190716 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
190636 TATGAAATAA
*
190646 GAAATGGAAGAAGAATG
1 GAAATGG-A-AAGAAAG
190663 GAAAT-GATAAGAAAG
1 GAAATGGA-AAGAAAG
190678 GAAATGGAAAGAAA-
1 GAAATGGAAAGAAAG
*
190692 -AGAT---AAGAAAG
1 GAAATGGAAAGAAAG
190703 GAAATGGAAAGAAA
1 GAAATGGAAAGAAA
190717 TGATATCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
10 6 0.14
12 3 0.07
13 3 0.07
15 24 0.55
16 3 0.07
17 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.10
Consensus pattern (15 bp):
GAAATGGAAAGAAAG
Found at i:190727 original size:25 final size:25
Alignment explanation
Indices: 190663--190721 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
190653 AAGAAGAATG
190663 GAAATGATAAGAAAGGAAATGGAAA
1 GAAATGATAAGAAAGGAAATGGAAA
*
190688 GAAAAGATAAGAAAGGAAATGGAAA
1 GAAATGATAAGAAAGGAAATGGAAA
190713 GAAATGATA
1 GAAATGATA
190722 TCAAAGTAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (25 bp):
GAAATGATAAGAAAGGAAATGGAAA
Found at i:194341 original size:12 final size:13
Alignment explanation
Indices: 194324--194352 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
194314 TTATATATTG
194324 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
194336 GAAATAAAGAAAT
1 GAAATAAAGAAAT
194349 GAAA
1 GAAA
194353 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:201394 original size:30 final size:30
Alignment explanation
Indices: 201358--201414 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
201348 GTGCTGGCAC
201358 GCACATGGGTGCTGTTTTGTTCCAAATCAT
1 GCACATGGGTGCTGTTTTGTTCCAAATCAT
*
201388 GCACATGGGTGTTGTTTTGTTCCAAAT
1 GCACATGGGTGCTGTTTTGTTCCAAAT
201415 GGTGAGTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (30 bp):
GCACATGGGTGCTGTTTTGTTCCAAATCAT
Found at i:207788 original size:29 final size:29
Alignment explanation
Indices: 207746--207801 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
207736 GTGCTGGCAC
207746 GCACATGGGTGTTGTTTTGTTCCAAATCA
1 GCACATGGGTGTTGTTTTGTTCCAAATCA
207775 GCACATGGGTGTTGTTTTGTTCCAAAT
1 GCACATGGGTGTTGTTTTGTTCCAAAT
207802 GGTGAGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (29 bp):
GCACATGGGTGTTGTTTTGTTCCAAATCA
Found at i:214958 original size:33 final size:33
Alignment explanation
Indices: 214916--214984 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
214906 GTTGATGAAT
*
214916 GAAGGATGAT-TTAATGGTGATGAGATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAGATGGTAATG
* * *
214949 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAGATGGTAATG
214982 GAA
1 GAA
214985 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.01, G:0.38, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAGATGGTAATG
Found at i:219019 original size:12 final size:13
Alignment explanation
Indices: 219002--219031 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
218992 GTTGTAGGAG
219002 TCTTTTCTTTTC-
1 TCTTTTCTTTTCT
219014 TCTTTTCTTTTCT
1 TCTTTTCTTTTCT
219027 TCTTT
1 TCTTT
219032 CTTATTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTCT
Found at i:219430 original size:33 final size:33
Alignment explanation
Indices: 219388--219456 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
219378 GTTGATGAAT
*
219388 GAAGGATGAT-TTAATGGTGATGAGATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAGATGGTAATG
* * *
219421 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAGATGGTAATG
219454 GAA
1 GAA
219457 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.01, G:0.38, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAGATGGTAATG
Found at i:227096 original size:19 final size:19
Alignment explanation
Indices: 227056--227105 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
227046 GAAACCCTTT
**
227056 TGAAAATACATGTTTTTTA
1 TGAAAATACATGTTTTAAA
227075 TGAAAATACAT-TATTTAAA
1 TGAAAATACATGT-TTTAAA
*
227094 TGAATATACATG
1 TGAAAATACATG
227106 CTCTTGGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (19 bp):
TGAAAATACATGTTTTAAA
Found at i:227806 original size:24 final size:25
Alignment explanation
Indices: 227774--227823 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
227764 ACCATTTGTT
*
227774 CTTCATGAT-CTCCCGTGATGTAAGG
1 CTTCATGATGC-CACGTGATGTAAGG
*
227799 CTTC-TGATGCCACTTGATGTAAGG
1 CTTCATGATGCCACGTGATGTAAGG
227823 C
1 C
227824 ATTTATACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (25 bp):
CTTCATGATGCCACGTGATGTAAGG
Found at i:228288 original size:13 final size:12
Alignment explanation
Indices: 228269--228354 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
228259 ATATAGGCGT
228269 GATATGGTGATG
1 GATATGGTGATG
228281 GAATATGGTGAT-
1 G-ATATGGTGATG
*
228293 GATATAGGCG-T-
1 GATAT-GGTGATG
228304 GATAATGGTGATG
1 GAT-ATGGTGATG
228317 GACTATGGTGAT-
1 GA-TATGGTGATG
*
228329 GATATAGGCG-T-
1 GATAT-GGTGATG
228340 GATAATGGTGATG
1 GAT-ATGGTGATG
228353 GA
1 GA
228355 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:228324 original size:36 final size:36
Alignment explanation
Indices: 228251--228355 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
228241 ATTTATAAGT
* *
228251 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
228286 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
228322 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
228356 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:228745 original size:19 final size:20
Alignment explanation
Indices: 228698--228748 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
228688 GAAACCCCTT
**
228698 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
228718 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
228737 TGAAGATACATG
1 TGAAAATACATG
228749 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:230804 original size:13 final size:12
Alignment explanation
Indices: 230785--230870 Score: 67
Period size: 11 Copynumber: 7.2 Consensus size: 12
230775 ATATAGGCGT
230785 GATATGGTGATG
1 GATATGGTGATG
230797 GAATATGGTGAT-
1 G-ATATGGTGATG
230809 GATATAGGTG-T-
1 GATAT-GGTGATG
230820 GATAATGGTGATG
1 GAT-ATGGTGATG
230833 GACTATGGTGAT-
1 GA-TATGGTGATG
*
230845 GATATAGGCG-T-
1 GATAT-GGTGATG
230856 GATAATGGTGATG
1 GAT-ATGGTGATG
230869 GA
1 GA
230871 CAGATTGTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 22 0.35
12 17 0.27
13 22 0.35
14 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:230822 original size:11 final size:12
Alignment explanation
Indices: 230768--230852 Score: 65
Period size: 11 Copynumber: 7.2 Consensus size: 12
230758 TTTATAAGTT
*
230768 GGTGATAATATA
1 GGTGATGATATA
*
230780 GGCG-TGATAT-
1 GGTGATGATATA
230790 GGTGATGGA-ATA
1 GGTGAT-GATATA
230802 TGGTGATGATATA
1 -GGTGATGATATA
230815 GGTG-TGATA-A
1 GGTGATGATATA
230825 TGGTGATGGACTAT-
1 -GGTGAT-GA-TATA
230839 GGTGATGATATA
1 GGTGATGATATA
230851 GG
1 GG
230853 CGTGATAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
10 4 0.07
11 20 0.34
12 16 0.27
13 17 0.29
14 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.32
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:230840 original size:36 final size:36
Alignment explanation
Indices: 230767--230871 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
230757 ATTTATAAGT
* *
230767 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
230802 TGGTGATGATATAGGTGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
230838 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
230872 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:234716 original size:19 final size:19
Alignment explanation
Indices: 234692--234728 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
234682 TGTTTCACTT
*
234692 TTCTTTTGCTTTTGTTTTC
1 TTCTTTTGCTTTTCTTTTC
*
234711 TTCTTTTTCTTTTCTTTT
1 TTCTTTTGCTTTTCTTTT
234729 GCACTCCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (19 bp):
TTCTTTTGCTTTTCTTTTC
Found at i:234779 original size:21 final size:21
Alignment explanation
Indices: 234754--234795 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
234744 TGTAGGAGTC
*
234754 TTTTTCTT-TTCTATTTTTGTT
1 TTTTTCTTCTTCT-TTCTTGTT
234775 TTTTTCTTCTTCTTTCTTGTT
1 TTTTTCTTCTTCTTTCTTGTT
234796 GCTTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (21 bp):
TTTTTCTTCTTCTTTCTTGTT
Found at i:234801 original size:24 final size:21
Alignment explanation
Indices: 234754--234802 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
234744 TGTAGGAGTC
*
234754 TTTTTCTTTTCTATTTTTGTT
1 TTTTTCTTTTCTATTTTTGCT
*
234775 TTTTTCTTCTTCTTTCTTGTTGCT
1 TTTTTCTT-TTCTAT-TT-TTGCT
234799 TTTT
1 TTTT
234803 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 5 0.22
23 2 0.09
24 8 0.35
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (21 bp):
TTTTTCTTTTCTATTTTTGCT
Found at i:235219 original size:13 final size:12
Alignment explanation
Indices: 235200--235285 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
235190 ATATAGGAGT
235200 GATATGGTGATG
1 GATATGGTGATG
235212 GAATATGGTGAT-
1 G-ATATGGTGATG
*
235224 GATATAGGCG-T-
1 GATAT-GGTGATG
235235 GATAATGGTGATG
1 GAT-ATGGTGATG
235248 GACTATGGTGAT-
1 GA-TATGGTGATG
*
235260 GATATAGGCG-T-
1 GATAT-GGTGATG
235271 GATAATGGTGATG
1 GAT-ATGGTGATG
235284 GA
1 GA
235286 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:235255 original size:36 final size:36
Alignment explanation
Indices: 235182--235286 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
235172 ATTTATAAGT
* * *
235182 TGGTGATAATATAGGAGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
235217 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
235253 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
235287 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:238848 original size:13 final size:12
Alignment explanation
Indices: 238812--238858 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
238802 ATTGGAGTGC
*
238812 AAAAAGAAGAGA
1 AAAAAGAAAAGA
238824 AAAATCAGAAAAGA
1 AAAA--AGAAAAGA
238838 ATAAAAGAAAAGA
1 A-AAAAGAAAAGA
238851 AAAAAGAA
1 AAAAAGAA
238859 TTCAAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 11 0.35
13 9 0.29
14 8 0.26
15 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:245542 original size:13 final size:12
Alignment explanation
Indices: 245523--245608 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
245513 ATATAGGCGT
245523 GATATGGTGATG
1 GATATGGTGATG
245535 GAATATGGTGAT-
1 G-ATATGGTGATG
*
245547 GATATAGGCG-T-
1 GATAT-GGTGATG
245558 GATAATGGTGATG
1 GAT-ATGGTGATG
245571 GACTATGGTGAT-
1 GA-TATGGTGATG
*
245583 GATATAGGCG-T-
1 GATAT-GGTGATG
245594 GATAATGGTGATG
1 GAT-ATGGTGATG
245607 GA
1 GA
245609 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:245578 original size:36 final size:36
Alignment explanation
Indices: 245505--245609 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
245495 ATTTATAAGT
* *
245505 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
245540 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
245576 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
245610 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:245995 original size:19 final size:20
Alignment explanation
Indices: 245948--245998 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
245938 TGAAACCCTT
**
245948 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
245968 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
245987 TGAAGATACATG
1 TGAAAATACATG
245999 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:256731 original size:15 final size:15
Alignment explanation
Indices: 256696--256724 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
256686 GTGCTTCAAC
256696 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
256710 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
256725 CTTTTTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:261378 original size:23 final size:23
Alignment explanation
Indices: 261333--261378 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
261323 TTATACCTAT
*
261333 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
261356 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
261379 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:263016 original size:9 final size:9
Alignment explanation
Indices: 263002--263054 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
262992 CAAAAAGAAG
263002 AGAAAAATC
1 AGAAAAATC
**
263011 AGAAAAGAAG
1 AGAAAA-ATC
263021 AGAAAAATC
1 AGAAAAATC
**
263030 AGAAAAGAAG
1 AGAAAA-ATC
263040 AGAAAAATC
1 AGAAAAATC
263049 AGAAAA
1 AGAAAA
263055 GAAGAAAAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
9 20 0.59
10 14 0.41
ACGTcount: A:0.70, C:0.06, G:0.19, T:0.06
Consensus pattern (9 bp):
AGAAAAATC
Found at i:263018 original size:19 final size:19
Alignment explanation
Indices: 262994--263059 Score: 132
Period size: 19 Copynumber: 3.5 Consensus size: 19
262984 TTGGAGTGCA
262994 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAATCAG
263013 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAATCAG
263032 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAATCAG
263051 AAAAGAAGA
1 AAAAGAAGA
263060 AAAGAAAGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.70, C:0.05, G:0.21, T:0.05
Consensus pattern (19 bp):
AAAAGAAGAGAAAAATCAG
Found at i:263084 original size:38 final size:37
Alignment explanation
Indices: 262994--263076 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 37
262984 TTGGAGTGCA
*
262994 AAAAGAAGAGAAAAATCAGAAAAGAAGAGAAAAATCAG
1 AAAAGAAGACAAAAATCAGAAAAGAAGAGAAAAA-CAG
*
263032 AAAAGAAGAGAAAAATCAGAAAAGAAGA-AAAGAA-AG
1 AAAAGAAGACAAAAATCAGAAAAGAAGAGAAA-AACAG
263068 AAAAAGAAG
1 -AAAAGAAG
263077 TTCAAAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
36 2 0.05
37 11 0.26
38 30 0.70
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.04
Consensus pattern (37 bp):
AAAAGAAGACAAAAATCAGAAAAGAAGAGAAAAACAG
Found at i:266001 original size:23 final size:23
Alignment explanation
Indices: 265956--266001 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
265946 TTATACCTAT
*
265956 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
265979 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
266002 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:273377 original size:5 final size:5
Alignment explanation
Indices: 273367--273402 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
273357 CTTCAACTTC
*
273367 TTTCT TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
273403 CTTTTTGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:277455 original size:16 final size:16
Alignment explanation
Indices: 277422--277470 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
277412 TAAGGTAATG
277422 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
277440 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
277456 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
277471 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:278777 original size:19 final size:20
Alignment explanation
Indices: 278747--278797 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
278737 CGGCCAAGAG
* *
278747 CATGTATCTTCATTA-AAAT
1 CATGTATTTTCATCACAAAT
*
278766 CATGTGTTTTCATCACAAAT
1 CATGTATTTTCATCACAAAT
278786 CATGTATTTTCA
1 CATGTATTTTCA
278798 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCACAAAT
Found at i:285538 original size:22 final size:21
Alignment explanation
Indices: 285507--285547 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
285497 CATCTCCATT
*
285507 TCATCATCAATACCATCAACA
1 TCATCATCAAGACCATCAACA
*
285528 TCATCCATCAAGACTATCAA
1 TCAT-CATCAAGACCATCAA
285548 TTCAGACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.32, G:0.02, T:0.24
Consensus pattern (21 bp):
TCATCATCAAGACCATCAACA
Found at i:290273 original size:6 final size:6
Alignment explanation
Indices: 290250--290292 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
290240 GTTGTAGGAG
* *
290250 TCTTTT TCTTTC TC-TTT TGTTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
290293 GTGCTTTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 3 0.10
6 22 0.71
7 6 0.19
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:290280 original size:20 final size:19
Alignment explanation
Indices: 290255--290292 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
290245 AGGAGTCTTT
*
290255 TTCTTTCTCTTTTGTTTTTC
1 TTCTTTCT-TTTTCTTTTTC
290275 TTCTTTCTTTTTCTTTTT
1 TTCTTTCTTTTTCTTTTT
290293 GTGCTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (19 bp):
TTCTTTCTTTTTCTTTTTC
Found at i:290729 original size:13 final size:13
Alignment explanation
Indices: 290706--290739 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
290696 GTTATAGGCG
290706 TGAAA-ATGGTGA
1 TGAAAGATGGTGA
290718 TGAAAGATGGTGA
1 TGAAAGATGGTGA
290731 TGAACAGAT
1 TGAA-AGAT
290740 TGTATCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 11 0.55
14 4 0.20
ACGTcount: A:0.41, C:0.03, G:0.32, T:0.24
Consensus pattern (13 bp):
TGAAAGATGGTGA
Found at i:292123 original size:19 final size:19
Alignment explanation
Indices: 292095--292137 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
292085 AGTAAAGATG
292095 TGAAAACATAT-GTTATGCA
1 TGAAAACATATAG-TATGCA
*
292114 TGAAATCATATAGTATGCA
1 TGAAAACATATAGTATGCA
*
292133 AGAAA
1 TGAAA
292138 GTGATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (19 bp):
TGAAAACATATAGTATGCA
Found at i:292888 original size:17 final size:17
Alignment explanation
Indices: 292866--292898 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
292856 AAATTAGAGT
292866 ACAAAAAGAAAGAAAAG
1 ACAAAAAGAAAGAAAAG
*
292883 ACAAAAGGAAAGAAAA
1 ACAAAAAGAAAGAAAA
292899 TAAGAAAATA
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:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (17 bp):
ACAAAAAGAAAGAAAAG
Found at i:293166 original size:12 final size:14
Alignment explanation
Indices: 293136--293167 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
293126 TAATCTTTTC
293136 TTCTACTTTTCCAT
1 TTCTACTTTTCCAT
293150 TTCTA-TTTTCC-T
1 TTCTACTTTTCCAT
293162 TTCTAC
1 TTCTAC
293168 CCTAACCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 6 0.35
14 5 0.29
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCTACTTTTCCAT
Found at i:294537 original size:19 final size:21
Alignment explanation
Indices: 294513--294564 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
294503 CGGCCAAGAG
*
294513 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
294532 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
294553 CATGTATTTTCA
1 CATGTATTTTCA
294565 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:295295 original size:8 final size:8
Alignment explanation
Indices: 295284--295308 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
295274 GAGAAAAATT
295284 AGAAAAGA
1 AGAAAAGA
295292 AGAAAAGA
1 AGAAAAGA
295300 AGAAAAGA
1 AGAAAAGA
295308 A
1 A
295309 AAGAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:296527 original size:28 final size:29
Alignment explanation
Indices: 296496--296551 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
296486 TTTGTTTTGC
296496 AGGACA-ATTCAAGAGA-CATATCTTTTCA
1 AGGACAGATTCAAGA-ATCATATCTTTTCA
*
296524 AGGAGATGATTCAAGAATCATATCTTTT
1 AGGACA-GATTCAAGAATCATATCTTTT
296552 GGAGGACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.21
29 1 0.04
30 18 0.75
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (29 bp):
AGGACAGATTCAAGAATCATATCTTTTCA
Found at i:298657 original size:19 final size:21
Alignment explanation
Indices: 298633--298684 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
298623 CGGCCAAGAG
*
298633 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
298652 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
*
298673 CGTGTATTTTCA
1 CATGTATTTTCA
298685 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 6 0.21
21 12 0.41
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Done.