Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005036.1 Hibiscus syriacus cultivar Beakdansim tig00011305_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: 80907
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3961 original size:28 final size:28
Alignment explanation
Indices: 3928--4061 Score: 118
Period size: 28 Copynumber: 4.9 Consensus size: 28
3918 TCGTGGGGTT
3928 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* *
3956 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* * * ** **
3984 --TAA-ATTCACGTGCACTCA---CATTCA
1 CATAACA-GCATGTTCA-TCATTTGTTTTG
4008 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
*
4036 CATAACAACATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
4062 AGTTAATTCA
Statistics
Matches: 79, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
24 2 0.03
25 4 0.05
26 16 0.20
27 4 0.05
28 53 0.67
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:4028 original size:80 final size:79
Alignment explanation
Indices: 3928--4087 Score: 257
Period size: 80 Copynumber: 2.0 Consensus size: 79
3918 TCGTGGGGTT
* * *
3928 CATAACAGCATGTTCATCATTTGTTTTGCATAACAGCATATTTATCATTTGTTTTGTAAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
3993 GTGCACTCACATTCA
66 GTGCAC-CACATTCA
* *
4008 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATGTTCATCATTTGTTTAGTTAATTCAC
1 CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
*
4073 GTGCACCCCATTCA
66 GTGCACCACATTCA
4087 C
1 C
4088 TTTACAACAT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
79 8 0.11
80 66 0.89
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (79 bp):
CATAACAGCATGTTCATCATTTGTTTTGCATAACAACATATTCATCATTTGTTTAGTAAATTCAC
GTGCACCACATTCA
Found at i:5811 original size:19 final size:19
Alignment explanation
Indices: 5787--5823 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5777 CGGCCAAGAG
5787 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
*
5806 CATGTATTTTCATTAAAA
1 CATGTATCTTCATTAAAA
5824 AAATCATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:6410 original size:10 final size:10
Alignment explanation
Indices: 6378--6421 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
6368 TTGGTGCTGG
6378 AAACAAGATA
1 AAACAAGATA
*
6388 AAATAAGATTA
1 AAACAAGA-TA
6399 AAACAAGATA
1 AAACAAGATA
*
6409 AAGAAAAGATA
1 AA-ACAAGATA
6420 AA
1 AA
6422 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 11 0.38
11 18 0.62
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (10 bp):
AAACAAGATA
Found at i:6421 original size:21 final size:21
Alignment explanation
Indices: 6378--6418 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6368 TTGGTGCTGG
*
6378 AAACAAGATAAAATAAGATTA
1 AAACAAGATAAAAAAAGATTA
6399 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAA-AAAAGAT
6419 AAATGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (21 bp):
AAACAAGATAAAAAAAGATTA
Found at i:9981 original size:10 final size:10
Alignment explanation
Indices: 9968--10027 Score: 75
Period size: 10 Copynumber: 5.7 Consensus size: 10
9958 AAATTTTGGC
9968 TTTTTTGTTTT
1 TTTTTTG-TTT
9979 TTTTTTGTTT
1 TTTTTTGTTT
9989 TTTTTTGCCTTT
1 TTTTTTG--TTT
**
10001 TTTTTTCCTT
1 TTTTTTGTTT
10011 TTTTTTGTTT
1 TTTTTTGTTT
10021 TTTTTTG
1 TTTTTTG
10028 AAAAAATAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
10 27 0.63
11 7 0.16
12 9 0.21
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:10368 original size:11 final size:11
Alignment explanation
Indices: 10344--10388 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
10334 TTGATGTTGG
10344 AAACAAGATAA
1 AAACAAGATAA
* *
10355 AAATAAGATTA
1 AAACAAGATAA
10366 AAACAAGATAA
1 AAACAAGATAA
10377 AGAA-AAGATAA
1 A-AACAAGATAA
10388 A
1 A
10389 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:10372 original size:22 final size:22
Alignment explanation
Indices: 10344--10385 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
10334 TTGATGTTGG
10344 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
10366 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
10386 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:10911 original size:22 final size:23
Alignment explanation
Indices: 10870--10912 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
10860 CAACCTTAAT
10870 TCCTAATAAAATAATAAATCAGA
1 TCCTAATAAAATAATAAATCAGA
* *
10893 TCCTAA-AAGATAATTAATCA
1 TCCTAATAAAATAATAAATCA
10913 TCCTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (23 bp):
TCCTAATAAAATAATAAATCAGA
Found at i:13760 original size:33 final size:33
Alignment explanation
Indices: 13718--13786 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
13708 GTTGATGAAT
*
13718 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
13751 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
13784 GAA
1 GAA
13787 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:13791 original size:13 final size:12
Alignment explanation
Indices: 13772--13868 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
13762 TTATTGGCGT
13772 GATATGGTGATG
1 GATATGGTGATG
13784 GAATATGGTGAT-
1 G-ATATGGTGATG
*
13796 GATATAGGCG-T-
1 GATAT-GGTGATG
13807 GATAATGGTGATG
1 GAT-ATGGTGATG
13820 GACTATGGTGAT-
1 GA-TATGGTGATG
*
13832 GATATAGGCG-T-
1 GATAT-GGTGATG
*
13843 GATAATGGAGATG
1 GAT-ATGGTGATG
13856 GATTATGGTGATG
1 GA-TATGGTGATG
13869 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:13827 original size:36 final size:36
Alignment explanation
Indices: 13757--13869 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
13747 AATGGAAGGA
* *
13757 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
13792 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
13828 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
13864 TGATGA
1 TGATGA
13870 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:18308 original size:13 final size:12
Alignment explanation
Indices: 18289--18385 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
18279 TTATTGGCGT
18289 GATATGGTGATG
1 GATATGGTGATG
18301 GAATATGGTGAT-
1 G-ATATGGTGATG
*
18313 GATATAGGCG-T-
1 GATAT-GGTGATG
18324 GATAATGGTGATG
1 GAT-ATGGTGATG
18337 GACTATGGTGAT-
1 GA-TATGGTGATG
*
18349 GATATAGGCG-T-
1 GATAT-GGTGATG
*
18360 GATAATGGAGATG
1 GAT-ATGGTGATG
18373 GATTATGGTGATG
1 GA-TATGGTGATG
18386 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:18344 original size:36 final size:36
Alignment explanation
Indices: 18274--18386 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
18264 AATGGAAGGA
* *
18274 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
18309 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
18345 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
18381 TGATGA
1 TGATGA
18387 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:21895 original size:1 final size:1
Alignment explanation
Indices: 21891--21939 Score: 80
Period size: 1 Copynumber: 49.0 Consensus size: 1
21881 AAATTTTGGC
* *
21891 TTTTTTTTTGTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
21940 GAAAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (1 bp):
T
Found at i:21909 original size:22 final size:22
Alignment explanation
Indices: 21884--21931 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
21874 TTTTTTGAAA
21884 TTTTGGCTTTTTTTTTGTTTTT
1 TTTTGGCTTTTTTTTTGTTTTT
** *
21906 TTTTGTTTTTTTTTTTTTTTTT
1 TTTTGGCTTTTTTTTTGTTTTT
21928 TTTT
1 TTTT
21932 TTTTTTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (22 bp):
TTTTGGCTTTTTTTTTGTTTTT
Found at i:22279 original size:11 final size:11
Alignment explanation
Indices: 22255--22299 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
22245 TTGGTGCTGG
22255 AAACAAGATAA
1 AAACAAGATAA
* *
22266 AAATAAGATTA
1 AAACAAGATAA
22277 AAACAAGATAA
1 AAACAAGATAA
22288 AGAA-AAGATAA
1 A-AACAAGATAA
22299 A
1 A
22300 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:22283 original size:22 final size:22
Alignment explanation
Indices: 22255--22296 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
22245 TTGGTGCTGG
22255 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
22277 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
22297 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:26489 original size:18 final size:18
Alignment explanation
Indices: 26468--26503 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
26458 TTTTTTTAAA
26468 TTTTGGTATTTTTGTTTT
1 TTTTGGTATTTTTGTTTT
* *
26486 TTTTGTTTTTTTTGTTTT
1 TTTTGGTATTTTTGTTTT
26504 GCCTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.83
Consensus pattern (18 bp):
TTTTGGTATTTTTGTTTT
Found at i:26528 original size:20 final size:19
Alignment explanation
Indices: 26476--26542 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 19
26466 AATTTTGGTA
26476 TTTTTGTTTTTTTTG----
1 TTTTTGTTTTTTTTGCCTT
*
26491 TTTTT-TTTGTTTTGCCTT
1 TTTTTGTTTTTTTTGCCTT
26509 TTTTTGCCTTTTTTTT-CCTT
1 TTTTTG--TTTTTTTTGCCTT
26529 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
26543 TGAAAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
14 8 0.19
15 5 0.12
18 13 0.30
20 10 0.23
21 7 0.16
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (19 bp):
TTTTTGTTTTTTTTGCCTT
Found at i:26542 original size:9 final size:9
Alignment explanation
Indices: 26476--26503 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
26466 AATTTTGGTA
26476 TTTTTGTTT
1 TTTTTGTTT
26485 TTTTTGTTT
1 TTTTTGTTT
26494 TTTTTGTTT
1 TTTTTGTTT
26503 T
1 T
26504 GCCTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:26877 original size:11 final size:11
Alignment explanation
Indices: 26861--26905 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
26851 TTGGTGCTGG
26861 AAATAAGATAA
1 AAATAAGATAA
*
26872 AAATAAGATTA
1 AAATAAGATAA
*
26883 AAACAAGATAA
1 AAATAAGATAA
26894 AGAA-AAGATAA
1 A-AATAAGATAA
26905 A
1 A
26906 TGAATTGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (11 bp):
AAATAAGATAA
Found at i:28239 original size:17 final size:18
Alignment explanation
Indices: 28219--28260 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
28209 AAGAAACAAA
28219 AAGAGAAAAAAT-GAAAG
1 AAGAGAAAAAATAGAAAG
*
28236 AAGAAAAAAAATAGAAAG
1 AAGAGAAAAAATAGAAAG
*
28254 AAAAGAA
1 AAGAGAA
28261 TCCTACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (18 bp):
AAGAGAAAAAATAGAAAG
Found at i:28500 original size:17 final size:17
Alignment explanation
Indices: 28449--28503 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
28439 GTAAGTTATC
* *
28449 TTCACTTTC-TTACTAT
1 TTCATTTTCTTTAGTAT
*
28465 TTCA-TTTCTTTAGTCT
1 TTCATTTTCTTTAGTAT
* *
28481 TTCATTTTTTTTATTAT
1 TTCATTTTCTTTAGTAT
28498 TTCATT
1 TTCATT
28504 ACCATATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 4 0.12
16 13 0.41
17 15 0.47
ACGTcount: A:0.16, C:0.16, G:0.02, T:0.65
Consensus pattern (17 bp):
TTCATTTTCTTTAGTAT
Found at i:30573 original size:19 final size:19
Alignment explanation
Indices: 30549--30586 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30539 ATCACTTACT
*
30549 TGCATACTATATGATTTCA
1 TGCATACCATATGATTTCA
*
30568 TGCATACCATATGTTTTCA
1 TGCATACCATATGATTTCA
30587 CATCTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (19 bp):
TGCATACCATATGATTTCA
Found at i:34385 original size:19 final size:21
Alignment explanation
Indices: 34361--34412 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
34351 CGGCCAAGAG
* *
34361 CATGTATCTTCA-TTACAA-T
1 CATGTATTTTCATTTAAAAGT
34380 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
34401 CATGTATTTTCA
1 CATGTATTTTCA
34413 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 5 0.17
21 13 0.45
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:39849 original size:13 final size:13
Alignment explanation
Indices: 39831--39899 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
39821 AGATACTAAA
*
39831 CATCACCATCTTC
1 CATCACCATATTC
*
39844 CATCACCAT-TTT
1 CATCACCATATTC
* **
39856 CA-CGCC-TATAA
1 CATCACCATATTC
*
39867 CATCACCATCTTC
1 CATCACCATATTC
*
39880 CATCACCATAGTC
1 CATCACCATATTC
39893 CATCACC
1 CATCACC
39900 TTCACGCCAG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.14
12 7 0.16
13 29 0.67
ACGTcount: A:0.28, C:0.42, G:0.03, T:0.28
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:43055 original size:13 final size:13
Alignment explanation
Indices: 43037--43105 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
43027 AGATACTAAA
*
43037 CATCACCATCTTC
1 CATCACCATATTC
*
43050 CATCACCAT-TTT
1 CATCACCATATTC
* **
43062 CAT-GCC-TATAA
1 CATCACCATATTC
*
43073 CATCACCATCTTC
1 CATCACCATATTC
*
43086 CATCACCATAGTC
1 CATCACCATATTC
43099 CATCACC
1 CATCACC
43106 TTCACGCCAG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.14
12 7 0.16
13 29 0.67
ACGTcount: A:0.28, C:0.41, G:0.03, T:0.29
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:46369 original size:15 final size:15
Alignment explanation
Indices: 46351--46416 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 15
46341 CATTTCTATC
*
46351 CATTTCCTTTCTTAT
1 CATTTCCTATCTTAT
*
46366 CATTTCC-ATTCTTTTT
1 CATTTCCTA-TC-TTAT
46382 CCATTTCCTAT-TTAT
1 -CATTTCCTATCTTAT
46397 -ATTTCC-ATCTTAAT
1 CATTTCCTATCTT-AT
46411 CATTTC
1 CATTTC
46417 TCTCTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
12 2 0.05
13 8 0.20
14 2 0.05
15 17 0.41
16 3 0.07
17 8 0.20
18 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (15 bp):
CATTTCCTATCTTAT
Found at i:49987 original size:19 final size:20
Alignment explanation
Indices: 49963--50007 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
49953 CGACCAAGAG
49963 CATGTAACTTCATTAAA-AT
1 CATGTAACTTCATTAAATAT
**
49982 CATGTATTTTCATTAAATAT
1 CATGTAACTTCATTAAATAT
50002 CATGTA
1 CATGTA
50008 TTTTCAAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (20 bp):
CATGTAACTTCATTAAATAT
Found at i:50005 original size:20 final size:19
Alignment explanation
Indices: 49971--50013 Score: 77
Period size: 20 Copynumber: 2.2 Consensus size: 19
49961 AGCATGTAAC
49971 TTCATTAAAATCATGTATT
1 TTCATTAAAATCATGTATT
49990 TTCATTAAATATCATGTATT
1 TTCATTAAA-ATCATGTATT
50010 TTCA
1 TTCA
50014 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:50431 original size:33 final size:34
Alignment explanation
Indices: 50354--50419 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 34
50344 ACTACCTAAG
*
50354 CATCACCATCTTCCATCACCATTTTCACGCCTATAA
1 CATCACCATCTTCCATCACC--TTTCACGCCAATAA
50390 CATCACCATCTTCCATCACC-TTCACGCCAA
1 CATCACCATCTTCCATCACCTTTCACGCCAA
50420 CTCCATTACC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 9 0.31
36 20 0.69
ACGTcount: A:0.27, C:0.42, G:0.03, T:0.27
Consensus pattern (34 bp):
CATCACCATCTTCCATCACCTTTCACGCCAATAA
Found at i:50854 original size:23 final size:22
Alignment explanation
Indices: 50828--50874 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
50818 CAAAAGTAAC
50828 AAAAAGAGAAAA-AAAAAACAAGA
1 AAAAAGA-AAAATAAAAAAC-AGA
*
50851 AAAAATAAAAATAAAAAACAGA
1 AAAAAGAAAAATAAAAAACAGA
50873 AA
1 AA
50875 GAAAAGACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.83, C:0.04, G:0.09, T:0.04
Consensus pattern (22 bp):
AAAAAGAAAAATAAAAAACAGA
Found at i:50932 original size:7 final size:6
Alignment explanation
Indices: 50910--50943 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
50900 AGTGCAAAAG
*
50910 AAAGAA AAAGAA AAAGAA TAAAGAA AAACAA AAA
1 AAAGAA AAAGAA AAAGAA -AAAGAA AAAGAA AAA
50944 TTCAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:50934 original size:13 final size:12
Alignment explanation
Indices: 50910--50943 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
50900 AGTGCAAAAG
50910 AAAGAAAAAGAA
1 AAAGAAAAAGAA
50922 AAAGAATAAAGAA
1 AAAGAA-AAAGAA
*
50935 AAACAAAAA
1 AAAGAAAAA
50944 TTCAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAGAAAAAGAA
Found at i:51972 original size:21 final size:22
Alignment explanation
Indices: 51934--51986 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
51924 AATATTCAAA
*
51934 TGAAGAAAAGCTTTTTTGAAGT
1 TGAACAAAAGCTTTTTTGAAGT
51956 TGAACAAAAGC-TTTTTGAAGT
1 TGAACAAAAGCTTTTTTGAAGT
51977 TGAACAAAAG
1 TGAACAAAAG
51987 AGAGTGGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 20 0.67
22 10 0.33
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.30
Consensus pattern (22 bp):
TGAACAAAAGCTTTTTTGAAGT
Found at i:52837 original size:19 final size:20
Alignment explanation
Indices: 52796--52846 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
52786 GAAACCCCTT
*
52796 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
52816 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
52835 TGAAGATACATG
1 TGAAAATACATG
52847 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:57012 original size:19 final size:20
Alignment explanation
Indices: 56971--57021 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
56961 GAAACCCCTT
*
56971 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
56991 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
57010 TGAAGATACATG
1 TGAAAATACATG
57022 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:59379 original size:37 final size:37
Alignment explanation
Indices: 59336--59411 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
59326 CATATCATGG
59336 CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
1 CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
59373 CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
1 CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
59410 CA
1 CA
59412 TGCTATGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (37 bp):
CAGCATGTATCATTCATTTATTAGCCCATGTCATGTT
Found at i:59930 original size:15 final size:16
Alignment explanation
Indices: 59912--59943 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
59902 TTAGAAGACC
59912 AAAGCTAACTAG-TTG
1 AAAGCTAACTAGCTTG
59927 AAAGCTAACTAGCTTG
1 AAAGCTAACTAGCTTG
59943 A
1 A
59944 GTTCATCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (16 bp):
AAAGCTAACTAGCTTG
Found at i:61197 original size:25 final size:25
Alignment explanation
Indices: 61145--61193 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
61135 AGAAAAAGGT
*
61145 TAAGAAAGATGATAAGATAATGGAA
1 TAAGAAAGATGATAAGATAAAGGAA
61170 TAAGAAAAGATGA-AAGA-AAAGGAA
1 TAAG-AAAGATGATAAGATAAAGGAA
61194 ATAAAATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 8 0.36
26 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.14
Consensus pattern (25 bp):
TAAGAAAGATGATAAGATAAAGGAA
Found at i:68919 original size:19 final size:20
Alignment explanation
Indices: 68897--68939 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
68887 AGCATGTATC
68897 TTCATT-AAAATCATGAATT
1 TTCATTAAAAATCATGAATT
*
68916 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGAATT
68936 TTCA
1 TTCA
68940 AAGGGGTTTC
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:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (20 bp):
TTCATTAAAAATCATGAATT
Found at i:69297 original size:13 final size:13
Alignment explanation
Indices: 69279--69347 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
69269 ACTACCTAAA
*
69279 CATCACCATCTTC
1 CATCACCATATTC
*
69292 CATCACCAT-TTT
1 CATCACCATATTC
* **
69304 CA-CGCC-TATAA
1 CATCACCATATTC
*
69315 CATCACCATCTTC
1 CATCACCATATTC
*
69328 CATCACCATAGTC
1 CATCACCATATTC
69341 CATCACC
1 CATCACC
69348 TTCACTTCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
10 1 0.02
11 6 0.14
12 7 0.16
13 29 0.67
ACGTcount: A:0.28, C:0.42, G:0.03, T:0.28
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:70256 original size:19 final size:19
Alignment explanation
Indices: 70232--70281 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
70222 GAAACCCCTT
*
70232 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
70251 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
70270 TGAAGATACATG
1 TGAAAATACATG
70282 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:74402 original size:19 final size:20
Alignment explanation
Indices: 74361--74411 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
74351 GAAACCCCTT
*
74361 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
74381 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
74400 TGAAGATACATG
1 TGAAAATACATG
74412 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:78505 original size:18 final size:20
Alignment explanation
Indices: 78465--78514 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
78455 GAAACCCCTT
*
78465 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
78485 TGAAAA-ACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
78503 TGAAGATACATG
1 TGAAAATACATG
78515 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 10 0.37
19 11 0.41
20 6 0.22
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Done.