Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_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: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 25
Found at i:1399047 original size:16 final size:16
Alignment explanation
Indices: 1398996--1399047 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
1398986 TTGGAGTTCA
1398996 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAAA--AG
*
1399015 AAAAGAAGAAAATAAG
1 AAAAGAAGAAAAAAAG
1399031 AAAAGAA-AAGAAAAAG
1 AAAAGAAGAA-AAAAAG
1399047 A
1 A
1399048 GAAGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
18 4 0.13
19 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:1401225 original size:22 final size:20
Alignment explanation
Indices: 1401200--1401239 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1401190 ATGTTTGTTT
1401200 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
1401222 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
1401240 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:1402596 original size:13 final size:13
Alignment explanation
Indices: 1402574--1402603 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1402564 ACTAAACACC
1402574 TTTC-ACATACCT
1 TTTCAACATACCT
1402586 TTTCAACATACCT
1 TTTCAACATACCT
1402599 TTTCA
1 TTTCA
1402604 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1410498 original size:19 final size:20
Alignment explanation
Indices: 1410474--1410513 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1410464 TATCCTTTCT
1410474 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
1410493 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
1410513 T
1 T
1410514 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:1430101 original size:21 final size:21
Alignment explanation
Indices: 1430076--1430116 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1430066 GACATCTCTC
*
1430076 TTCA-TTAAAACATCATGTATT
1 TTCATTTAAAA-ACCATGTATT
1430097 TTCATTTAAAAACCATGTAT
1 TTCATTTAAAAACCATGTAT
1430117 CTAGCCGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (21 bp):
TTCATTTAAAAACCATGTATT
Found at i:1433583 original size:24 final size:24
Alignment explanation
Indices: 1433525--1433583 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
1433515 CATTCATGAT
* *
1433525 CCAATGAACATGCCTATTGGAGAG
1 CCAAGGAACATGACTATTGGAGAG
* * *
1433549 CCATGGCACATGACTTTTGG-GATG
1 CCAAGGAACATGACTATTGGAGA-G
1433573 CCAAGGAACAT
1 CCAAGGAACAT
1433584 AATCGTTCAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (24 bp):
CCAAGGAACATGACTATTGGAGAG
Found at i:1442316 original size:34 final size:34
Alignment explanation
Indices: 1442269--1442343 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
1442259 TAACATGTGA
1442269 TATGATAACTTATACTAACATGTGAATGCATGCT
1 TATGATAACTTATACTAACATGTGAATGCATGCT
* * *
1442303 TATGATAATTTATACTAACATGTGAATGTATGTT
1 TATGATAACTTATACTAACATGTGAATGCATGCT
1442337 TATGATA
1 TATGATA
1442344 TAATAGAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (34 bp):
TATGATAACTTATACTAACATGTGAATGCATGCT
Found at i:1443281 original size:24 final size:24
Alignment explanation
Indices: 1443253--1443303 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1443243 TCACCATTGG
*
1443253 AGGCCAATTTCATCTTCCATTTAA
1 AGGCCAATTTCACCTTCCATTTAA
*
1443277 AGGCCAATTTCACCTTCCATTTGA
1 AGGCCAATTTCACCTTCCATTTAA
1443301 AGG
1 AGG
1443304 ATACTTCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (24 bp):
AGGCCAATTTCACCTTCCATTTAA
Found at i:1447802 original size:23 final size:22
Alignment explanation
Indices: 1447775--1447824 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
1447765 CTCTATCTTT
*
1447775 TTATTTA-TTTCATTTCATTATTA
1 TTATTTATTTTCATTAC-TTA-TA
1447798 TTATTTATTTTCATTACTTATA
1 TTATTTATTTTCATTACTTATA
1447820 TTATT
1 TTATT
1447825 ACCCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 10 0.40
24 8 0.32
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTTATTTTCATTACTTATA
Found at i:1448094 original size:14 final size:13
Alignment explanation
Indices: 1448077--1448126 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
1448067 GTACAAAAAG
1448077 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
1448091 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
1448104 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
1448115 AAAGAAAAAGAA
1 AAAGAAAAAGAA
1448127 TTAAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:1448123 original size:19 final size:18
Alignment explanation
Indices: 1448071--1448126 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
1448061 ATTGGAGTAC
1448071 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
1448088 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
1448107 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
1448126 A
1 A
1448127 TTAAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:1452409 original size:22 final size:21
Alignment explanation
Indices: 1452360--1452411 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1452350 TCTATCTTTT
1452360 TTAT-TTATTTCATTTCATTA
1 TTATATTATTTCATTTCATTA
1452380 TTATATTATTT-ATTTTCATTA
1 TTATATTATTTCA-TTTCATTA
1452401 CTTATATTATT
1 -TTATATTATT
1452412 ACCCTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.17
21 14 0.48
22 10 0.34
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATATTATTTCATTTCATTA
Found at i:1456450 original size:10 final size:10
Alignment explanation
Indices: 1456435--1456460 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1456425 TTCAACTTTC
1456435 TTTCTTTCCT
1 TTTCTTTCCT
1456445 TTTCTTTCCT
1 TTTCTTTCCT
1456455 TTTCTT
1 TTTCTT
1456461 CTTTTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTTCCT
Found at i:1457869 original size:20 final size:22
Alignment explanation
Indices: 1457841--1457882 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1457831 ATGTGTAAGA
1457841 CATAGGAGCT-A-AAATGAATG
1 CATAGGAGCTAACAAATGAATG
*
1457861 CATATGAGCTAACAAATGAATG
1 CATAGGAGCTAACAAATGAATG
1457883 ATTAAACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (22 bp):
CATAGGAGCTAACAAATGAATG
Found at i:1459287 original size:26 final size:26
Alignment explanation
Indices: 1459253--1459309 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1459243 CTTGGCTTGC
1459253 TTTC-TCTTTT-TGAACTTCTTTTTCT
1 TTTCTTCTTTTCTGAA-TTCTTTTTCT
*
1459278 TTTCTTCTTTTCTGAATTTTTTTTCT
1 TTTCTTCTTTTCTGAATTCTTTTTCT
*
1459304 CTTCTT
1 TTTCTT
1459310 TTTGTCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 4 0.14
26 20 0.71
27 4 0.14
ACGTcount: A:0.07, C:0.19, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTCTTCTTTTCTGAATTCTTTTTCT
Found at i:1459297 original size:23 final size:20
Alignment explanation
Indices: 1459271--1459327 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 20
1459261 TTTGAACTTC
1459271 TTTTTCTTTTCTTCTTTTCTG
1 TTTTTCTTTTCTTCTTTT-TG
1459292 AATTTTT-TTTCTCTTCTTTTTG
1 --TTTTTCTTT-TCTTCTTTTTG
1459314 TCTTTTCTTTTCTT
1 T-TTTTCTTTTCTT
1459328 TTTGCACTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 1 0.03
21 8 0.26
22 8 0.26
23 14 0.45
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTTCTTTTCTTCTTTTTG
Found at i:1465915 original size:30 final size:30
Alignment explanation
Indices: 1465872--1465967 Score: 138
Period size: 30 Copynumber: 3.2 Consensus size: 30
1465862 GTTGTTTGTG
* *
1465872 AGTTGTTTATGTCTCCCAAATGCTCCACTA
1 AGTTGTATATGTCTTCCAAATGCTCCACTA
* *
1465902 AATTGTATATGTCTTCCAAATGCTCCACCA
1 AGTTGTATATGTCTTCCAAATGCTCCACTA
* *
1465932 AGCTGTATATGTCTTCAAAATGCTCCACTA
1 AGTTGTATATGTCTTCCAAATGCTCCACTA
1465962 AGTTGT
1 AGTTGT
1465968 TTGAGAGCTG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (30 bp):
AGTTGTATATGTCTTCCAAATGCTCCACTA
Found at i:1472792 original size:11 final size:13
Alignment explanation
Indices: 1472760--1472789 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1472750 TGGCCAAAGA
1472760 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1472773 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1472785 TGAAA
1 TGAAA
1472790 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1478847 original size:1 final size:1
Alignment explanation
Indices: 1478843--1478886 Score: 79
Period size: 1 Copynumber: 44.0 Consensus size: 1
1478833 AAATTTTGGC
*
1478843 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1478887 AAAATAGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.02, T:0.98
Consensus pattern (1 bp):
T
Found at i:1484848 original size:18 final size:18
Alignment explanation
Indices: 1484805--1484842 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1484795 GTGAAGTATG
*
1484805 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
1484823 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
1484841 AA
1 AA
1484843 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:1531364 original size:11 final size:11
Alignment explanation
Indices: 1531348--1531372 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1531338 TTTCATGCTC
1531348 TTTGTGAGCTG
1 TTTGTGAGCTG
1531359 TTTGTGAGCTG
1 TTTGTGAGCTG
1531370 TTT
1 TTT
1531373 ATGTCTCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (11 bp):
TTTGTGAGCTG
Found at i:1531406 original size:30 final size:30
Alignment explanation
Indices: 1531365--1531460 Score: 147
Period size: 30 Copynumber: 3.2 Consensus size: 30
1531355 GCTGTTTGTG
* *
1531365 AGCTGTTTATGTCTCCCAAATGCTCCACCA
1 AGCTGTATATGTCTTCCAAATGCTCCACCA
*
1531395 AGCTGTATATGTCTTTCAAATGCTCCACCA
1 AGCTGTATATGTCTTCCAAATGCTCCACCA
* *
1531425 AGCTGTATATGTCTTCAAAATGCTCCACTA
1 AGCTGTATATGTCTTCCAAATGCTCCACCA
1531455 AGCTGT
1 AGCTGT
1531461 TTGTGAGCTG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (30 bp):
AGCTGTATATGTCTTCCAAATGCTCCACCA
Found at i:1532123 original size:19 final size:20
Alignment explanation
Indices: 1532099--1532137 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1532089 GGTAAAGATG
1532099 TGAAAA-CAAATAGTATGCA
1 TGAAAATCAAATAGTATGCA
*
1532118 TGAAAATCATATAGTATGCA
1 TGAAAATCAAATAGTATGCA
1532138 AGTGAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (20 bp):
TGAAAATCAAATAGTATGCA
Found at i:1546095 original size:24 final size:24
Alignment explanation
Indices: 1546060--1546110 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1546050 TCACTTCAAG
* *
1546060 TTGAAGATTCAAGAAACATGTCTT
1 TTGAAGAATCAAGAAACATGACTT
* *
1546084 TTGAAGAATCAATAAACGTGACTT
1 TTGAAGAATCAAGAAACATGACTT
1546108 TTG
1 TTG
1546111 GTGATCCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (24 bp):
TTGAAGAATCAAGAAACATGACTT
Found at i:1549078 original size:29 final size:29
Alignment explanation
Indices: 1549041--1549096 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1549031 CTTATAAGTT
1549041 ATGGAATGATATCA-TGAGCTAAGTATAAG
1 ATGGAATGATATCAGTGAGCTAA-TATAAG
* *
1549070 ATGGTATGATATTAGTGAGCTAATATA
1 ATGGAATGATATCAGTGAGCTAATATA
1549097 TATGACTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.32
Consensus pattern (29 bp):
ATGGAATGATATCAGTGAGCTAATATAAG
Found at i:1552884 original size:17 final size:17
Alignment explanation
Indices: 1552862--1552897 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1552852 GTGCTTTCAA
1552862 CTTTTC-TTTCTTTCTTT
1 CTTTTCTTTTC-TTCTTT
1552879 CTTTTCTTTTCTTCTTT
1 CTTTTCTTTTCTTCTTT
1552896 CT
1 CT
1552898 CTGAGTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
CTTTTCTTTTCTTCTTT
Found at i:1552978 original size:11 final size:11
Alignment explanation
Indices: 1552962--1552986 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1552952 TTTATTTTTG
1552962 TTCACTTGCAC
1 TTCACTTGCAC
1552973 TTCACTTGCAC
1 TTCACTTGCAC
1552984 TTC
1 TTC
1552987 TTTTTGGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:1553738 original size:352 final size:345
Alignment explanation
Indices: 1553068--1553740 Score: 839
Period size: 353 Copynumber: 1.9 Consensus size: 345
1553058 AAGTTAATTC
* *
1553068 TACCTTTTCAATTGATTATGGATCTAGGAAGGAAGCAAAATAACCTGCATAAGTGAATGGCTCAA
1 TACCTTTTCAAATGATTATGGATCTAGGAAGGAAGCAAAACAACCTGCATAAGTGAATGGCTCAA
* * * *
1553133 ATAGATGGTTTGGTGGTAGATGCAAAGGTGAATAGGTAGGCTATTTATGATAAGAGAGATGGTAG
66 ATAGATGGTTGGGTGGTAGACGCAAAGGTGAATAGGTAGGCTATTTATAATAAGAGAGATGGAAG
* * *
1553198 CAGAAGGATGTTATGGCTATGGTGAGGTTGATGAAACAATGGAATGGTTGTGAGGTAGTGTCTTA
131 CAGAAGGATGTTATGGCTATGGTGAGGTTGATGAAAAAAAGGAATGGTTGTGAGGTAGTATCTTA
* *
1553263 AAGAAGACTCAAAAAAGAACCAATACTATAGAGAGCAAAGACTCATACTTTATATTACTTATTTA
196 AAGAAGACTCAAAAAAGAACCAATACTATAGAGAGCAAAGACCCATACTTTATATTACTTATTCA
1553328 AGGGATGGTAGTAAGGACTTGGACCCACTATATATATGGAGATAGGAACCACAAGTATCAAAGGG
261 AGGGATGGTAGTAAGGACTTGGACCCACTATATATATGGAGATAGGAACCACAAGTATCAAAGGG
1553393 AAGGTGATGTATGGTACTTG
326 AAGGTGATGTATGGTACTTG
*
1553413 TACCTTTTTCAAATGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCA-AAGTGAATGGCTCA
1 TACC-TTTTCAAATGATTATGGATCTAGGAAGGAAGCAAAACAACCTGCATAAGTGAATGGCTC-
* * *
1553477 AAATAGAATGGTTAAGGGTGGTAGACGTATAGGTGAATTGGTAGGCTATTTA-AATAATGAGTA-
64 AAATAG-ATGGTT--GGGTGGTAGACGCAAAGGTGAATAGGTAGGCTATTTATAATAA-GAG-AG
* *
1553540 ATGGAAGCGGAA-GATAGTTGATAAGGCTATGGTTATGG-TGATGAAATAAAAGG-ATGGTTGTG
124 ATGGAAGCAGAAGGAT-GTT-AT--GGCTATGGTGA-GGTTGATGAAA-AAAAGGAATGGTTGTG
* * * * *
1553602 AGGATAGTATCTTGAAGAA-ATCTCAAAGAAGAACCAATGCTATATAGAGCAGAGACCCA-ATCT
183 AGG-TAGTATCTTAAAGAAGA-CTCAAAAAAGAACCAATACTATAGAGAGCAAAGACCCATA-CT
** * * *
1553665 TTATATTGTTTCTTCAAGGGATGGT-GTTAAGTACTTTGACCCACTAGT-TATAT-GA-ACTAGG
245 TTATATTACTTATTCAAGGGATGGTAG-TAAGGACTTGGACCCACTA-TATATATGGAGA-TAGG
*
1553726 AACCAGAAGTATCAA
307 AACCACAAGTATCAA
1553741 GATGAAAGGA
Statistics
Matches: 281, Mismatches: 28, Indels: 31
0.83 0.08 0.09
Matches are distributed among these distances:
345 17 0.06
346 48 0.17
347 6 0.02
348 7 0.02
349 48 0.17
350 3 0.01
351 1 0.00
352 53 0.19
353 97 0.35
354 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (345 bp):
TACCTTTTCAAATGATTATGGATCTAGGAAGGAAGCAAAACAACCTGCATAAGTGAATGGCTCAA
ATAGATGGTTGGGTGGTAGACGCAAAGGTGAATAGGTAGGCTATTTATAATAAGAGAGATGGAAG
CAGAAGGATGTTATGGCTATGGTGAGGTTGATGAAAAAAAGGAATGGTTGTGAGGTAGTATCTTA
AAGAAGACTCAAAAAAGAACCAATACTATAGAGAGCAAAGACCCATACTTTATATTACTTATTCA
AGGGATGGTAGTAAGGACTTGGACCCACTATATATATGGAGATAGGAACCACAAGTATCAAAGGG
AAGGTGATGTATGGTACTTG
Found at i:1554608 original size:22 final size:20
Alignment explanation
Indices: 1554583--1554622 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1554573 ATGTTTGTTT
1554583 ATGGTAATGTAAGCTAAGTATG
1 ATGGTAATG--AGCTAAGTATG
*
1554605 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
1554623 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:1555978 original size:13 final size:13
Alignment explanation
Indices: 1555956--1555985 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1555946 ACTAAACACC
1555956 TTTC-ACATACCT
1 TTTCAACATACCT
1555968 TTTCAACATACCT
1 TTTCAACATACCT
1555981 TTTCA
1 TTTCA
1555986 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1564011 original size:31 final size:31
Alignment explanation
Indices: 1563973--1564034 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1563963 TATGGAAGAT
1563973 GTTCTCTCTTTGTTCATCCTCTTGACTTTGA
1 GTTCTCTCTTTGTTCATCCTCTTGACTTTGA
*
1564004 GTTCTCTCTTTGTTCATCCTCTTGATTTTGA
1 GTTCTCTCTTTGTTCATCCTCTTGACTTTGA
1564035 ATGTTCAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.10, C:0.24, G:0.13, T:0.53
Consensus pattern (31 bp):
GTTCTCTCTTTGTTCATCCTCTTGACTTTGA
Found at i:1568578 original size:24 final size:24
Alignment explanation
Indices: 1568546--1568597 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1568536 CCTTGGCACT
* * *
1568546 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAACTGTTGGAACA
*
1568570 TCAAGTGGCATAACTGTTGGAACA
1 TCAAGTGGCACAACTGTTGGAACA
1568594 TCAA
1 TCAA
1568598 AGGACATGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAACTGTTGGAACA
Found at i:1570871 original size:86 final size:86
Alignment explanation
Indices: 1570756--1570930 Score: 341
Period size: 86 Copynumber: 2.0 Consensus size: 86
1570746 CATATGCAAG
*
1570756 GCACATAGGGGCTGATCACATGCAAAACACATGGCTTGGCCGAATAGGGAGGGAACTCTTCATCT
1 GCACAAAGGGGCTGATCACATGCAAAACACATGGCTTGGCCGAATAGGGAGGGAACTCTTCATCT
1570821 TGGCGCCTAAATGACCCATAT
66 TGGCGCCTAAATGACCCATAT
1570842 GCACAAAGGGGCTGATCACATGCAAAACACATGGCTTGGCCGAATAGGGAGGGAACTCTTCATCT
1 GCACAAAGGGGCTGATCACATGCAAAACACATGGCTTGGCCGAATAGGGAGGGAACTCTTCATCT
1570907 TGGCGCCTAAATGACCCATAT
66 TGGCGCCTAAATGACCCATAT
1570928 GCA
1 GCA
1570931 AGGCACATGG
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.20
Consensus pattern (86 bp):
GCACAAAGGGGCTGATCACATGCAAAACACATGGCTTGGCCGAATAGGGAGGGAACTCTTCATCT
TGGCGCCTAAATGACCCATAT
Found at i:1572529 original size:11 final size:11
Alignment explanation
Indices: 1572513--1572552 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
1572503 TATTTTTTTT
1572513 CAAAAAAAAGG
1 CAAAAAAAAGG
1572524 C-AAAAAAAGG
1 CAAAAAAAAGG
*
1572534 CAAAAAAAA-A
1 CAAAAAAAAGG
1572544 CAAAAAAAA
1 CAAAAAAAA
1572553 CAAAAAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGG
Found at i:1572552 original size:10 final size:10
Alignment explanation
Indices: 1572513--1572559 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1572503 TATTTTTTTT
*
1572513 CAAAAAAAAGG
1 CAAAAAAAA-A
**
1572524 CAAAAAAAGG
1 CAAAAAAAAA
1572534 CAAAAAAAAA
1 CAAAAAAAAA
1572544 C-AAAAAAAA
1 CAAAAAAAAA
1572553 CAAAAAA
1 CAAAAAA
1572560 TCCAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 9 0.28
10 15 0.47
11 8 0.25
ACGTcount: A:0.81, C:0.11, G:0.09, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:1576998 original size:50 final size:50
Alignment explanation
Indices: 1576892--1576999 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 50
1576882 TTCACACTCC
* * * * *
1576892 ATTTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGT
1 ATTTT-CCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
* *
1576943 GTTTTCCTTTTCATTGCGACTAGGAGGGCTCGATAG-GACATTATCCATCG-
1 ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACA-TAT-CATCGT
1576993 ATTTTCC
1 ATTTTCC
1577000 ACATCCATCC
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
49 3 0.06
50 36 0.77
51 8 0.17
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.37
Consensus pattern (50 bp):
ATTTTCCTTTTCATCGCGACTAGGAGGGCTCGATAGAGACATATCATCGT
Found at i:1577528 original size:19 final size:19
Alignment explanation
Indices: 1577461--1577528 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
1577451 CTATTTTTTT
1577461 CCAAAAAAA-CAAAAAAA-
1 CCAAAAAAACCAAAAAAAG
* *
1577478 --AAAACACCCAAAAAAAG
1 CCAAAAAAACCAAAAAAAG
* *
1577495 GCAAAAAAACAAAAAAAAG
1 CCAAAAAAACCAAAAAAAG
*
1577514 CCAAAAAAGCCAAAA
1 CCAAAAAAACCAAAA
1577529 TTTCAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 5 0.13
16 8 0.21
19 26 0.67
ACGTcount: A:0.75, C:0.19, G:0.06, T:0.00
Consensus pattern (19 bp):
CCAAAAAAACCAAAAAAAG
Found at i:1587194 original size:12 final size:11
Alignment explanation
Indices: 1587177--1587207 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1587167 GGCTTTATTA
1587177 TTTTTTTTGCTT
1 TTTTTTTTG-TT
1587189 TTTTTTTTGTT
1 TTTTTTTTGTT
1587200 TTTTTTTT
1 TTTTTTTT
1587208 AAAAATAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.90
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:1597324 original size:11 final size:11
Alignment explanation
Indices: 1597310--1597350 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
1597300 CTTTTTTTTA
*
1597310 TTTTTTTCCCTT
1 TTTTTTTGCC-T
1597322 TTTTTTTGCCT
1 TTTTTTTGCCT
1597333 TTTTTTTGCCT
1 TTTTTTTGCCT
1597344 TTTTTTT
1 TTTTTTT
1597351 TGTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:1597336 original size:23 final size:23
Alignment explanation
Indices: 1597310--1597362 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1597300 CTTTTTTTTA
1597310 TTTTTTTCCCTTTTTTTTTGCCT
1 TTTTTTTCCCTTTTTTTTTGCCT
* **
1597333 TTTTTTTGCCTTTTTTTTTGTTT
1 TTTTTTTCCCTTTTTTTTTGCCT
1597356 TTTTTTT
1 TTTTTTT
1597363 TTGAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (23 bp):
TTTTTTTCCCTTTTTTTTTGCCT
Found at i:1597362 original size:11 final size:11
Alignment explanation
Indices: 1597319--1597361 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
1597309 ATTTTTTTCC
1597319 CTTTTTTTTTG
1 CTTTTTTTTTG
*
1597330 CCTTTTTTTTG
1 CTTTTTTTTTG
1597341 CCTTTTTTTTTG
1 -CTTTTTTTTTG
1597353 -TTTTTTTTT
1 CTTTTTTTTT
1597362 TTTGAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.31
11 10 0.34
12 10 0.34
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (11 bp):
CTTTTTTTTTG
Found at i:1597363 original size:12 final size:12
Alignment explanation
Indices: 1597310--1597361 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
1597300 CTTTTTTTTA
*
1597310 TTTTTTTCCCTT
1 TTTTTTTGCCTT
1597322 TTTTTTTGCC-T
1 TTTTTTTGCCTT
1597333 TTTTTTTGCCTT
1 TTTTTTTGCCTT
1597345 TTTTTTTG--TT
1 TTTTTTTGCCTT
1597355 TTTTTTT
1 TTTTTTT
1597362 TTTGAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
10 9 0.24
11 11 0.29
12 18 0.47
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:1599404 original size:14 final size:14
Alignment explanation
Indices: 1599386--1599421 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1599376 TCCAGCACTC
1599386 AAAAGAAGAGAAAG
1 AAAAGAAGAGAAAG
* *
1599400 CAAAGAAAAGAAAG
1 AAAAGAAGAGAAAG
1599414 AAAAGAAG
1 AAAAGAAG
1599422 TTGAAGCACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAGAAAG
Found at i:1605094 original size:36 final size:35
Alignment explanation
Indices: 1605029--1605125 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 35
1605019 GTTGGGGATA
* *
1605029 ATATAGGCGTGATATGGTGATGGAATATGGTGATG
1 ATATAGGCGTGATATGGTGATGGACTATGGCGATG
1605064 ATATAGGCGTGATAATGGTGATGGACTATGGCGATG
1 ATATAGGCGTGAT-ATGGTGATGGACTATGGCGATG
*
1605100 ATATAGGTGTGATGATGGTGATGGAC
1 ATATAGGCGTGAT-ATGGTGATGGAC
1605126 AGATTGTATC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 13 0.23
36 44 0.77
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (35 bp):
ATATAGGCGTGATATGGTGATGGACTATGGCGATG
Found at i:1605108 original size:25 final size:23
Alignment explanation
Indices: 1605053--1605112 Score: 56
Period size: 25 Copynumber: 2.6 Consensus size: 23
1605043 TGGTGATGGA
1605053 ATAT-GGTGATGATATAGGCGTG
1 ATATAGGTGATGATATAGGCGTG
1605075 ATA-ATGGTGATGGACTAT-GGCGATG
1 ATATA-GGTGAT-GA-TATAGGCG-TG
1605100 ATATAGGTG-TGAT
1 ATATAGGTGATGAT
1605113 GATGGTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 7 0.22
25 12 0.38
26 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.32
Consensus pattern (23 bp):
ATATAGGTGATGATATAGGCGTG
Found at i:1609126 original size:26 final size:22
Alignment explanation
Indices: 1609081--1609130 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 22
1609071 TGATGTAGGA
1609081 TTCTTTTTCTTTTCTCTTTTGTT
1 TTCTTTTTCTTTTCTCTTTT-TT
*
1609104 TTCTTCTTTCTTGTTGCTTTTTTTT
1 TTCTT-TTTCTT-TT-CTCTTTTTT
1609129 TT
1 TT
1609131 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.22
24 6 0.26
25 6 0.26
26 6 0.26
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (22 bp):
TTCTTTTTCTTTTCTCTTTTTT
Found at i:1609583 original size:36 final size:35
Alignment explanation
Indices: 1609518--1609614 Score: 158
Period size: 36 Copynumber: 2.7 Consensus size: 35
1609508 GTTGGGGATA
* *
1609518 ATATAGGCGTGATATGGTGATGGAATATGGTGATG
1 ATATAGGCGTGATATGGTGATGGACTATGGCGATG
1609553 ATATAGGCGTGATAATGGTGATGGACTATGGCGATG
1 ATATAGGCGTGAT-ATGGTGATGGACTATGGCGATG
1609589 ATATAGGCGTGATGATGGTGATGGAC
1 ATATAGGCGTGAT-ATGGTGATGGAC
1609615 AGATTGTATC
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 13 0.22
36 45 0.78
ACGTcount: A:0.28, C:0.06, G:0.37, T:0.29
Consensus pattern (35 bp):
ATATAGGCGTGATATGGTGATGGACTATGGCGATG
Found at i:1610502 original size:15 final size:16
Alignment explanation
Indices: 1610466--1610504 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1610456 TGATAATTAA
*
1610466 GAAATGAAAAGTAATG
1 GAAATGGAAAGTAATG
*
1610482 GAAATGGAAAG-AATT
1 GAAATGGAAAGTAATG
1610497 GAAATGGA
1 GAAATGGA
1610505 TATAATAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.28, T:0.18
Consensus pattern (16 bp):
GAAATGGAAAGTAATG
Found at i:1610699 original size:35 final size:36
Alignment explanation
Indices: 1610652--1610719 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
1610642 ATTTATAAGT
*
1610652 TGGTGATAATATAGGCGTGAT-ATGTTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
1610687 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
1610720 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:1616363 original size:35 final size:36
Alignment explanation
Indices: 1616316--1616383 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
1616306 ATTTATAAGT
*
1616316 TGGTGATAATATAGGCGTGAT-ATGTTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
1616351 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
1616384 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:1624015 original size:13 final size:11
Alignment explanation
Indices: 1623971--1624055 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
1623961 ACAATCTGTC
1623971 CATCACCATCAT
1 CATCACCAT-AT
*
1623983 CA-CCCCTATAT
1 CATCACC-ATAT
*
1623994 CATCGCCATAGT
1 CATCACCATA-T
1624006 CCATCACCATTAT
1 -CATCACCA-TAT
*
1624019 CA-CGCCTATAT
1 CATCACC-ATAT
1624030 CATCACCATATT
1 CATCACCATA-T
1624042 CCATCACCATAT
1 -CATCACCATAT
1624054 CA
1 CA
1624056 CGCCTATATT
Statistics
Matches: 59, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
11 23 0.39
12 16 0.27
13 18 0.31
14 2 0.03
ACGTcount: A:0.31, C:0.39, G:0.04, T:0.27
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1624015 original size:36 final size:35
Alignment explanation
Indices: 1623968--1624064 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 35
1623958 GATACAATCT
* *
1623968 GTCCATCACCATCATCACCCCTATATCATCGCCATA
1 GTCCATCACCAT-ATCACGCCTATATCATCACCATA
1624004 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCA-TATCACGCCTATATCATCACCATA
*
1624040 TTCCATCACCATATCACGCCTATAT
1 GTCCATCACCATATCACGCCTATAT
1624065 TATCCCCAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
35 14 0.25
36 42 0.74
37 1 0.02
ACGTcount: A:0.29, C:0.38, G:0.05, T:0.28
Consensus pattern (35 bp):
GTCCATCACCATATCACGCCTATATCATCACCATA
Found at i:1624550 original size:14 final size:15
Alignment explanation
Indices: 1624516--1624562 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1624506 AATTTGGAGG
1624516 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
1624531 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
1624545 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
1624562 G
1 G
1624563 TGAAGTGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:1629731 original size:13 final size:11
Alignment explanation
Indices: 1629687--1629771 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
1629677 ACAATCTGTC
1629687 CATCACCATCAT
1 CATCACCAT-AT
*
1629699 CA-CGCCTATAT
1 CATCACC-ATAT
*
1629710 CATCGCCATAGT
1 CATCACCATA-T
1629722 CCATCACCATTAT
1 -CATCACCA-TAT
*
1629735 CA-CGCCTATAT
1 CATCACC-ATAT
1629746 CATCACCATATT
1 CATCACCATA-T
1629758 CCATCACCATAT
1 -CATCACCATAT
1629770 CA
1 CA
1629772 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 23 0.38
12 17 0.28
13 18 0.30
14 2 0.03
ACGTcount: A:0.31, C:0.38, G:0.05, T:0.27
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1629731 original size:36 final size:35
Alignment explanation
Indices: 1629684--1629780 Score: 158
Period size: 36 Copynumber: 2.7 Consensus size: 35
1629674 GATACAATCT
*
1629684 GTCCATCACCATCATCACGCCTATATCATCGCCATA
1 GTCCATCACCAT-ATCACGCCTATATCATCACCATA
1629720 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCA-TATCACGCCTATATCATCACCATA
*
1629756 TTCCATCACCATATCACGCCTATAT
1 GTCCATCACCATATCACGCCTATAT
1629781 TATCCCCAAC
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
35 14 0.24
36 43 0.74
37 1 0.02
ACGTcount: A:0.29, C:0.37, G:0.06, T:0.28
Consensus pattern (35 bp):
GTCCATCACCATATCACGCCTATATCATCACCATA
Found at i:1633102 original size:24 final size:24
Alignment explanation
Indices: 1633056--1633107 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1633046 CCTTGGCACT
* * *
1633056 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAACTGTTGGAACA
* *
1633080 TCAAGTGGCATAACTGTTGGAACG
1 TCAAGTGGCACAACTGTTGGAACA
1633104 TCAA
1 TCAA
1633108 AGGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAACTGTTGGAACA
Found at i:1637509 original size:23 final size:25
Alignment explanation
Indices: 1637464--1637515 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
1637454 AATAAAGGGG
*
1637464 ATAATAATATAAGTAATGAAAATAA
1 ATAATAATATAAGAAATGAAAATAA
*
1637489 ATAATAATA-ATGAAATG-AAATAA
1 ATAATAATATAAGAAATGAAAATAA
1637512 ATAA
1 ATAA
1637516 AGGATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 6 0.24
25 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (25 bp):
ATAATAATATAAGAAATGAAAATAA
Found at i:1637619 original size:13 final size:13
Alignment explanation
Indices: 1637597--1637626 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1637587 ACTAAACACA
1637597 TTTC-ACATACCT
1 TTTCAACATACCT
1637609 TTTCAACATACCT
1 TTTCAACATACCT
1637622 TTTCA
1 TTTCA
1637627 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1642237 original size:35 final size:35
Alignment explanation
Indices: 1642191--1642266 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
1642181 AAAACAGTCC
* *
1642191 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
1642226 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1642261 TCAATT
1 TCAATT
1642267 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1642809 original size:130 final size:130
Alignment explanation
Indices: 1642664--1642911 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
1642654 TATTTATATA
* **
1642664 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1642729 TTAGCACATGATCATGACACGTGTCATTGGTGACATATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
1642794 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATGTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1642859 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
1642912 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1642942 original size:130 final size:129
Alignment explanation
Indices: 1642678--1642942 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
1642668 ATTTGGTCCT
* ** *
1642678 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * * ** *
1642743 TGACACGTGTCATTGGTGACATATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAATAAGT-CA
*
1642808 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATGTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
1642873 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAATAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAATAAGT
1642937 -A
128 CA
1642938 AAATT
1 AAATT
1642943 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 98 0.88
132 9 0.08
133 5 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAATAAGTCA
Found at i:1643245 original size:28 final size:27
Alignment explanation
Indices: 1643214--1643276 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1643204 AGTTGATACA
*
1643214 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1643242 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1643270 ATATTTT
1 ATATTTT
1643277 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1657742 original size:2 final size:2
Alignment explanation
Indices: 1657735--1657759 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1657725 ATGTAGCGGA
1657735 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1657760 AGTTGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1661459 original size:36 final size:35
Alignment explanation
Indices: 1661408--1661517 Score: 152
Period size: 34 Copynumber: 3.2 Consensus size: 35
1661398 TAAGATACTA
1661408 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* *
1661443 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * *
1661478 -CTATATCATTACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
1661512 CCTATA
1 CCTATA
1661518 TAACCACCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 29 0.44
35 15 0.23
36 22 0.33
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:1662252 original size:27 final size:26
Alignment explanation
Indices: 1662222--1662282 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
1662212 CATTTTCCTA
*
1662222 AACCTTTTTCTACCCTACCCCTATCAT
1 AACCATTTT-TACCCTACCCCTATCAT
*
1662249 AACCATTTTTATCCTACCCCTATCAT
1 AACCATTTTTACCCTACCCCTATCAT
1662275 AACCATTT
1 AACCATTT
1662283 CTAGATCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 24 0.75
27 8 0.25
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (26 bp):
AACCATTTTTACCCTACCCCTATCAT
Found at i:1664874 original size:20 final size:21
Alignment explanation
Indices: 1664838--1664883 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1664828 CTATTTTTTT
* *
1664838 CAAAACAAAAACAAAAAAAGG
1 CAAAAAAAAAACAAAAAAAGC
1664859 CAAAAAAAAAAC-AAAAAAGC
1 CAAAAAAAAAACAAAAAAAGC
1664879 CAAAA
1 CAAAA
1664884 TTTCAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAACAAAAAAAGC
Found at i:1669850 original size:19 final size:19
Alignment explanation
Indices: 1669826--1669867 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
1669816 ATCCTTTCTT
1669826 TATTTCATTTCATT-CTTAA
1 TATTTCATTTCATTACTT-A
1669845 TATTTCATTTCATTACTTA
1 TATTTCATTTCATTACTTA
1669864 TATT
1 TATT
1669868 ATTATCACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTCATTTCATTACTTA
Found at i:1670407 original size:36 final size:35
Alignment explanation
Indices: 1670313--1670412 Score: 137
Period size: 35 Copynumber: 2.8 Consensus size: 35
1670303 ATTGGTGGTT
* *
1670313 ATATAGGCATGAAATGGTGATAGAAGATGGTAATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
* * *
1670348 ATATAGGCGTGCAATGGTAATGGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
*
1670383 TTATAGGCGTGAAAATGGTGATGGAAGATG
1 ATATAGGCGTG-AAATGGTGATGGAAGATG
1670413 ATAAGTGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 40 0.71
36 16 0.29
ACGTcount: A:0.35, C:0.04, G:0.35, T:0.26
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATGGAAGATGGTAATG
Found at i:1670550 original size:26 final size:26
Alignment explanation
Indices: 1670521--1670571 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1670511 AAGCTTTTTC
1670521 TATCCTACCCCTATCATAACCATTTA
1 TATCCTACCCCTATCATAACCATTTA
1670547 TATCCTACCCCTATCATAACCATTT
1 TATCCTACCCCTATCATAACCATTT
1670572 CTAGACCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (26 bp):
TATCCTACCCCTATCATAACCATTTA
Found at i:1689189 original size:19 final size:19
Alignment explanation
Indices: 1689135--1689190 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
1689125 ATTGGAGTGC
* *
1689135 AAAAAGAAAAGTAAAAGAC
1 AAAAAGAAAAGAAAAAGAA
**
1689154 AAAAAG--AAGAATCAGAA
1 AAAAAGAAAAGAAAAAGAA
1689171 AAAAAGAAAAGAAAAAGAA
1 AAAAAGAAAAGAAAAAGAA
1689190 A
1 A
1689191 TTCAAAAGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 13 0.45
19 16 0.55
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAAGAA
Found at i:1693025 original size:19 final size:20
Alignment explanation
Indices: 1693001--1693040 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1692991 TATCTTTTCT
1693001 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
**
1693020 TTATTTGTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
1693040 T
1 T
1693041 ACTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:1693657 original size:74 final size:74
Alignment explanation
Indices: 1693573--1693730 Score: 307
Period size: 74 Copynumber: 2.1 Consensus size: 74
1693563 GTTAGCTCAT
1693573 ATGCATTCATTTTAGCTCCTATGTCTTACACATTAGCTTACATATATTATATCATTATGTACTTA
1 ATGCATTCATTTTAGCTCCTATGTCTTACACATTAGCTTACATATATTATATCATTATGTACTTA
1693638 ACTCATGAC
66 ACTCATGAC
1693647 ATGCATTCATTTTAGCTCCTATGTCTTACACATTAGCTTACATATATTATATCATTATGTACTTA
1 ATGCATTCATTTTAGCTCCTATGTCTTACACATTAGCTTACATATATTATATCATTATGTACTTA
*
1693712 GCTCATGAC
66 ACTCATGAC
1693721 ATGCATTCAT
1 ATGCATTCAT
1693731 AGCTTATATC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 83 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (74 bp):
ATGCATTCATTTTAGCTCCTATGTCTTACACATTAGCTTACATATATTATATCATTATGTACTTA
ACTCATGAC
Found at i:1696604 original size:24 final size:25
Alignment explanation
Indices: 1696558--1696612 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1696548 ACAGTTATGC
*
1696558 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
1696582 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
1696607 CA-TTGA
1 CACTTGA
1696613 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:1704757 original size:30 final size:31
Alignment explanation
Indices: 1704721--1704780 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1704711 CGTAGCTTTA
**
1704721 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
1704751 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
1704781 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:1705653 original size:19 final size:21
Alignment explanation
Indices: 1705629--1705679 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1705619 GGCCAAGAGC
*
1705629 ATGTATCTTCA-TT-AAAATA
1 ATGTATTTTCATTTAAAAATA
*
1705648 ATGTATTTTCATTTAAAAATC
1 ATGTATTTTCATTTAAAAATA
1705669 ATGTATTTTCA
1 ATGTATTTTCA
1705680 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (21 bp):
ATGTATTTTCATTTAAAAATA
Found at i:1708300 original size:14 final size:15
Alignment explanation
Indices: 1708283--1708318 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1708273 TCTAGCACTC
1708283 AAAAGAAGAA-AAAG
1 AAAAGAAGAAGAAAG
1708297 AAAAGAA-AAGAAAG
1 AAAAGAAGAAGAAAG
1708311 AAAAGAAG
1 AAAAGAAG
1708319 TTGAAGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAGAAAG
Found at i:1711227 original size:20 final size:20
Alignment explanation
Indices: 1711191--1711229 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1711181 TCATCACATA
*
1711191 AGGAGCTTAAACTTAGCTGG
1 AGGAGCTTAAAATTAGCTGG
1711211 AGGAGC-TAAAATGTAGCTG
1 AGGAGCTTAAAAT-TAGCTG
1711230 AACTTAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (20 bp):
AGGAGCTTAAAATTAGCTGG
Found at i:1741399 original size:22 final size:21
Alignment explanation
Indices: 1741344--1741402 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 21
1741334 TGAGATACAA
1741344 CATCAACACCATC-TCCATTTCAT
1 CATCAACACCATCAT-C--TTCAT
1741367 CATCAACACCATCATCTTCAT
1 CATCAACACCATCATCTTCAT
*
1741388 CCATCAAGACCATCA
1 -CATCAACACCATCA
1741403 ATTCTACGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 5 0.15
22 13 0.39
23 14 0.42
24 1 0.03
ACGTcount: A:0.34, C:0.39, G:0.02, T:0.25
Consensus pattern (21 bp):
CATCAACACCATCATCTTCAT
Found at i:1741755 original size:15 final size:14
Alignment explanation
Indices: 1741717--1741766 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 14
1741707 ATTTGATTGC
*
1741717 AAAAAGAAAAG-AA
1 AAAAAAAAAAGAAA
* *
1741730 AAGACAAAAAGAATA
1 AAAAAAAAAAGAA-A
1741745 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
1741759 AAAAAAAA
1 AAAAAAAA
1741767 TTCGAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 8 0.27
14 10 0.33
15 12 0.40
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:1744571 original size:22 final size:21
Alignment explanation
Indices: 1744531--1744571 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1744521 CCATCTCTAT
*
1744531 TTCATCATCAACACCATCATC
1 TTCATCATCAACACAATCATC
*
1744552 TTCATCCATCAAGACAATCA
1 TTCAT-CATCAACACAATCA
1744572 ATTCCGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.37, C:0.34, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACAATCATC
Found at i:1744892 original size:1 final size:1
Alignment explanation
Indices: 1744886--1744950 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
1744876 ATTGGAATGC
* * * * * * * *
1744886 AAAAAAAAAAAAAAAAAAAAAAAAGAGAAAAAGAAAAAGAAGAAAAAAAAGAAAAGAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1744951 TTCAAAAAGA
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.88, C:0.00, G:0.11, T:0.02
Consensus pattern (1 bp):
A
Found at i:1746513 original size:22 final size:21
Alignment explanation
Indices: 1746473--1746513 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1746463 CCATCTCTAT
*
1746473 TTCATCATCAACACCATCATC
1 TTCATCATCAACACAATCATC
*
1746494 TTCATCCATCAAGACAATCA
1 TTCAT-CATCAACACAATCA
1746514 ATTCCGTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.37, C:0.34, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACAATCATC
Found at i:1746866 original size:27 final size:26
Alignment explanation
Indices: 1746829--1746884 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
1746819 TTGGAATGCA
1746829 AAAAAAAAATAAAAAGACAAAAAGAAG
1 AAAAAAAAATAAAAAGACAAAAAG-AG
* **
1746856 AAAAGAAAATAAAAATTCAAAAAGAG
1 AAAAAAAAATAAAAAGACAAAAAGAG
1746882 AAA
1 AAA
1746885 GCAAGCCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.79, C:0.04, G:0.11, T:0.07
Consensus pattern (26 bp):
AAAAAAAAATAAAAAGACAAAAAGAG
Found at i:1753761 original size:19 final size:20
Alignment explanation
Indices: 1753737--1753779 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1753727 AGCATTTATC
*
1753737 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
1753756 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
1753776 TTCA
1 TTCA
1753780 AATGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:1756131 original size:5 final size:5
Alignment explanation
Indices: 1756121--1756170 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
1756111 TTGGAGTGCA
1756121 AAAAG AAAAG AAAAG ACAAA- AAGAAG AAAA- AAAACG AAAAG AAAAG
1 AAAAG AAAAG AAAAG A-AAAG AA-AAG AAAAG AAAA-G AAAAG AAAAG
1756167 AAAA
1 AAAA
1756171 ATTCAAAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
4 5 0.12
5 26 0.65
6 9 0.22
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1756142 original size:18 final size:18
Alignment explanation
Indices: 1756119--1756186 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
1756109 AATTGGAGTG
*
1756119 CAAAAAGAAAAGAAAAGA
1 CAAAAAGAAAAGAAAAAA
1756137 CAAAAAGAAGAA-AAAAAA
1 CAAAAAGAA-AAGAAAAAA
* *
1756155 CGAAAAGAAAAGAAAAATT
1 CAAAAAGAAAAGAAAAA-A
1756174 CAAAAAGAGAAAG
1 CAAAAAGA-AAAG
1756187 CAACCCAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.05
18 27 0.64
19 9 0.21
20 4 0.10
ACGTcount: A:0.75, C:0.06, G:0.16, T:0.03
Consensus pattern (18 bp):
CAAAAAGAAAAGAAAAAA
Found at i:1761810 original size:13 final size:13
Alignment explanation
Indices: 1761788--1761817 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1761778 ACTAAACACC
1761788 TTTC-ACATACCT
1 TTTCAACATACCT
1761800 TTTCAACATACCT
1 TTTCAACATACCT
1761813 TTTCA
1 TTTCA
1761818 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1769974 original size:14 final size:15
Alignment explanation
Indices: 1769940--1769986 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1769930 AATTTGGAGT
1769940 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
1769955 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
1769969 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
1769986 G
1 G
1769987 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:1773411 original size:35 final size:37
Alignment explanation
Indices: 1773342--1773421 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1773332 ATACTATTTC
*
1773342 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
1773379 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
1773414 CATCACCA
1 CATCACCA
1773422 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:1779022 original size:35 final size:37
Alignment explanation
Indices: 1778953--1779030 Score: 115
Period size: 35 Copynumber: 2.2 Consensus size: 37
1778943 ATATTATTTC
* *
1778953 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACAATAATCCATCTACCATTATCACGCCTATAT
*
1778990 CATCACAATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACAATAATCCATCTACCATTATCACGCCTATAT
1779025 CATCAC
1 CATCAC
1779031 CAAATTCTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 20 0.53
36 3 0.08
37 15 0.39
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACAATAATCCATCTACCATTATCACGCCTATAT
Found at i:1780643 original size:5 final size:5
Alignment explanation
Indices: 1780633--1780674 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
1780623 CTTCAACTTC
*
1780633 TTTCT TTTCT TTTCT TTTCC TTT-T TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1780675 ATTCTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 3 0.09
5 31 0.91
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:1780661 original size:19 final size:18
Alignment explanation
Indices: 1780630--1780682 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 18
1780620 GTTCTTCAAC
1780630 TTCTTTCTTTTCTTTTCTT
1 TTCTTT-TTTTCTTTTCTT
1780649 TTCCTTTTTTTCTTTTCTT
1 TT-CTTTTTTTCTTTTCTT
*
1780668 TTCTTTTATTCTTTT
1 TTCTTTTTTTCTTTT
1780683 TGAGTGCTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 12 0.38
19 16 0.50
20 4 0.12
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (18 bp):
TTCTTTTTTTCTTTTCTT
Found at i:1780682 original size:24 final size:24
Alignment explanation
Indices: 1780633--1780683 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
1780623 CTTCAACTTC
*
1780633 TTTCTTTTCTTTTCTTTTCCTTTT
1 TTTCTTTTCTTTTCTTTTCATTTT
1780657 TTTCTTTTCTTTTCTTTT-ATTCTT
1 TTTCTTTTCTTTTCTTTTCATT-TT
1780681 TTT
1 TTT
1780684 GAGTGCTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTCTTTTCTTTTCTTTTCATTTT
Found at i:1780683 original size:19 final size:19
Alignment explanation
Indices: 1780639--1780682 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
1780629 CTTCTTTCTT
*
1780639 TTCTTTTCTTTTCCTTTTT
1 TTCTTTTCTTTTCCTTTTA
1780658 TTCTTTTCTTTT-CTTTTA
1 TTCTTTTCTTTTCCTTTTA
1780676 TTCTTTT
1 TTCTTTT
1780683 TGAGTGCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TTCTTTTCTTTTCCTTTTA
Found at i:1783874 original size:13 final size:12
Alignment explanation
Indices: 1783858--1783897 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
1783848 GGGCAAAAGG
1783858 AAAAGAAAAGACA
1 AAAAGAAAAGA-A
1783871 AAAAG-AAAGAAA
1 AAAAGAAAAG-AA
1783883 AAAAGAAAAGAA
1 AAAAGAAAAGAA
1783895 AAA
1 AAA
1783898 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:1783879 original size:12 final size:12
Alignment explanation
Indices: 1783858--1783897 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
1783848 GGGCAAAAGG
*
1783858 AAAAGAAAAGACA
1 AAAAG-AAAGAAA
1783871 AAAAGAAAGAAA
1 AAAAGAAAGAAA
1783883 AAAAGAAAAGAAA
1 AAAAG-AAAGAAA
1783896 AA
1 AA
1783898 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:1783887 original size:8 final size:9
Alignment explanation
Indices: 1783859--1783895 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
1783849 GGCAAAAGGA
1783859 AAAGAAAAG
1 AAAGAAAAG
*
1783868 ACA-AAAAG
1 AAAGAAAAG
1783876 AAAGAAAA-
1 AAAGAAAAG
1783884 AAAGAAAAG
1 AAAGAAAAG
1783893 AAA
1 AAA
1783896 AATTCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 15 0.62
9 9 0.38
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:1787799 original size:13 final size:12
Alignment explanation
Indices: 1787783--1787822 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
1787773 GGGCAAAAGG
1787783 AAAAGAAAAGACA
1 AAAAGAAAAGA-A
1787796 AAAAG-AAAGAAA
1 AAAAGAAAAG-AA
1787808 AAAAGAAAAGAA
1 AAAAGAAAAGAA
1787820 AAA
1 AAA
1787823 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:1787804 original size:12 final size:12
Alignment explanation
Indices: 1787783--1787822 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
1787773 GGGCAAAAGG
*
1787783 AAAAGAAAAGACA
1 AAAAG-AAAGAAA
1787796 AAAAGAAAGAAA
1 AAAAGAAAGAAA
1787808 AAAAGAAAAGAAA
1 AAAAG-AAAGAAA
1787821 AA
1 AA
1787823 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:1787812 original size:8 final size:9
Alignment explanation
Indices: 1787784--1787820 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
1787774 GGCAAAAGGA
1787784 AAAGAAAAG
1 AAAGAAAAG
*
1787793 ACA-AAAAG
1 AAAGAAAAG
1787801 AAAGAAAA-
1 AAAGAAAAG
1787809 AAAGAAAAG
1 AAAGAAAAG
1787818 AAA
1 AAA
1787821 AATTCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 15 0.62
9 9 0.38
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:1794628 original size:21 final size:21
Alignment explanation
Indices: 1794594--1794633 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1794584 TAGTTCAACT
* *
1794594 AGCTGAGTTTAGCTCTCCTCC
1 AGCTGAATTGAGCTCTCCTCC
*
1794615 AGCTGAATTGAGCTTTCCT
1 AGCTGAATTGAGCTCTCCT
1794634 TAGTGTTCCA
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:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (21 bp):
AGCTGAATTGAGCTCTCCTCC
Found at i:1799690 original size:16 final size:16
Alignment explanation
Indices: 1799659--1799705 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
1799649 TGGTAATGAA
1799659 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
1799676 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
1799693 ATAAAAAAATGAA
1 ATAAAAAAATGAA
1799706 GATAACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:1808828 original size:36 final size:36
Alignment explanation
Indices: 1808755--1808855 Score: 159
Period size: 36 Copynumber: 2.8 Consensus size: 36
1808745 ATTTATAAGT
*
1808755 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
1808790 TGGTGATGATATAGGCTTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
1808826 TGGTGATGATATAGACGTGATAATGGTGAT
1 TGGTGATGATATAGGCGTGATAATGGTGAT
1808856 AGACAGATTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 19 0.32
36 41 0.68
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.33
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:1808830 original size:13 final size:12
Alignment explanation
Indices: 1808773--1808837 Score: 55
Period size: 13 Copynumber: 5.4 Consensus size: 12
1808763 ATATAGGCGT
1808773 GATATGGTGATG
1 GATATGGTGATG
1808785 GAATATGGTGAT-
1 G-ATATGGTGATG
* * *
1808797 GATATAG-GCTT
1 GATATGGTGATG
1808808 GATAATGGTGATG
1 GAT-ATGGTGATG
1808821 GACTATGGTGAT-
1 GA-TATGGTGATG
1808833 GATAT
1 GATAT
1808838 AGACGTGATA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
10 2 0.05
11 11 0.26
12 7 0.16
13 22 0.51
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:1809245 original size:19 final size:20
Alignment explanation
Indices: 1809198--1809248 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1809188 GAAACCCCTT
**
1809198 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1809218 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1809237 TGAAGATACATG
1 TGAAAATACATG
1809249 CTCTTGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1812343 original size:11 final size:11
Alignment explanation
Indices: 1812324--1812354 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1812314 TGTAGGAGTC
*
1812324 TTTTATTTTCT
1 TTTTCTTTTCT
1812335 TTTTCTTTTCT
1 TTTTCTTTTCT
1812346 TTTTCTTTT
1 TTTTCTTTT
1812355 ATTCTTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:1815045 original size:187 final size:190
Alignment explanation
Indices: 1814727--1815102 Score: 731
Period size: 188 Copynumber: 2.0 Consensus size: 190
1814717 AAGAACCTTG
1814727 CATTGTTGCTTCTCTATCTTCATCCACATTGGCTCGGATCATGGCAATCTCCATCTCCTTGAAAT
1 CATTGTTGCTTCTCTATCTTCATCCACATTGGCTCGGATCATGGCAATCTCCATCTCCTTGAAAT
1814792 AATCTTCAACGTTCTTGCTTCCTTGTTTCAGATTTTGTAACTTATGATAGAGATCTCGGTGATAG
66 AATCTTCAACGTTCTTGCTTCCTTGTTTCAGATTTTGTAACTTATGATAGAGATCTCGGTGATAG
1814857 TGA-TAGGAACAACTTTTTTCTCATAAGGGCCTTCATTTC-TTCCCAAGTTGTGATGGGC
131 TGATTAGGAACAACTTTTTTCTCATAAGGGCCTTCATTTCTTTCCCAAGTTGTGATGGGC
1814915 CATTGTTGCTTCTCTATCTTCATCCACATTGGCTCGGATCATGGCAATCTCCATCTCCTTGAAAT
1 CATTGTTGCTTCTCTATCTTCATCCACATTGGCTCGGATCATGGCAATCTCCATCTCCTTGAAAT
1814980 -ATCTTCAACGTTCTTGCTTCCTTGTTTCAGATTTTGTAACTTATGATAGAGATCTCGGTGATAG
66 AATCTTCAACGTTCTTGCTTCCTTGTTTCAGATTTTGTAACTTATGATAGAGATCTCGGTGATAG
1815044 TGATTAGGAACAACTTTTTTCTCATAAGGGCCTTCATTTCTTTCCCAAGTTGTGATGGG
131 TGATTAGGAACAACTTTTTTCTCATAAGGGCCTTCATTTCTTTCCCAAGTTGTGATGGG
1815103 GCGTTCACCA
Statistics
Matches: 186, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
187 67 0.36
188 101 0.54
189 18 0.10
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (190 bp):
CATTGTTGCTTCTCTATCTTCATCCACATTGGCTCGGATCATGGCAATCTCCATCTCCTTGAAAT
AATCTTCAACGTTCTTGCTTCCTTGTTTCAGATTTTGTAACTTATGATAGAGATCTCGGTGATAG
TGATTAGGAACAACTTTTTTCTCATAAGGGCCTTCATTTCTTTCCCAAGTTGTGATGGGC
Found at i:1818050 original size:36 final size:36
Alignment explanation
Indices: 1817973--1818074 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
1817963 ATTTATAAGT
*
1817973 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
* *
1818008 TTGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
1818044 TGGTGATGATATAGACGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
1818075 AACAGATTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.31
36 42 0.69
ACGTcount: A:0.29, C:0.04, G:0.34, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:1821334 original size:11 final size:11
Alignment explanation
Indices: 1821318--1821342 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1821308 ATTTTTTTCT
1821318 TTCACTTGCAC
1 TTCACTTGCAC
1821329 TTCACTTGCAC
1 TTCACTTGCAC
1821340 TTC
1 TTC
1821343 TTTTTGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:1827496 original size:23 final size:23
Alignment explanation
Indices: 1827461--1827532 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
1827451 TTTCTTTTTC
1827461 TTCTT-TTTTGAGTGCTTTCAAT
1 TTCTTCTTTTGAGTGCTTTCAAT
1827483 TTCTTCTTTTGAGTGCTTTCAAT
1 TTCTTCTTTTGAGTGCTTTCAAT
* *
1827506 TTATTCTTTTGAGTGC-TTCGAT
1 TTCTTCTTTTGAGTGCTTTCAAT
1827528 TTCTT
1 TTCTT
1827533 TGCTGGATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 14 0.30
23 32 0.70
ACGTcount: A:0.12, C:0.15, G:0.14, T:0.58
Consensus pattern (23 bp):
TTCTTCTTTTGAGTGCTTTCAAT
Found at i:1833536 original size:35 final size:35
Alignment explanation
Indices: 1833451--1833561 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
1833441 TAAGATACTA
*
1833451 CCTA-AACATCACCATCATCCATCACCATTTTCATG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCATG
* * *
1833486 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCATG
* * *
1833521 CCTATAACCTTACCATCTTCTATCACCATTTCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCATG
1833556 CCTATA
1 CCTATA
1833562 TAACCACCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 44 0.68
36 21 0.32
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCATG
Found at i:1833607 original size:11 final size:11
Alignment explanation
Indices: 1833587--1833616 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1833577 TACCATATAT
1833587 TCATCATTCAA
1 TCATCATTCAA
*
1833598 TCATCCTTCAA
1 TCATCATTCAA
1833609 TCATCATT
1 TCATCATT
1833617 AAGGCATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (11 bp):
TCATCATTCAA
Found at i:1839200 original size:257 final size:257
Alignment explanation
Indices: 1838744--1839256 Score: 832
Period size: 257 Copynumber: 2.0 Consensus size: 257
1838734 AGTCCTACTA
*
1838744 ACACAAGGAAGATAATGTGTTAGATAATGCAAAAGAACAATAACAGGGAAAAACAAAAGAACCTA
1 ACACAAGGAAGATAATGTGTTAGATAATGCAAAAGAACAATAACAAGGAAAAACAAAAGAACCTA
*
1838809 AAGCACTAAGAGTTAAAGAAATAAAGGACCAAACCAGAAAACCTAGAAAACACTGGATCAACTTG
66 AAGCACTAAGAGTCAAAGAAATAAAGGACCAAACCAGAAAACCTAGAAAACACTGGATCAACTTG
*
1838874 AGAAACGTTTTTGAGGGGGTTACCGGTATCCAAAAATACTGGAAAATTCTTGAATGTCTTTTGAT
131 AGAAACGTTTTTGAGGGGGTTACCGGTATCCAAAAATACTGGAAAATTCTTGAATGTCTTTCGAT
* * * * *
1838939 GCGTCAAGAAACCACCTGTAAAATGTCAGAATCAAATACCTTTAGTAGTATCCAGTAGACTG
196 GCGTCAAGAAACCACATGTAAAATATCAGAACCAAATAACTTCAGTAGTATCCAGTAGACTG
1839001 ACACAAGGAAGATAATGTGTTAGATAATGCAAAAGAACAATAACAAGGAAAAACAAAAGAACCTA
1 ACACAAGGAAGATAATGTGTTAGATAATGCAAAAGAACAATAACAAGGAAAAACAAAAGAACCTA
* * *
1839066 AAGCACTAAGAGTCAAAGAAA-AAGGGACCAAACCAGAAAACCTAGAAAACGCTTGATCAACTTG
66 AAGCACTAAGAGTCAAAGAAATAAAGGACCAAACCAGAAAACCTAGAAAACACTGGATCAACTTG
* * * *
1839130 AGCAACGTTTTTGAGGGGGTTACTGGTGTCCAAAAATTCT-GAAACATTTCTTGAATGTCTTTCG
131 AGAAACGTTTTTGAGGGGGTTACCGGTATCCAAAAATACTGGAAA-A-TTCTTGAATGTCTTTCG
* * *
1839194 ATGCGTCACGAAACCACATGTTAAATATCATAACCAAATAACTTCAGTAGTATCCAGTAGACT
194 ATGCGTCAAGAAACCACATGTAAAATATCAGAACCAAATAACTTCAGTAGTATCCAGTAGACT
1839257 CTGTTGAACG
Statistics
Matches: 236, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
255 4 0.02
256 77 0.33
257 155 0.66
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.22
Consensus pattern (257 bp):
ACACAAGGAAGATAATGTGTTAGATAATGCAAAAGAACAATAACAAGGAAAAACAAAAGAACCTA
AAGCACTAAGAGTCAAAGAAATAAAGGACCAAACCAGAAAACCTAGAAAACACTGGATCAACTTG
AGAAACGTTTTTGAGGGGGTTACCGGTATCCAAAAATACTGGAAAATTCTTGAATGTCTTTCGAT
GCGTCAAGAAACCACATGTAAAATATCAGAACCAAATAACTTCAGTAGTATCCAGTAGACTG
Found at i:1842263 original size:16 final size:16
Alignment explanation
Indices: 1842242--1842274 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1842232 TTGACGCCAC
1842242 AAGTATAAAATACTTG
1 AAGTATAAAATACTTG
1842258 AAGTATAAAATACTTG
1 AAGTATAAAATACTTG
1842274 A
1 A
1842275 TAAGTCGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (16 bp):
AAGTATAAAATACTTG
Found at i:1845362 original size:19 final size:19
Alignment explanation
Indices: 1845338--1845387 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1845328 GAAACCCCTT
*
1845338 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
*
1845357 TGAAAATGCATGATTTTAA
1 TGAAAATACATGATTTTAA
*
1845376 TGAAGATACATG
1 TGAAAATACATG
1845388 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:1846325 original size:30 final size:31
Alignment explanation
Indices: 1846286--1846345 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
1846276 ACATGCTGCC
**
1846286 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
1846317 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
1846346 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:1847678 original size:32 final size:32
Alignment explanation
Indices: 1847637--1847701 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1847627 GGGGAAGAAG
1847637 TAAGGTTAGATAAAAATTGTTCTTCACTCTCC
1 TAAGGTTAGATAAAAATTGTTCTTCACTCTCC
1847669 TAAGGTTAGATAAAAATTGTTCTTCACTCTCC
1 TAAGGTTAGATAAAAATTGTTCTTCACTCTCC
1847701 T
1 T
1847702 CTTTTCCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (32 bp):
TAAGGTTAGATAAAAATTGTTCTTCACTCTCC
Found at i:1849690 original size:19 final size:20
Alignment explanation
Indices: 1849649--1849699 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1849639 GAATCCCCTT
*
1849649 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1849669 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1849688 TGAAGATACATG
1 TGAAAATACATG
1849700 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1856811 original size:16 final size:16
Alignment explanation
Indices: 1856780--1856826 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
1856770 TGGTAATGAA
1856780 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAACG
*
1856797 AATAAAGAAATGAAACG
1 -ATAAAAAAATGAAACG
1856814 ATAAAAAAATGAA
1 ATAAAAAAATGAA
1856827 GATAACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.02, G:0.17, T:0.13
Consensus pattern (16 bp):
ATAAAAAAATGAAACG
Found at i:1858821 original size:23 final size:23
Alignment explanation
Indices: 1858795--1858858 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
1858785 CACATCAAGA
1858795 AGCCTTACATCAAGTGGTATCAG
1 AGCCTTACATCAAGTGGTATCAG
* *
1858818 AGCCATACATAAAGTGGTATCAG
1 AGCCTTACATCAAGTGGTATCAG
1858841 AGCCTTACATCAAGTGGT
1 AGCCTTACATCAAGTGGT
1858859 TTTATAACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (23 bp):
AGCCTTACATCAAGTGGTATCAG
Done.