Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007978.1 Hibiscus syriacus cultivar Beakdansim tig00110415_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: 1479011
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 7 of 7
Found at i:1430324 original size:20 final size:20
Alignment explanation
Indices: 1430274--1430329 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1430264 TCGCGTTGCG
*
1430274 ATTCTCTCGTTGCGATAGTT
1 ATTCTCTCGTTGCGATAGTC
*
1430294 ATT-TCCACGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
1430314 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
1430330 TTTCATTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:1430335 original size:20 final size:20
Alignment explanation
Indices: 1430274--1430336 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
1430264 TCGCGTTGCG
1430274 ATTCTCTCGTTGCGATAGTT-
1 ATTCTCTCGTTGCGATA-TTC
* *
1430294 ATT-TCCACGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATATTC
*
1430314 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATATTC
1430334 ATT
1 ATT
1430337 TCAACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 2 0.06
20 32 0.91
21 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATATTC
Found at i:1432223 original size:94 final size:95
Alignment explanation
Indices: 1432008--1432241 Score: 389
Period size: 95 Copynumber: 2.5 Consensus size: 95
1431998 TAGATTGCTT
* * * *
1432008 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
1432073 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
** * *
1432103 AGTAAATTTGTTTAGTTGCTGTCAATTCTGCTAAACTGTGTATTTTTTAACACTATGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
1432168 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
1432197 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC
1432242 ACGTTGCGAT
Statistics
Matches: 127, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
94 63 0.50
95 64 0.50
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (95 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
ATTTGTCTTTTGTTTTGTCTTTTGGTTGAA
Found at i:1434144 original size:14 final size:14
Alignment explanation
Indices: 1434125--1434160 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1434115 ATTGTTTAAT
1434125 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1434139 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1434153 TGATTTGT
1 TGATTTGT
1434161 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1434291 original size:19 final size:19
Alignment explanation
Indices: 1434267--1434351 Score: 92
Period size: 19 Copynumber: 4.7 Consensus size: 19
1434257 AAAAGTGACT
1434267 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1434286 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1434300 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1434319 ATCGCAATGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
* *
1434338 ATCACAACGCGAAA
1 ATCGCAATGCGAAA
1434352 CTAAATTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.70
20 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1434352 original size:19 final size:19
Alignment explanation
Indices: 1434316--1434356 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1434306 ATGCGAAATG
* *
1434316 AAAATCGCAATGCGAAACT
1 AAAATCACAACGCGAAACT
1434335 AAAATCACAACGCGAAACT
1 AAAATCACAACGCGAAACT
1434354 AAA
1 AAA
1434357 TTCGCGTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.22, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAATCACAACGCGAAACT
Found at i:1434473 original size:20 final size:19
Alignment explanation
Indices: 1434357--1434528 Score: 140
Period size: 19 Copynumber: 9.7 Consensus size: 19
1434347 CGAAACTAAA
1434357 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1434376 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1434391 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1434409 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1434424 -TCACGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1434442 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
1434461 TTCCGCGTTGCGATTTTCAT
1 TT-CGCGTTGCGATTTTCAT
1434481 ATTCGCGTTGCGATTTTCA-
1 -TTCGCGTTGCGATTTTCAT
1434500 ----CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1434515 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
1434529 CTCTCGTTGC
Statistics
Matches: 119, Mismatches: 17, Indels: 34
0.70 0.10 0.20
Matches are distributed among these distances:
14 31 0.26
16 6 0.05
17 6 0.05
19 44 0.37
20 30 0.25
21 2 0.02
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1434504 original size:106 final size:106
Alignment explanation
Indices: 1434359--1434568 Score: 314
Period size: 106 Copynumber: 2.0 Consensus size: 106
1434349 AAACTAAATT
* *
1434359 CGCGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTC
1 CGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCACGTTGCGATTTTCATTTCGCATTGCGATTC
** * *
1434424 TCACGTTGCGATTTTCATTT-CGCATTGCGATAGTCATTTC
66 TCACGTTGCGATAGTAATTTCCGCATTGCGATAGACATTTC
**
1434464 CGCGTTGCGATTTTCATATTCGCGTTGCGATTTTCACGTTGCGATTTTCATTTCGCATTGCGATT
1 CGCGTTGCGATTTTCAT-TTCGCGTTGCGATTCCCACGTTGCGATTTTCATTTCGCATTGCGATT
* *
1434529 CTCTCGTTGCGATAGTAATTTCCGCGTTGCGATAGACATT
65 CTCACGTTGCGATAGTAATTTCCGCATTGCGATAGACATT
1434569 AAGATGATTG
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
105 17 0.18
106 60 0.65
107 16 0.17
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.41
Consensus pattern (106 bp):
CGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCACGTTGCGATTTTCATTTCGCATTGCGATTC
TCACGTTGCGATAGTAATTTCCGCATTGCGATAGACATTTC
Found at i:1434505 original size:14 final size:14
Alignment explanation
Indices: 1434486--1434513 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1434476 TTCATATTCG
1434486 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1434500 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
1434514 TTTCGCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:1434512 original size:73 final size:66
Alignment explanation
Indices: 1434361--1434541 Score: 245
Period size: 73 Copynumber: 2.6 Consensus size: 66
1434351 ACTAAATTCG
* *
1434361 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCGCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1434426 A
66 A
*
1434427 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATTTTCATATTCGCGTTGC
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC----CCGCGTTGCGATTTTCAT-TTCGCATTGC
*
1434492 GATTTTCA
59 GATTCTCA
* *
1434500 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCGCGTTGCGAT
1434542 AGTAATTTCC
Statistics
Matches: 102, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
66 27 0.26
67 10 0.10
68 2 0.02
71 2 0.02
72 17 0.17
73 44 0.43
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCGCGTTGCGATTTTCATTTCGCATTGCGATTCTC
A
Found at i:1434550 original size:33 final size:33
Alignment explanation
Indices: 1434361--1434541 Score: 236
Period size: 33 Copynumber: 5.3 Consensus size: 33
1434351 ACTAAATTCG
* * *
1434361 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
1434394 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
*
1434427 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CA
* *
1434466 CGTTGCGATTTTCATATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCA
*
1434500 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
1434533 CGTTGCGAT
1 CGTTGCGAT
1434542 AGTAATTTCC
Statistics
Matches: 131, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
33 82 0.63
34 16 0.12
35 3 0.02
38 2 0.02
39 16 0.12
40 12 0.09
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCA
Found at i:1434607 original size:20 final size:20
Alignment explanation
Indices: 1434534--1434607 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
1434524 CGATTCTCTC
* *
1434534 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
1434554 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
1434574 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
1434595 GTTGCGATAGTCA
1 GTTGCGATAGTCA
1434608 AATGAATGTC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:1437111 original size:24 final size:24
Alignment explanation
Indices: 1437077--1437130 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1437067 CTGAAAAATA
1437077 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1437101 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1437125 ATCAAA
1 ATCAAA
1437131 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1437144 original size:24 final size:24
Alignment explanation
Indices: 1437077--1437144 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1437067 CTGAAAAATA
* * *
1437077 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1437101 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1437125 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1437145 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1438018 original size:20 final size:20
Alignment explanation
Indices: 1437995--1438033 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1437985 GAATCTCGTT
1437995 GCGATTTAC-TAAATCGCAAC
1 GCGA-TTACGTAAATCGCAAC
1438015 GCGATTACGTAAATCGCAA
1 GCGATTACGTAAATCGCAA
1438034 TGTGAATACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
GCGATTACGTAAATCGCAAC
Found at i:1438043 original size:20 final size:20
Alignment explanation
Indices: 1438004--1438064 Score: 79
Period size: 19 Copynumber: 3.1 Consensus size: 20
1437994 TGCGATTTAC
* * *
1438004 TAAATCGCAACGCGATTACG
1 TAAATCGCAATGTGAATACG
1438024 TAAATCGCAATGTGAATACG
1 TAAATCGCAATGTGAATACG
*
1438044 T-ATTCGCAATGTGAATACG
1 TAAATCGCAATGTGAATACG
1438063 TA
1 TA
1438065 TTCGCATTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (20 bp):
TAAATCGCAATGTGAATACG
Found at i:1438052 original size:19 final size:19
Alignment explanation
Indices: 1438028--1438070 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1438018 ATTACGTAAA
1438028 TCGCAATGTGAATACGTAT
1 TCGCAATGTGAATACGTAT
1438047 TCGCAATGTGAATACGTAT
1 TCGCAATGTGAATACGTAT
1438066 TCGCA
1 TCGCA
1438071 TTGCGATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (19 bp):
TCGCAATGTGAATACGTAT
Found at i:1438084 original size:20 final size:20
Alignment explanation
Indices: 1438040--1438116 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1438030 GCAATGTGAA
* * *
1438040 TACGTATTCGCAATGTGA-A
1 TACGTATTCGCATTGCGATT
1438059 TACGTATTCGCATTGCGATT
1 TACGTATTCGCATTGCGATT
* *
1438079 TACGTAATCGCGTTGCGATT
1 TACGTATTCGCATTGCGATT
1438099 TACGTATTCGCATTGCGA
1 TACGTATTCGCATTGCGA
1438117 ATTAGGAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 16 0.32
20 34 0.68
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
TACGTATTCGCATTGCGATT
Found at i:1438137 original size:21 final size:21
Alignment explanation
Indices: 1438113--1438158 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1438103 TATTCGCATT
1438113 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1438134 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1438155 GCGA
1 GCGA
1438159 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1440180 original size:18 final size:21
Alignment explanation
Indices: 1440143--1440180 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1440133 CATTTTATCC
1440143 ATTCAACTATAATTTGAAATA
1 ATTCAACTATAATTTGAAATA
1440164 ATTCAA-TA-AATTT-AAAT
1 ATTCAACTATAATTTGAAAT
1440181 CTTTACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 2 0.12
21 6 0.35
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (21 bp):
ATTCAACTATAATTTGAAATA
Found at i:1440685 original size:4 final size:4
Alignment explanation
Indices: 1440676--1440711 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
1440666 TAATAATAGT
1440676 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA -TTAA TTA
1440712 TATTTTTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:1443843 original size:21 final size:22
Alignment explanation
Indices: 1443805--1443845 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1443795 TTAGAAATTA
*
1443805 TAAAGGAAATATCGATACTCAT
1 TAAAGGAAATATCAATACTCAT
*
1443827 TAAAGG-AGTATCAATACTC
1 TAAAGGAAATATCAATACTC
1443846 TCAGTCCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (22 bp):
TAAAGGAAATATCAATACTCAT
Found at i:1445803 original size:11 final size:11
Alignment explanation
Indices: 1445766--1445803 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1445756 TTACATAATC
1445766 TAAAAATAAAA
1 TAAAAATAAAA
*
1445777 TATAAAA-AATA
1 TA-AAAATAAAA
1445788 TAAAAATAAAA
1 TAAAAATAAAA
1445799 TAAAA
1 TAAAA
1445804 TTATAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 4 0.17
11 15 0.65
12 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:1445944 original size:17 final size:16
Alignment explanation
Indices: 1445922--1445970 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
1445912 ATAATTTTGA
1445922 AATTTAAAATAAAATAT
1 AATTTAAAATAAAA-AT
*
1445939 AATTTAAAACAAAAAT
1 AATTTAAAATAAAAAT
*
1445955 AATAATAAAATAAAAA
1 AAT-TTAAAATAAAAA
1445971 AAGAATTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 5 0.18
17 23 0.82
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AATTTAAAATAAAAAT
Found at i:1449198 original size:5 final size:5
Alignment explanation
Indices: 1449179--1449217 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
1449169 GTCCGTCCGT
* * *
1449179 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1449218 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.03, C:0.41, G:0.33, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:1449226 original size:6 final size:6
Alignment explanation
Indices: 1449215--1449317 Score: 179
Period size: 6 Copynumber: 17.2 Consensus size: 6
1449205 TCGGCTCGGC
*
1449215 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* *
1449263 TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1449311 TCGTGG T
1 TCGTGG T
1449318 AATACGTGTC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 95 1.00
ACGTcount: A:0.03, C:0.17, G:0.50, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:1449620 original size:22 final size:22
Alignment explanation
Indices: 1449595--1449649 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1449585 TCAGGAGTTA
* *
1449595 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1449617 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1449639 CGGGAGTTATA
1 CAGGAGTTATA
1449650 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1455199 original size:5 final size:5
Alignment explanation
Indices: 1455180--1455218 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
1455170 GTCCGTCCGT
* * *
1455180 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1455219 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.03, C:0.41, G:0.33, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:1455227 original size:6 final size:6
Alignment explanation
Indices: 1455216--1455315 Score: 152
Period size: 6 Copynumber: 17.2 Consensus size: 6
1455206 TCGGCTCGGC
*
1455216 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* *
1455264 TCGAGG TCGAGG TC---G TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1455309 TCGTGG T
1 TCGTGG T
1455316 AATACGTGTC
Statistics
Matches: 90, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
3 3 0.03
6 87 0.97
ACGTcount: A:0.03, C:0.17, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:1455618 original size:22 final size:22
Alignment explanation
Indices: 1455593--1455647 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1455583 TCAGGAGTTA
* *
1455593 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1455615 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1455637 CGGGAGTTATA
1 CAGGAGTTATA
1455648 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1456499 original size:14 final size:14
Alignment explanation
Indices: 1456480--1456510 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1456470 AGTCAAATAC
*
1456480 ATTGGACAAAAGGA
1 ATTGGACAAAAGAA
1456494 ATTGGACAAAAGAA
1 ATTGGACAAAAGAA
1456508 ATT
1 ATT
1456511 TCTTGAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (14 bp):
ATTGGACAAAAGAA
Found at i:1458584 original size:25 final size:25
Alignment explanation
Indices: 1458556--1458620 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
1458546 GACGTGGCTT
1458556 TTTCTTCTTCTTCATTCTATTCTGC
1 TTTCTTCTTCTTCATTCTATTCTGC
* * * *
1458581 TTTCTTCTTATTCCTCCTCTTCTGC
1 TTTCTTCTTCTTCATTCTATTCTGC
1458606 TTT-TT-TTCTT-ATTCT
1 TTTCTTCTTCTTCATTCT
1458621 TCCTCCTTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 3 0.09
23 4 0.12
24 2 0.06
25 24 0.73
ACGTcount: A:0.06, C:0.28, G:0.03, T:0.63
Consensus pattern (25 bp):
TTTCTTCTTCTTCATTCTATTCTGC
Found at i:1463951 original size:14 final size:14
Alignment explanation
Indices: 1463932--1463959 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1463922 TGTTCGAAAT
1463932 GAACATAAATGAAC
1 GAACATAAATGAAC
1463946 GAACATAAATGAAC
1 GAACATAAATGAAC
1463960 ATATAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:1477155 original size:26 final size:27
Alignment explanation
Indices: 1477126--1477179 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
1477116 GTATTAAACG
1477126 TTTTTCAATGCAAA-TTTAGGTAATTA
1 TTTTTCAATGCAAAGTTTAGGTAATTA
* *
1477152 -TTTTCGATGTAAAGTTTAGGTAATTA
1 TTTTTCAATGCAAAGTTTAGGTAATTA
1477178 TT
1 TT
1477180 GTAAACCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.46
26 12 0.50
27 1 0.04
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (27 bp):
TTTTTCAATGCAAAGTTTAGGTAATTA
Found at i:1478713 original size:211 final size:213
Alignment explanation
Indices: 1478330--1478750 Score: 552
Period size: 209 Copynumber: 2.0 Consensus size: 213
1478320 AAAAAACTCG
* * *
1478330 AATAAAAGATAGATACGATCAGATCTAATCGCATCGGGAAACGAACCACGAAAGGGAATGAAACT
1 AATAAAAGATAGATACAAACAGATCTAATCGCATCGGCAAACGAACCACGAAAGGGAATGAAACT
* * *
1478395 ATTGAAAGGCGATTAAAAAATTACAAACCAAAATTAAGCAACGTGAAATACTATCAACGATCACA
66 ATTGAAA-GCGATTAAAAAATTACAAACAAAAATTAAGCAACGTAAAATACTATCAACAATCACA
* * *
1478460 AAATCGCGTATTCAAATCCAATATATGTCCAAAGCAAAGAAGA-A-CATGATAACAAAT-AAGTG
130 AAATCGAGTATTCAAATCCAATATATGTCCAAAACAAAGAAGACATCATGATAACAAATAAAATG
1478522 TCATCTTGATCAGTATAAA
195 TCATCTTGATCAGTATAAA
* * *
1478541 AATATAAAGATAGATACAAACAGATCTAATCGCATTGGCAAACGAGCCA-TAAAGAGG-ATGAAA
1 AATA-AAAGATAGATACAAACAGATCTAATCGCATCGGCAAACGAACCACGAAAG-GGAATGAAA
* * *
1478604 CTATTGAAA-CGATTGAAAAATTGCAAACAAAAATTAAGCAACGTAAAAATACTATCAACAATCG
64 CTATTGAAAGCGATTAAAAAATTACAAACAAAAATTAAGCAACGT-AAAATACTATCAACAATCA
* *
1478668 CAAAAT-TAGTATTTAAATCCAATCCA-ATAGTCCAAAACAAAGAAGATCATCATGATAACAAAT
128 CAAAATCGAGTATTCAAATCCAAT--ATAT-GTCCAAAACAAAGAAGA-CATCATGATAACAAAT
*
1478731 AAAATGTCATTTTGATCAGT
189 AAAATGTCATCTTGATCAGT
1478751 CATGACAATG
Statistics
Matches: 182, Mismatches: 18, Indels: 16
0.84 0.08 0.07
Matches are distributed among these distances:
209 46 0.25
210 24 0.13
211 40 0.22
212 41 0.23
213 1 0.01
214 13 0.07
215 17 0.09
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (213 bp):
AATAAAAGATAGATACAAACAGATCTAATCGCATCGGCAAACGAACCACGAAAGGGAATGAAACT
ATTGAAAGCGATTAAAAAATTACAAACAAAAATTAAGCAACGTAAAATACTATCAACAATCACAA
AATCGAGTATTCAAATCCAATATATGTCCAAAACAAAGAAGACATCATGATAACAAATAAAATGT
CATCTTGATCAGTATAAA
Done.