Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002743.1 Hibiscus syriacus cultivar Beakdansim tig00005653_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: 65805
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:8412 original size:29 final size:26
Alignment explanation
Indices: 8359--8411 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
8349 CATTTTGATC
8359 ATCTCTAGGAGTTTTCATAGAAGAAG
1 ATCTCTAGGAGTTTTCATAGAAGAAG
8385 ATCTCTAGGAGTTTTCATAGAAGAAG
1 ATCTCTAGGAGTTTTCATAGAAGAAG
8411 A
1 A
8412 AATATTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (26 bp):
ATCTCTAGGAGTTTTCATAGAAGAAG
Found at i:15000 original size:194 final size:194
Alignment explanation
Indices: 14651--15027 Score: 610
Period size: 194 Copynumber: 1.9 Consensus size: 194
14641 CCAATCATGG
* * *
14651 ATAAGAGGTTGGAAGTAATAGAGCAGTCTCAAGGTGATTTACGAGATCAGTTGCAAGATTAGAGA
1 ATAAGAGGTTAGAAGTAATAGAGCAATCTCAAGGTGATTTACGAGATCAATTGCAAGATTAGAGA
* * *
14716 TAAACTTAAACAGATAGGGAAATTGGTTGAAGTAGTGAAATGTGTTGATGTCTCCCACAAGAATC
66 TAAACTTAAACAGATAGAGAAATTCGTTGAAGTAATGAAATGTGTTGATGTCTCCCACAAGAATC
* * *
14781 TAGATGAGAGAGAACTTAGTTTAGTTCCTGATTTGGTCATCCCACAAGAGTTTTTGGTCATCCA
131 TAAATGAGAGAGAACCTACTTTAGTTCCTGATTTGGTCATCCCACAAGAGTTTTTGGTCATCCA
* *
14845 ATAATAGGTTAGAAGTAATAGAGCAATCTCAAGGTGATTTATGAGATCAATTGCAAGATTAGAGA
1 ATAAGAGGTTAGAAGTAATAGAGCAATCTCAAGGTGATTTACGAGATCAATTGCAAGATTAGAGA
* *
14910 TAAACTTATACAGTTAGAGAAATTCGTTGAAGTAATGAAATGTGTTGATGTCTCCCACAAGAATC
66 TAAACTTAAACAGATAGAGAAATTCGTTGAAGTAATGAAATGTGTTGATGTCTCCCACAAGAATC
* * *
14975 TAAATGCGAGAGATCCTACTTTAGTTCCTGATTTGGTCATCCCACGAGAGTTT
131 TAAATGAGAGAGAACCTACTTTAGTTCCTGATTTGGTCATCCCACAAGAGTTT
15028 AAGTTGTCCG
Statistics
Matches: 167, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
194 167 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (194 bp):
ATAAGAGGTTAGAAGTAATAGAGCAATCTCAAGGTGATTTACGAGATCAATTGCAAGATTAGAGA
TAAACTTAAACAGATAGAGAAATTCGTTGAAGTAATGAAATGTGTTGATGTCTCCCACAAGAATC
TAAATGAGAGAGAACCTACTTTAGTTCCTGATTTGGTCATCCCACAAGAGTTTTTGGTCATCCA
Found at i:15851 original size:18 final size:18
Alignment explanation
Indices: 15828--15865 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
15818 ATTTTCATTG
15828 TTTTGT-TTTAATTTGTTT
1 TTTTGTCTTT-ATTTGTTT
*
15846 TTTTGTCTTTCTTTGTTT
1 TTTTGTCTTTATTTGTTT
15864 TT
1 TT
15866 AGGTTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.79
Consensus pattern (18 bp):
TTTTGTCTTTATTTGTTT
Found at i:18396 original size:74 final size:74
Alignment explanation
Indices: 18274--18424 Score: 232
Period size: 74 Copynumber: 2.0 Consensus size: 74
18264 GTGGGGCATG
* **
18274 TTACCCGACCAATATGATTTTTGAAATGAATATTTTAAAGAAGCCAAGTTTTCTTTTCAAAGGTT
1 TTACCCGACCAATATGATTTCTGAAATGAATATTTTAAAGAAGCCAAGTTTGATTTTCAAAGGTT
*
18339 TCTTGATGA
66 TCTAGATGA
* *
18348 TTACCCGACTAATATGATGTTCTGAAATGAAT-TTTTAAAGAAGTCAAGTTTGATTTTCAAAGGT
1 TTACCCGACCAATATGAT-TTCTGAAATGAATATTTTAAAGAAGCCAAGTTTGATTTTCAAAGGT
18412 TTCTAGATGA
65 TTCTAGATGA
18422 TTA
1 TTA
18425 AATCCTTCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
74 58 0.83
75 12 0.17
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (74 bp):
TTACCCGACCAATATGATTTCTGAAATGAATATTTTAAAGAAGCCAAGTTTGATTTTCAAAGGTT
TCTAGATGA
Found at i:19981 original size:20 final size:20
Alignment explanation
Indices: 19956--19994 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19946 TGGTTTAAGT
19956 AAAAGTATTT-GGTCAATGAG
1 AAAAGT-TTTAGGTCAATGAG
19976 AAAAGTTTTACGGTCAATG
1 AAAAGTTTTA-GGTCAATG
19995 TAAAATAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 6 0.35
21 8 0.47
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (20 bp):
AAAAGTTTTAGGTCAATGAG
Found at i:20275 original size:20 final size:21
Alignment explanation
Indices: 20250--20342 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
20240 TTTTCCCAAT
*
20250 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
20270 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
20291 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
20311 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
20332 TCGCAATGCGA
1 TCGCAATGCGA
20343 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:20295 original size:41 final size:41
Alignment explanation
Indices: 20250--20342 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
20240 TTTTCCCAAT
20250 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
20291 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
20332 TCGCAATGCGA
1 TCGCAATGCGA
20343 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:20355 original size:41 final size:41
Alignment explanation
Indices: 20269--20403 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
20259 GAATAAGTAA
** *
20269 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
20310 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
20351 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
* *
20392 TTCGCAATGCGA
1 ATCGCAACGCGA
20404 TACTGACTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
40 5 0.06
41 75 0.91
42 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:20356 original size:20 final size:20
Alignment explanation
Indices: 20331--20424 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
20321 AATTGGGAAA
20331 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTTACT
* * **
20351 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-TACT
* *
20372 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTTACT
* *
20392 TTCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTTACT
* *
20412 TTCGCAACGCGAT
1 ATCGCAATGCGAT
20425 TTACATAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTTACT
Found at i:21008 original size:38 final size:39
Alignment explanation
Indices: 20939--21028 Score: 155
Period size: 38 Copynumber: 2.3 Consensus size: 39
20929 TAGTTTCGAG
20939 AATGAAAATCGCAACGCGGAAATAAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGGAAATAAAAATCGCAACGCGA
20978 AATGAAAATCGCAACGC-GAAATAAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGGAAATAAAAATCGCAACGCGA
**
21016 AACCAAAATCGCA
1 AATGAAAATCGCA
21029 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 32 0.65
39 17 0.35
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (39 bp):
AATGAAAATCGCAACGCGGAAATAAAAATCGCAACGCGA
Found at i:21034 original size:19 final size:19
Alignment explanation
Indices: 20943--21028 Score: 136
Period size: 19 Copynumber: 4.5 Consensus size: 19
20933 TTCGAGAATG
20943 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
*
20963 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATA
20982 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
21001 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
21020 AAAATCGCA
1 AAAATCGCA
21029 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
19 49 0.79
20 13 0.21
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:21046 original size:19 final size:19
Alignment explanation
Indices: 21024--21208 Score: 183
Period size: 19 Copynumber: 10.1 Consensus size: 19
21014 GAAACCAAAA
*
21024 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21043 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21062 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21081 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
21101 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
21117 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
21134 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
21148 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
21167 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
21187 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
21207 TC
1 TC
21209 AACCAAAAGA
Statistics
Matches: 140, Mismatches: 13, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 61 0.44
20 50 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:21133 original size:33 final size:33
Alignment explanation
Indices: 21096--21183 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
21086 GTTGCGATTT
* *
21096 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
21129 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
21162 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
21184 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:21185 original size:20 final size:20
Alignment explanation
Indices: 21151--21208 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
21141 GCGATTCTCT
**
21151 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
21171 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
21191 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
21209 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:23268 original size:42 final size:42
Alignment explanation
Indices: 23208--23291 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
23198 GCCCGACTCG
* * *
23208 CCTATCATTCCTCCAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCCAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
23250 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCCAGAGTCCACTCCCACCGTTCAAGAGGCC
23292 ACTGTCATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.39, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCCAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:23288 original size:21 final size:21
Alignment explanation
Indices: 23264--23330 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
23254 TCATTCCTCG
23264 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
23285 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
23306 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
23327 AGAG
1 AGAG
23331 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:24705 original size:14 final size:14
Alignment explanation
Indices: 24686--24721 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
24676 ATTGTTTAAT
24686 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
24700 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
24714 TGATTTGT
1 TGATTTGT
24722 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:24852 original size:19 final size:19
Alignment explanation
Indices: 24828--24894 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
24818 AAAAAGTACT
*
24828 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
24847 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
24861 ATCGCAACGCGAAAATG-AA
1 ATCGCAACGCG-AAATGAAA
24880 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
24895 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 4 0.10
19 20 0.50
20 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:24948 original size:33 final size:32
Alignment explanation
Indices: 24903--25029 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
24893 ATTAAATTCG
*
24903 CGTTGCGCTTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
24936 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
24969 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
25002 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
25030 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:24962 original size:19 final size:19
Alignment explanation
Indices: 24899--25029 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
24889 CGAAATTAAA
* *
24899 TTCGCGTTGCGCTTTTCAT
1 TTCGCATTGCGATTTTCAT
*
24918 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
24934 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
24951 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
24965 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
24984 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
25000 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
25017 TTCGCATTGCGAT
1 TTCGCATTGCGAT
25030 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 23 0.28
16 13 0.16
17 13 0.16
19 34 0.41
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:24982 original size:66 final size:66
Alignment explanation
Indices: 24896--25028 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
24886 ACGCGAAATT
* *
24896 AAATTCGCGTTGCGCTTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
24961 G
66 G
*
24962 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
25027 G
66 G
25028 A
1 A
25029 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:27339 original size:12 final size:12
Alignment explanation
Indices: 27322--27346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27312 TCTTCGGGGA
27322 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27334 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27346 C
1 C
27347 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:27555 original size:24 final size:24
Alignment explanation
Indices: 27521--27574 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
27511 CTGAAACATC
* *
27521 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAA
*
27545 ATCAAAGTCCGGGTATTGACCAAA
1 ATCAAAATCCGGGTATTGACCAAA
27569 ATCAAA
1 ATCAAA
27575 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAA
Found at i:28734 original size:19 final size:19
Alignment explanation
Indices: 28712--28757 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
28702 TTTCTCGTTG
28712 CGATTTTCATTTCGCATTA
1 CGATTTTCATTTCGCATTA
*
28731 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTA
28750 CGATTTTC
1 CGATTTTC
28758 TCGTTGCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.22, G:0.13, T:0.48
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTA
Found at i:30668 original size:19 final size:19
Alignment explanation
Indices: 30644--30699 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
30634 GAAACTTAAA
30644 ATCGCAATGCGAAATGACT
1 ATCGCAATGCGAAATGACT
* *
30663 ATCGCAACGCGGAAATGGCT
1 ATCGCAATGC-GAAATGACT
30683 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
30700 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:30668 original size:39 final size:37
Alignment explanation
Indices: 30625--30741 Score: 102
Period size: 39 Copynumber: 3.2 Consensus size: 37
30615 TAGTTTACTT
*
30625 TCGCAACACGAAACTTAAAATCGCAATGCGAAATGACTA
1 TCGCAACACGAAAC-TAAAATCGCAATGCGAAATGA-AA
* ***
30664 TCGCAACGCGGAAA-TGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACAC-GAAACT-AAAATCGCAATGCGAAATG-AAA
30703 TCGC-A-ACG--AC-AAAATCGCAATGCGAAATGAAA
1 TCGCAACACGAAACTAAAATCGCAATGCGAAATGAAA
30735 TCGCAAC
1 TCGCAAC
30742 TACAAAATCG
Statistics
Matches: 63, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
32 7 0.11
33 17 0.27
34 1 0.02
36 1 0.02
37 1 0.02
38 2 0.03
39 29 0.46
40 5 0.08
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (37 bp):
TCGCAACACGAAACTAAAATCGCAATGCGAAATGAAA
Found at i:30705 original size:19 final size:19
Alignment explanation
Indices: 30641--30740 Score: 86
Period size: 19 Copynumber: 5.5 Consensus size: 19
30631 CACGAAACTT
30641 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
** *
30660 ACTATCGCAACGCGGAAATG
1 AAAATCGCAATGC-GAAATG
***
30680 GCTATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
30699 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
30713 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
30732 -AAATCGCAA
1 AAAATCGCAA
30741 CTACAAAATC
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 10 0.15
19 23 0.35
20 17 0.26
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.15
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:30718 original size:14 final size:14
Alignment explanation
Indices: 30699--30756 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
30689 ATGCGAAATG
30699 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
30713 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
30729 ATGAAATCGCAACTAC
1 A--AAATCGCAACGAC
30745 AAAATCGCAACG
1 AAAATCGCAACG
30757 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 7 0.19
18 9 0.25
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:30741 original size:32 final size:33
Alignment explanation
Indices: 30683--30761 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
30673 GGAAATGGCT
30683 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
30716 ATCGCAATGCGAAATG-AAATCGCAACTACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
30748 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
30762 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 28 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:30849 original size:50 final size:51
Alignment explanation
Indices: 30768--30901 Score: 198
Period size: 50 Copynumber: 2.6 Consensus size: 51
30758 GAAACACAAA
*
30768 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCATT
1 TCGCATTGCGA-TTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATT
*
30819 TCGCGTTGCGATTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATT
**
30870 TCGCATTGCGATAGCCATTTCCGCATTGCGAT
1 TCGCATTGCGAT-TTCATTT-CGCATTGCGAT
30902 AGCCATTTCC
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 31 0.41
51 28 0.37
52 5 0.07
53 11 0.15
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (51 bp):
TCGCATTGCGATTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATT
Found at i:30896 original size:20 final size:20
Alignment explanation
Indices: 30866--30929 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
30856 TTGCGATTTT
30866 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
30885 CATTTCCGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
30905 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
30925 CATTT
1 CATTT
30930 TCGTGTTGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
19 5 0.12
20 37 0.88
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:30937 original size:20 final size:20
Alignment explanation
Indices: 30866--30940 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
30856 TTGCGATTTT
*
30866 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
30885 CATTTCCGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
30905 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
* *
30925 CATTTTCGTGTTGCGA
1 CATTTCCGCGTTGCGA
30941 AAGTAAACTA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 5 0.10
20 46 0.90
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:31439 original size:18 final size:18
Alignment explanation
Indices: 31413--31457 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
31403 GTCGATCAGA
*
31413 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
31431 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
31449 TGATGGCTC
1 TGATGGCTC
31458 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:32800 original size:20 final size:20
Alignment explanation
Indices: 32777--32814 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32767 AATAGTTTCT
32777 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
32797 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
32815 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:33104 original size:22 final size:22
Alignment explanation
Indices: 33079--33122 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
33069 GATTTAGATA
33079 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
33101 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
33123 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:33335 original size:20 final size:20
Alignment explanation
Indices: 33310--33362 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
33300 GATTATGTAT
*
33310 TATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCAAAAGTAAG
*
33330 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCAAAAGTAAG
*
33350 TATCTCGTTGCAA
1 TATCGCGTTGCAA
33363 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCAAAAGTAAG
Found at i:33396 original size:20 final size:20
Alignment explanation
Indices: 33290--33404 Score: 70
Period size: 20 Copynumber: 5.7 Consensus size: 20
33280 CGCTTTGAAA
*
33290 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
33311 ATCGCGTTGCAAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
33331 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * * ** * *
33351 ATCTCGTTGCAATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
33372 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
33392 ATCGCATTGCGAT
1 ATCGCATTGCGAT
33405 TTTCCCAATT
Statistics
Matches: 72, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
19 2 0.03
20 48 0.67
21 22 0.31
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:33407 original size:41 final size:41
Alignment explanation
Indices: 33330--33407 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
33320 CAAAAGTCAG
* * *
33330 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCAATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTTTAT
* * *
33371 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTT
33408 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTTTAT
Found at i:33422 original size:21 final size:21
Alignment explanation
Indices: 33393--33485 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
33383 ATAGTCAGTA
33393 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
33414 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
33434 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
33455 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
33475 TCGCATTGCGA
1 TCGCATTGCGA
33486 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:33423 original size:41 final size:41
Alignment explanation
Indices: 33393--33485 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
33383 ATAGTCAGTA
* *
33393 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
33434 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
33475 TCGCATTGCGA
1 TCGCATTGCGA
33486 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:36317 original size:14 final size:13
Alignment explanation
Indices: 36300--36338 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
36290 TAATTTTAAA
36300 AATTTATAAAATAT
1 AATTTATAAAA-AT
36314 AATTTTATAAAAAT
1 AA-TTTATAAAAAT
36328 AATTT-TAAAAA
1 AATTTATAAAAA
36339 ATTAAAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 3 0.12
14 6 0.25
15 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTTATAAAAAT
Found at i:36322 original size:15 final size:15
Alignment explanation
Indices: 36302--36340 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
36292 ATTTTAAAAA
36302 TTTATAAAATATAAT
1 TTTATAAAATATAAT
36317 TTTATAAAA-ATAAT
1 TTTATAAAATATAAT
*
36331 TTTAAAAAAT
1 TTTATAAAAT
36341 TAAAAGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTATAAAATATAAT
Found at i:37665 original size:23 final size:25
Alignment explanation
Indices: 37613--37669 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
37603 TTGTTATTAA
37613 TTAATTTA--TATTTTTATGCATGTT
1 TTAATTTATTTATTTTTAT-CATGTT
37637 TT-ATTTATTTATTTTTAT-AT-TT
1 TTAATTTATTTATTTTTATCATGTT
37659 TTAATTTATTT
1 TTAATTTATTT
37670 TTCTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 4 0.13
23 15 0.50
24 2 0.07
25 9 0.30
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (25 bp):
TTAATTTATTTATTTTTATCATGTT
Found at i:37679 original size:19 final size:19
Alignment explanation
Indices: 37643--37679 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
37633 TGTTTTATTT
*
37643 ATTTATTTTTATATTTTTA
1 ATTTATTTTTATAATTTTA
*
37662 ATTTATTTTTCTAATTTT
1 ATTTATTTTTATAATTTT
37680 TTTTAATTCA
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:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTATTTTTATAATTTTA
Found at i:42079 original size:2 final size:2
Alignment explanation
Indices: 42005--42060 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
41995 CAGTAAAAAG
42005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42047 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
42061 TTTAAAGCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42268 original size:24 final size:24
Alignment explanation
Indices: 42241--42312 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
42231 GTAAACGGAG
42241 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * *
42265 ATATCAGATATCATAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTC
* *
42289 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
42312 A
1 A
42313 GGTAACTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 14 0.34
24 27 0.66
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:42313 original size:12 final size:12
Alignment explanation
Indices: 42245--42313 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
42235 ACGGAGATAT
* *
42245 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
42257 CAGAATTCATAT
1 CAGAATTCAGAA
*
42269 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
42281 CAGAATCCAGAT
1 CAGAATTCAGAA
42293 CAGAA-TCAGAA
1 CAGAATTCAGAA
42304 CAGAATTCAG
1 CAGAATTCAG
42314 GTAACTTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 11 0.24
12 32 0.71
13 2 0.04
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:43455 original size:18 final size:18
Alignment explanation
Indices: 43434--43468 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43424 TGCCATCCGG
*
43434 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
43452 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
43469 GTTCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:44779 original size:8 final size:8
Alignment explanation
Indices: 44766--44806 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
44756 GTTCAACGCC
44766 GGTCAACG
1 GGTCAACG
44774 GGTCAACG
1 GGTCAACG
44782 GGT---CG
1 GGTCAACG
44787 GGTCAACG
1 GGTCAACG
*
44795 GGTAAACG
1 GGTCAACG
44803 GGTC
1 GGTC
44807 GGATCGGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
5 5 0.18
8 23 0.82
ACGTcount: A:0.22, C:0.22, G:0.41, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:44790 original size:13 final size:13
Alignment explanation
Indices: 44772--44797 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44762 CGCCGGTCAA
44772 CGGGTCAACGGGT
1 CGGGTCAACGGGT
44785 CGGGTCAACGGGT
1 CGGGTCAACGGGT
44798 AAACGGGTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:44792 original size:21 final size:21
Alignment explanation
Indices: 44766--44808 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
44756 GTTCAACGCC
*
44766 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGTAAACGGGTCG
44787 GGTCAACGGGTAAACGGGTCG
1 GGTCAACGGGTAAACGGGTCG
44808 G
1 G
44809 ATCGGGTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.44, T:0.14
Consensus pattern (21 bp):
GGTCAACGGGTAAACGGGTCG
Found at i:48818 original size:31 final size:31
Alignment explanation
Indices: 48783--48842 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
48773 TTAACATTAC
48783 AAAATCAAAATAAATATATAAAAAA-TAATAA
1 AAAATCAAAATAAATA-ATAAAAAACTAATAA
** *
48814 AAAATGTAAATAAGTAATAAAAAACTAAT
1 AAAATCAAAATAAATAATAAAAAACTAAT
48843 TTAAATAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (31 bp):
AAAATCAAAATAAATAATAAAAAACTAATAA
Found at i:48876 original size:52 final size:51
Alignment explanation
Indices: 48798--48950 Score: 190
Period size: 49 Copynumber: 3.1 Consensus size: 51
48788 CAAAATAAAT
*
48798 ATATAAAAA-A-TAATAAAAAATGTAAATAAGTAATAAAAAACTAATTTAA
1 ATATAAAAACATTAATTAAAAATGTAAATAAGTAATAAAAAACTAATTTAA
* * * *
48847 ATA-AAGACAATATTTATTAAAAATGTAAATAAGTAAT--AAAATTAATTAAA
1 ATATAA-A-AACATTAATTAAAAATGTAAATAAGTAATAAAAAACTAATTTAA
* *
48897 ATATAAAAACATTAATTAAAAATGTAAATAAGTAGTAAATAACTAATTTAA
1 ATATAAAAACATTAATTAAAAATGTAAATAAGTAATAAAAAACTAATTTAA
48948 ATA
1 ATA
48951 GAGTTCTAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
48 2 0.02
49 30 0.34
50 17 0.20
51 16 0.18
52 22 0.25
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (51 bp):
ATATAAAAACATTAATTAAAAATGTAAATAAGTAATAAAAAACTAATTTAA
Found at i:48924 original size:21 final size:19
Alignment explanation
Indices: 48879--48924 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
48869 ATGTAAATAA
48879 GTAATAAAATTAATTAAAAT
1 GTAA-AAAATTAATTAAAAT
*
48899 ATAAAAACATTAATTAAAAAT
1 GTAAAAA-ATTAATT-AAAAT
48920 GTAAA
1 GTAAA
48925 TAAGTAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 3 0.14
20 10 0.45
21 9 0.41
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
GTAAAAAATTAATTAAAAT
Found at i:49788 original size:15 final size:15
Alignment explanation
Indices: 49768--49806 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
49758 TTCCCTTTTT
49768 TTCTCTTTTTTATCC
1 TTCTCTTTTTTATCC
49783 TTCTCTTTTTTATCC
1 TTCTCTTTTTTATCC
49798 TTCTCTTTT
1 TTCTCTTTT
49807 ACATAACATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCTCTTTTTTATCC
Found at i:50645 original size:33 final size:33
Alignment explanation
Indices: 50601--50665 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
50591 GAAGGTATCG
50601 ACACTTCAGTGCATTTGGACCTACGAGTTCATA
1 ACACTTCAGTGCATTTGGACCTACGAGTTCATA
* *
50634 ACACTTTAGTGCATTTGGACCTTCGAGTTCAT
1 ACACTTCAGTGCATTTGGACCTACGAGTTCAT
50666 CTGCTATAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (33 bp):
ACACTTCAGTGCATTTGGACCTACGAGTTCATA
Found at i:50851 original size:36 final size:35
Alignment explanation
Indices: 50792--50867 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
50782 TACATTATAT
* * * * *
50792 ATATATATGCTCTTGCTATTGATGAACATATTCATG
1 ATATACATGCGCTTACTACTGATGAA-ATATACATG
50828 ATATACATGCGCTTACTACTGATGAAATATACATG
1 ATATACATGCGCTTACTACTGATGAAATATACATG
*
50863 GTATA
1 ATATA
50868 TATATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 12 0.35
36 22 0.65
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (35 bp):
ATATACATGCGCTTACTACTGATGAAATATACATG
Found at i:50871 original size:2 final size:2
Alignment explanation
Indices: 50864--50889 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50854 ATATACATGG
50864 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
50890 CTTGCTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51054 original size:36 final size:36
Alignment explanation
Indices: 50890--51043 Score: 161
Period size: 36 Copynumber: 4.3 Consensus size: 36
50880 TATATATATA
* * *
50890 CTTGCTATTGATGATAATATGAATGATAAACATGTG
1 CTTGCTATTGATGATTATATGCATGATATACATGTG
* * *
50926 -TGTGCTATTAATTATTATATGCATGATACACATGT-
1 CT-TGCTATTGATGATTATATGCATGATATACATGTG
** * *
50961 CTTTGCTACCGATGATTATATACATTATATACATGTG
1 C-TTGCTATTGATGATTATATGCATGATATACATGTG
*
50998 CTTGAC-ATTAATGATTATATGCATGATATACATGTG
1 CTTG-CTATTGATGATTATATGCATGATATACATGTG
51034 CTTGCTATTG
1 CTTGCTATTG
51044 GGGTTTATAT
Statistics
Matches: 94, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
35 2 0.02
36 89 0.95
37 3 0.03
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (36 bp):
CTTGCTATTGATGATTATATGCATGATATACATGTG
Found at i:60946 original size:19 final size:19
Alignment explanation
Indices: 60924--61178 Score: 183
Period size: 19 Copynumber: 13.2 Consensus size: 19
60914 GAAACCAAAT
* *
60924 TTTTAGGTTGCAACCTAGA
1 TTTTAGGTTGCAACCCATA
* * * *
60943 TTTTAAGTTGTAGCCTAGT-
1 TTTTAGGTTGCAACCCA-TA
** *
60962 TTTTAGGTTGGGATCCATA
1 TTTTAGGTTGCAACCCATA
* *
60981 TTTTAGGTTTCAACCCAGA
1 TTTTAGGTTGCAACCCATA
*
61000 TATTTAGGCTGCAACCCATA
1 T-TTTAGGTTGCAACCCATA
* * * *
61020 TTTTTATGTTGGAATCCAAA
1 -TTTTAGGTTGCAACCCATA
61040 TTTTAGGTTGCAACCCATA
1 TTTTAGGTTGCAACCCATA
* *
61059 TTATTAGGTTACAACCCAAA
1 TT-TTAGGTTGCAACCCATA
* *
61079 TTTTTGGGTTGGAACCCATA
1 -TTTTAGGTTGCAACCCATA
** *
61099 TTTTAGGTTAAAAGCCGA-A
1 TTTTAGGTTGCAA-CCCATA
61118 TTTTAGGTTGCAACCCATA
1 TTTTAGGTTGCAACCCATA
*
61137 TTTTTAGGTTGACAA-CCAGA
1 -TTTTAGGTTG-CAACCCATA
* *
61157 TTTTAGGTTGAAAACCATA
1 TTTTAGGTTGCAACCCATA
61176 TTT
1 TTT
61179 CTGGTTAGAA
Statistics
Matches: 182, Mismatches: 43, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
18 6 0.03
19 97 0.53
20 73 0.40
21 6 0.03
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (19 bp):
TTTTAGGTTGCAACCCATA
Found at i:61037 original size:59 final size:59
Alignment explanation
Indices: 60909--61165 Score: 222
Period size: 59 Copynumber: 4.4 Consensus size: 59
60899 AGATTTTAAG
* * * * * * *
60909 GGTTGGAAACCAAATTTTTAGGTTGCAACCTAGAT-TTTAAGTTG-TAGCC-TAGTTTTTA
1 GGTTGGAATCCATA-TTTTAGGTTACAACCCAGATATTTAGGTTGCAACCCATA-TTTTTA
* * *
60967 GGTTGGGATCCATATTTTAGGTTTCAACCCAGATATTTAGGCTGCAACCCATATTTTTA
1 GGTTGGAATCCATATTTTAGGTTACAACCCAGATATTTAGGTTGCAACCCATATTTTTA
* * * * * * *
61026 TGTTGGAATCCAAATTTTAGGTTGCAACCCATAT-TATTAGGTTACAACCCAAATTTTTG
1 GGTTGGAATCCATATTTTAGGTTACAACCCAGATAT-TTAGGTTGCAACCCATATTTTTA
* * *
61085 GGTTGGAACCCATATTTTAGGTTAAAAGCC-GA-ATTTTAGGTTGCAACCCATATTTTTA
1 GGTTGGAATCCATATTTTAGGTTACAACCCAGATA-TTTAGGTTGCAACCCATATTTTTA
* *
61143 GGTT-GACAACCAGATTTTAGGTT
1 GGTTGGA-ATCCATATTTTAGGTT
61166 GAAAACCATA
Statistics
Matches: 162, Mismatches: 30, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
57 20 0.12
58 58 0.36
59 82 0.51
60 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (59 bp):
GGTTGGAATCCATATTTTAGGTTACAACCCAGATATTTAGGTTGCAACCCATATTTTTA
Found at i:61200 original size:39 final size:38
Alignment explanation
Indices: 60909--61203 Score: 211
Period size: 39 Copynumber: 7.6 Consensus size: 38
60899 AGATTTTAAG
* * *
60909 GGTTGGAAACCAAATTTTTAGGTTGCAACCTAGATTTTA
1 GGTTAGAAACCAAA-TTTTAGGTTGCAACCCATATTTTA
* * * ** ** *
60948 AGTT-GTAGCCTAGTTTTTAGGTTGGGATCCATATTTTA
1 GGTTAGAAACC-AAATTTTAGGTTGCAACCCATATTTTA
** * * *
60986 GGTTTCAACCCAGATATTTAGGCTGCAACCCATATTTTTA
1 GGTTAGAAACCAAAT-TTTAGGTTGCAACCCATA-TTTTA
* * *
61026 TGTTGGAATCCAAATTTTAGGTTGCAACCCATATTATTA
1 GGTTAGAAACCAAATTTTAGGTTGCAACCCATATT-TTA
* * * *
61065 GGTTACAACCCAAATTTTTGGGTTGGAACCCATATTTTA
1 GGTTAGAAACCAAA-TTTTAGGTTGCAACCCATATTTTA
*
61104 GGTTA-AAAGCCGAATTTTAGGTTGCAACCCATATTTTTA
1 GGTTAGAAA-CCAAATTTTAGGTTGCAACCCATA-TTTTA
* * *
61143 GGTT-GACAACCAGATTTTAGGTTGAAAACCATATTTCT-
1 GGTTAGA-AACCAAATTTTAGGTTGCAACCCATATTT-TA
*
61181 GGTTAGAAATCAAATTTTTAGGT
1 GGTTAGAAACCAAA-TTTTAGGT
61204 GTAAGTTTGT
Statistics
Matches: 202, Mismatches: 41, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
38 62 0.31
39 104 0.51
40 36 0.18
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (38 bp):
GGTTAGAAACCAAATTTTAGGTTGCAACCCATATTTTA
Found at i:61200 original size:78 final size:77
Alignment explanation
Indices: 60962--61203 Score: 242
Period size: 78 Copynumber: 3.1 Consensus size: 77
60952 GTAGCCTAGT
** * * * *
60962 TTTTAGGTTGGGATCCATA-TTTTAGGTTTCAACCCAGATATTTAGGCTGCAACCCATATTTTTA
1 TTTTAGGTTGCAACCCATATTTTTAGGTTACAACCCAGAT-TTTAGGTTGAAACCCATA-TTTTA
* *
61026 TGTT-GGAATCCAAA
64 GGTTAGAAAT-CAAA
* * * *
61040 TTTTAGGTTGCAACCCATATTATTAGGTTACAACCCAAATTTTTGGGTTGGAACCCATATTTTAG
1 TTTTAGGTTGCAACCCATATTTTTAGGTTACAACCCAGA-TTTTAGGTTGAAACCCATATTTTAG
* *
61105 GTTA-AAAGCCGAA
65 GTTAGAAA-TCAAA
*
61118 TTTTAGGTTGCAACCCATATTTTTAGGTTGACAA-CCAGATTTTAGGTTGAAAACCATATTTCT-
1 TTTTAGGTTGCAACCCATATTTTTAGGTT-ACAACCCAGATTTTAGGTTGAAACCCATATTT-TA
61181 GGTTAGAAATCAAA
64 GGTTAGAAATCAAA
61195 TTTTTAGGT
1 -TTTTAGGT
61204 GTAAGTTTGT
Statistics
Matches: 136, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
77 27 0.20
78 73 0.54
79 35 0.26
80 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (77 bp):
TTTTAGGTTGCAACCCATATTTTTAGGTTACAACCCAGATTTTAGGTTGAAACCCATATTTTAGG
TTAGAAATCAAA
Done.