Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 28
Found at i:5371372 original size:81 final size:82
Alignment explanation
Indices: 5371189--5371377 Score: 263
Period size: 82 Copynumber: 2.3 Consensus size: 82
5371179 TAGATCATCA
* * * * * *
5371189 TTCAACTTGATTCAATCATGGTAACATGAAATAATTCAACATTCGATTCAATACAATCAAGGTAG
1 TTCAATTTGATTCGATCATGGTAGCACGAAATAATTCAACATTCGATTAAATACAAACAAGGTAG
*
5371254 TGTATAATAGTTTATCC
66 TATATAATAGTTTATCC
* * *
5371271 TTCAATTTGATTCGATCATGGTAGCACGCAATAATTCAATATTCGATTAAATTCAAACAAGGTA-
1 TTCAATTTGATTCGATCATGGTAGCACGAAATAATTCAACATTCGATTAAATACAAACAAGGTAG
5371335 TATATAATAGTTTATCC
66 TATATAATAGTTTATCC
* *
5371352 TTCTATTTGATTTGATCATGGTAGCA
1 TTCAATTTGATTCGATCATGGTAGCA
5371378 TACAATAGAT
Statistics
Matches: 95, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 40 0.42
82 55 0.58
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (82 bp):
TTCAATTTGATTCGATCATGGTAGCACGAAATAATTCAACATTCGATTAAATACAAACAAGGTAG
TATATAATAGTTTATCC
Found at i:5371438 original size:204 final size:205
Alignment explanation
Indices: 5371075--5371507 Score: 575
Period size: 204 Copynumber: 2.1 Consensus size: 205
5371065 GGGTATTACA
* ** *
5371075 ATTCGATCATGGTAGCATGCAATAATTCACTATTCAATTTTATTCAATCAAGACATCATATAATA
1 ATTCGATCATGGTAGCATGCAATAATTCAATATTCAATTAAATTCAAACAAGACATCATATAATA
*
5371140 ATTCATCATTCAATTTGATTTGATCATGGTAGAATGCAATAGATCATCATTCAACTTGATTCAAT
66 ATTCATCATTCAATTTGATTTGATCATGGTAGAATACAATAGATCATCATTCAACTTGATTCAAT
* * * * *
5371205 CATGGTAACATGAAATAATTCAACATTCGATTCAATACAATCAAGGTAGT-GTATAATAGTTTAT
131 CATGATAACATGAAATAAATCAACATTCGATTCAATACAATCAAGGCA-TCATATAATAGTTCA-
* *
5371269 CC-TTCAATTTG
194 CCATCCAATTGG
* * **
5371280 ATTCGATCATGGTAGCACGCAATAATTCAATATTCGATTAAATTCAAACAAGGTAT-ATATAATA
1 ATTCGATCATGGTAGCATGCAATAATTCAATATTCAATTAAATTCAAACAAGACATCATATAATA
* * * * * *
5371344 GTTTATCCTTCTATTTGATTTGATCATGGTAGCATACAATAGATTATCATTCAACTTGATTCAAT
66 ATTCATCATTCAATTTGATTTGATCATGGTAGAATACAATAGATCATCATTCAACTTGATTCAAT
* * * **
5371409 CATGATAGCATGCAATAAATCATCATTCGATTCAATTTAATCAAGGCATCATATAATAGTTCACC
131 CATGATAACATGAAATAAATCAACATTCGATTCAATACAATCAAGGCATCATATAATAGTTCACC
5371474 ATCCAATTGG
196 ATCCAATTGG
*
5371484 ATTCAATCATGGTAGCATGCAATA
1 ATTCGATCATGGTAGCATGCAATA
5371508 CCAATTGGTC
Statistics
Matches: 197, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
203 3 0.02
204 146 0.74
205 48 0.24
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (205 bp):
ATTCGATCATGGTAGCATGCAATAATTCAATATTCAATTAAATTCAAACAAGACATCATATAATA
ATTCATCATTCAATTTGATTTGATCATGGTAGAATACAATAGATCATCATTCAACTTGATTCAAT
CATGATAACATGAAATAAATCAACATTCGATTCAATACAATCAAGGCATCATATAATAGTTCACC
ATCCAATTGG
Found at i:5372417 original size:41 final size:41
Alignment explanation
Indices: 5372352--5372824 Score: 313
Period size: 41 Copynumber: 11.6 Consensus size: 41
5372342 ACCCTATTTT
* * *
5372352 TAGCATGCAATATATCATCGTTCAACTTGATTCGATCATGG
1 TAGCATGCAATAAATTATCATTCAACTTGATTCGATCATGG
*
5372393 TAGCATTCAATAAATTATCATTCAACTTGATTCGATCATGG
1 TAGCATGCAATAAATTATCATTCAACTTGATTCGATCATGG
* ** * * *
5372434 TAGCATGCAAT-AATTCACCATTTGA-TTCAATTCAATCA-AG
1 TAGCATGCAATAAATT-ATCATTCAACTT-GATTCGATCATGG
* *
5372474 -A-CAT-CATATAATAGTTCAACATTCAATTTGATTCGATCATGG
1 TAGCATGCA-ATAA-A-TT-ATCATTCAACTTGATTCGATCATGG
* * *
5372516 TAGCATGCAATATATCATCATTCAAC-TAATTCGATCATGG
1 TAGCATGCAATAAATTATCATTCAACTTGATTCGATCATGG
* * * *
5372556 CAGCATGAAATAGATCATCATTCAACTTGATTCGATCATGG
1 TAGCATGCAATAAATTATCATTCAACTTGATTCGATCATGG
* * * * * * *
5372597 TAACATGTAAT-AATTCAAT-ATTCGA-TTCAATACAATCAAGG
1 TAGCATGCAATAAATT--ATCATTCAACTT-GATTCGATCATGG
** ** * * *
5372638 TAGCATATAATAGTTTATCCTTCAATTTGATTTGATCATGG
1 TAGCATGCAATAAATTATCATTCAACTTGATTCGATCATGG
* * * *
5372679 TAGCATGCAAT-AATTCAACATTCAA-TTCAATTCAATCAAGG
1 TAGCATGCAATAAATT-ATCATTCAACTT-GATTCGATCATGG
* ** ** * * *
5372720 TAACATATAATATTTTATCCTTCTATTTGATTCGATCATGG
1 TAGCATGCAATAAATTATCATTCAACTTGATTCGATCATGG
* * *
5372761 TAGCATGCAATAGATTATCATTCAATTTGATTCGGTCATGG
1 TAGCATGCAATAAATTATCATTCAACTTGATTCGATCATGG
* *
5372802 TAGCATGCAATAGATCATCATTC
1 TAGCATGCAATAAATTATCATTC
5372825 GATTCAATTT
Statistics
Matches: 333, Mismatches: 77, Indels: 44
0.73 0.17 0.10
Matches are distributed among these distances:
37 2 0.01
38 5 0.02
39 2 0.01
40 54 0.16
41 246 0.74
42 14 0.04
43 2 0.01
44 6 0.02
45 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (41 bp):
TAGCATGCAATAAATTATCATTCAACTTGATTCGATCATGG
Found at i:5372505 original size:82 final size:82
Alignment explanation
Indices: 5372409--5372787 Score: 442
Period size: 82 Copynumber: 4.6 Consensus size: 82
5372399 TCAATAAATT
* * **
5372409 ATCATTCAACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTTGATTCAATTCAATCAAG
1 ATCATTCAATTTGATTCGATCATGGTAGCATGCAATAATTCAACATTCAATTCAATTCAATCAAG
* *
5372474 ACATCATATAATAGTTC
66 GCAGCATATAATAGTTC
* * * * *
5372491 AACATTCAATTTGATTCGATCATGGTAGCATGCAAT-ATATCATCATTCAACT-AATTCGATCAT
1 ATCATTCAATTTGATTCGATCATGGTAGCATGCAATAAT-TCAACATTCAATTCAATTCAATCAA
*
5372554 GGCAGCATGA-AATAGATC
65 GGCAGCAT-ATAATAGTTC
* * * * * *
5372572 ATCATTCAACTTGATTCGATCATGGTAACATGTAATAATTCAATATTCGATTCAATACAATCAAG
1 ATCATTCAATTTGATTCGATCATGGTAGCATGCAATAATTCAACATTCAATTCAATTCAATCAAG
* *
5372637 GTAGCATATAATAGTTT
66 GCAGCATATAATAGTTC
* *
5372654 ATCCTTCAATTTGATTTGATCATGGTAGCATGCAATAATTCAACATTCAATTCAATTCAATCAAG
1 ATCATTCAATTTGATTCGATCATGGTAGCATGCAATAATTCAACATTCAATTCAATTCAATCAAG
* * * *
5372719 GTAACATATAATATTTT
66 GCAGCATATAATAGTTC
* * *
5372736 ATCCTTCTATTTGATTCGATCATGGTAGCATGCAATAGATT-ATCATTCAATT
1 ATCATTCAATTTGATTCGATCATGGTAGCATGCAATA-ATTCAACATTCAATT
5372788 TGATTCGGTC
Statistics
Matches: 253, Mismatches: 38, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
81 66 0.26
82 184 0.73
83 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (82 bp):
ATCATTCAATTTGATTCGATCATGGTAGCATGCAATAATTCAACATTCAATTCAATTCAATCAAG
GCAGCATATAATAGTTC
Found at i:5372626 original size:163 final size:164
Alignment explanation
Indices: 5372352--5372772 Score: 499
Period size: 163 Copynumber: 2.6 Consensus size: 164
5372342 ACCCTATTTT
* * * ** *
5372352 TAGCATGCAATATATCATCGTTCAACTTGATTCGATCATGGTAGCATTCAATAAATTATCATTCA
1 TAGCATGCAATATATCATCATTCAACTTAATTCGATCATGGCAGCATGAAATAAATCATCATTCA
* * * * *
5372417 ACTTGATTCGATCATGGTAGCATGCAATAATTCACCATTTGATTCAATTCAATCAAGACATCATA
66 ACTTGATTCGATCATGGTAACATGCAATAATTCAACATTCGATTCAATACAATCAAGACAGCATA
5372482 TAATAGTTCAACATTCAATTTGATTCGATCATGG
131 TAATAGTTCAACATTCAATTTGATTCGATCATGG
*
5372516 TAGCATGCAATATATCATCATTCAAC-TAATTCGATCATGGCAGCATGAAATAGATCATCATTCA
1 TAGCATGCAATATATCATCATTCAACTTAATTCGATCATGGCAGCATGAAATAAATCATCATTCA
* * **
5372580 ACTTGATTCGATCATGGTAACATGTAATAATTCAATATTCGATTCAATACAATCAAGGTAGCATA
66 ACTTGATTCGATCATGGTAACATGCAATAATTCAACATTCGATTCAATACAATCAAGACAGCATA
* * * *
5372645 TAATAGTTTATCCTTCAATTTGATTTGATCATGG
131 TAATAGTTCAACATTCAATTTGATTCGATCATGG
* * * * * ** * *
5372679 TAGCATGCAATA-ATTCAACATTCAA-TTCAATTCAATCAAGGTAACAT-ATAATATTTTATCCT
1 TAGCATGCAATATA-TCATCATTCAACTT-AATTCGATCATGGCAGCATGA-AATAAATCATCAT
* * *
5372741 TCTATTTGATTCGATCATGGTAGCATGCAATA
63 TCAACTTGATTCGATCATGGTAACATGCAATA
5372773 GATTATCATT
Statistics
Matches: 220, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
162 1 0.00
163 142 0.65
164 77 0.35
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (164 bp):
TAGCATGCAATATATCATCATTCAACTTAATTCGATCATGGCAGCATGAAATAAATCATCATTCA
ACTTGATTCGATCATGGTAACATGCAATAATTCAACATTCGATTCAATACAATCAAGACAGCATA
TAATAGTTCAACATTCAATTTGATTCGATCATGG
Found at i:5372722 original size:123 final size:123
Alignment explanation
Indices: 5372372--5372895 Score: 513
Period size: 123 Copynumber: 4.3 Consensus size: 123
5372362 TATATCATCG
* * ** *
5372372 TTCAACTTGATTCGATCATGGTAGCATTCAATAAATTATCATTCAACTTGATTCGATCATGGTAG
1 TTCAATTTGATTCGATCATGGTAGCATGCAATAGTTTATCATTCAATTTGATTCGATCATGGTAG
* ** ** * * *
5372437 CATGCAATA-ATTCACCATTTGATTCAATTCAATCAAGACATCATATAATAGTTCAACA
66 CATGCAATAGA-TCATCATTCAATTCAATTCAATCAAGGTAACATATAATAATTCAATA
* * * *
5372495 TTCAATTTGATTCGATCATGGTAGCATGCAATA-TATCATCATTCAA-CTAATTCGATCATGGCA
1 TTCAATTTGATTCGATCATGGTAGCATGCAATAGT-TTATCATTCAATTTGATTCGATCATGGTA
* * * * *
5372558 GCATGAAATAGATCATCATTCAACTT-GATTCGATCATGGTAACATGTAATAATTCAATA
65 GCATGCAATAGATCATCATTCAA-TTCAATTCAATCAAGGTAACATATAATAATTCAATA
* ** * * * ** * *
5372617 TTCGATTCAATACAATCAAGGTAGCATATAATAGTTTATCCTTCAATTTGATTTGATCATGGTAG
1 TTCAATTTGATTCGATCATGGTAGCATGCAATAGTTTATCATTCAATTTGATTCGATCATGGTAG
* ** *
5372682 CATGCAATA-ATTCAACATTCAATTCAATTCAATCAAGGTAACATATAAT-ATTTTATCC
66 CATGCAATAGA-TCATCATTCAATTCAATTCAATCAAGGTAACATATAATAATTCAAT-A
* * *
5372740 TTCTATTTGATTCGATCATGGTAGCATGCAATAGATTATCATTCAATTTGATTCGGTCATGGTAG
1 TTCAATTTGATTCGATCATGGTAGCATGCAATAGTTTATCATTCAATTTGATTCGATCATGGTAG
* * * * *
5372805 CATGCAATAGATCATCATTCGATTCAATTTAATCAAGGCATCATATAATAGTTC-ATCA
66 CATGCAATAGATCATCATTCAATTCAATTCAATCAAGGTAACATATAATAATTCAAT-A
* * * *
5372863 TCCAATTGGATTCAATCATGGTAGTATGCAATA
1 TTCAATTTGATTCGATCATGGTAGCATGCAATA
5372896 ACCAATTTAT
Statistics
Matches: 323, Mismatches: 68, Indels: 20
0.79 0.17 0.05
Matches are distributed among these distances:
122 97 0.30
123 223 0.69
124 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (123 bp):
TTCAATTTGATTCGATCATGGTAGCATGCAATAGTTTATCATTCAATTTGATTCGATCATGGTAG
CATGCAATAGATCATCATTCAATTCAATTCAATCAAGGTAACATATAATAATTCAATA
Found at i:5372829 original size:36 final size:39
Alignment explanation
Indices: 5372352--5372895 Score: 218
Period size: 41 Copynumber: 13.3 Consensus size: 39
5372342 ACCCTATTTT
5372352 TAGCATGCAATA-TATCATCGTTCAACTT-GATTCGATCATGG
1 TAGCATGCAATAGTATCA---TTCAA-TTCGATTCGATCATGG
* *
5372393 TAGCATTCAATAAATTATCATTCAACTT-GATTCGATCATGG
1 TAGCATGCAAT--AGTATCATTCAA-TTCGATTCGATCATGG
* * ** * * * *
5372434 TAGCATGCAATAATTCACCATTTGATTCAATTCAATCAAGA
1 TAGCATGCAAT-AGT-ATCATTCAATTCGATTCGATCATGG
* * ** * *
5372475 CATCATATAATAGTTCAACATTCAATTTGATTCGATCATGG
1 TAGCATGCAATAG-T-ATCATTCAATTCGATTCGATCATGG
* * *
5372516 TAGCATGCAATATATCATCATTCAACT-AATTCGATCATGG
1 TAGCATGCAATA-GT-ATCATTCAATTCGATTCGATCATGG
* *
5372556 CAGCATGAAATAGATCATCATTCAACTT-GATTCGATCATGG
1 TAGCATGCAATAG-T-ATCATTCAA-TTCGATTCGATCATGG
* * * * * * * *
5372597 TAACATGTAATAAT-TCAATATTCGATTCAATACAATCAAGG
1 TAGCATGCAATAGTATC---ATTCAATTCGATTCGATCATGG
** * * *
5372638 TAGCATATAATAGTTTATCCTTCAATTTGATTTGATCATGG
1 TAGCATGCAATAG--TATCATTCAATTCGATTCGATCATGG
* * * * *
5372679 TAGCATGCAATAATTCAACATTCAATTCAATTCAATCAAGG
1 TAGCATGCAAT-AGT-ATCATTCAATTCGATTCGATCATGG
* ** * * * *
5372720 TAACATATAATATTTTATCCTTCTATTTGATTCGATCATGG
1 TAGCATGCAATA--GTATCATTCAATTCGATTCGATCATGG
* *
5372761 TAGCATGCAATAGATTATCATTCAATTTGATTCGGTCATGG
1 TAGCATGCAATAG--TATCATTCAATTCGATTCGATCATGG
* * ** *
5372802 TAGCATGCAATAGATCATCATTCGATTCAATTTAATCAAGG
1 TAGCATGCAATAG-T-ATCATTCAATTCGATTCGATCATGG
* * ** * * *
5372843 CATCATATAATAGTTCATCATCCAATTGGATTCAATCATGG
1 TAGCATGCAATAG-T-ATCATTCAATTCGATTCGATCATGG
*
5372884 TAGTATGCAATA
1 TAGCATGCAATA
5372896 ACCAATTTAT
Statistics
Matches: 374, Mismatches: 106, Indels: 46
0.71 0.20 0.09
Matches are distributed among these distances:
38 2 0.01
40 46 0.12
41 314 0.84
42 3 0.01
43 2 0.01
44 7 0.02
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (39 bp):
TAGCATGCAATAGTATCATTCAATTCGATTCGATCATGG
Found at i:5377305 original size:21 final size:20
Alignment explanation
Indices: 5377280--5377341 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
5377270 CAAAACCCCA
5377280 GGGGGTATCGATTCCCCTGT
1 GGGGGTATCGATTCCCCTGT
* * * *
5377300 GGGGGGAATCGGTT-CCTTCAT
1 -GGGGGTATCGATTCCCCT-GT
5377321 GGGGGTATCGATTCCCTCTGT
1 GGGGGTATCGATTCCC-CTGT
5377342 ACCAAAATGC
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
20 14 0.47
21 15 0.50
22 1 0.03
ACGTcount: A:0.11, C:0.23, G:0.35, T:0.31
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCTGT
Found at i:5380752 original size:159 final size:161
Alignment explanation
Indices: 5380542--5380864 Score: 623
Period size: 159 Copynumber: 2.0 Consensus size: 161
5380532 TTCTTCCTCA
5380542 TTTTGGCATTAAGCTCAATGAACCGATTTTTTCCTCCGGTCATGTGTCTTGAGCATCCACTATCA
1 TTTTGGCATTAAGCTCAATGAACCGATTTTTTCCTCCGGTCATGTGTCTTGAGCATCCACTATCA
5380607 AGGTACCATGAATTTGGA-TTTTTTCTCGTTCCTTGTAGCAATGCTCCTTTTCCTACAAACAT-G
66 AGGTACCATGAATTTGGATTTTTTTCTCGTTCCTTGTAGCAATGCTCCTTTTCCTACAAACATAG
5380670 ATTAATTTCTAATTTTTGGTACCCAAATTCT
131 ATTAATTTCTAATTTTTGGTACCCAAATTCT
*
5380701 TTTTGGCATTAAGCTCAATGAACCGATTTTTTTCTCCGGTCATGTGTCTTGAGCATCCACTATCA
1 TTTTGGCATTAAGCTCAATGAACCGATTTTTTCCTCCGGTCATGTGTCTTGAGCATCCACTATCA
5380766 AGGTACCATGAATTTGGATTTTTTTCTCGTTCCTTGTAGCAATGCTCCTTTTCCTACAAACATAG
66 AGGTACCATGAATTTGGATTTTTTTCTCGTTCCTTGTAGCAATGCTCCTTTTCCTACAAACATAG
5380831 ATTAATTTCTAATTTTTGGTACCCAAATTCT
131 ATTAATTTCTAATTTTTGGTACCCAAATTCT
5380862 TTT
1 TTT
5380865 GGGTTCATAT
Statistics
Matches: 161, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
159 82 0.51
160 44 0.27
161 35 0.22
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.41
Consensus pattern (161 bp):
TTTTGGCATTAAGCTCAATGAACCGATTTTTTCCTCCGGTCATGTGTCTTGAGCATCCACTATCA
AGGTACCATGAATTTGGATTTTTTTCTCGTTCCTTGTAGCAATGCTCCTTTTCCTACAAACATAG
ATTAATTTCTAATTTTTGGTACCCAAATTCT
Found at i:5381298 original size:22 final size:21
Alignment explanation
Indices: 5381256--5381295 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5381246 TAGTTTATTT
*
5381256 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5381277 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5381296 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5385239 original size:24 final size:25
Alignment explanation
Indices: 5385193--5385242 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
5385183 TTTTGTTTCA
*
5385193 AAAATAAAACAAAACATTTTAATAT
1 AAAATAAAACAAAACATTGTAATAT
**
5385218 AAAATAAAAC-ATTCATTGTAATAT
1 AAAATAAAACAAAACATTGTAATAT
5385242 A
1 A
5385243 TTACAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (25 bp):
AAAATAAAACAAAACATTGTAATAT
Found at i:5385893 original size:112 final size:111
Alignment explanation
Indices: 5385696--5385925 Score: 381
Period size: 112 Copynumber: 2.1 Consensus size: 111
5385686 ATTGAAGTGC
* * * *
5385696 CGAAATGGTAATTCACCTCGTTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGCACCGT
1 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTCTTATGCCAAAAATGCACAGT
5385761 TATGCATTAAGAAAAATCGATCGATAACTT-TCATACACAAAGTATGT
66 TATGCATTAAGAAAAATCGATCGAT-A-TTATCATACACAAAGTATGT
5385808 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTCTTATGCCAAAAATGCACAGT
1 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTCTTATGCCAAAAATGCACAGT
*
5385873 TATGCATTAAGCAAAATCGATCGATATTATCATACACAAAGTATGT
66 TATGCATTAAGAAAAATCGATCGATATTATCATACACAAAGTATGT
*
5385919 TGAAATG
1 CGAAATG
5385926 AAATTATGAC
Statistics
Matches: 111, Mismatches: 6, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
110 2 0.02
111 24 0.22
112 85 0.77
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (111 bp):
CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTCTTATGCCAAAAATGCACAGT
TATGCATTAAGAAAAATCGATCGATATTATCATACACAAAGTATGT
Found at i:5392845 original size:112 final size:111
Alignment explanation
Indices: 5392648--5392878 Score: 383
Period size: 112 Copynumber: 2.1 Consensus size: 111
5392638 ACCAAAGTGC
*
5392648 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGAACTGT
1 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGAACCGT
*
5392713 TATGCAATAAGCAAAATCGATCGATAACTTTCATACA-AGAAGTATGT
66 TATGCAATAAGCAAAATCGATCGAT-ACTATCATACACA-AAGTATGT
* *
5392760 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACTTTTTATGCCAAAAATGCACCGT
1 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGAACCGT
*
5392825 TATGCATTAAGCAAAATCGATCGATACTATCATACACAAAGTATGT
66 TATGCAATAAGCAAAATCGATCGATACTATCATACACAAAGTATGT
*
5392871 CAAAATGG
1 CGAAATGG
5392879 ACTTATGACT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
111 25 0.22
112 87 0.78
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (111 bp):
CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGAACCGT
TATGCAATAAGCAAAATCGATCGATACTATCATACACAAAGTATGT
Found at i:5396886 original size:21 final size:21
Alignment explanation
Indices: 5396860--5396903 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5396850 GAGTTAAAAA
5396860 GTGTATAAATGCCACTAGGAT
1 GTGTATAAATGCCACTAGGAT
5396881 GTGTATAAATGCCACTAGGAT
1 GTGTATAAATGCCACTAGGAT
5396902 GT
1 GT
5396904 CAAAAGTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTATAAATGCCACTAGGAT
Found at i:5397805 original size:6 final size:6
Alignment explanation
Indices: 5397794--5397818 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5397784 AAGACCTATG
5397794 GGTCAT GGTCAT GGTCAT GGTCAT G
1 GGTCAT GGTCAT GGTCAT GGTCAT G
5397819 ATACAAGGGT
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:0.16, G:0.36, T:0.32
Consensus pattern (6 bp):
GGTCAT
Found at i:5403375 original size:22 final size:22
Alignment explanation
Indices: 5403350--5403402 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
5403340 AAAAGGGTAC
5403350 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
5403372 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
5403394 CGATTCCCC
1 CGATTCCCC
5403403 CACTGTTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (22 bp):
CGATTCCCCTGCTACAGGGAAT
Found at i:5405714 original size:17 final size:17
Alignment explanation
Indices: 5405688--5405721 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5405678 AGTTAGGACC
*
5405688 GAAAAATTATTATTTTA
1 GAAAAATTATTAATTTA
*
5405705 GAAAATTTATTAATTTA
1 GAAAAATTATTAATTTA
5405722 TCAATTATTA
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:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
GAAAAATTATTAATTTA
Found at i:5406422 original size:21 final size:21
Alignment explanation
Indices: 5406398--5406437 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5406388 AAATAACGGT
*
5406398 GATATTGACATGTCATCATAC
1 GATAATGACATGTCATCATAC
* *
5406419 GATAATGTCATGTCCTCAT
1 GATAATGACATGTCATCAT
5406438 TGAAAAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (21 bp):
GATAATGACATGTCATCATAC
Found at i:5407154 original size:61 final size:61
Alignment explanation
Indices: 5407112--5407262 Score: 198
Period size: 61 Copynumber: 2.5 Consensus size: 61
5407102 GATTCTGACT
5407112 ATAGCAACGAGTATCCGTAAAATCGCAACGCGTAGTC-GTAAATCGCAACGACAATACGTAAA
1 ATAGCAACGAGTATCCGT-AAATCGCAACGCGTA-TCTGTAAATCGCAACGACAATACGTAAA
* * * *
5407174 ATCGCAACGCGTATCCGTAAATCGCAATGCGTATCTGTAAATCGCAACGAGAATACGT-AA
1 ATAGCAACGAGTATCCGTAAATCGCAACGCGTATCTGTAAATCGCAACGACAATACGTAAA
* * * *
5407234 ATCGCAATGCGTATCCGTTAATCGCAACG
1 ATAGCAACGAGTATCCGTAAATCGCAACG
5407263 ACAATACGTA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
60 30 0.37
61 35 0.43
62 16 0.20
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (61 bp):
ATAGCAACGAGTATCCGTAAATCGCAACGCGTATCTGTAAATCGCAACGACAATACGTAAA
Found at i:5407156 original size:20 final size:20
Alignment explanation
Indices: 5407115--5407302 Score: 159
Period size: 20 Copynumber: 9.2 Consensus size: 20
5407105 TCTGACTATA
* *
5407115 GCAACGAGTATCCGTAAAATC
1 GCAACGCGTATACGT-AAATC
5407136 GCAACGCGTAGT-CGTAAATC
1 GCAACGCGTA-TACGTAAATC
*
5407156 GCAACGAC-AATACGTAAAATC
1 GCAACG-CGTATACGT-AAATC
*
5407177 GCAACGCGTATCCGTAAATC
1 GCAACGCGTATACGTAAATC
*
5407197 GCAATGCGTAT-CTGTAAATC
1 GCAACGCGTATAC-GTAAATC
* *
5407217 GCAACGAGAATACGTAAATC
1 GCAACGCGTATACGTAAATC
* * *
5407237 GCAATGCGTATCCGTTAATC
1 GCAACGCGTATACGTAAATC
*
5407257 GCAACGAC-AATACGTAAAATC
1 GCAACG-CGTATACGT-AAATC
* * *
5407278 ACAACGCATATCCGTAAATC
1 GCAACGCGTATACGTAAATC
5407298 GCAAC
1 GCAAC
5407303 CCGATCTCCA
Statistics
Matches: 136, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.01
20 88 0.65
21 45 0.33
22 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
GCAACGCGTATACGTAAATC
Found at i:5407233 original size:40 final size:40
Alignment explanation
Indices: 5407122--5407302 Score: 177
Period size: 41 Copynumber: 4.5 Consensus size: 40
5407112 ATAGCAACGA
* * *
5407122 GTATCCGTAAAATCGCAACGCGTAGT-CGTAAATCGCAACGAC
1 GTATCCGT-AAATCGCAACGAG-AATACGTAAATCGCAATG-C
* * * * *
5407164 -AATACGTAAAATCGCAACGCGTATCCGTAAATCGCAATGC
1 GTATCCGT-AAATCGCAACGAGAATACGTAAATCGCAATGC
*
5407204 GTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGC
1 GTATCCGTAAATCGCAACGAGAATACGTAAATCGCAATGC
* * * *
5407244 GTATCCGTTAATCGCAACGACAATACGTAAAATCACAACGC
1 GTATCCGTAAATCGCAACGAGAATACGT-AAATCGCAATGC
*
5407285 ATATCCGTAAATCGCAAC
1 GTATCCGTAAATCGCAAC
5407303 CCGATCTCCA
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
40 56 0.47
41 62 0.53
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (40 bp):
GTATCCGTAAATCGCAACGAGAATACGTAAATCGCAATGC
Found at i:5407271 original size:101 final size:102
Alignment explanation
Indices: 5407115--5407301 Score: 297
Period size: 101 Copynumber: 1.8 Consensus size: 102
5407105 TCTGACTATA
* * *
5407115 GCAACGAGTATCCGTAAAATCGCAACGCGTAGTCGTAAATCGCAACGACAATACGTAAAATCGCA
1 GCAACGAGAATACGTAAAATCGCAACGCGTAGTCGTAAATCGCAACGACAATACGTAAAATCACA
*
5407180 ACGCGTATCCGTAAATCGCAATGCGTATCTGTAAATC
66 ACGCATATCCGTAAATCGCAATGCGTATCTGTAAATC
* *
5407217 GCAACGAGAATACGT-AAATCGCAATGCGTA-TCCGTTAATCGCAACGACAATACGTAAAATCAC
1 GCAACGAGAATACGTAAAATCGCAACGCGTAGT-CGTAAATCGCAACGACAATACGTAAAATCAC
5407280 AACGCATATCCGTAAATCGCAA
65 AACGCATATCCGTAAATCGCAA
5407302 CCCGATCTCC
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 1 0.01
101 64 0.82
102 13 0.17
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (102 bp):
GCAACGAGAATACGTAAAATCGCAACGCGTAGTCGTAAATCGCAACGACAATACGTAAAATCACA
ACGCATATCCGTAAATCGCAATGCGTATCTGTAAATC
Found at i:5407341 original size:101 final size:100
Alignment explanation
Indices: 5407131--5407321 Score: 260
Period size: 101 Copynumber: 1.9 Consensus size: 100
5407121 AGTATCCGTA
* *
5407131 AAATCGCAACGCGTAGTCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAAT
1 AAATCGCAACGCGTAGTCGTAAATCGCAACGACAATACGTAAAATCACAACGCATATCCGTAAAT
** **
5407196 CGCAATGCGTATCTGTAAATCGCAACGAGAATACG
66 CGCAACCCGTATCTCCAAATCGCAACGAGAATACG
* *
5407231 TAAATCGCAATGCGTA-TCCGTTAATCGCAACGACAATACGTAAAATCACAACGCATATCCGTAA
1 -AAATCGCAACGCGTAGT-CGTAAATCGCAACGACAATACGTAAAATCACAACGCATATCCGTAA
*
5407295 ATCGCAACCCG-ATCTCCAGTATCGCAA
64 ATCGCAACCCGTATCTCCA-AATCGCAA
5407322 ATCAGTTTCC
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
100 6 0.08
101 73 0.92
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (100 bp):
AAATCGCAACGCGTAGTCGTAAATCGCAACGACAATACGTAAAATCACAACGCATATCCGTAAAT
CGCAACCCGTATCTCCAAATCGCAACGAGAATACG
Found at i:5407398 original size:21 final size:21
Alignment explanation
Indices: 5407356--5407402 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5407346 ATTCTGACTA
*
5407356 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCACAAAT
* * *
5407377 TCGCGTTGCGATTTTACTAAT
1 TCGCATTGCGATTTCACAAAT
5407398 TCGCA
1 TCGCA
5407403 ACGCGAATAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCACAAAT
Found at i:5407423 original size:20 final size:20
Alignment explanation
Indices: 5407398--5407505 Score: 173
Period size: 20 Copynumber: 5.4 Consensus size: 20
5407388 TTTTACTAAT
5407398 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
5407418 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
5407438 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
5407458 TCGCAACGCAAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
5407478 TCGCAATGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
5407498 TCGCAACG
1 TCGCAACG
5407506 AGATTCTGAC
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
19 1 0.01
20 80 0.99
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:5407443 original size:40 final size:40
Alignment explanation
Indices: 5407390--5407510 Score: 174
Period size: 40 Copynumber: 3.0 Consensus size: 40
5407380 CGTTGCGATT
*
5407390 TTAC-TAATTCGCAACGCGAATACGTAAATCGCAACGCGA
1 TTACGTAAATCGCAACGCGAATACGTAAATCGCAACGCGA
*
5407429 TTACGTAAATCGCAACGCGAATACGTAAATCGCAACGCAA
1 TTACGTAAATCGCAACGCGAATACGTAAATCGCAACGCGA
* * *
5407469 ATACGTAAATCGCAATGCGAAT-CTGTAAATCGCAACGAGA
1 TTACGTAAATCGCAACGCGAATAC-GTAAATCGCAACGCGA
5407509 TT
1 TT
5407511 CTGACTATCG
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 5 0.07
40 68 0.93
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (40 bp):
TTACGTAAATCGCAACGCGAATACGTAAATCGCAACGCGA
Found at i:5407513 original size:20 final size:19
Alignment explanation
Indices: 5407089--5407511 Score: 133
Period size: 20 Copynumber: 20.9 Consensus size: 19
5407079 CGCGCACATA
5407089 TAAATCGCAACGCGATTC-
1 TAAATCGCAACGCGATTCG
* * * *
5407107 TGACTATAGCAACGAGTATCCG
1 T-A-AATCGCAACGCG-ATTCG
*
5407129 TAAAATCGCAACGCGTAGTCG
1 T-AAATCGCAACGCG-ATTCG
* *
5407150 TAAATCGCAACGACAATACG
1 TAAATCGCAACG-CGATTCG
*
5407170 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCG-ATTCG
*
5407191 TAAATCGCAATGCG-TATCTG
1 TAAATCGCAACGCGAT-TC-G
* *
5407211 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGCG-ATTCG
* *
5407231 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCG-ATTCG
* * *
5407251 TTAATCGCAACGACAATACG
1 TAAATCGCAACG-CGATTCG
*
5407271 TAAAATCACAACGC-ATATCCG
1 T-AAATCGCAACGCGAT-T-CG
*
5407292 TAAATCGCAACCCGATCTCCAG
1 TAAATCGCAACGCGAT-T-C-G
** *
5407314 T--ATCGCAAATCAGTTTC-
1 TAAATCGCAACGC-GATTCG
* * *
5407331 CAGATTCGCAACACGATTC-
1 TA-AATCGCAACGCGATTCG
* ** *
5407350 TGACTATCGCATTGCGATTTCC
1 T-A-AATCGCAACGCGA-TTCG
* ***
5407372 CAAATTCGCGTTGCGATTTTAC-
1 TAAA-TCGCAACGCGA--TT-CG
* *
5407394 TAATTCGCAACGCGAATACG
1 TAAATCGCAACGCG-ATTCG
5407414 TAAATCGCAACGCGATTACG
1 TAAATCGCAACGCGATT-CG
*
5407434 TAAATCGCAACGCGAATACG
1 TAAATCGCAACGCG-ATTCG
* *
5407454 TAAATCGCAACGCAAATACG
1 TAAATCGCAACGC-GATTCG
* *
5407474 TAAATCGCAATGCGAATCTG
1 TAAATCGCAACGCGATTC-G
*
5407494 TAAATCGCAACGAGATTC
1 TAAATCGCAACGCGATTC
5407512 TGACTATCGC
Statistics
Matches: 303, Mismatches: 69, Indels: 64
0.69 0.16 0.15
Matches are distributed among these distances:
18 2 0.01
19 14 0.05
20 197 0.65
21 78 0.26
22 11 0.04
23 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (19 bp):
TAAATCGCAACGCGATTCG
Found at i:5408392 original size:24 final size:24
Alignment explanation
Indices: 5408365--5408418 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
5408355 GTATTTGAAA
5408365 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
5408389 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
5408413 TTTGAT
1 TTTGAT
5408419 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:5410859 original size:20 final size:20
Alignment explanation
Indices: 5410834--5410927 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
5410824 GACATTCATT
5410834 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
5410854 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* * *
5410874 AGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
5410894 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
5410914 TAACTATCGCAACG
1 TGACTATCGCAACG
5410928 AGAGAATCAC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 61 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:5410956 original size:33 final size:34
Alignment explanation
Indices: 5410919--5410994 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
5410909 GGAAATAACT
5410919 ATCGCAACGAGAGAATCACAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCACAATGCGAAAATGAAA
* *
5410952 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCACAATGCGAAAATGAAA
5410986 ATCGCAACG
1 ATCGCAACG
5410995 TGAAACTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 23 0.57
34 17 0.43
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCACAATGCGAAAATGAAA
Found at i:5411050 original size:20 final size:20
Alignment explanation
Indices: 5411025--5411074 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5411015 GATTTTCATT
* *
5411025 TATCGCAATGCGGAATTGAC
1 TATCGCAATGCAGAAATGAC
*
5411045 TATCGCAACGCAGAAATGAC
1 TATCGCAATGCAGAAATGAC
5411065 TATCGCAATG
1 TATCGCAATG
5411075 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
TATCGCAATGCAGAAATGAC
Found at i:5411266 original size:14 final size:14
Alignment explanation
Indices: 5411247--5411283 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5411237 CATCAATTAA
5411247 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5411261 ACAAATCATCTTTT
1 ACAAATCAACATTT
5411275 ACAAATCAA
1 ACAAATCAA
5411284 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5412692 original size:42 final size:42
Alignment explanation
Indices: 5412625--5412716 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
5412615 GTGAATCGGG
* * *
5412625 CTCTAGAATGTTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* ** *
5412667 CTCTTGAATGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGGGGC
5412709 CTCTTGAA
1 CTCTTGAA
5412717 CGATAGGGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:5413285 original size:20 final size:20
Alignment explanation
Indices: 5413192--5413276 Score: 143
Period size: 20 Copynumber: 4.2 Consensus size: 20
5413182 AAATCGCAGC
*
5413192 GCGAAAATGACTATCACAAT
1 GCGAAAATGACTATCGCAAT
5413212 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
5413232 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
**
5413252 GCGAATTTGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
5413272 GCGAA
1 GCGAA
5413277 TTTTACTATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
GCGAAAATGACTATCGCAAT
Found at i:5413347 original size:19 final size:19
Alignment explanation
Indices: 5413325--5413368 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5413315 AAATCGCAAC
*
5413325 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCACGTT
* *
5413344 GCGATTTTGGTTTCACGTT
1 GCGATTATAGTTTCACGTT
*
5413363 GTGATT
1 GCGATT
5413369 TTGTCATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.27, T:0.45
Consensus pattern (19 bp):
GCGATTATAGTTTCACGTT
Found at i:5413369 original size:19 final size:19
Alignment explanation
Indices: 5413334--5413420 Score: 67
Period size: 19 Copynumber: 4.8 Consensus size: 19
5413324 CGCGATTATA
*
5413334 GTTTCGCGTTGCGATTTTG
1 GTTTCACGTTGCGATTTTG
*
5413353 GTTTCACGTTGTGATTTT-
1 GTTTCACGTTGCGATTTTG
*
5413371 G--TCA--TTGTGATTTTG
1 GTTTCACGTTGCGATTTTG
** *
5413386 GTTTTGCGTTGCGATTTTC
1 GTTTCACGTTGCGATTTTG
* *
5413405 ATTTCTCGTTGCGATT
1 GTTTCACGTTGCGATT
5413421 CTCTCGTTGC
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 3 0.06
17 1 0.02
18 1 0.02
19 38 0.70
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (19 bp):
GTTTCACGTTGCGATTTTG
Found at i:5413427 original size:14 final size:14
Alignment explanation
Indices: 5413408--5413435 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5413398 GATTTTCATT
5413408 TCTCGTTGCGATTC
1 TCTCGTTGCGATTC
5413422 TCTCGTTGCGATTC
1 TCTCGTTGCGATTC
5413436 ATTTCACGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.21, T:0.43
Consensus pattern (14 bp):
TCTCGTTGCGATTC
Found at i:5413684 original size:94 final size:93
Alignment explanation
Indices: 5413538--5413914 Score: 655
Period size: 94 Copynumber: 4.0 Consensus size: 93
5413528 ATGGATTGCA
* *
5413538 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
5413603 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
5413631 TTACTTTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
5413696 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
5413725 TTACTTTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
5413790 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
5413819 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
5413884 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
5413913 TT
1 TT
5413915 CTTAAGCAAT
Statistics
Matches: 275, Mismatches: 7, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
93 23 0.08
94 252 0.92
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:5415661 original size:19 final size:19
Alignment explanation
Indices: 5415606--5415662 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
5415596 TGAAATGAAA
*
5415606 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
*
5415626 ATCGCAATGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
5415646 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
5415663 AAATCGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.21
20 24 0.73
21 2 0.06
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:5415673 original size:39 final size:40
Alignment explanation
Indices: 5415597--5415676 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
5415587 TCTTTTGGTT
**
5415597 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAATGCG
1 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAATGCG
** *
5415637 GAAATGACTATCGCAACGCGA-AATGAAAATCGCAATGCG
1 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAATGCG
5415676 G
1 G
5415677 TTTTCATTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 17 0.49
40 18 0.51
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (40 bp):
GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAATGCG
Found at i:5415694 original size:19 final size:19
Alignment explanation
Indices: 5415672--5415793 Score: 92
Period size: 20 Copynumber: 6.5 Consensus size: 19
5415662 AAAATCGCAA
*
5415672 TGCGGTTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
5415691 TGCGA--TT-A--TCTCGT
1 TGCGATTTTCATTTCGCGT
*
5415705 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
5415724 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGT
** *
5415745 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
**
5415765 TGCGATTTTCATTTTCATGT
1 TGCGATTTTCA-TTTCGCGT
5415785 TGCGATTTT
1 TGCGATTTT
5415794 AAGTTTAGAA
Statistics
Matches: 83, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 19 0.23
20 32 0.39
21 16 0.19
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:5415757 original size:40 final size:40
Alignment explanation
Indices: 5415699--5415790 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
5415689 GTTGCGATTA
**
5415699 TCTCGTTGCGATTTTCA-TTTCGCATTGCGATTTTCATTT
1 TCTCGTTGCGATAGTCATTTTCGCATTGCGATTTTCATTT
**
5415738 CTCTCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTT
1 -TCTCGTTGCGATAGTCATTTTCGCATTGCGATTTTCATTT
5415779 TCAT-GTTGCGAT
1 TC-TCGTTGCGAT
5415791 TTTAAGTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 25 0.54
41 21 0.46
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (40 bp):
TCTCGTTGCGATAGTCATTTTCGCATTGCGATTTTCATTT
Found at i:5415791 original size:20 final size:21
Alignment explanation
Indices: 5415703--5415793 Score: 102
Period size: 20 Copynumber: 4.5 Consensus size: 21
5415693 CGATTATCTC
*
5415703 GTTGCGATTTTCATTTCGCA-
1 GTTGCGATTTTCATTTCTCAT
5415723 -TTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTTCTCAT
** *
5415742 CGTTGCGATAGTCATTT-TCGT
1 -GTTGCGATTTTCATTTCTCAT
5415763 GTTGCGATTTTCATTT-TCAT
1 GTTGCGATTTTCATTTCTCAT
5415783 GTTGCGATTTT
1 GTTGCGATTTT
5415794 AAGTTTAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
19 17 0.28
20 30 0.49
21 14 0.23
ACGTcount: A:0.13, C:0.18, G:0.19, T:0.51
Consensus pattern (21 bp):
GTTGCGATTTTCATTTCTCAT
Found at i:5416377 original size:20 final size:20
Alignment explanation
Indices: 5416352--5416588 Score: 221
Period size: 20 Copynumber: 11.7 Consensus size: 20
5416342 CTTTAAAAAT
*
5416352 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
*
5416372 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
5416392 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
5416413 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
5416433 CTCGTTGCGATTTACATATA
1 CGCGTTGCGATTTACGGATA
* *
5416453 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
5416473 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
5416493 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
5416513 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
5416534 CGCGTTGCGATTTTATGGATA
1 CGCGTTGCGA-TTTACGGATA
* * *
5416555 CTCGTTACGATAGTTA-GAAT-
1 CGCGTTGCGAT--TTACGGATA
5416575 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
5416589 TATGTTCGCG
Statistics
Matches: 179, Mismatches: 29, Indels: 20
0.79 0.13 0.09
Matches are distributed among these distances:
18 3 0.02
20 120 0.67
21 53 0.30
22 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5416438 original size:40 final size:40
Alignment explanation
Indices: 5416354--5416546 Score: 314
Period size: 40 Copynumber: 4.8 Consensus size: 40
5416344 TTAAAAATCG
* *
5416354 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
*
5416395 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
**
5416435 CGTTGCGATTTACATATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
5416475 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
5416516 CGTTGCGATTTACGGATACGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTT
5416547 TATGGATACT
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
40 77 0.54
41 65 0.46
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:5416560 original size:41 final size:41
Alignment explanation
Indices: 5416354--5416587 Score: 323
Period size: 41 Copynumber: 5.8 Consensus size: 41
5416344 TTAAAAATCG
* *
5416354 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
5416395 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
5416435 CGTTGCGATTTACATATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
5416475 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
5416516 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
5416557 CGTTACGATAGTTA-GAAT-CGCGTTGCGATTT
1 CGTTGCGAT--TTACGGATACGCGTTGCGATTT
5416588 ATATGTTCGC
Statistics
Matches: 175, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
40 74 0.42
41 95 0.54
42 3 0.02
43 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:5416597 original size:20 final size:19
Alignment explanation
Indices: 5416574--5416626 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
5416564 ATAGTTAGAA
5416574 TCGCGTTGCGATTT-ATATGT
1 TCGCGTTGCGATTTCATA--T
5416594 TCGCGTTGCGAATTTCATAT
1 TCGCGTTGCG-ATTTCATAT
5416614 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5416627 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.10
20 21 0.68
21 4 0.13
22 3 0.10
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTCATAT
Found at i:5416725 original size:20 final size:19
Alignment explanation
Indices: 5416676--5416729 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
5416666 ATTCTTCATA
5416676 ATCGAGTTGCGATTCTGGG
1 ATCGAGTTGCGATTCTGGG
* *
5416695 AACTGATTTGCGATTCTGGAG
1 ATC-GAGTTGCGATTCTGG-G
5416716 ATCGAGTTGCGATT
1 ATCGAGTTGCGATT
5416730 TTTATTTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.20, C:0.15, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGAGTTGCGATTCTGGG
Found at i:5418128 original size:16 final size:16
Alignment explanation
Indices: 5418075--5418128 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
5418065 CTTTTAAAAT
* *
5418075 ATTAATATATATTTAG
1 ATTAATATTTATTTTG
*
5418091 -TTAAATATTTATTTTA
1 ATT-AATATTTATTTTG
*
5418107 AATAATATTTATTTTG
1 ATTAATATTTATTTTG
5418123 ATTAAT
1 ATTAAT
5418129 CATCAACATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 27 0.90
17 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (16 bp):
ATTAATATTTATTTTG
Found at i:5418635 original size:22 final size:20
Alignment explanation
Indices: 5418590--5418635 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
5418580 TGTGTATTTG
*
5418590 ATTTTATATTTTAAATAATA
1 ATTTTATATTTTAAACAATA
*
5418610 ATTTTATATATTTAAAACAATT
1 ATTTTATAT-TTT-AAACAATA
5418632 ATTT
1 ATTT
5418636 AAAATAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 3 0.14
22 10 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTATATTTTAAACAATA
Found at i:5418763 original size:3 final size:3
Alignment explanation
Indices: 5418755--5418812 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
5418745 ATTTTAATCA
5418755 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5418803 ATT ATT ATT A
1 ATT ATT ATT A
5418813 GAAAAATTAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5419447 original size:18 final size:19
Alignment explanation
Indices: 5419412--5419448 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5419402 CACGGAATGT
5419412 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
5419432 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
5419449 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:5420828 original size:7 final size:7
Alignment explanation
Indices: 5420816--5420843 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5420806 GGTGACGGTC
5420816 GGAAGTG
1 GGAAGTG
5420823 GGAAGTG
1 GGAAGTG
5420830 GGAAGTG
1 GGAAGTG
5420837 GGAAGTG
1 GGAAGTG
5420844 ACCATCGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.57, T:0.14
Consensus pattern (7 bp):
GGAAGTG
Found at i:5429604 original size:21 final size:22
Alignment explanation
Indices: 5429578--5429650 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 22
5429568 AGGGAATCAA
5429578 TCCCCCCTTGA-GGGAACCGAT
1 TCCCCCCTTGAGGGGAACCGAT
*
5429599 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTG-AGGGGAACCGAT
* *
5429622 TCCCCCCAT-AGGGGAATCGAT
1 TCCCCCCTTGAGGGGAACCGAT
*
5429643 ACCCCCCT
1 TCCCCCCT
5429651 GGGGTTCTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
21 26 0.59
22 1 0.02
23 17 0.39
ACGTcount: A:0.21, C:0.38, G:0.22, T:0.19
Consensus pattern (22 bp):
TCCCCCCTTGAGGGGAACCGAT
Found at i:5433127 original size:25 final size:25
Alignment explanation
Indices: 5433098--5433161 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
5433088 ATTAAGGTTC
5433098 CATTTTGAGAAGTTCCATGAATAAG
1 CATTTTGAGAAGTTCCATGAATAAG
5433123 CATTTTGAGAAGTTCCATGAATAAG
1 CATTTTGAGAAGTTCCATGAATAAG
5433148 CATTTTGAGAAGTT
1 CATTTTGAGAAGTT
5433162 TGAAAATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (25 bp):
CATTTTGAGAAGTTCCATGAATAAG
Found at i:5435925 original size:2 final size:2
Alignment explanation
Indices: 5435918--5435967 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
5435908 ATTATTTTAA
5435918 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
*
5435960 AT TT AT AT
1 AT AT AT AT
5435968 GACTAAGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5437311 original size:3 final size:3
Alignment explanation
Indices: 5437303--5437402 Score: 146
Period size: 3 Copynumber: 32.7 Consensus size: 3
5437293 TTATTTATTA
*
5437303 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* **
5437350 AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5437398 AAT AA
1 AAT AA
5437403 ATTTAAATGA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
3 81 0.93
4 6 0.07
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:5437999 original size:75 final size:76
Alignment explanation
Indices: 5437528--5438393 Score: 1556
Period size: 76 Copynumber: 11.5 Consensus size: 76
5437518 GATGGAAATG
* *
5437528 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTTGAAAACATCAAAAAG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTGAAAACATCAAAAAG
5437593 CTCCCGAAGGC-T
64 CTCCCGAAGGCTT
5437605 TTTGGAAAC-TCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGC
5437669 TCCCGAAGGCTT
65 TCCCGAAGGCTT
5437681 TTTGGAAACATCATGCACTGAAGGACTTACAGAT-ACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGC
5437745 TCCCGAAGGCTT
65 TCCCGAAGGCTT
5437757 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTG-AAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
5437820 CCCGAAGGCTT
66 CCCGAAGGCTT
*
5437831 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGC
5437896 TCCCGAAGGCTT
65 TCCCGAAGGCTT
5437908 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
5437972 CCCGAAGGCTT
66 CCCGAAGGCTT
5437983 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGC
5438048 TCCCGAAGGCTT
65 TCCCGAAGGCTT
5438060 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
5438124 CCCGAAGGCTT
66 CCCGAAGGCTT
*
5438135 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
5438200 CCCGAAGGCTT
66 CCCGAAGGCTT
5438211 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA-CCGAA-GTTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
5438273 CCCGAAGGC-T
66 CCCGAAGGCTT
*
5438283 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
5438348 CCCGAAGGCTT
66 CCCGAAGGCTT
5438359 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
5438394 TGGGAAATAG
Statistics
Matches: 769, Mismatches: 7, Indels: 27
0.96 0.01 0.03
Matches are distributed among these distances:
72 37 0.05
73 29 0.04
74 71 0.09
75 216 0.28
76 244 0.32
77 172 0.22
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:5443791 original size:10 final size:11
Alignment explanation
Indices: 5443771--5443800 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5443761 TCAATTTTCC
5443771 TTTTTCTTTTT
1 TTTTTCTTTTT
5443782 TTTTTCTTTTT
1 TTTTTCTTTTT
5443793 TTTTTCTT
1 TTTTTCTT
5443801 CTTTCTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:5443792 original size:18 final size:17
Alignment explanation
Indices: 5443765--5443808 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
5443755 CTTGATTCAA
*
5443765 TTTTCCTTTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
5443782 TTTTTCTTTTT-TTTTT
1 TTTTTCTTTTTCTTTTT
5443798 CTTCTTTCTTT
1 -TT-TTTCTTT
5443809 GCTGGATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 12 0.50
18 7 0.29
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTT
Found at i:5444102 original size:2 final size:2
Alignment explanation
Indices: 5444095--5444150 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
5444085 ACAACAAAGG
5444095 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
5444137 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
5444151 TAAAGGATAA
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:5448453 original size:17 final size:15
Alignment explanation
Indices: 5448428--5448471 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
5448418 TTAATACCTG
*
5448428 AATAAAAAAATAATA
1 AATATAAAAATAATA
5448443 TTAATATAAAAATAATA
1 --AATATAAAAATAATA
5448460 AATAATAAAAAT
1 AAT-ATAAAAAT
5448472 TTGAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 8 0.32
17 14 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATAAAAATAATA
Found at i:5450521 original size:3 final size:3
Alignment explanation
Indices: 5450513--5450612 Score: 146
Period size: 3 Copynumber: 32.7 Consensus size: 3
5450503 TTATTTATTA
*
5450513 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* **
5450560 AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5450608 AAT AA
1 AAT AA
5450613 ATTTAAATGA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
3 81 0.93
4 6 0.07
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:5451633 original size:33 final size:35
Alignment explanation
Indices: 5451570--5451634 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
5451560 TTGCACTTTG
*
5451570 TGTGCATATTATGATTATGATATGATAGCACTATA
1 TGTGCATATTATGATTATGAGATGATAGCACTATA
5451605 TGTGCATATTATGA-T-TGAGATGATAGCACT
1 TGTGCATATTATGATTATGAGATGATAGCACT
5451635 GAAGTGCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 14 0.48
34 1 0.03
35 14 0.48
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (35 bp):
TGTGCATATTATGATTATGAGATGATAGCACTATA
Found at i:5452686 original size:45 final size:46
Alignment explanation
Indices: 5452601--5452688 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
5452591 AAAAAGCCTA
*
5452601 AGTGCATCGATGCATGGTCATGTGCATCGATGCATCAAATGCACTG
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTG
*
5452647 AGTGCATCGATGCATGGT-ATGTGCATCGATGTATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
5452689 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 22 0.55
46 18 0.45
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTG
Found at i:5452736 original size:20 final size:20
Alignment explanation
Indices: 5452708--5452746 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5452698 CAAGAAATTA
5452708 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
5452728 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
5452747 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:5455410 original size:44 final size:44
Alignment explanation
Indices: 5455321--5455417 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
5455311 GCTCTTGTGC
* * *
5455321 ATCGATGCACATTCAAGGGCGTGCATCGGTGTATCAGCTGATGT
1 ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
* *
5455365 ATCGATGCACATTCAAAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATCGATGCACATTC-AAGGGCATGCATCGGTGCATCAGCTAA-TGT
5455409 ATCGATGCA
1 ATCGATGCA
5455418 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 4 0.09
44 37 0.80
45 5 0.11
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
Found at i:5460851 original size:19 final size:20
Alignment explanation
Indices: 5460815--5460860 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
5460805 TAAGTACATT
*
5460815 GATGCATGGTCTTGTGCATC
1 GATGCATGGTCATGTGCATC
5460835 GATGCATGGT-ATGTGCATC
1 GATGCATGGTCATGTGCATC
5460854 GATGCAT
1 GATGCAT
5460861 AAAATGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (20 bp):
GATGCATGGTCATGTGCATC
Found at i:5465990 original size:31 final size:31
Alignment explanation
Indices: 5465952--5466027 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
5465942 ATTTTAAAAC
*
5465952 TTGTAATACAGTCCCCCAACATTTAGTCCGT
1 TTGTAATATAGTCCCCCAACATTTAGTCCGT
* *
5465983 TTGTAATATGGTCCCCCAACATTTAGTCTGT
1 TTGTAATATAGTCCCCCAACATTTAGTCCGT
*
5466014 TTGCAATATAGTCC
1 TTGTAATATAGTCC
5466028 ATGACCATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (31 bp):
TTGTAATATAGTCCCCCAACATTTAGTCCGT
Found at i:5467835 original size:19 final size:19
Alignment explanation
Indices: 5467811--5467856 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
5467801 AGAGAAGCGA
5467811 AAAAGGAAATTCAAGATCG
1 AAAAGGAAATTCAAGATCG
*
5467830 AAAAGGAAATTCAAGATTG
1 AAAAGGAAATTCAAGATCG
5467849 AAAAGGAA
1 AAAAGGAA
5467857 TTTGGGGTTT
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:0.57, C:0.07, G:0.22, T:0.15
Consensus pattern (19 bp):
AAAAGGAAATTCAAGATCG
Found at i:5468035 original size:31 final size:30
Alignment explanation
Indices: 5467989--5468066 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 30
5467979 TCAAATAGTC
* *
5467989 GGGGACCATAATGCAAACAGACTAAATGTTG
1 GGGGA-CATATTGCAAACAGACTAAATGTTA
5468020 GGGGATCATATTGCAAACAGACTAAATGTTA
1 GGGGA-CATATTGCAAACAGACTAAATGTTA
5468051 GGGGACTATATTGCAA
1 GGGGAC-ATATTGCAA
5468067 GTTTAGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (30 bp):
GGGGACATATTGCAAACAGACTAAATGTTA
Found at i:5473284 original size:30 final size:30
Alignment explanation
Indices: 5473248--5473322 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
5473238 CGATTTTGCT
* *
5473248 GGTTTTCAGCTGGTTTACCCCGGTTTTACC
1 GGTTTTCAGCCGGTTCACCCCGGTTTTACC
*
5473278 GGTTTTCAGCCGGTTCACCCCGGTTTTATC
1 GGTTTTCAGCCGGTTCACCCCGGTTTTACC
*
5473308 GGTTTTCAGTCGGTT
1 GGTTTTCAGCCGGTT
5473323 TTATCAGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.40
Consensus pattern (30 bp):
GGTTTTCAGCCGGTTCACCCCGGTTTTACC
Found at i:5473292 original size:20 final size:20
Alignment explanation
Indices: 5473248--5473359 Score: 72
Period size: 20 Copynumber: 5.6 Consensus size: 20
5473238 CGATTTTGCT
*
5473248 GGTTTTCAGCTGG-TTTACCCC
1 GGTTTTCAGCCGGTTTTA--CC
5473269 GGTTTT-A-CCGGTTTTCAGCC
1 GGTTTTCAGCCGGTTTT-A-CC
* *
5473289 GG--TTCACCCCGGTTTTATC
1 GGTTTTCAGC-CGGTTTTACC
* *
5473308 GGTTTTCAGTCGGTTTTATC
1 GGTTTTCAGCCGGTTTTACC
* *
5473328 AGTTTTCAGCCGGTTCTACC
1 GGTTTTCAGCCGGTTTTACC
*
5473348 AGTTTTCAGCCG
1 GGTTTTCAGCCG
5473360 ATTCATTGCC
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.03
19 7 0.09
20 48 0.64
21 18 0.24
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (20 bp):
GGTTTTCAGCCGGTTTTACC
Found at i:5477722 original size:77 final size:79
Alignment explanation
Indices: 5477635--5477783 Score: 191
Period size: 77 Copynumber: 1.9 Consensus size: 79
5477625 TTAATAAATT
*
5477635 TCTTATTTAATTAATTC-AAATTAAATAT-ACATT-AAAGACTTATAAT-ATGAATTACATTC-A
1 TCTTATTTAATT-ATTCTAAATTAAATATCA-ATTAAAAGACTTATAATCA-AAATTACATTCTA
5477695 TTAATGTTTATTTAAAA
63 TTAATGTTTATTTAAAA
* * * *
5477712 TCTTATTTAATTATTCTGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACATTCTTTTA
1 TCTTATTTAATTATTCTAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACATTCTATTA
5477777 ATGTTTA
66 ATGTTTA
5477784 CTTACTATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
76 4 0.06
77 25 0.40
78 22 0.35
79 11 0.18
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (79 bp):
TCTTATTTAATTATTCTAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACATTCTATTA
ATGTTTATTTAAAA
Found at i:5481763 original size:24 final size:24
Alignment explanation
Indices: 5481736--5481835 Score: 67
Period size: 24 Copynumber: 4.2 Consensus size: 24
5481726 GATATAAAAA
*
5481736 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
5481760 ATCAGAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* * * *
5481784 ATCAGAATAGATTTCAGATCAAAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
5481808 GTCAAAACAAAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
5481832 ATCA
1 ATCA
5481836 GATAAAATAT
Statistics
Matches: 54, Mismatches: 20, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
23 1 0.02
24 51 0.94
25 2 0.04
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:5483062 original size:17 final size:18
Alignment explanation
Indices: 5483029--5483062 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5483019 TCCATTCTAT
*
5483029 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
5483047 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
5483063 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:5490015 original size:17 final size:18
Alignment explanation
Indices: 5489982--5490015 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5489972 TCCATTCTAT
*
5489982 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
5490000 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
5490016 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:5499567 original size:18 final size:19
Alignment explanation
Indices: 5499544--5499580 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5499534 TGATTGACTC
*
5499544 AAAAATAAA-ATAAAAAAG
1 AAAAATAAACAAAAAAAAG
5499562 AAAAATAAACAAAAAAAAG
1 AAAAATAAACAAAAAAAAG
5499581 TTTACGTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (19 bp):
AAAAATAAACAAAAAAAAG
Found at i:5504569 original size:10 final size:10
Alignment explanation
Indices: 5504520--5504569 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
5504510 CATATTAGGG
5504520 ATTT-AATTA
1 ATTTAAATTA
*
5504529 TTTTAAATTA
1 ATTTAAATTA
5504539 A-TTAAATCTA
1 ATTTAAAT-TA
5504549 TATTT-AATTA
1 -ATTTAAATTA
5504559 ATTTAAATTA
1 ATTTAAATTA
5504569 A
1 A
5504570 ATATTTGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 13 0.38
10 15 0.44
11 4 0.12
12 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTAAATTA
Found at i:5511337 original size:90 final size:90
Alignment explanation
Indices: 5511184--5511361 Score: 295
Period size: 90 Copynumber: 2.0 Consensus size: 90
5511174 CCTAACACAC
* *
5511184 CCTTTTATAGCCAAGTTACCCTAATCATATTAGTGTTTTTATTTTTCCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTTTTCCAAATTAATTAAATCTAT
* *
5511249 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
5511274 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTT-CAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATT-TTTCCAAATTAATTAAATCTA
5511338 TATTTAATTAATTGAAATTAAATA
65 TATTTAATTAATTGAAATTAAATA
5511362 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 79 0.96
91 3 0.04
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTTTTCCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:5513718 original size:20 final size:20
Alignment explanation
Indices: 5513693--5513734 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5513683 GCATGCAAAA
5513693 ATGTCAATATCTAATGCGTC
1 ATGTCAATATCTAATGCGTC
5513713 ATGTCAATATCTAATGCGTC
1 ATGTCAATATCTAATGCGTC
5513733 AT
1 AT
5513735 AGTTTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTCAATATCTAATGCGTC
Found at i:5514891 original size:21 final size:22
Alignment explanation
Indices: 5514867--5514958 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 22
5514857 TTTACCCATT
*
5514867 TTATTTATT-TATTTATTATAA
1 TTATTTATTATATTTATTATTA
*
5514888 TTA-TTATTATAATTATTATTA
1 TTATTTATTATATTTATTATTA
5514909 TTA-TTATTATCATTATATATATTA
1 TTATTTATTAT-ATT-TAT-TATTA
*
5514933 TTATATA-TAT-TATTATTATTA
1 TTATTTATTATAT-TTATTATTA
5514954 TTATT
1 TTATT
5514959 AAAAAATAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
20 5 0.08
21 32 0.53
22 6 0.10
23 4 0.07
24 11 0.18
25 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATTTATTATATTTATTATTA
Found at i:5514893 original size:3 final size:3
Alignment explanation
Indices: 5514879--5514959 Score: 103
Period size: 3 Copynumber: 27.0 Consensus size: 3
5514869 ATTTATTTAT
* * *
5514879 TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TCA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5514926 TATA TTA TTA -TA TATA TTA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
5514960 AAAAATAATA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.06
3 58 0.85
4 6 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5515987 original size:2 final size:2
Alignment explanation
Indices: 5515980--5516040 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
5515970 TCCTTATCAG
5515980 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
5516022 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
5516041 TTAGGTAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5516251 original size:15 final size:15
Alignment explanation
Indices: 5516206--5516253 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
5516196 TTTATTTTTG
*
5516206 ATTATTTTTTTATATT
1 ATTATATTTTTA-ATT
5516222 -TTATA-TTTTAA-T
1 ATTATATTTTTAATT
5516234 ATTATATTTTTAATT
1 ATTATATTTTTAATT
5516249 ATTAT
1 ATTAT
5516254 TTGCAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 1 0.04
13 6 0.21
14 11 0.39
15 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTATATTTTTAATT
Found at i:5516266 original size:3 final size:3
Alignment explanation
Indices: 5516260--5516305 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
5516250 TTATTTGCAA
* *
5516260 TAT TAT T-T TAT TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
5516305 T
1 T
5516306 TATATAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:5516307 original size:19 final size:19
Alignment explanation
Indices: 5516260--5516308 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
5516250 TTATTTGCAA
5516260 TATTATTTTATTATTATTAT
1 TATTA-TTTATTATTATTAT
*
5516280 TACTT-TTTATTATTATTCT
1 TA-TTATTTATTATTATTAT
5516299 TATTATTTAT
1 TATTATTTAT
5516309 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 20 0.77
20 2 0.08
21 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATTTATTATTATTAT
Found at i:5516329 original size:18 final size:16
Alignment explanation
Indices: 5516306--5516340 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5516296 TCTTATTATT
5516306 TATATA-AATAAATATA
1 TATATATAATAAATA-A
5516322 TATATATAATAAATAA
1 TATATATAATAAATAA
5516338 TAT
1 TAT
5516341 TTGTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATAATAAATAA
Found at i:5516521 original size:112 final size:111
Alignment explanation
Indices: 5516405--5516618 Score: 263
Period size: 113 Copynumber: 1.9 Consensus size: 111
5516395 TTAATATATA
* * * *
5516405 TTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACT-GGATGTCCATTTTCTGA
1 TTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAT-T-CATTTTCTGA
*
5516467 TATTTTTAAATAAATAAATATCTTATTTTATAAATTATATAGTAATTGTT
64 TATTTCTAAATAAATAAATATCTTA-TTTATAAA-TATATAGTAATTGTT
* * ** * *
5516517 TTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAATTCATTTTCTTATA
1 TTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAATTCATTTTCTGATA
*
5516582 TTTCTAAATAAATAAATATTTTATTTATAAATATATA
66 TTTCTAAATAAATAAATATCTTATTTATAAATATATA
5516619 AATTAATATA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
111 6 0.07
112 26 0.30
113 35 0.40
114 17 0.20
115 3 0.03
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (111 bp):
TTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAATTCATTTTCTGATA
TTTCTAAATAAATAAATATCTTATTTATAAATATATAGTAATTGTT
Found at i:5522309 original size:8 final size:8
Alignment explanation
Indices: 5522287--5522368 Score: 60
Period size: 8 Copynumber: 9.9 Consensus size: 8
5522277 TATACTTGAA
*
5522287 AAAAAAAC
1 AAAAAAAG
5522295 AACAAAAAG
1 AA-AAAAAG
5522304 -AAAAAAG
1 AAAAAAAG
*
5522311 AAAGAAAG
1 AAAAAAAG
*
5522319 AAAGAAAG
1 AAAAAAAG
*
5522327 AAAGAAAG
1 AAAAAAAG
5522335 AAAAGGAAA-
1 AAAA--AAAG
5522344 AAAAGGAAAG
1 AAAA--AAAG
*
5522354 AAAAAAGG
1 AAAAAAAG
5522362 AAAAAAA
1 AAAAAAA
5522369 AGGGAGAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
7 6 0.09
8 37 0.58
9 14 0.22
10 7 0.11
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5522316 original size:4 final size:4
Alignment explanation
Indices: 5522300--5522360 Score: 72
Period size: 4 Copynumber: 15.0 Consensus size: 4
5522290 AAAACAACAA
*
5522300 AAAG AAA- AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAAGG AAAA AAAGG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAA-G AAAG AAA-G
5522350 AAAG AAA- AAAG
1 AAAG AAAG AAAG
5522361 GAAAAAAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
3 6 0.12
4 34 0.68
5 9 0.18
6 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:5522324 original size:12 final size:11
Alignment explanation
Indices: 5522300--5522370 Score: 72
Period size: 12 Copynumber: 6.0 Consensus size: 11
5522290 AAAACAACAA
5522300 AAAGAAAAAAG
1 AAAGAAAAAAG
5522311 AAAGAAAGAAAG
1 AAAGAAA-AAAG
5522323 AAAGAAAGAAAG
1 AAAGAAA-AAAG
5522335 AAAAGGAAAAAAAGG
1 -AAA-G-AAAAAA-G
5522350 AAAGAAAAAAG
1 AAAGAAAAAAG
*
5522361 GAA-AAAAAAG
1 AAAGAAAAAAG
5522371 GGAGAAATTG
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
10 7 0.13
11 10 0.19
12 22 0.41
13 4 0.07
14 7 0.13
15 4 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:5522377 original size:21 final size:21
Alignment explanation
Indices: 5522304--5522368 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
5522294 CAACAAAAAG
5522304 AAAAAA-GAAAGAAAGAAA-GA
1 AAAAAAGGAAAGAAA-AAAGGA
*
5522324 AAGAAA-GAAAG--AAAAGGA
1 AAAAAAGGAAAGAAAAAAGGA
5522342 AAAAAAGGAAAGAAAAAAGGA
1 AAAAAAGGAAAGAAAAAAGGA
5522363 AAAAAA
1 AAAAAA
5522369 AGGGAGAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.08
18 8 0.21
19 5 0.13
20 10 0.26
21 13 0.33
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AAAAAAGGAAAGAAAAAAGGA
Found at i:5527097 original size:22 final size:22
Alignment explanation
Indices: 5527066--5527120 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
5527056 ATCTACACTC
*
5527066 TTCAAAGATGATAGATTC-CTTT
1 TTCAAAGATGACAGATTCTC-TT
*
5527088 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
5527110 TTCAAAGATGA
1 TTCAAAGATGA
5527121 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:5527856 original size:114 final size:114
Alignment explanation
Indices: 5527508--5527945 Score: 806
Period size: 114 Copynumber: 3.9 Consensus size: 114
5527498 TTTCAAAGAT
* *
5527508 TCAAATCCATCATTTGATGGATCATCTTTTTCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
5527573 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
5527622 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
5527686 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
5527735 TCAAATCCATCATTTGATGGATCAGCTTTTCTAGAAAAAAGTTCATAATGAGAAGAACTCATCTA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
5527800 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
5527849 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
5527914 AAGAAAGAAGAAAAAATTCATAATGAGAAGAA
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAA
5527946 CTCATCTGAA
Statistics
Matches: 314, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
113 112 0.36
114 202 0.64
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (114 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:5527937 original size:40 final size:40
Alignment explanation
Indices: 5527881--5527985 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 40
5527871 CAGCTTTTCC
*
5527881 AGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGA
1 AGAAAAAA-TTCATAATGAGAAGAACTCATCTGAAGAAAGA
*
5527922 AGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAAGA
**
5527962 AGAGGAAATTCATAATGAGAAGAA
1 AGAAAAAATTCATAATGAGAAGAA
5527986 ATTGATCAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 52 0.87
41 8 0.13
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.17
Consensus pattern (40 bp):
AGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAAGA
Found at i:5527951 original size:154 final size:153
Alignment explanation
Indices: 5527767--5528098 Score: 493
Period size: 154 Copynumber: 2.2 Consensus size: 153
5527757 CAGCTTTTCT
5527767 AGAAAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
1 AGAAAAAA-TTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
* * * *
5527832 TTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAA
65 ATTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAG-AAAAAGTTCATAA
5527897 TAAGAAGAACTCATCTGAAGAAAGA
129 TAAGAAGAACTCATCTGAAGAAAGA
* *
5527922 AGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAA
1 AGAAAAAATTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
* ** * *
5527987 TTGATCAACCTTTTGTTTGAATTCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATG
66 TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATA
* * *
5528052 AGGAGGACTCATCTGAAGAAGGA
131 AGAAGAACTCATCTGAAGAAAGA
* * *
5528075 AGAAGAAGTTCATAATGAGGAGAA
1 AGAAAAAATTCATAATGAGAAGAA
5528099 TTTGTTCAAC
Statistics
Matches: 160, Mismatches: 17, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
153 55 0.34
154 97 0.61
155 8 0.05
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (153 bp):
AGAAAAAATTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATA
AGAAGAACTCATCTGAAGAAAGA
Found at i:5528120 original size:113 final size:113
Alignment explanation
Indices: 5527922--5528341 Score: 569
Period size: 113 Copynumber: 3.7 Consensus size: 113
5527912 TGAAGAAAGA
* * * *
5527922 AGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAA
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
5527987 TTGATCAACCTTTTGTTTGAATTCATCACTTGATAGATCAGCTTTTCC
66 TTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATCAGCTTTTCC
* * * *
5528035 AGAAAAAGTTCATAATGAGGAGGACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGGAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * *
5528100 TTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAGC-ATCCC
66 TTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATCAGCTTTTCC
*
5528147 TAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAG
1 -A--GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
* * *
5528211 AACTTGTTCAA-CTTTTCGCTCGAATTCATCACTCGATGGATCA-CTTTTTCC
63 AACTTGTTCAACCTTTT-GTTTGAATTCATCACTTGATGGATCAGC-TTTTCC
* * * *
5528262 AGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
*
5528327 TTGTTCGACCTTTTG
66 TTGTTCAACCTTTTG
5528342 CATGACTCTA
Statistics
Matches: 273, Mismatches: 26, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
112 38 0.14
113 138 0.51
114 61 0.22
115 36 0.13
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (113 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATCAGCTTTTCC
Found at i:5528162 original size:268 final size:267
Alignment explanation
Indices: 5527654--5528214 Score: 847
Period size: 268 Copynumber: 2.1 Consensus size: 267
5527644 CAGCTTTTCC
*
5527654 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
* * * *
5527719 TTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCTAGAAAAAAGTTCATAAT
66 TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAAGTTCATAAT
5527784 GAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
131 GAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
5527849 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
196 TCAAATCCATCATTTGATGGATCAGCTATCCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
5527914 AAGAAAGA
261 AAG-AAGA
* *
5527922 AGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAA
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
* ** *
5527987 TTGATCAACCTTTTGTTTGAATTCATCACTTGATAGATCAGCTTTTCCAG-AAAAAGTTCATAAT
66 TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAAGTTCATAAT
* * * * * *
5528051 GAGGAGGACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGGAGAATTTGTTCAACCTTTTGT
131 GAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * *
5528116 TTGAATTCATCATTTGATGGATCAGC-ATCCCTAGTGAAAGAGTTCATAATGAGAAGAACTCATC
196 TCAAATCCATCATTTGATGGATCAGCTATCCC-AG-AAAAAAGTTCATAATAAGAAGAACTCATC
5528180 TGAAGAAGA
259 TGAAGAAGA
*
5528189 AGAAGAAGTTCATAATGAGAAGAACT
1 AGAAAAAGTTCATAATGAGAAGAACT
5528215 TGTTCAACTT
Statistics
Matches: 264, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
266 3 0.01
267 126 0.48
268 135 0.51
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (267 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAAGTTCATAAT
GAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
TCAAATCCATCATTTGATGGATCAGCTATCCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTG
AAGAAGA
Found at i:5528238 original size:227 final size:228
Alignment explanation
Indices: 5527930--5528341 Score: 632
Period size: 227 Copynumber: 1.8 Consensus size: 228
5527920 GAAGAAAAAA
*
5527930 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAATTGATCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAATTGATCAA
* * * * *
5527995 CCTTTTGTTTGAATTCATCACTTGATAGATCAGC-TTTTCCAGAAAAAGTTCATAATGAGGAGGA
66 CCTTTTGCTCGAATTCATCACTCGATAGATCA-CTTTTTCCAGAAAAAGTTCATAATGAGAAGAA
* * *
5528059 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGGAGAATTTGTTCAACCTTTTGTTTGAATTC
130 CTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTC
5528124 ATCATTTGATGGATCAGCATCCCTAGTGAAAGAG
195 ATCATTTGATGGATCAGCATCCCTAGTGAAAGAG
* * *
5528158 TTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAATTGATCAA
* * *
5528222 -CTTTTCGCTCGAATTCATCACTCGATGGATCACTTTTTCCAGAGAGAGTTCATAATGAGAAGAA
66 CCTTTT-GCTCGAATTCATCACTCGATAGATCACTTTTTCCAGAAAAAGTTCATAATGAGAAGAA
* *
5528286 CTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTG
130 CTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
5528342 CATGACTCTA
Statistics
Matches: 165, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
226 6 0.04
227 130 0.79
228 29 0.18
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (228 bp):
TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAATTGATCAA
CCTTTTGCTCGAATTCATCACTCGATAGATCACTTTTTCCAGAAAAAGTTCATAATGAGAAGAAC
TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCA
TCATTTGATGGATCAGCATCCCTAGTGAAAGAG
Found at i:5528252 original size:381 final size:380
Alignment explanation
Indices: 5527540--5528324 Score: 1198
Period size: 381 Copynumber: 2.1 Consensus size: 380
5527530 CATCTTTTTC
5527540 AGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
1 AGAAAAAA-TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
* * * *
5527605 TTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAAT
65 ATTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAAT
5527670 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
130 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* **
5527735 TCAAATCCATCATTTGATGGATCAGCTTTTCTAGAAAAAAGTTCATAATGAGAAGAACTCATCTA
195 TCAAATCCATCATTTGATGGATCAGCATCCCTAGAAAAAAGTTCATAATGAGAAGAACTCATCTA
* * *
5527800 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTG
260 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCG
5527865 ATGGATCAGC-TTTTCCAGAAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGA
325 ATGGATCA-CTTTTTCCAG-AAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGA
*
5527922 AGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAATTCATAATGAGAAGAAA
1 AGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
* ** *
5527987 TTGATCAACCTTTTGTTTGAATTCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATG
66 TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATG
* * * * *
5528052 AGGAGGACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGGAGAATTTGTTCAACCTTTTGTT
131 AGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
** * * * *
5528117 TGAATTCATCATTTGATGGATCAGCATCCCTAGTGAAAGAGTTCATAATGAGAAGAACTCATCTG
196 CAAATCCATCATTTGATGGATCAGCATCCCTAG-AAAAAAGTTCATAATGAGAAGAACTCATCTA
* * *
5528182 AAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTCGAATTCATCACTC
260 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCAAATCCATCACTC
* * *
5528245 GATGGATCACTTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
324 GATGGATCACTTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGA
* *
5528302 AGAAGAAGTTCATAATGAGAAGA
1 AGAAAAAATTCATAATGAGAAGA
5528325 GCTTGTTCGA
Statistics
Matches: 366, Mismatches: 34, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
380 62 0.17
381 263 0.72
382 41 0.11
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (380 bp):
AGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAA
TTGATCAACCTTTTGCTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAAAAAGTTCATAATG
AGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
CAAATCCATCATTTGATGGATCAGCATCCCTAGAAAAAAGTTCATAATGAGAAGAACTCATCTAA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGA
TGGATCACTTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAGA
Found at i:5528408 original size:17 final size:17
Alignment explanation
Indices: 5528386--5528444 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
5528376 CAGCATTTCT
5528386 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
5528403 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
5528421 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
5528439 AGAAGA
1 AGAAGA
5528445 GCTTGTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 3 0.09
17 16 0.47
18 2 0.06
19 10 0.29
20 3 0.09
ACGTcount: A:0.49, C:0.12, G:0.24, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:5528706 original size:3 final size:3
Alignment explanation
Indices: 5528698--5528778 Score: 103
Period size: 3 Copynumber: 27.0 Consensus size: 3
5528688 ATTTATTTAT
* * *
5528698 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5528746 -TA TATA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
5528779 AAAAATAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
2 4 0.06
3 59 0.86
4 6 0.09
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5529820 original size:2 final size:2
Alignment explanation
Indices: 5529813--5529844 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5529803 TCCTTATCAG
5529813 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
5529845 GGTAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5530025 original size:13 final size:15
Alignment explanation
Indices: 5530009--5530040 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5529999 TATTTATATT
5530009 TTATA-TTTTAA-TA
1 TTATATTTTTAATTA
5530022 TTATATTTTTAATTA
1 TTATATTTTTAATTA
5530037 TTAT
1 TTAT
5530041 TTGCAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 6 0.35
15 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATTTTTAATTA
Found at i:5530041 original size:26 final size:26
Alignment explanation
Indices: 5529998--5530067 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
5529988 CATTCAAATT
*
5529998 TTATTTATATT-TTA-TATTT-TAATA
1 TTATTT-TATTATTATTATTTGCAATA
5530022 TTATATTT-TTAATTATTATTTGCAATA
1 TTAT-TTTATT-ATTATTATTTGCAATA
5530049 TTATTTTATTATTATTATT
1 TTATTTTATTATTATTATT
5530068 ACTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
23 2 0.05
24 5 0.13
25 5 0.13
26 17 0.44
27 10 0.26
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
TTATTTTATTATTATTATTTGCAATA
Found at i:5530042 original size:33 final size:34
Alignment explanation
Indices: 5529968--5530042 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
5529958 TACTCTAGTT
* *
5529968 TTATAATTTTATATTTTAATCATTCAAATTTTAT
1 TTATTATTTTATATTTTAATCATTCAAATTTTAA
*
5530002 TTA-TATTTTATATTTTAAT-ATT-ATATTTTTAA
1 TTATTATTTTATATTTTAATCATTCA-AATTTTAA
5530034 TTATTATTT
1 TTATTATTT
5530043 GCAATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 1 0.03
32 12 0.33
33 20 0.56
34 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (34 bp):
TTATTATTTTATATTTTAATCATTCAAATTTTAA
Found at i:5530053 original size:3 final size:3
Alignment explanation
Indices: 5530047--5530092 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
5530037 TTATTTGCAA
* *
5530047 TAT TAT T-T TAT TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
5530092 T
1 T
5530093 TATATAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:5530094 original size:19 final size:19
Alignment explanation
Indices: 5530047--5530095 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
5530037 TTATTTGCAA
5530047 TATTATTTTATTATTATTAT
1 TATTA-TTTATTATTATTAT
*
5530067 TACTT-TTTATTATTATTCT
1 TA-TTATTTATTATTATTAT
5530086 TATTATTTAT
1 TATTATTTAT
5530096 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 20 0.77
20 2 0.08
21 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATTTATTATTATTAT
Found at i:5530308 original size:113 final size:114
Alignment explanation
Indices: 5530191--5530412 Score: 270
Period size: 114 Copynumber: 2.0 Consensus size: 114
5530181 TTAATATATA
* * * * *
5530191 TTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCCATTTTCTGAT
1 TTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-CATTTTCTGAT
* *
5530254 ATTTTTAAATAAATAAATATCTTATTTTATAAAT-TATATAGTAATTGTTT
65 ATTTCTAAATAAATAAATATCTTA-TTTATAAATATATAAAGTAATTGTTT
* * ** * * *
5530304 TTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCGTTTTCTTATA
1 TTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTTTCTGATA
*
5530369 TTTCTAAATAAATAAATATTTTATTTATAAATATATAAAGTAAT
66 TTTCTAAATAAATAAATATCTTATTTATAAATATATAAAGTAAT
5530413 ATATATTTTT
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
113 27 0.30
114 44 0.48
115 20 0.22
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (114 bp):
TTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTTTCTGATA
TTTCTAAATAAATAAATATCTTATTTATAAATATATAAAGTAATTGTTT
Found at i:5533743 original size:19 final size:19
Alignment explanation
Indices: 5533716--5533757 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
5533706 CTTATTATAG
*
5533716 GTGCCTTAAAGAAGAGCAA
1 GTGCATTAAAGAAGAGCAA
5533735 GTGCATTAAAGAAGAGCAA
1 GTGCATTAAAGAAGAGCAA
5533754 GTGC
1 GTGC
5533758 CTCCGGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (19 bp):
GTGCATTAAAGAAGAGCAA
Found at i:5543391 original size:21 final size:21
Alignment explanation
Indices: 5543365--5543405 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5543355 TGAGTCGAGC
*
5543365 CATCCTTGATCAGCCATTAAA
1 CATCCTTGACCAGCCATTAAA
*
5543386 CATCCTTGACCAGCCGTTAA
1 CATCCTTGACCAGCCATTAA
5543406 CTTTTTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.27
Consensus pattern (21 bp):
CATCCTTGACCAGCCATTAAA
Found at i:5548649 original size:201 final size:204
Alignment explanation
Indices: 5548301--5548708 Score: 795
Period size: 201 Copynumber: 2.0 Consensus size: 204
5548291 TTAAGCTCAC
5548301 AAATAATGAATACAAAGATATTCAATAAGGCTCAATATACTATATCCAAGAGAAAATGAAAAAAT
1 AAATAATGAATACAAAGATATTCAATAAGGCTCAATATACTATATCCAAGAGAAAATGAAAAAAT
5548366 AAGAATGAAATACACTTTTCTCTTGATCCTTAAGCTTGGATAAGTGTAGTAACCTTCTTTGAGTG
66 AAGAATGAAATACACTTTTCTCTTGATCCTTAAGCTTGGATAAGTGTAGTAACCTTCTTTGAGTG
5548431 TCATTGGGTTGTTTTTATATAATGGAACGAGTTTGTGGATATTTCTAACCATTGTGGATGTTTTG
131 TCATTGGGTTGTTTTTATATAATGGAACGAGTTTGTGGATATTTCTAACCATTGTGGATGTTTTG
5548496 GAGCCATTG
196 GAGCCATTG
5548505 AAATAATGAATACAAAGATA-TC-ATAAGGCTCAATATACTATATCCAAGAGAAAATGAAAAAA-
1 AAATAATGAATACAAAGATATTCAATAAGGCTCAATATACTATATCCAAGAGAAAATGAAAAAAT
5548567 AAGAATGAAATACACTTTTCTCTTGATCCTTAAGCTTGGATAAGTGTAGTAACCTTCTTTGAGTG
66 AAGAATGAAATACACTTTTCTCTTGATCCTTAAGCTTGGATAAGTGTAGTAACCTTCTTTGAGTG
5548632 TCATTGGGTTGTTTTTATATAATGGAACGAGTTTGTGGATATTTCTAACCATTGTGGATGTTTTG
131 TCATTGGGTTGTTTTTATATAATGGAACGAGTTTGTGGATATTTCTAACCATTGTGGATGTTTTG
5548697 GAGCCATTG
196 GAGCCATTG
5548706 AAA
1 AAA
5548709 GCTTTTAATC
Statistics
Matches: 204, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
201 142 0.70
202 40 0.20
203 2 0.01
204 20 0.10
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (204 bp):
AAATAATGAATACAAAGATATTCAATAAGGCTCAATATACTATATCCAAGAGAAAATGAAAAAAT
AAGAATGAAATACACTTTTCTCTTGATCCTTAAGCTTGGATAAGTGTAGTAACCTTCTTTGAGTG
TCATTGGGTTGTTTTTATATAATGGAACGAGTTTGTGGATATTTCTAACCATTGTGGATGTTTTG
GAGCCATTG
Found at i:5549933 original size:29 final size:29
Alignment explanation
Indices: 5549901--5549986 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
5549891 CTCAGTTTCA
5549901 TACATAAAGTTTAAATATTCTCGATTAAC
1 TACATAAAGTTTAAATATTCTCGATTAAC
*
5549930 TACATAATA-TTT---TATGC-CG-TT-A-
1 TACATAA-AGTTTAAATATTCTCGATTAAC
*
5549952 -ACGTAAAGTTTAAATATTCTCGATTAAC
1 TACATAAAGTTTAAATATTCTCGATTAAC
5549980 TACATAA
1 TACATAA
5549987 TATTTTATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 20
0.64 0.06 0.30
Matches are distributed among these distances:
20 1 0.02
21 8 0.19
23 1 0.02
24 6 0.14
25 4 0.09
26 6 0.14
27 1 0.02
29 15 0.35
30 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (29 bp):
TACATAAAGTTTAAATATTCTCGATTAAC
Found at i:5549964 original size:50 final size:50
Alignment explanation
Indices: 5549905--5550004 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
5549895 GTTTCATACA
5549905 TAAAGTTTAAATATTCTCGATTAACTACATAATATTTTATGCCGTTAACG
1 TAAAGTTTAAATATTCTCGATTAACTACATAATATTTTATGCCGTTAACG
5549955 TAAAGTTTAAATATTCTCGATTAACTACATAATATTTTATGCCGTTAACG
1 TAAAGTTTAAATATTCTCGATTAACTACATAATATTTTATGCCGTTAACG
5550005 AATTCACCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (50 bp):
TAAAGTTTAAATATTCTCGATTAACTACATAATATTTTATGCCGTTAACG
Found at i:5552240 original size:19 final size:21
Alignment explanation
Indices: 5552208--5552249 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
5552198 TCAAAACTTC
5552208 ATTTTGCTTTTCAAAAT-CAA
1 ATTTTGCTTTTCAAAATCCAA
5552228 ATTTTGC-TTTCAAAATCCAA
1 ATTTTGCTTTTCAAAATCCAA
5552248 AT
1 AT
5552250 CATTTCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (21 bp):
ATTTTGCTTTTCAAAATCCAA
Found at i:5554147 original size:20 final size:20
Alignment explanation
Indices: 5554117--5554193 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
5554107 GACCACTGGA
* *
5554117 TAGGGGGTTTAGAAACCAAT
1 TAGGGGTTTTAGAAACCATT
5554137 TAGGGGTTTTA-AAA-C---
1 TAGGGGTTTTAGAAACCATT
*
5554152 TAGAGG-TTTAGAAACCATT
1 TAGGGGTTTTAGAAACCATT
5554171 TAGGAGGTTTT-GAAACCATT
1 TAGG-GGTTTTAGAAACCATT
5554191 TAG
1 TAG
5554194 AAAATTTGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.09
15 8 0.17
16 1 0.02
18 1 0.02
19 6 0.13
20 24 0.51
21 3 0.06
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (20 bp):
TAGGGGTTTTAGAAACCATT
Found at i:5556302 original size:21 final size:21
Alignment explanation
Indices: 5556263--5556302 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5556253 AAGGAATATT
*
5556263 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
5556284 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
5556303 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:5556439 original size:28 final size:28
Alignment explanation
Indices: 5556407--5556467 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
5556397 CCATCCTTTT
* *
5556407 TGGGCACAAGTAACATTGGAATAGCACA
1 TGGGCACAAGTAACACTGGAACAGCACA
** *
5556435 TGGGCTTAAGTAACACTGGAACATCACA
1 TGGGCACAAGTAACACTGGAACAGCACA
5556463 TGGGC
1 TGGGC
5556468 TTAAACTCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (28 bp):
TGGGCACAAGTAACACTGGAACAGCACA
Found at i:5556468 original size:28 final size:28
Alignment explanation
Indices: 5556414--5556471 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
5556404 TTTTGGGCAC
* *
5556414 AAGTAACATTGGAATAGCACATGGGCTT
1 AAGTAACACTGGAACAGCACATGGGCTT
*
5556442 AAGTAACACTGGAACATCACATGGGCTT
1 AAGTAACACTGGAACAGCACATGGGCTT
5556470 AA
1 AA
5556472 ACTCTCTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (28 bp):
AAGTAACACTGGAACAGCACATGGGCTT
Done.