Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008717.1 Hibiscus syriacus cultivar Beakdansim tig00111772_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: 3453450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 16
Found at i:2360569 original size:83 final size:85
Alignment explanation
Indices: 2360467--2360651 Score: 250
Period size: 83 Copynumber: 2.2 Consensus size: 85
2360457 CTAAAAATCG
* * ** * *
2360467 CAAAAAATCAAAAATTCTAAATTGTAATCCTTAAAAAT-CATAAAAATCATAAGATTCA-TTTTT
1 CAAAAAATCATAAACTCTAAATCATAAACCCTAAAAATAC-TAAAAATCATAAGATTCATTTTTT
**
2360530 TGGAATGAATTTAGGGATTA-
65 TACAATGAATTTAGGGATTAC
* *
2360550 CAAAAAATTATAAACTCTAAATCATAAACCCTAAAAATACTAAAAATCATAAGATTTATTTTTTT
1 CAAAAAATCATAAACTCTAAATCATAAACCCTAAAAATACTAAAAATCATAAGATTCATTTTTTT
2360615 ACAATGAATTTAGGGATTAC
66 ACAATGAATTTAGGGATTAC
2360635 CAAAAAATCATAAACTC
1 CAAAAAATCATAAACTC
2360652 CCTAAAAATG
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
83 48 0.55
84 24 0.27
85 16 0.18
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (85 bp):
CAAAAAATCATAAACTCTAAATCATAAACCCTAAAAATACTAAAAATCATAAGATTCATTTTTTT
ACAATGAATTTAGGGATTAC
Found at i:2360960 original size:3 final size:3
Alignment explanation
Indices: 2360945--2360996 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
2360935 GGTTAAAAAA
*
2360945 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2360992 TAT TA
1 TAT TA
2360997 AGTGTGTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 1 0.02
3 45 0.98
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2367269 original size:172 final size:172
Alignment explanation
Indices: 2366925--2367274 Score: 661
Period size: 172 Copynumber: 2.0 Consensus size: 172
2366915 GTCTTGGTTG
2366925 ATTAA-AGAAGTTGTCGAACTTAATCGGATGGCTAGGCCATATCTGTAGAAGTGAATTATTGTGT
1 ATTAATAGAAGTTGTCGAACTTAATCGGATGGCTAGGCCATATCTGTAGAAGTGAATTATTGTGT
2366989 AATAAAAACTTTGTGTTCCAATGGAAGTTGTTCTATGATAATTAACTTTTGAGATCAATACCTTT
66 AATAAAAACTTTGTGTTCCAATGGAAGTTGTTCTATGATAATTAACTTTTGAGATCAATACCTTT
2367054 TACATACATTCATTCTGCATTGCATTTATTTTAAATATTTGC
131 TACATACATTCATTCTGCATTGCATTTATTTTAAATATTTGC
2367096 ATTAATAGAAGTTGTCGAACTTAATCGGATGGCTAGGCCATATCTGTAGAAGTGAATTATTGTGT
1 ATTAATAGAAGTTGTCGAACTTAATCGGATGGCTAGGCCATATCTGTAGAAGTGAATTATTGTGT
2367161 AATAAAAACTTTGTGTTCCAATGGAAGTTGTTTCTATGATAATTAACTTTTTGAGATCAATACCT
66 AATAAAAACTTTGTGTTCCAATGGAAGTTG-TTCTATGATAATTAAC-TTTTGAGATCAATACCT
2367226 TTTACATACATTCATTCTGCATTGCATTTA-TTTAAAT-TTTGC
129 TTTACATACATTCATTCTGCATTGCATTTATTTTAAATATTTGC
2367268 ATTAATA
1 ATTAATA
2367275 CATGCATTCA
Statistics
Matches: 176, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
171 5 0.03
172 101 0.57
173 23 0.13
174 47 0.27
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (172 bp):
ATTAATAGAAGTTGTCGAACTTAATCGGATGGCTAGGCCATATCTGTAGAAGTGAATTATTGTGT
AATAAAAACTTTGTGTTCCAATGGAAGTTGTTCTATGATAATTAACTTTTGAGATCAATACCTTT
TACATACATTCATTCTGCATTGCATTTATTTTAAATATTTGC
Found at i:2374530 original size:26 final size:26
Alignment explanation
Indices: 2374496--2374576 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 26
2374486 GGAACAAATA
2374496 AAAAGATGAAAAATGAAAAAGAAAAAG
1 AAAA-ATGAAAAATGAAAAAGAAAAAG
2374523 AAAAATGAAAAATGAAAAATGAAAAA-
1 AAAAATGAAAAATGAAAAA-GAAAAAG
* *
2374549 AGAAATGAAAAAATTAAAAGAGAAAAAG
1 AAAAATG-AAAAATGAAAA-AGAAAAAG
2374577 GAGGGTTTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
26 21 0.44
27 26 0.54
28 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (26 bp):
AAAAATGAAAAATGAAAAAGAAAAAG
Found at i:2374559 original size:33 final size:34
Alignment explanation
Indices: 2374474--2374575 Score: 104
Period size: 34 Copynumber: 3.0 Consensus size: 34
2374464 TATGCTTAAA
2374474 GAAAAA-AAAAAGGGAACAAATAAAAAGATGAAAAAT
1 GAAAAAGAAAAA--GAA-AAATAAAAAGATGAAAAAT
*
2374510 GAAAAAGAAAAAGAAAAATGAAAA-ATGAAAAAT
1 GAAAAAGAAAAAGAAAAATAAAAAGATGAAAAAT
* *
2374543 GAAAAA-AGAAATGAAAAAATTAAAAGA-GAAAAA
1 GAAAAAGA-AAAAG-AAAAATAAAAAGATGAAAAA
2374576 GGAGGGTTTG
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
32 1 0.02
33 19 0.32
34 24 0.41
35 4 0.07
36 6 0.10
37 5 0.08
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.09
Consensus pattern (34 bp):
GAAAAAGAAAAAGAAAAATAAAAAGATGAAAAAT
Found at i:2374561 original size:13 final size:13
Alignment explanation
Indices: 2374496--2374560 Score: 80
Period size: 12 Copynumber: 4.9 Consensus size: 13
2374486 GGAACAAATA
2374496 AAAAGATGAAAAATG
1 AAAA-ATGAAAAA-G
2374511 AAAAA-GAAAAAG
1 AAAAATGAAAAAG
2374523 AAAAATGAAAAATG
1 AAAAATGAAAAA-G
2374537 AAAAATGAAAAA-
1 AAAAATGAAAAAG
*
2374549 AGAAATGAAAAA
1 AAAAATGAAAAA
2374561 ATTAAAAGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
12 17 0.36
13 12 0.26
14 14 0.30
15 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAAATGAAAAAG
Found at i:2374567 original size:7 final size:7
Alignment explanation
Indices: 2374491--2374553 Score: 85
Period size: 7 Copynumber: 9.1 Consensus size: 7
2374481 AAAAGGGAAC
*
2374491 AAATAAA
1 AAATGAA
2374498 AAGATGAA
1 AA-ATGAA
2374506 AAATGAA
1 AAATGAA
2374513 AAA-GAA
1 AAATGAA
2374519 AAA-GAA
1 AAATGAA
2374525 AAATGAA
1 AAATGAA
2374532 AAATGAA
1 AAATGAA
2374539 AAATGAA
1 AAATGAA
*
2374546 AAAAGAA
1 AAATGAA
2374553 A
1 A
2374554 TGAAAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
6 12 0.23
7 34 0.65
8 6 0.12
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (7 bp):
AAATGAA
Found at i:2374567 original size:19 final size:20
Alignment explanation
Indices: 2374491--2374573 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
2374481 AAAAGGGAAC
*
2374491 AAATAAAAAGATGAAAAATGA-
1 AAATGAAAA-ATGAAAAA-GAG
* *
2374512 AAAAGAAAAA-GAAAAATGAA
1 AAATGAAAAATGAAAAA-GAG
2374532 AAATGAAAAATGAAAAA-AG
1 AAATGAAAAATGAAAAAGAG
*
2374551 AAATGAAAAAAT-TAAAAGAG
1 AAATG-AAAAATGAAAAAGAG
2374571 AAA
1 AAA
2374574 AAGGAGGGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
19 19 0.36
20 21 0.40
21 13 0.25
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (20 bp):
AAATGAAAAATGAAAAAGAG
Found at i:2374574 original size:14 final size:14
Alignment explanation
Indices: 2374481--2374575 Score: 74
Period size: 14 Copynumber: 6.9 Consensus size: 14
2374471 AAAGAAAAAA
* *
2374481 AAAAGGGAACAAATA
1 AAAAGAGAA-AAATG
2374496 AAAAGATGAAAAATG
1 AAAAGA-GAAAAATG
2374511 AAAA-AGAAAAA-G
1 AAAAGAGAAAAATG
2374523 AAAA-ATGAAAAATG
1 AAAAGA-GAAAAATG
*
2374537 AAAA-ATGAAAAAAG
1 AAAAGA-GAAAAATG
* *
2374551 AAATGA-AAAAATT
1 AAAAGAGAAAAATG
2374564 AAAAGAGAAAAA
1 AAAAGAGAAAAA
2374576 GGAGGGTTTG
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
12 6 0.09
13 22 0.32
14 23 0.34
15 14 0.21
16 3 0.04
ACGTcount: A:0.74, C:0.01, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAAGAGAAAAATG
Found at i:2375690 original size:134 final size:136
Alignment explanation
Indices: 2375446--2375789 Score: 540
Period size: 135 Copynumber: 2.6 Consensus size: 136
2375436 GGTGAACCAG
2375446 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATG
* * *
2375511 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCA-TGACACCTTGCTTGAAG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
*
2375575 GATCAG
131 GATCAA
* *
2375581 TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGA-AAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATG
* *
2375645 AGAAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACACCTCGCTTGAGG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
2375710 GATCAA
131 GATCAA
* *
2375716 CATTTCCAGTGAAGAGTTCATAAT--GAAGAACTCAT-C-AAAGA-GGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATG
*
2375776 AGAAGAACTTGTTC
66 AGAAGAGCTTGTTC
2375790 AACTTCGCAT
Statistics
Matches: 194, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
130 3 0.02
131 32 0.16
132 1 0.01
133 11 0.06
134 59 0.30
135 88 0.45
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (136 bp):
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
GATCAA
Found at i:2375867 original size:92 final size:87
Alignment explanation
Indices: 2375711--2375881 Score: 243
Period size: 92 Copynumber: 1.9 Consensus size: 87
2375701 CGCTTGAGGG
* *
2375711 ATCAACATTTCCAGTGAAGAGTTCATAATGAAGAACTCATCAAAGAGGAGAAGAAGTTCATAATG
1 ATCAACATTTCCAATGAAGAGCTCATAATGAAGAACTCATCAAAGAGGAGAAGAAGTTCATAATG
2375776 AGAAGAACTTGTTCAACTTCGC
66 AGAAGAACTTGTTCAACTTCGC
* * *
2375798 ATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCGTCCGAAAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAATGAAGAGCTCATAAT--GAAGAACTCAT-C-AAAGA-GGAGAAGAAGTTCA
*
2375863 TAATGAGAAGAGCTTGTTC
61 TAATGAGAAGAACTTGTTC
2375882 GACCTATCAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
87 25 0.34
89 10 0.14
90 1 0.01
91 5 0.07
92 32 0.44
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (87 bp):
ATCAACATTTCCAATGAAGAGCTCATAATGAAGAACTCATCAAAGAGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACTTCGC
Found at i:2375967 original size:16 final size:16
Alignment explanation
Indices: 2375946--2376001 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2375936 TGATATTTTC
2375946 AGAAGAGTTCATAATG
1 AGAAGAGTTCATAATG
* * *
2375962 AGAAGACTCATCCTAAAGG
1 AGAAGAGT--TCAT-AATG
2375981 AGAA-AGTTCATAATG
1 AGAAGAGTTCATAATG
2375996 AGAAGA
1 AGAAGA
2376002 ACTTGTTCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 7 0.23
16 11 0.37
18 5 0.17
19 7 0.23
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (16 bp):
AGAAGAGTTCATAATG
Found at i:2376328 original size:18 final size:18
Alignment explanation
Indices: 2376275--2376328 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
2376265 TCCAATGAAG
2376275 AGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
* *
2376293 ACTCATCATAA--AGGAGAA
1 AGT--TCATAATGAGAAGAA
2376311 AGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
2376329 CTTGTTCCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
16 6 0.21
18 16 0.57
20 6 0.21
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20
Consensus pattern (18 bp):
AGTTCATAATGAGAAGAA
Found at i:2376340 original size:326 final size:326
Alignment explanation
Indices: 2375709--2376342 Score: 965
Period size: 323 Copynumber: 1.9 Consensus size: 326
2375699 CTCGCTTGAG
*
2375709 GGATCAACATTTCCAGTGAAGAGTTCATAATGAAGAACTCATCAAAGAGGAGAAGAAGTTCATAA
1 GGATCAACATTTCCAATGAAGAGTTCATAAT-AAGAACTCATCAAAGAGGAGAAGAAGTTCATAA
* *
2375774 TGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCG
65 TGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCA
*
2375839 TCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGAC
130 TCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGAC
* * * * *
2375904 ATTTCAAATTAGTGACATCTCGCTTGAGGGATTGATATTTTCAGAAGAGTTCATAATGAGAAGAC
195 ATTTCAAATCAGTGACACCTCGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGAC
*
2375969 TCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAG
260 TCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAG
2376034 AT
325 AT
* *
2376036 GGATCAACATTTCCAATGGAGAGTTCATAAT-A-AACTCATCCAATGAGAGAGAAGAAGTTCAT-
1 GGATCAACATTTCCAATGAAGAGTTCATAATAAGAACTCAT-CAAAGAG-GAGAAGAAGTTCATA
* *
2376098 ATGAGAAGAACTTGTTCAACTTCGCATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAACTC
64 ATGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTC
* * * * *
2376163 AT-CGATAGA-GGAGAAGAAGTTCATAATGAGAAGAGTTTTTTTGACCTATCACTTGATTCACGA
129 ATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGA
* **
2376226 CATTTCGAATCAGTGATGCCTCGCTT-AGGGATCGACATTTCCAATGAAGAGTTCATAATGAGAA
194 CATTTCAAATCAGTGACACCTCGCTTGAGGGATCGACATTTCC-A-GAAGAGTTCATAATGAGAA
2376290 GAAACTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
257 G--ACTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAA
2376343 ATTTCACCAC
Statistics
Matches: 279, Mismatches: 22, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
322 13 0.05
323 71 0.25
324 33 0.12
325 70 0.25
326 63 0.23
327 29 0.10
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (326 bp):
GGATCAACATTTCCAATGAAGAGTTCATAATAAGAACTCATCAAAGAGGAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCAT
CCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACA
TTTCAAATCAGTGACACCTCGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGACT
CATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGA
T
Found at i:2376386 original size:325 final size:325
Alignment explanation
Indices: 2375713--2376389 Score: 954
Period size: 325 Copynumber: 2.1 Consensus size: 325
2375703 CTTGAGGGAT
2375713 CAACATTTCCAGTGAAGAGTTCATAATGAAGAACTCATCAAAGAGGAGAAGAAGTTCATAATGAG
1 CAACATTTCCA-TGAAGAGTTCATAAT-AAGAACTCATCAAAGAGGAGAAGAAGTTCATAATGAG
* *
2375778 AAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAGAAGAACTCGTCCG
64 AAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCATCCG
*
2375843 AAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTT
129 AAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTT
* * * * *
2375908 CAAATTAGTGACATCTCGCTTGAGGGATTGATATTTTCAGAAGAGTTCATAATGAGAAGACTCAT
194 CAAATCAGTGACACCTCGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGACTCAT
* * *
2375973 CCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGG
259 CATAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGATGA
*
2376038 AT
324 AC
* *
2376040 CAACATTTCCAATGGAGAGTTCATAAT-A-AACTCATCCAATGAGAGAGAAGAAGTTCAT-ATGA
1 CAACATTTCC-ATGAAGAGTTCATAATAAGAACTCAT-CAAAGAG-GAGAAGAAGTTCATAATGA
* *
2376102 GAAGAACTTGTTCAACTTCGCATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAACTCAT-C
63 GAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCATCC
* * * * *
2376166 GATAGA-GGAGAAGAAGTTCATAATGAGAAGAGTTTTTTTGACCTATCACTTGATTCACGACATT
128 GAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATT
* **
2376230 TCGAATCAGTGATGCCTCGCTT-AGGGATCGACATTTCCAATGAAGAGTTCATAATGAGAAGAAA
193 TCAAATCAGTGACACCTCGCTTGAGGGATCGACATTTCC-A-GAAGAGTTCATAATGAGAAG--A
* * **
2376294 CTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTTCACCACAGATGG
254 CTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTC-AAGTCCACCACAGAAAG
*
2376359 AGGTGAAC
318 AGATGAAC
2376367 CAACATTTCC-TGAAGAGTTCATA
1 CAACATTTCCATGAAGAGTTCATA
2376390 TGAGAAGAAC
Statistics
Matches: 312, Mismatches: 30, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
322 13 0.04
323 71 0.23
324 33 0.11
325 82 0.26
326 61 0.20
327 51 0.16
328 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (325 bp):
CAACATTTCCATGAAGAGTTCATAATAAGAACTCATCAAAGAGGAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACTCATCCGAA
AGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCA
AATCAGTGACACCTCGCTTGAGGGATCGACATTTCCAGAAGAGTTCATAATGAGAAGACTCATCA
TAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCACCACAGAAAGAGATGAAC
Found at i:2376569 original size:3 final size:3
Alignment explanation
Indices: 2376561--2376603 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2376551 AGGGTTAAAA
2376561 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2376604 AGTGTGTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2379867 original size:55 final size:57
Alignment explanation
Indices: 2379749--2379872 Score: 200
Period size: 55 Copynumber: 2.2 Consensus size: 57
2379739 GTAATCGATT
* *
2379749 AAAAGTATGCAAGAAATTTTGTTAGTCAAAAAGGTTATTTTTTCTAAAAGGATAAAG
1 AAAAGTATGCAAGAAATTTTATTAGTCAAAAAGGTTATATTTTCTAAAAGGATAAAG
2379806 AAAAGTATGCAAGAAA-TTTATTAGTCAAAAA-GTT-TATTTTCTAAAAAGGATAAAG
1 AAAAGTATGCAAGAAATTTTATTAGTCAAAAAGGTTATATTTTCT-AAAAGGATAAAG
2379861 AAAAGTATGCAA
1 AAAAGTATGCAA
2379873 TTTATCGCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
54 7 0.11
55 27 0.42
56 14 0.22
57 16 0.25
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.31
Consensus pattern (57 bp):
AAAAGTATGCAAGAAATTTTATTAGTCAAAAAGGTTATATTTTCTAAAAGGATAAAG
Found at i:2382988 original size:61 final size:62
Alignment explanation
Indices: 2382913--2383036 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 62
2382903 ATTCCTTCAC
2382913 GATCCTGGTAATCACATCACAGATCAGGTTATTGATACCCTCTC-TTGCAATACGAGTGGAA
1 GATCCTGGTAATCACATCACAGATCAGGTTATTGATACCCTCTCTTTGCAATACGAGTGGAA
2382974 GATCCTGGTAATCACATCACAGATCAGGTTATTGATACCCTCTCTTTGCAATACGAGTGGAA
1 GATCCTGGTAATCACATCACAGATCAGGTTATTGATACCCTCTCTTTGCAATACGAGTGGAA
2383036 G
1 G
2383037 CAATAACCCG
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 44 0.71
62 18 0.29
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (62 bp):
GATCCTGGTAATCACATCACAGATCAGGTTATTGATACCCTCTCTTTGCAATACGAGTGGAA
Found at i:2384480 original size:20 final size:20
Alignment explanation
Indices: 2384457--2384494 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2384447 TAGAAAATCG
2384457 CAATGCGAATATGTAAATTA
1 CAATGCGAATATGTAAATTA
*
2384477 CAATGTGAATATGTAAAT
1 CAATGCGAATATGTAAAT
2384495 CGCAACGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (20 bp):
CAATGCGAATATGTAAATTA
Found at i:2384539 original size:20 final size:20
Alignment explanation
Indices: 2384514--2384607 Score: 170
Period size: 20 Copynumber: 4.7 Consensus size: 20
2384504 ATAATACATA
2384514 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2384534 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
2384554 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2384574 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
2384594 ATCACAACGCGATT
1 ATCGCAACGCGATT
2384608 TTCAAAGCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:2385263 original size:20 final size:20
Alignment explanation
Indices: 2385167--2385256 Score: 110
Period size: 20 Copynumber: 4.5 Consensus size: 20
2385157 CGATTTTCTC
*
2385167 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
** **
2385186 GTTGCGATAGTCAAATTCGT
1 GTTGCGATTTTCATTTTCGT
**
2385206 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
2385226 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
2385246 GTTGCGATTTT
1 GTTGCGATTTT
2385257 AAGTTTCATA
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
19 11 0.18
20 51 0.82
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.47
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:2386752 original size:95 final size:98
Alignment explanation
Indices: 2386562--2386754 Score: 356
Period size: 95 Copynumber: 2.0 Consensus size: 98
2386552 ATGGCACGGA
2386562 TGATTAGCAGCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCACACT
1 TGATTAGCAGCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCACACT
2386627 ATACACCTCTACAACGAGAGCCATCACCTATTC
66 ATACACCTCTACAACGAGAGCCATCACCTATTC
2386660 TGATTAGCAGCCTCCACTTCGAGAGCC-TCACCTCACCCAGAGCCATCACCTGATCGA-C-CACT
1 TGATTAGCAGCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCACACT
*
2386722 ATACACCTCTACACCGAGAGCCATCACCTATTC
66 ATACACCTCTACAACGAGAGCCATCACCTATTC
2386755 CGTCACATCA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
95 36 0.38
96 1 0.01
97 30 0.32
98 27 0.29
ACGTcount: A:0.27, C:0.39, G:0.13, T:0.20
Consensus pattern (98 bp):
TGATTAGCAGCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCACACT
ATACACCTCTACAACGAGAGCCATCACCTATTC
Found at i:2387326 original size:33 final size:34
Alignment explanation
Indices: 2387253--2387351 Score: 92
Period size: 34 Copynumber: 2.9 Consensus size: 34
2387243 CACGAAACTT
* * ** *
2387253 AAAATCGCAACGCGAAAATGACTATCGCAACGGG
1 AAAATCGCAAAGCGAAAATAAAAATCACAACGGG
* *
2387287 ATAATCGCAAAGCG-AAATAAAAATCACAACGTG
1 AAAATCGCAAAGCGAAAATAAAAATCACAACGGG
* * * *
2387320 AAAATCGCAATGCAAAAATGAAAATCGCAACG
1 AAAATCGCAAAGCGAAAATAAAAATCACAACG
2387352 CGAATTTAGT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 25 0.48
34 27 0.52
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.13
Consensus pattern (34 bp):
AAAATCGCAAAGCGAAAATAAAAATCACAACGGG
Found at i:2387373 original size:19 final size:19
Alignment explanation
Indices: 2387351--2387392 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2387341 AAATCGCAAC
2387351 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
2387370 GCGATTTTGGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
2387389 GCGA
1 GCGA
2387393 TTTTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.17, G:0.31, T:0.40
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:2387393 original size:19 final size:19
Alignment explanation
Indices: 2387360--2387396 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2387350 CGCGAATTTA
2387360 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
2387379 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
2387397 CTCGTTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.30, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:2387416 original size:32 final size:33
Alignment explanation
Indices: 2387361--2387439 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
2387351 GCGAATTTAG
* * *
2387361 TTTCGCGTTGCGATTTTGGTTTCGCGTTGCGAT
1 TTTCTCGTTGCGATTTTGATTTCGCATTGCGAT
*
2387394 TTTCTCGTTGC-ATTTTTATTTCGCATTGCGAT
1 TTTCTCGTTGCGATTTTGATTTCGCATTGCGAT
* *
2387426 TATCTTGTTGCGAT
1 TTTCTCGTTGCGAT
2387440 AGTCAAATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 27 0.69
33 12 0.31
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCTCGTTGCGATTTTGATTTCGCATTGCGAT
Found at i:2387457 original size:20 final size:20
Alignment explanation
Indices: 2387432--2387479 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2387422 CGATTATCTT
2387432 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
2387452 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
2387472 GTTGCGAT
1 GTTGCGAT
2387480 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:2387489 original size:20 final size:20
Alignment explanation
Indices: 2387432--2387490 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
2387422 CGATTATCTT
*
2387432 GTTGCGATAGTCAA-ATTCGC
1 GTTGCGATAGT-AAGTTTCGC
* *
2387452 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTAAGTTTCGC
**
2387472 GTTGCGATTTTAAGTTTCG
1 GTTGCGATAGTAAGTTTCG
2387491 TGTTACGACT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGTAAGTTTCGC
Found at i:2388906 original size:29 final size:29
Alignment explanation
Indices: 2388864--2388922 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2388854 TGTATCGACC
2388864 TACATCATCATGTCTGAAGCGTAGACTAG
1 TACATCATCATGTCTGAAGCGTAGACTAG
2388893 TACATCATCATGTCTGAAGCGTAGACTAG
1 TACATCATCATGTCTGAAGCGTAGACTAG
2388922 T
1 T
2388923 GATTAAGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (29 bp):
TACATCATCATGTCTGAAGCGTAGACTAG
Found at i:2389436 original size:20 final size:20
Alignment explanation
Indices: 2389413--2389499 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
2389403 TATGAAACTT
2389413 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
2389433 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
2389453 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
2389473 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
2389492 AAAATCGC
1 AAAATCGC
2389500 CACGAGAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
19 9 0.16
20 49 0.84
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:2390087 original size:20 final size:20
Alignment explanation
Indices: 2390062--2390111 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2390052 GCGCTTTGAA
2390062 AATCGCGTTGTAATAGTCAG
1 AATCGCGTTGTAATAGTCAG
* *
2390082 AATCGCATTGTGATAGTCAG
1 AATCGCGTTGTAATAGTCAG
2390102 AATCGCGTTG
1 AATCGCGTTG
2390112 CGATTTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (20 bp):
AATCGCGTTGTAATAGTCAG
Found at i:2390129 original size:21 final size:21
Alignment explanation
Indices: 2390103--2390159 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2390093 GATAGTCAGA
2390103 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
*
2390124 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTTTGTATT
2390145 ATCGCGTTGCGATTT
1 ATCGCGTTGCGATTT
2390160 ACATATTCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.16, C:0.16, G:0.25, T:0.44
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:2390179 original size:20 final size:20
Alignment explanation
Indices: 2390151--2390199 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2390141 TATTATCGCG
2390151 TTGCGATTTACATATTCACA
1 TTGCGATTTACATATTCACA
* *
2390171 TTGCAATTTACATATTCGCA
1 TTGCGATTTACATATTCACA
2390191 TTGCGATTT
1 TTGCGATTT
2390200 TCTAAAATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (20 bp):
TTGCGATTTACATATTCACA
Found at i:2390308 original size:19 final size:19
Alignment explanation
Indices: 2390284--2390320 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2390274 TGCGATATTG
*
2390284 GAGATCGCGTTGCAATTTA
1 GAGATCGCATTGCAATTTA
*
2390303 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCAATTT
2390321 TGTTGGTCAT
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:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCAATTTA
Found at i:2394965 original size:55 final size:56
Alignment explanation
Indices: 2394887--2395011 Score: 182
Period size: 57 Copynumber: 2.2 Consensus size: 56
2394877 TTGCGATAAA
* *
2394887 TTGCATACTTTTCTTTATTCTTTTTAG-AAAATAAACTTTTTGACTAA-TAAATTTC
1 TTGCATACTTTTCTTTA-TCCTTTTAGAAAAATAAACTTTTTGACTAACAAAATTTC
*
2394942 TTGCATACTTTTCTTTATCCTTTTAGAAAAAAATAACCTTTTTGACTAACAAAATTTC
1 TTGCATACTTTTCTTTATCCTTTTAG--AAAAATAAACTTTTTGACTAACAAAATTTC
2395000 TTGCATACTTTT
1 TTGCATACTTTT
2395012 AATCGATTAC
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
54 8 0.13
55 17 0.27
57 19 0.30
58 19 0.30
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (56 bp):
TTGCATACTTTTCTTTATCCTTTTAGAAAAATAAACTTTTTGACTAACAAAATTTC
Found at i:2396017 original size:28 final size:29
Alignment explanation
Indices: 2395985--2396040 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
2395975 GATTTTTTGC
2395985 GATTTT-TAGAAATTT-AGGAGTTTTTTTA
1 GATTTTCT-GAAATTTAAGGAGTTTTTTTA
* *
2396013 GATTTTCTGGAATTTAAGGTGTTTTTTT
1 GATTTTCTGAAATTTAAGGAGTTTTTTT
2396041 TTAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.23, C:0.02, G:0.20, T:0.55
Consensus pattern (29 bp):
GATTTTCTGAAATTTAAGGAGTTTTTTTA
Found at i:2397623 original size:31 final size:30
Alignment explanation
Indices: 2397585--2397651 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
2397575 AATTTAGGAG
* *
2397585 TTTTTTTAGATTTTCATGAATTT-AAGGTGTT
1 TTTTTTTAAATTTTAAT-AATTTCAAGG-GTT
*
2397616 TTTTTTTAAATTTTAATAATTTCATGGGTT
1 TTTTTTTAAATTTTAATAATTTCAAGGGTT
2397646 TTTTTT
1 TTTTTT
2397652 AGAAAGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 14 0.44
31 18 0.56
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.63
Consensus pattern (30 bp):
TTTTTTTAAATTTTAATAATTTCAAGGGTT
Found at i:2401634 original size:21 final size:21
Alignment explanation
Indices: 2401608--2401686 Score: 113
Period size: 21 Copynumber: 3.8 Consensus size: 21
2401598 ATGCTTGATA
*
2401608 GTATCGATACTACTATTCACG
1 GTATCGATACTACTATTCATG
* *
2401629 GTATCGATATTACTGTTCATG
1 GTATCGATACTACTATTCATG
*
2401650 GTATCGATACTACTGTTCATG
1 GTATCGATACTACTATTCATG
*
2401671 GTAACGATACTACTAT
1 GTATCGATACTACTAT
2401687 AGCAGTATCG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (21 bp):
GTATCGATACTACTATTCATG
Found at i:2401754 original size:18 final size:18
Alignment explanation
Indices: 2401728--2401775 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
2401718 ATTTTTTAGC
*
2401728 ATCGGTACTGTTCATGGT
1 ATCGATACTGTTCATGGT
*
2401746 ATCGATACTACTGTTTATGGT
1 ATCG--A-TACTGTTCATGGT
2401767 ATCGATACT
1 ATCGATACT
2401776 ATTGTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.32
19 1 0.04
21 16 0.64
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (18 bp):
ATCGATACTGTTCATGGT
Found at i:2401759 original size:21 final size:21
Alignment explanation
Indices: 2401733--2401783 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
2401723 TTAGCATCGG
2401733 TACTGTTCATGGTATCGATAC
1 TACTGTTCATGGTATCGATAC
*
2401754 TACTGTTTATGGTATCGATAC
1 TACTGTTCATGGTATCGATAC
*
2401775 TATTGTTCA
1 TACTGTTCA
2401784 CACAGTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (21 bp):
TACTGTTCATGGTATCGATAC
Found at i:2401819 original size:19 final size:19
Alignment explanation
Indices: 2401780--2401843 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
2401770 GATACTATTG
* *
2401780 TTCACACAGTATTGGTACTA
1 TTCATACAGT-TTGATACTA
2401800 TTCATACAGTTTGATACTA
1 TTCATACAGTTTGATACTA
* *
2401819 TTCATACAGTATGATATTA
1 TTCATACAGTTTGATACTA
2401838 TTCATA
1 TTCATA
2401844 AAAATTTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 31 0.77
20 9 0.22
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (19 bp):
TTCATACAGTTTGATACTA
Found at i:2409022 original size:76 final size:73
Alignment explanation
Indices: 2408942--2409168 Score: 246
Period size: 76 Copynumber: 3.1 Consensus size: 73
2408932 TAAACTCAAG
* *
2408942 TTTAGGATAATATTTTAAACATTATATTTTTCTCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAGGATATTATTTTAAATATT-TATTTTT-T-TTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
2409007 TTTAATTAAGT
63 TTTAATTAAGA
* * *
2409018 TTTAGGATATTGTTTT-TATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTA
1 TTTAGGATATTATTTTAAATA-TTTAT-TTT-TTTT-TGTATTTTAGTTTAAATAGGTTTTAGTA
**
2409082 TTTTAATTCGGA
62 TTTTAATTAAGA
* * * *
2409094 TTTAGAATATTATTTTAAATA-TTA-TTTTTTTGGTATTTTATTTTAAATA-GTTTTAAGTTTTT
1 TTTAGGATATTATTTTAAATATTTATTTTTTTTTGTATTTTAGTTTAAATAGGTTTT-AGTATTT
2409156 TAATTAAGA
65 TAATTAAGA
2409165 TTTA
1 TTTA
2409169 AGGTGTTTTA
Statistics
Matches: 130, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
70 5 0.04
71 34 0.26
72 4 0.03
73 3 0.02
75 10 0.08
76 70 0.54
77 4 0.03
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (73 bp):
TTTAGGATATTATTTTAAATATTTATTTTTTTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTT
AATTAAGA
Found at i:2409780 original size:18 final size:18
Alignment explanation
Indices: 2409757--2409799 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2409747 TCTTAGATTA
*
2409757 TTTATTTAATTTTTTTCT
1 TTTATTTAATTTTTATCT
2409775 TTTATTTAATTTTTATCT
1 TTTATTTAATTTTTATCT
2409793 TTTATTT
1 TTTATTT
2409800 TAAAAACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTAATTTTTATCT
Found at i:2409857 original size:15 final size:16
Alignment explanation
Indices: 2409839--2409895 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 16
2409829 TCTTTATTAC
2409839 TATTATTTA-TTATTT
1 TATTATTTACTTATTT
*
2409854 TATTATTTACCT-TTT
1 TATTATTTACTTATTT
*
2409869 TATTTACTATTATTTATTT
1 TA-TTA-T-TTACTTATTT
2409888 TATTATTT
1 TATTATTT
2409896 TTTTCTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
15 14 0.41
16 6 0.18
17 2 0.06
18 7 0.21
19 5 0.15
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTTACTTATTT
Found at i:2409877 original size:37 final size:35
Alignment explanation
Indices: 2409831--2409931 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 35
2409821 TTTTTTTATC
2409831 TTTATTACTATTATTTATTATTTTATTATTTACCTT
1 TTTATTACTATTATTTATT-TTTTATTATTTACCTT
**
2409867 TTTATTTACTATTATTTATTTTATTATT-TTTTTCTT
1 TTTA-TTACTATTATTTATTTT-TTATTATTTACCTT
2409903 TTTAAATTA-TAATTATTTATTTTTT-TTAT
1 TTT--ATTACT-ATTATTTATTTTTTATTAT
2409932 ATATTTTCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
35 2 0.04
36 19 0.33
37 35 0.61
38 1 0.02
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (35 bp):
TTTATTACTATTATTTATTTTTTATTATTTACCTT
Found at i:2410259 original size:13 final size:14
Alignment explanation
Indices: 2410241--2410271 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2410231 CAAACGCTTC
2410241 AAGAAAAG-AGAAA
1 AAGAAAAGAAGAAA
2410254 AAGAAAAGAAGAAA
1 AAGAAAAGAAGAAA
2410268 AAGA
1 AAGA
2410272 GCAAAGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAGAAA
Found at i:2414910 original size:5 final size:5
Alignment explanation
Indices: 2414902--2415024 Score: 88
Period size: 5 Copynumber: 23.8 Consensus size: 5
2414892 TCATTCTATT
* * * *
2414902 TTTTA TTTTA TTTTCA TTTCA TTTCA TTTCA TTTTA TTTCA TTTTTA TTTTA
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA
** * *
2414954 TTTT- TTAGCAAA CTTTA TTTTCA TTATA -TTTA TTTTA TTTTA TTTTA
1 TTTTA TT---TTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA
* *
2415001 TTTTA ATTAA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT
2415025 TCTCTTAACA
Statistics
Matches: 94, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
4 5 0.05
5 76 0.81
6 12 0.13
8 1 0.01
ACGTcount: A:0.23, C:0.07, G:0.01, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:2417124 original size:18 final size:17
Alignment explanation
Indices: 2417082--2417115 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2417072 TCTTAGATTA
2417082 TTTATTTAATTATTTTAT
1 TTTATTTAA-TATTTTAT
2417100 TTTATTTAA-ATTTTAT
1 TTTATTTAATATTTTAT
2417116 CTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTAATATTTTAT
Found at i:2417206 original size:25 final size:24
Alignment explanation
Indices: 2417168--2417220 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
2417158 ACTACTATTA
2417168 TTTATTATTTTATTATTTTCCCTT
1 TTTATTATTTTATTATTTTCCCTT
**
2417192 TTTATTTATTTTATTATTTTTTCTT
1 TTTA-TTATTTTATTATTTTCCCTT
2417217 TTTA
1 TTTA
2417221 AATTATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTATTATTTTATTATTTTCCCTT
Found at i:2421345 original size:21 final size:20
Alignment explanation
Indices: 2421319--2421368 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2421309 GCATTCGTAC
2421319 TTAGCTCATTTCATGATTAT
1 TTAGCTCATTTCATGATTAT
* *
2421339 GTTAGCTTA-TTCATTATTAT
1 -TTAGCTCATTTCATGATTAT
*
2421359 CTAGCTCATT
1 TTAGCTCATT
2421369 CATATACTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.50
Consensus pattern (20 bp):
TTAGCTCATTTCATGATTAT
Found at i:2421369 original size:19 final size:20
Alignment explanation
Indices: 2421320--2421371 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2421310 CATTCGTACT
*
2421320 TAGCTCATTTCATGATTATGT
1 TAGCTCA-TTCATGATTATGC
* *
2421341 TAGCTTATTCATTATTAT-C
1 TAGCTCATTCATGATTATGC
2421360 TAGCTCATTCAT
1 TAGCTCATTCAT
2421372 ATACTTTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 10 0.37
21 6 0.22
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (20 bp):
TAGCTCATTCATGATTATGC
Found at i:2421722 original size:13 final size:12
Alignment explanation
Indices: 2421683--2421732 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
2421673 CACTCGGTGC
2421683 CTAGCTATCTAG
1 CTAGCTATCTAG
* *
2421695 CTACACTACCTAG
1 CTA-GCTATCTAG
2421708 CTAGCTATCTAAG
1 CTAGCTATCT-AG
*
2421721 CTAGCTAGCTAG
1 CTAGCTATCTAG
2421733 GTAAGTGACC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (12 bp):
CTAGCTATCTAG
Found at i:2421737 original size:17 final size:17
Alignment explanation
Indices: 2421704--2421737 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2421694 GCTACACTAC
*
2421704 CTAGCTAGCTATCTAAG
1 CTAGCTAGCTAGCTAAG
*
2421721 CTAGCTAGCTAGGTAAG
1 CTAGCTAGCTAGCTAAG
2421738 TGACCTAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (17 bp):
CTAGCTAGCTAGCTAAG
Found at i:2428947 original size:43 final size:43
Alignment explanation
Indices: 2428894--2429037 Score: 177
Period size: 42 Copynumber: 3.4 Consensus size: 43
2428884 TGCCCCAATT
* *
2428894 TTTTTTCAATCCCACTTTTTACGTTTATAATTAAGGCCCCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTAAGGCCCCTAA
* *
2428937 TTTTTTCAATCTCACTTTCTACCTTTAT-ATTGAA-GCTCCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATT-AAGGCCCCTAA
* * * *
2428979 TTTTTTTAAGCTCACTTTTTACTTTTATAA-TGAGGCCCCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTAAGGCCCCTAA
*
2429021 TTTATTCAATCTCACTT
1 TTTTTTCAATCTCACTT
2429038 AATTTAATTA
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 56 0.66
43 28 0.33
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.47
Consensus pattern (43 bp):
TTTTTTCAATCTCACTTTTTACCTTTATAATTAAGGCCCCTAA
Found at i:2431482 original size:28 final size:28
Alignment explanation
Indices: 2431451--2431537 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 28
2431441 ATATTTAAAT
*
2431451 ATATTTATTATTTTTTTAATAATATATA
1 ATATTTATTATTATTTTAATAATATATA
* * * *
2431479 ATATTTTTTAATATTATAATAATATACTC
1 ATATTTATTATTATTTTAATAATATA-TA
** *
2431508 AT-TACATTCTTATTTTAATAATATATA
1 ATATTTATTATTATTTTAATAATATATA
2431535 ATA
1 ATA
2431538 AATTATTAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
27 3 0.07
28 39 0.87
29 3 0.07
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (28 bp):
ATATTTATTATTATTTTAATAATATATA
Found at i:2431485 original size:20 final size:21
Alignment explanation
Indices: 2431462--2431503 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2431452 TATTTATTAT
2431462 TTTTTTAATAATAT-ATAATA
1 TTTTTTAATAATATAATAATA
*
2431482 TTTTTTAATATTATAATAATA
1 TTTTTTAATAATATAATAATA
2431503 T
1 T
2431504 ACTCATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTTAATAATATAATAATA
Found at i:2431672 original size:37 final size:37
Alignment explanation
Indices: 2431631--2431721 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
2431621 AATCTAATAA
2431631 TATTTTAATAAAGATACATAATATAA-TATAATATTCT
1 TATTTTAATAAA-ATACATAATATAATTATAATATTCT
** * *
2431668 TATTTTAAT-AAATATTTAATATAATTTATGATATTTT
1 TATTTTAATAAAATACATAATATAA-TTATAATATTCT
2431705 TATTTTAATAAAATACA
1 TATTTTAATAAAATACA
2431722 CTATTGTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
35 11 0.24
36 2 0.04
37 27 0.60
38 5 0.11
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (37 bp):
TATTTTAATAAAATACATAATATAATTATAATATTCT
Found at i:2431683 original size:18 final size:18
Alignment explanation
Indices: 2431630--2431683 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2431620 TAATCTAATA
* *
2431630 ATATTTTAATAAAGATAC
1 ATATTTTAATAAATATTC
* *
2431648 ATAATATAATATAATATTC
1 ATATTTTAATA-AATATTC
*
2431667 TTATTTTAATAAATATT
1 ATATTTTAATAAATATT
2431684 TAATATAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
ATATTTTAATAAATATTC
Found at i:2433927 original size:23 final size:23
Alignment explanation
Indices: 2433868--2433928 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2433858 CTCGTATAAA
*
2433868 TGCACCGAAGTGCAACGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
*
2433891 TGCACCGAAGTGCTGCGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
*
2433914 TGCACCGTAGTGCTA
1 TGCACCGAAGTGCTA
2433929 TATGAGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCTACGTAGAAT
Found at i:2437245 original size:5 final size:5
Alignment explanation
Indices: 2437235--2437304 Score: 50
Period size: 5 Copynumber: 12.4 Consensus size: 5
2437225 CACCAGTCAA
* *
2437235 CGGGT CGGGT CAACGGT CGGGT CGGGT CAACGGGT CGGGT CGGGT CGGTT
1 CGGGT CGGGT C--GGGT CGGGT CGGGT ---CGGGT CGGGT CGGGT CGGGT
2437285 CGGGT CAACGGGT CGGGT CG
1 CGGGT ---CGGGT CGGGT CG
2437305 TGACCGGTCA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
5 39 0.74
7 4 0.08
8 10 0.19
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.19
Consensus pattern (5 bp):
CGGGT
Found at i:2437254 original size:12 final size:13
Alignment explanation
Indices: 2437230--2437303 Score: 67
Period size: 13 Copynumber: 5.2 Consensus size: 13
2437220 AATAGCACCA
2437230 GTCAACGGGTCGG
1 GTCAACGGGTCGG
2437243 GTCAACGGTCGGGTCGG
1 GTCAA----CGGGTCGG
2437260 GTCAACGGGTCGG
1 GTCAACGGGTCGG
** *
2437273 GTCGGGTCGGTTCGG
1 GTC--AACGGGTCGG
2437288 GTCAACGGGTCGG
1 GTCAACGGGTCGG
2437301 GTC
1 GTC
2437304 GTGACCGGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 26 0.53
15 10 0.20
17 13 0.27
ACGTcount: A:0.11, C:0.23, G:0.47, T:0.19
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:2437257 original size:17 final size:18
Alignment explanation
Indices: 2437235--2437280 Score: 85
Period size: 17 Copynumber: 2.6 Consensus size: 18
2437225 CACCAGTCAA
2437235 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
2437252 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2437270 CGGGTCGGGTC
1 CGGGTCGGGTC
2437281 GGTTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.09, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2437289 original size:28 final size:28
Alignment explanation
Indices: 2437230--2437304 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
2437220 AATAGCACCA
*
2437230 GTCAACGGGTCGGGTCAACGGTCGGGTCGG
1 GTCAACGGGTCGGGTC--GGGTCGGGTCGG
*
2437260 GTCAACGGGTCGGGTCGGGTCGGTTCGG
1 GTCAACGGGTCGGGTCGGGTCGGGTCGG
2437288 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
2437305 TGACCGGTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 27 0.63
30 16 0.37
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.19
Consensus pattern (28 bp):
GTCAACGGGTCGGGTCGGGTCGGGTCGG
Found at i:2437313 original size:23 final size:23
Alignment explanation
Indices: 2437270--2437315 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2437260 GTCAACGGGT
* *
2437270 CGGGTCGGGTCGGTTCGGGTCAA
1 CGGGTCGGGTCGGTACCGGTCAA
2437293 CGGGTCGGGTC-GTGACCGGTCAA
1 CGGGTCGGGTCGGT-ACCGGTCAA
2437316 AACCGGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.11, C:0.24, G:0.46, T:0.20
Consensus pattern (23 bp):
CGGGTCGGGTCGGTACCGGTCAA
Found at i:2444455 original size:12 final size:13
Alignment explanation
Indices: 2444431--2444499 Score: 72
Period size: 13 Copynumber: 5.2 Consensus size: 13
2444421 AATAGCACCA
2444431 GTCAACGGGTCGG
1 GTCAACGGGTCGG
2444444 GTCAACGGTCGGGTCGG
1 GTCAA----CGGGTCGG
2444461 GTCAACGGGTCGG
1 GTCAACGGGTCGG
*
2444474 GT---CGGTTCGG
1 GTCAACGGGTCGG
2444484 GTCAACGGGTCGG
1 GTCAACGGGTCGG
2444497 GTC
1 GTC
2444500 GTGACCGGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
10 9 0.19
13 25 0.53
17 13 0.28
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.19
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:2444458 original size:17 final size:18
Alignment explanation
Indices: 2444436--2444478 Score: 79
Period size: 17 Copynumber: 2.4 Consensus size: 18
2444426 CACCAGTCAA
2444436 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
2444453 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
2444471 CGGGTCGG
1 CGGGTCGG
2444479 TTCGGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.09, C:0.23, G:0.51, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:2444478 original size:23 final size:23
Alignment explanation
Indices: 2444450--2444500 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
2444440 TCGGGTCAAC
2444450 GGTCGGGTCGGGTCAACGGGTCG
1 GGTCGGGTCGGGTCAACGGGTCG
*
2444473 GGTCGGTTCGGGTCAACGGGTCG
1 GGTCGGGTCGGGTCAACGGGTCG
2444496 GGTCG
1 GGTCG
2444501 TGACCGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.08, C:0.22, G:0.51, T:0.20
Consensus pattern (23 bp):
GGTCGGGTCGGGTCAACGGGTCG
Found at i:2444509 original size:23 final size:23
Alignment explanation
Indices: 2444460--2444511 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2444450 GGTCGGGTCG
* *
2444460 GGTCAACGGGTCGGGTCGGTTCG
1 GGTCAACGGGTCGGGTCGGTACC
2444483 GGTCAACGGGTCGGGTC-GTGACC
1 GGTCAACGGGTCGGGTCGGT-ACC
2444506 GGTCAA
1 GGTCAA
2444512 ACCGGTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.13, C:0.23, G:0.44, T:0.19
Consensus pattern (23 bp):
GGTCAACGGGTCGGGTCGGTACC
Found at i:2444533 original size:11 final size:10
Alignment explanation
Indices: 2444503--2444555 Score: 74
Period size: 9 Copynumber: 5.4 Consensus size: 10
2444493 TCGGGTCGTG
2444503 ACCGGTC-AA
1 ACCGGTCAAA
2444512 ACCGGTCAAA
1 ACCGGTCAAA
2444522 ACCGGTTCAAA
1 ACCGG-TCAAA
*
2444533 ACCGGT-TAA
1 ACCGGTCAAA
2444542 ACCGGTCAAA
1 ACCGGTCAAA
2444552 ACCG
1 ACCG
2444556 ATTTCCAGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
9 15 0.38
10 14 0.36
11 10 0.26
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:2450621 original size:21 final size:23
Alignment explanation
Indices: 2450595--2450644 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2450585 AGGGGATCGA
2450595 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
**
2450616 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
2450639 TCCCCC
1 TCCCCC
2450645 TGGGGTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.20, C:0.40, G:0.22, T:0.18
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCGAT
Found at i:2461130 original size:23 final size:25
Alignment explanation
Indices: 2461093--2461140 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
2461083 ATTTTAAATA
*
2461093 AAAATATAAATTTATTATTATTTTT
1 AAAATATAAATTTATTATTAATTTT
*
2461118 AAAATAT-AA-TTATTTTTAATTTT
1 AAAATATAAATTTATTATTAATTTT
2461141 GTTAGCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 2 0.10
25 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AAAATATAAATTTATTATTAATTTT
Found at i:2461685 original size:43 final size:43
Alignment explanation
Indices: 2461606--2461758 Score: 157
Period size: 42 Copynumber: 3.6 Consensus size: 43
2461596 GATATTCGAT
* * *
2461606 GCCCCAAATTTTTTTCAATCCCACTTTTTACGTTTATAATTGAG
1 GCCCCTAA-TTTTTTCAATCTCACTTTTTACCTTTATAATTGAG
* * * *
2461650 GCCCCTAATTTTTTAAATCTCGCTTTCTACCTTTAT-ATTGAA
1 GCCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAG
* * * *
2461692 GCTCCTAATTTTTTTAAGCTCACTTTTTACTTTTATAA-TGAG
1 GCCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAG
* * *
2461734 ACCCCTCATTTATTCAATCTCACTT
1 GCCCCTAATTTTTTCAATCTCACTT
2461759 AATTTAATTA
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
42 57 0.65
43 24 0.27
44 7 0.08
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (43 bp):
GCCCCTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAG
Found at i:2466652 original size:23 final size:23
Alignment explanation
Indices: 2466593--2466653 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
2466583 CTCGTATAAA
*
2466593 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
*
2466616 TGCACCGAAGTGCTGCGTAGAAT
1 TGCACCGAAGTGCTACGTAGAAT
*
2466639 TGCACCGTAGTGCTA
1 TGCACCGAAGTGCTA
2466654 TATGAGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCTACGTAGAAT
Found at i:2475034 original size:23 final size:25
Alignment explanation
Indices: 2474987--2475034 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
2474977 TTTTAAATAA
*
2474987 AAAATATAAATTTATTATTATTTTT
1 AAAATATAAATTTATTATTAATTTT
*
2475012 AAAATAT-AA-TTATTTTTAATTTT
1 AAAATATAAATTTATTATTAATTTT
2475035 GTTAGCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 2 0.10
25 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AAAATATAAATTTATTATTAATTTT
Found at i:2475465 original size:43 final size:44
Alignment explanation
Indices: 2475371--2475465 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 44
2475361 TGGAAGTCTC
* * *
2475371 TATTTTTTGTAATTTCATTTTTTTACCTTTATAATTAAGGCCCT
1 TATTTTTTGTAATGTCATCTTTTTAACTTTATAATTAAGGCCCT
* * *
2475415 TACTTTTTT-TAATGTCA-CTTTTTAACTTTATATTTGAGGCTCT
1 TA-TTTTTTGTAATGTCATCTTTTTAACTTTATAATTAAGGCCCT
2475458 TGATTTTT
1 T-ATTTTT
2475466 AAATCTCGCT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 27 0.63
44 10 0.23
45 6 0.14
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (44 bp):
TATTTTTTGTAATGTCATCTTTTTAACTTTATAATTAAGGCCCT
Found at i:2475654 original size:42 final size:42
Alignment explanation
Indices: 2475513--2475656 Score: 146
Period size: 42 Copynumber: 3.4 Consensus size: 42
2475503 TGCCCCAAAT
* * *
2475513 TTTTTTCAATCCCACTTTTTACGTTTATAATTGAGGCTCCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAA-TGAGACTCCTAA
* * * *
2475556 TTTTTTAAATCTCGCTTTCTACCTTTATATTGA-AGCTCCTAA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATGAGA-CTCCTAA
* * * * *
2475598 TTTTTTTAAGCTCACTTTTTACTTTTATAATGAGACCCCTCA
1 TTTTTTCAATCTCACTTTTTACCTTTATAATGAGACTCCTAA
*
2475640 TTTATTCAATCTCACTT
1 TTTTTTCAATCTCACTT
2475657 AATTTAATTA
Statistics
Matches: 81, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
42 56 0.69
43 25 0.31
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.48
Consensus pattern (42 bp):
TTTTTTCAATCTCACTTTTTACCTTTATAATGAGACTCCTAA
Found at i:2478119 original size:23 final size:23
Alignment explanation
Indices: 2478073--2478131 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
2478063 TTGTTAAATA
* *
2478073 TTTAA-AATAT-ATTTATTATTT
1 TTTAATAATATAATATAATATTT
2478094 TTTAATAATATAATATAATATTT
1 TTTAATAATATAATATAATATTT
*
2478117 TTTAATATTATAATA
1 TTTAATAATATAATA
2478132 ATATACTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 5 0.15
22 5 0.15
23 23 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTAATAATATAATATAATATTT
Found at i:2478306 original size:37 final size:36
Alignment explanation
Indices: 2478265--2478354 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 36
2478255 AATCTAGTAA
2478265 TATTTTAATAAAGATACATAATATAA-TAT-AATATTCT
1 TATTTTAATAAA-ATACATAATATAATTATGAAT-TT-T
**
2478302 TATTTTAAT-AAATATTTAATATAATTTATGAATTTT
1 TATTTTAATAAAATACATAATATAA-TTATGAATTTT
2478338 TATTTTAATAAAATACA
1 TATTTTAATAAAATACA
2478355 CTATTGTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
35 11 0.24
36 12 0.27
37 19 0.42
38 3 0.07
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (36 bp):
TATTTTAATAAAATACATAATATAATTATGAATTTT
Found at i:2478317 original size:18 final size:18
Alignment explanation
Indices: 2478264--2478317 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2478254 TAATCTAGTA
* *
2478264 ATATTTTAATAAAGATAC
1 ATATTTTAATAAATATTC
* *
2478282 ATAATATAATATAATATTC
1 ATATTTTAATA-AATATTC
*
2478301 TTATTTTAATAAATATT
1 ATATTTTAATAAATATT
2478318 TAATATAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
ATATTTTAATAAATATTC
Found at i:2480172 original size:2 final size:2
Alignment explanation
Indices: 2480165--2480199 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2480155 ACACCTCAGG
*
2480165 TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2480200 TACATACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2480333 original size:23 final size:24
Alignment explanation
Indices: 2480315--2480373 Score: 95
Period size: 23 Copynumber: 2.5 Consensus size: 24
2480305 CTCGTATAAA
2480315 TGCACCGAAGTGCCA-CGTAGAAT
1 TGCACCGAAGTGCCAGCGTAGAAT
2480338 TGCACCGAAGTG-CAGCGTAGAAT
1 TGCACCGAAGTGCCAGCGTAGAAT
*
2480361 TGCACCGTAGTGC
1 TGCACCGAAGTGC
2480374 TATATGAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.19
Consensus pattern (24 bp):
TGCACCGAAGTGCCAGCGTAGAAT
Found at i:2480449 original size:56 final size:55
Alignment explanation
Indices: 2480365--2480475 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 55
2480355 TAGAATTGCA
2480365 CCGTAGTGCTATATGAGATGTCCCTAAGGACCACGTAGAAAATTAATTAAGAATCAC
1 CCGTAGTGCTATATGAGATGTCCCTAAGGACCACGTA-AAAATTAATT-AGAATCAC
2480422 CCGTAGTGCTATAT-AGATGTCCCTAAGGACCACGTAAAAATTAATTAGAATCAC
1 CCGTAGTGCTATATGAGATGTCCCTAAGGACCACGTAAAAATTAATTAGAATCAC
2480476 ATACATATGC
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
54 8 0.15
55 10 0.19
56 22 0.41
57 14 0.26
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (55 bp):
CCGTAGTGCTATATGAGATGTCCCTAAGGACCACGTAAAAATTAATTAGAATCAC
Found at i:2481953 original size:23 final size:23
Alignment explanation
Indices: 2481927--2481988 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
2481917 TTTTCCTTTA
*
2481927 GGGGGGAATCGGTTCCCTACTGT
1 GGGGGGTATCGGTTCCCTACTGT
2481950 GGGGGGTATCGGTTCCCTACTGT
1 GGGGGGTATCGGTTCCCTACTGT
2481973 -GGGGGTATCGGTTCCC
1 GGGGGGTATCGGTTCCC
2481989 CCATGATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 16 0.42
23 22 0.58
ACGTcount: A:0.10, C:0.23, G:0.40, T:0.27
Consensus pattern (23 bp):
GGGGGGTATCGGTTCCCTACTGT
Found at i:2491991 original size:6 final size:6
Alignment explanation
Indices: 2491977--2492008 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2491967 TCCAATGTTT
*
2491977 TTCTTC TTCTCC TTCTCC TTCTCC TTCTCC TT
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TT
2492009 TGGTGTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (6 bp):
TTCTCC
Found at i:2493919 original size:2 final size:2
Alignment explanation
Indices: 2493912--2493951 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2493902 AATCTATGAC
2493912 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
2493952 TCAATTCAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2500676 original size:35 final size:35
Alignment explanation
Indices: 2500630--2500710 Score: 162
Period size: 35 Copynumber: 2.3 Consensus size: 35
2500620 AATCGCGGGG
2500630 AAACGGGTATCCCCGTTTAGCATAAACGGTTATTT
1 AAACGGGTATCCCCGTTTAGCATAAACGGTTATTT
2500665 AAACGGGTATCCCCGTTTAGCATAAACGGTTATTT
1 AAACGGGTATCCCCGTTTAGCATAAACGGTTATTT
2500700 AAACGGGTATC
1 AAACGGGTATC
2500711 TGGTCGAGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (35 bp):
AAACGGGTATCCCCGTTTAGCATAAACGGTTATTT
Found at i:2504246 original size:18 final size:19
Alignment explanation
Indices: 2504225--2504268 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
2504215 TTTTTATGAA
2504225 TTTTTTTGGCTTTTTCTT-
1 TTTTTTTGGCTTTTTCTTC
** *
2504243 TTTTTCAGTCTTTTTCTTC
1 TTTTTTTGGCTTTTTCTTC
2504262 TTTTTTT
1 TTTTTTT
2504269 TTGAAAAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTTTTGGCTTTTTCTTC
Found at i:2511278 original size:15 final size:17
Alignment explanation
Indices: 2511244--2511291 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 17
2511234 CGTTAGAGAA
*
2511244 TTTATACTTATATATAC
1 TTTATACCTATATATAC
2511261 TTTATACCTA-AT-TAC
1 TTTATACCTATATATAC
*
2511276 TTTATACTTATATATA
1 TTTATACCTATATATA
2511292 TACACTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTATACCTATATATAC
Found at i:2511359 original size:8 final size:7
Alignment explanation
Indices: 2511348--2511463 Score: 103
Period size: 8 Copynumber: 15.6 Consensus size: 7
2511338 CTTTAATACT
2511348 TATACTTA
1 TATA-TTA
2511356 TATA-TA
1 TATATTA
2511362 TATATATA
1 TATAT-TA
2511370 TATATATA
1 TATAT-TA
2511378 TATATATA
1 TATAT-TA
2511386 TATATATA
1 TATAT-TA
2511394 TATATATA
1 TATAT-TA
2511402 TATATATA
1 TATAT-TA
2511410 TATATATA
1 TATAT-TA
2511418 TATATATA
1 TATAT-TA
2511426 TATATATA
1 TATAT-TA
2511434 TATATTA
1 TATATTA
2511441 TATA-TA
1 TATATTA
*
2511447 TGTA-TA
1 TATATTA
*
2511453 TATATTT
1 TATATTA
2511460 TATA
1 TATA
2511464 CTAAAACTTT
Statistics
Matches: 102, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
6 16 0.16
7 11 0.11
8 75 0.74
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (7 bp):
TATATTA
Found at i:2511361 original size:2 final size:2
Alignment explanation
Indices: 2511354--2511457 Score: 192
Period size: 2 Copynumber: 52.5 Consensus size: 2
2511344 TACTTATACT
2511354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2511396 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2511438 T- TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2511458 TTTATACTAA
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 98 0.99
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2512669 original size:2 final size:2
Alignment explanation
Indices: 2512662--2512721 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
2512652 TGATTCGTGC
2512662 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
2512704 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2512722 GTAATTTTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2513727 original size:16 final size:16
Alignment explanation
Indices: 2513696--2513727 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2513686 TTTCAAGCTC
*
2513696 GACTCGAACTCGAAAA
1 GACTCGAACTCAAAAA
2513712 GACTCGAACTCAAAAA
1 GACTCGAACTCAAAAA
2513728 AAATCAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
GACTCGAACTCAAAAA
Found at i:2515787 original size:7 final size:7
Alignment explanation
Indices: 2515775--2515875 Score: 116
Period size: 7 Copynumber: 14.6 Consensus size: 7
2515765 GTATATAACT
2515775 TAAACCC
1 TAAACCC
2515782 TAAACCC
1 TAAACCC
**
2515789 TAAACTA
1 TAAACCC
*
2515796 TAAATCC
1 TAAACCC
2515803 T-AACCC
1 TAAACCC
*
2515809 T-AACACA
1 TAAAC-CC
*
2515816 TAAACAC
1 TAAACCC
2515823 TAAACCC
1 TAAACCC
2515830 TAAACCC
1 TAAACCC
2515837 TAAACCC
1 TAAACCC
*
2515844 TAAACTC
1 TAAACCC
*
2515851 TAAACTC
1 TAAACCC
2515858 TAAACCC
1 TAAACCC
2515865 TAAACCC
1 TAAACCC
2515872 TAAA
1 TAAA
2515876 TCTTATCACA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
6 8 0.10
7 69 0.86
8 3 0.04
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:2516602 original size:14 final size:14
Alignment explanation
Indices: 2516585--2516625 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2516575 TTTATTCATC
2516585 AATAATGTATTTTT
1 AATAATGTATTTTT
2516599 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
2516610 AATAATGTAATTTT
1 AATAATGTATTTTT
2516624 AA
1 AA
2516626 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:2516975 original size:30 final size:30
Alignment explanation
Indices: 2516916--2517009 Score: 104
Period size: 30 Copynumber: 3.1 Consensus size: 30
2516906 AAATTTATAA
2516916 TATTTTATATTCTTAACTT-TTAAAAATATATTT
1 TATTTT-TATT-TTAACTTATT--AAATATATTT
2516949 TATTTTTATTTTAACTTATTAAATATATTT
1 TATTTTTATTTTAACTTATTAAATATATTT
* *
2516979 TAATTTTATTTTAA--TATAAAATATATATT
1 TATTTTTATTTTAACTTATTAAATATAT-TT
2517008 TA
1 TA
2517010 CGCTGCCTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
28 11 0.19
29 4 0.07
30 23 0.40
31 7 0.12
32 6 0.11
33 6 0.11
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTTTTATTTTAACTTATTAAATATATTT
Found at i:2522269 original size:20 final size:20
Alignment explanation
Indices: 2522244--2522296 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2522234 GACCAACAAA
2522244 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
2522264 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
2522284 TTCGCAACGCGAA
1 TTCGCAACGCGAA
2522297 TTTGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:2522328 original size:20 final size:20
Alignment explanation
Indices: 2522284--2522375 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
2522274 AGTTTCCAAT
*
2522284 TTCGCAACGCGAATTTGT-AAA
1 TTCGCAACGCG-A-TAGTCAAA
* *
2522305 -TCGCAATGCGATAGCCAAA
1 TTCGCAACGCGATAGTCAAA
* * *
2522324 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
2522344 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
2522364 TTCGCAACGCGA
1 TTCGCAACGCGA
2522376 AACACAATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
18 2 0.03
19 4 0.07
20 52 0.90
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:2522328 original size:40 final size:41
Alignment explanation
Indices: 2522279--2522377 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 41
2522269 AACCCAGTTT
* ** *
2522279 CCAATTTCGCAACGCGAATTTGT-AAA-TCGCAATGCGATAG
1 CCAAATTCGCAACGCGAA-AAGTCAAATTCGCAACGCGATAG
*
2522319 CCAAATTCGCAACAC-AAAAGTCAAATTCGCAACGCGATAG
1 CCAAATTCGCAACGCGAAAAGTCAAATTCGCAACGCGATAG
*
2522359 TCAAATTCGCAACGCGAAA
1 CCAAATTCGCAACGCGAAA
2522378 CACAATATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
38 2 0.04
39 5 0.10
40 39 0.80
41 3 0.06
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CCAAATTCGCAACGCGAAAAGTCAAATTCGCAACGCGATAG
Found at i:2522515 original size:22 final size:22
Alignment explanation
Indices: 2522490--2522537 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2522480 CGGCGACATT
2522490 CGTCCCCATCTCCGACGAAATC
1 CGTCCCCATCTCCGACGAAATC
* *
2522512 CGTCCCCATCTCTGGCGAAATC
1 CGTCCCCATCTCCGACGAAATC
2522534 CGTC
1 CGTC
2522538 TATCTCCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.44, G:0.17, T:0.21
Consensus pattern (22 bp):
CGTCCCCATCTCCGACGAAATC
Found at i:2522906 original size:20 final size:20
Alignment explanation
Indices: 2522883--2522928 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2522873 AAACTTAAAT
2522883 TCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
2522903 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
2522923 TCGCAA
1 TCGCAA
2522929 AGCGATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:2522933 original size:20 final size:20
Alignment explanation
Indices: 2522891--2522933 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2522881 ATTCGCAACA
*
2522891 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAAAG
2522911 CGAAAATGAAAATCGCAAAG
1 CGAAAATGAAAATCGCAAAG
2522931 CGA
1 CGA
2522934 TTTTAGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.19, G:0.21, T:0.09
Consensus pattern (20 bp):
CGAAAATGAAAATCGCAAAG
Found at i:2522952 original size:19 final size:20
Alignment explanation
Indices: 2522930--2522976 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2522920 AAATCGCAAA
*
2522930 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTC
* *
2522949 GCGATTTTCATTTTCGTGTC
1 GCGATTTTCAGTTTCGCGTC
2522969 GCGATTTT
1 GCGATTTT
2522977 TTTCATTGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTC
Found at i:2523005 original size:20 final size:20
Alignment explanation
Indices: 2522940--2523007 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
2522930 GCGATTTTAG
*
2522940 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCTT
* *
2522960 TTTCGTGTCGCGA--TT-TT
1 TTTCGCGTTGCGATTTTCTT
*
2522977 TTT--CATTGCGATTTTCTT
1 TTTCGCGTTGCGATTTTCTT
2522995 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
2523008 ATTTAATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
15 5 0.14
17 6 0.17
18 7 0.19
20 18 0.50
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCTT
Found at i:2523017 original size:20 final size:20
Alignment explanation
Indices: 2522940--2523018 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 20
2522930 GCGATTTTAG
*
2522940 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTCAT
* *
2522960 TTTCGTGTCGCG-ATTT--T
1 TTTCGCGTTGCGAATTTCAT
* * *
2522977 TTT--CATTGCGATTTTCTT
1 TTTCGCGTTGCGAATTTCAT
*
2522995 TTTCGCGTTGCGAATTTAAT
1 TTTCGCGTTGCGAATTTCAT
2523015 TTTC
1 TTTC
2523019 AGAAACTACT
Statistics
Matches: 43, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
15 4 0.09
16 3 0.07
17 4 0.09
18 4 0.09
19 3 0.07
20 25 0.58
ACGTcount: A:0.11, C:0.18, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTCAT
Found at i:2524583 original size:6 final size:6
Alignment explanation
Indices: 2524572--2524596 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2524562 CGAGCCTCTT
2524572 CTCCAC CTCCAC CTCCAC CTCCAC C
1 CTCCAC CTCCAC CTCCAC CTCCAC C
2524597 ATCACCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CTCCAC
Found at i:2524742 original size:21 final size:21
Alignment explanation
Indices: 2524718--2524767 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2524708 GTTAGGGGAG
* *
2524718 TTACGTGATGAGGTCTGTGCT
1 TTACGTGATGAGGTCGGTACT
*
2524739 TTACGTCATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
*
2524760 ATACGTGA
1 TTACGTGA
2524768 AGATAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:2524871 original size:21 final size:21
Alignment explanation
Indices: 2524845--2524899 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
2524835 AATGGTGCGC
*
2524845 TACGTGGTGAGGTATCTACTT
1 TACGTGATGAGGTATCTACTT
2524866 TACGTGATGAGGTATCTACTT
1 TACGTGATGAGGTATCTACTT
2524887 TACGTGATGAGGT
1 TACGTGATGAGGT
2524900 TGCCGCTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (21 bp):
TACGTGATGAGGTATCTACTT
Found at i:2526502 original size:19 final size:19
Alignment explanation
Indices: 2526432--2526501 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
2526422 GGTCGGGTCA
* *
2526432 GGTCGAACCGGTTCAGATC
1 GGTCAAACCGGTTCAGACC
*
2526451 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
2526470 GGTTAAACCGGTTTAGACC
1 GGTCAAACCGGTTCAGACC
*
2526489 GATCAAACCGGTT
1 GGTCAAACCGGTT
2526502 TCAAGATGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:2534367 original size:20 final size:20
Alignment explanation
Indices: 2534350--2534398 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2534340 AACTATATAC
2534350 TCCTAAATGCATCTATATGA
1 TCCTAAATGCATCTATATGA
2534370 TCCTAAATGCATCTATATGA
1 TCCTAAATGCATCTATATGA
*
2534390 TCCAAAATG
1 TCCTAAATG
2534399 GGCTCTTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (20 bp):
TCCTAAATGCATCTATATGA
Found at i:2539378 original size:21 final size:21
Alignment explanation
Indices: 2539354--2539396 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2539344 TCATTTTTCA
*
2539354 ATTTTG-AAATATCTTTCTTAT
1 ATTTTGAAAATAAC-TTCTTAT
2539375 ATTTTGAAAATAACTTCTTAT
1 ATTTTGAAAATAACTTCTTAT
2539396 A
1 A
2539397 ATCCGAAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTTGAAAATAACTTCTTAT
Found at i:2542192 original size:2 final size:2
Alignment explanation
Indices: 2542185--2542387 Score: 103
Period size: 2 Copynumber: 110.5 Consensus size: 2
2542175 AAATAATTTA
*
2542185 AT AT AT AT ACT A- AT AT AT AT A- AT AT A- ACT AT A- AT AT AT AC
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
2542225 AT AT AT A- AT AT AA AA AT AT AT -T AT AT A- AT A- AT AA AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2542262 AT A- AT AT AT AT -T AT A- AT AT AT AT CT A- AT AT A- 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
* *
2542299 AT AT A- AT AT AA AT AT AT ACT AT A- AG A- AT AGT AT A- AT AT -T
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* *
2542338 A- AT AT A- AT AT AT -T AT AA AT A- AC AT AT AT AT AGT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
2542376 AT AT ACT AT AT A
1 AT AT A-T AT AT A
2542388 ATAATAGACT
Statistics
Matches: 158, Mismatches: 13, Indels: 60
0.68 0.06 0.26
Matches are distributed among these distances:
1 24 0.15
2 123 0.78
3 11 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:2542221 original size:30 final size:30
Alignment explanation
Indices: 2542187--2542390 Score: 156
Period size: 30 Copynumber: 6.6 Consensus size: 30
2542177 ATAATTTAAT
2542187 ATATATACTAATAT-ATATAATATAACTATA
1 ATATATACTAATATAATATAATATAA-TATA
2542217 ATATATAC-ATATATAATATAA-A-AATATA
1 ATATATACTA-ATATAATATAATATAATATA
* *
2542245 TTATATAATAATA-AATAATAATATATATTATA
1 ATATATACTAATATAAT-ATAATATA-A-TATA
2542277 ATATATATCTAATATAATATATATATAATATAA
1 ATATATA-CTAATATAATATA-ATATAATAT-A
* *
2542310 ATATATACTATAAGAATAGTATAATATTAATATA
1 ATATATAC--TAA-TATAATATAATA-TAATATA
* *
2542344 ATATATTA-TAA-ATAACATATATATAGTAT-
1 ATATA-TACTAATATAATATA-ATATAATATA
2542373 ATAATATACT-ATATAATA
1 AT-ATATACTAATATAATA
2542391 ATAGACTAAA
Statistics
Matches: 143, Mismatches: 10, Indels: 42
0.73 0.05 0.22
Matches are distributed among these distances:
27 3 0.02
28 17 0.12
29 10 0.07
30 34 0.24
31 10 0.07
32 17 0.12
33 17 0.12
34 20 0.14
35 15 0.10
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (30 bp):
ATATATACTAATATAATATAATATAATATA
Found at i:2542236 original size:45 final size:44
Alignment explanation
Indices: 2542148--2542390 Score: 155
Period size: 47 Copynumber: 5.6 Consensus size: 44
2542138 AAGAAAACTG
* *
2542148 TAATAA-ATATAT-A-ATAA-ATAATACTATAAATAATTTAATATA
1 TAATAATATATATAATATAATATAATA-TATACAT-ATATAATATA
2542190 TATACTAATATATATAATATAACTATAATATATACATATATAATATA
1 TA-A-TAATATATATAATATAA-TATAATATATACATATATAATATA
2542237 -AA-AATATAT-T-ATATAATAATAA-ATAATA-ATATAT-AT-TA
1 TAATAATATATATAATATAAT-ATAATAT-ATACATATATAATATA
*
2542275 TAAT-ATATATCTAATATAATAT-ATATATA-ATATA-AATATA
1 TAATAATATATATAATATAATATAATATATACATATATAATATA
* * * *
2542315 TACTATAAGAATAGTATAATATTAATATAATATAT-TATAAATAACATA
1 TA--ATAA-TATA-TATAATA-TAATATAATATATACATATATAATATA
2542363 T-AT-ATAGTATATAATATACTATATAATA
1 TAATAATA-TATATAATATA--ATATAATA
2542391 ATAGACTAAA
Statistics
Matches: 166, Mismatches: 7, Indels: 54
0.73 0.03 0.24
Matches are distributed among these distances:
38 2 0.01
39 21 0.13
40 18 0.11
41 20 0.12
42 7 0.04
43 17 0.10
44 17 0.10
45 15 0.09
46 8 0.05
47 23 0.14
48 12 0.07
49 6 0.04
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (44 bp):
TAATAATATATATAATATAATATAATATATACATATATAATATA
Found at i:2542386 original size:7 final size:6
Alignment explanation
Indices: 2542185--2542387 Score: 103
Period size: 5 Copynumber: 36.8 Consensus size: 6
2542175 AAATAATTTA
*
2542185 ATATAT ATACTA- ATATAT ATA-AT ATA-ACT ATA-AT ATATAC ATATAT
1 ATATAT ATA-TAT ATATAT ATATAT ATATA-T ATATAT ATATAT ATATAT
* * *
2542231 A-ATAT AAAAAT ATAT-T ATATA- ATA-AT AAATA- ATA-AT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
2542273 -TATA- ATATAT ATCTA- ATATA- ATATAT ATATA- ATATAA ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
2542316 ACTATA- AGA-AT AGTATA- ATAT-T A-ATAT A-ATAT AT-TAT AAATA-
1 A-TATAT ATATAT A-TATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
2542358 ACATAT ATATAGT ATATA- ATATACT ATATA
1 ATATAT ATATA-T ATATAT ATATA-T ATATA
2542388 ATAATAGACT
Statistics
Matches: 156, Mismatches: 15, Indels: 51
0.70 0.07 0.23
Matches are distributed among these distances:
4 5 0.03
5 80 0.51
6 53 0.34
7 18 0.12
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (6 bp):
ATATAT
Found at i:2544009 original size:54 final size:53
Alignment explanation
Indices: 2543899--2544030 Score: 219
Period size: 54 Copynumber: 2.5 Consensus size: 53
2543889 ACAATTTAGA
* * *
2543899 GCGCCCTTTCGGGTTTTCACTCTAAATATTTTTTCTTGAATCTTCTATTAAGG
1 GCGCCCTTTTGGGTTTTCGCCCTAAATATTTTTTCTTGAATCTTCTATTAAGG
*
2543952 GCGCCCTTTTGGGTTTTCGCCCTAAATATTTTTTTCTTGAATCTTCTATTATGG
1 GCGCCCTTTTGGGTTTTCGCCCTAAATA-TTTTTTCTTGAATCTTCTATTAAGG
2544006 GCGCCCTTTTGGGTTTTCGCCCTAA
1 GCGCCCTTTTGGGTTTTCGCCCTAA
2544031 GCGAAATATC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 25 0.34
54 49 0.66
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (53 bp):
GCGCCCTTTTGGGTTTTCGCCCTAAATATTTTTTCTTGAATCTTCTATTAAGG
Found at i:2549156 original size:30 final size:29
Alignment explanation
Indices: 2549104--2549161 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
2549094 TGTTAATAGA
* *
2549104 AATAAAAAAAAATATATCAAATATTAAAT
1 AATAAAAAAAAATAAATCAAATAATAAAT
* *
2549133 AATAGAAAAAAACTAAATTAAATAATAAA
1 AATA-AAAAAAAATAAATCAAATAATAAA
2549162 ACAAGAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (29 bp):
AATAAAAAAAAATAAATCAAATAATAAAT
Found at i:2550631 original size:24 final size:24
Alignment explanation
Indices: 2550604--2550710 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
2550594 AAACGGAGAT
*
2550604 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
2550628 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
2550652 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
2550676 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
2550700 ATCAGAAATCA
1 ATCAGAAATCA
2550711 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:2550710 original size:48 final size:48
Alignment explanation
Indices: 2550604--2550712 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
2550594 AAACGGAGAT
* * * *
2550604 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
2550652 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
2550700 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2550713 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:2553186 original size:7 final size:7
Alignment explanation
Indices: 2553174--2553205 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
2553164 TGGTCAACTC
2553174 CGGTCAA
1 CGGTCAA
2553181 CGGTCAA
1 CGGTCAA
2553188 CGGGTCAA
1 C-GGTCAA
2553196 CGGTCAA
1 CGGTCAA
2553203 CGG
1 CGG
2553206 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:2553195 original size:15 final size:15
Alignment explanation
Indices: 2553175--2553221 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
2553165 GGTCAACTCC
2553175 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
2553190 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
2553205 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
2553218 GGTC
1 GGTC
2553222 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Done.