Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007959.1 Hibiscus syriacus cultivar Beakdansim tig00110386_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: 1044826
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1023699 original size:4 final size:4
Alignment explanation
Indices: 1023690--1023775 Score: 54
Period size: 4 Copynumber: 20.2 Consensus size: 4
1023680 TCTTCTTCTT
1023690 TTTC TTTC TTTC TTTC TTTTC TTT- TCTT- TTTC TTTC TCTT- TTTCC
1 TTTC TTTC TTTC TTTC -TTTC TTTC T-TTC TTTC TTTC T-TTC TTT-C
*
1023735 TCTTC TTTC TTT- TTTC TCTATC TTTTGC TTTC TTTT TTTC T
1 T-TTC TTTC TTTC TTTC T-T-TC -TTT-C TTTC TTTC TTTC T
1023776 CTTTTCTCCC
Statistics
Matches: 68, Mismatches: 2, Indels: 24
0.72 0.02 0.26
Matches are distributed among these distances:
3 8 0.12
4 39 0.57
5 14 0.21
6 6 0.09
7 1 0.01
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:1023705 original size:24 final size:24
Alignment explanation
Indices: 1023678--1023775 Score: 89
Period size: 23 Copynumber: 4.2 Consensus size: 24
1023668 ATTTGTTTTA
1023678 TTTCTTCTTCTTTTTCTTTCTTTC
1 TTTCTTCTTCTTTTTCTTTCTTTC
*
1023702 TTTCTT-TTCTTTTCTTTTTCTTTC
1 TTTCTTCTTCTTTT-TCTTTCTTTC
* * *
1023726 --TCTTTTTCCTCTTCTTTCTTT-
1 TTTCTTCTTCTTTTTCTTTCTTTC
* *
1023747 TTTC-TCTATCTTTTGCTTTCTTTT
1 TTTCTTCT-TCTTTTTCTTTCTTTC
1023771 TTTCT
1 TTTCT
1023776 CTTTTCTCCC
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
22 14 0.24
23 26 0.44
24 19 0.32
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.74
Consensus pattern (24 bp):
TTTCTTCTTCTTTTTCTTTCTTTC
Found at i:1023708 original size:18 final size:18
Alignment explanation
Indices: 1023673--1023817 Score: 74
Period size: 19 Copynumber: 8.2 Consensus size: 18
1023663 GTTTAATTTG
*
1023673 TTTTATTTC-TTC-TTCT
1 TTTTCTTTCTTTCTTTCT
1023689 TTTTCTTTCTTTCTTTC-
1 TTTTCTTTCTTTCTTTCT
1023706 TTTTCTTT-TCTT-TTTCT
1 TTTTCTTTCT-TTCTTTCT
* *
1023723 TTCTC-TT-TTTC-CTCT
1 TTTTCTTTCTTTCTTTCT
1023738 TCTTTCTTT-TTTCTCTATCT
1 T-TTTCTTTCTTTCT-T-TCT
* *
1023758 TTTGCTTTCTTTTTTTCT
1 TTTTCTTTCTTTCTTTCT
** *
1023776 CTTTTCTCCCTTTTTTTCT
1 -TTTTCTTTCTTTCTTTCT
* *
1023795 CTTTCTCTTTTTTTGTTTCT
1 -TTT-TCTTTCTTTCTTTCT
1023815 TTT
1 TTT
1023818 ATGTGTTGTC
Statistics
Matches: 102, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
15 6 0.06
16 19 0.19
17 23 0.23
18 6 0.06
19 29 0.28
20 19 0.19
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.74
Consensus pattern (18 bp):
TTTTCTTTCTTTCTTTCT
Found at i:1023711 original size:29 final size:29
Alignment explanation
Indices: 1023678--1023816 Score: 103
Period size: 28 Copynumber: 4.8 Consensus size: 29
1023668 ATTTGTTTTA
1023678 TTTCTTCTTCTTTTTCTTTCTTTCTTTCT
1 TTTCTTCTTCTTTTTCTTTCTTTCTTTCT
1023707 TTTCTT-TTCTTTTTCTTTCTCTT-TTTCCT
1 TTTCTTCTTCTTTTTCTTTCT-TTCTTT-CT
* *
1023736 CTTCTTTCTT-TTTTCTCTATCTTTTGCTTTCT
1 TTTC-TTCTTCTTTT-TCTTTC-TTT-CTTTCT
* ** *
1023768 TTTTTTC-TC-TTTTCTCCCTTTTTTTCT
1 TTTCTTCTTCTTTTTCTTTCTTTCTTTCT
*
1023795 CTTTC-TCTT-TTTTTGTTTCTTT
1 -TTTCTTCTTCTTTTTCTTTCTTT
1023817 TATGTGTTGT
Statistics
Matches: 87, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
27 7 0.08
28 33 0.38
29 17 0.20
30 10 0.11
31 12 0.14
32 5 0.06
33 3 0.03
ACGTcount: A:0.01, C:0.24, G:0.01, T:0.74
Consensus pattern (29 bp):
TTTCTTCTTCTTTTTCTTTCTTTCTTTCT
Found at i:1023790 original size:41 final size:40
Alignment explanation
Indices: 1023699--1023778 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
1023689 TTTTCTTTCT
* *
1023699 TTCTTT-C-TTTTCTTTTCTTTTTCTTTCTCTTTTTCCTC
1 TTCTTTCCTTTTTCTTATCTTTTGCTTTCTCTTTTTCCTC
* *
1023737 TTCTTTCTTTTTTCTCTATCTTTTGCTTTCT-TTTTTTCTC
1 TTCTTTCCTTTTTCT-TATCTTTTGCTTTCTCTTTTTCCTC
1023777 TT
1 TT
1023779 TTCTCCCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 6 0.17
40 16 0.46
41 13 0.37
ACGTcount: A:0.01, C:0.24, G:0.01, T:0.74
Consensus pattern (40 bp):
TTCTTTCCTTTTTCTTATCTTTTGCTTTCTCTTTTTCCTC
Found at i:1024060 original size:2 final size:2
Alignment explanation
Indices: 1024053--1024086 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1024043 ACAACAAGGA
1024053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1024087 GAAATGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1027628 original size:15 final size:17
Alignment explanation
Indices: 1027608--1027639 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1027598 TAAAATAGGA
1027608 CTAAATT-AAA-AAAAT
1 CTAAATTGAAACAAAAT
1027623 CTAAATTGAAACAAAAT
1 CTAAATTGAAACAAAAT
1027640 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.62, C:0.09, G:0.03, T:0.25
Consensus pattern (17 bp):
CTAAATTGAAACAAAAT
Found at i:1030212 original size:30 final size:29
Alignment explanation
Indices: 1030108--1030212 Score: 77
Period size: 30 Copynumber: 3.4 Consensus size: 29
1030098 TTTTTAATTC
* * * *
1030108 AACCCATAAAATTATATAAAATGTTAATTT
1 AACCC-TAAATTTAGATAAAATATTCATTT
* * *
1030138 AACCACGAATTTTAGATGAAATA-TCATTTT
1 AACC-CTAAATTTAGATAAAATATTCA-TTT
*
1030168 CATCCCTAAAATTTAGATAAAATATTCATTT
1 -AACCCT-AAATTTAGATAAAATATTCATTT
1030199 AACCTCTAAATTTA
1 AACC-CTAAATTTA
1030213 ACCAAAATCT
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
29 2 0.04
30 29 0.51
31 23 0.40
32 3 0.05
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (29 bp):
AACCCTAAATTTAGATAAAATATTCATTT
Found at i:1035039 original size:20 final size:20
Alignment explanation
Indices: 1034996--1035347 Score: 383
Period size: 20 Copynumber: 17.4 Consensus size: 20
1034986 GATTCTGACT
*
1034996 ATCGCAACGAGTATCCGTTAA
1 ATCGCAACGCGTATCCG-TAA
1035017 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
1035037 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
1035057 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
1035077 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
1035098 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1035118 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
1035138 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1035158 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
1035178 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
1035198 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
1035219 ATCGCAACGCG-ATTCCGTAA
1 ATCGCAACGCGTA-TCCGTAA
*
1035239 ATCGCAACGCG-ATTACGTAA
1 ATCGCAACGCGTA-TCCGTAA
*
1035259 ATCGCAACGCG-ATTACGTAA
1 ATCGCAACGCGTA-TCCGTAA
* *
1035279 ATCGCAACGCGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
1035299 ATCGCAACGCG-ATTACGTAA
1 ATCGCAACGCGTA-TCCGTAA
* * *
1035319 ATCGCAATGCGAATCTGTAA
1 ATCGCAACGCGTATCCGTAA
1035339 ATCGCAACG
1 ATCGCAACG
1035348 AGATTCTGAC
Statistics
Matches: 290, Mismatches: 31, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.00
20 239 0.82
21 50 0.17
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:1035069 original size:40 final size:40
Alignment explanation
Indices: 1034954--1035347 Score: 462
Period size: 40 Copynumber: 9.8 Consensus size: 40
1034944 ATCGCAACGC
* ** *
1034954 AAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-T
1 AAATCGCAACGCGAATACGTAAATCGCAACGCGTATCCGT
* * * *
1034992 GACTATCGCAACGAGTATCCGTTAAATCGCAACGCGTATCCGT
1 -A-AATCGCAACGCGAATACG-TAAATCGCAACGCGTATCCGT
* *
1035035 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACGTAAATCGCAACGCGTATCCGT
*
1035075 AAATCGCAACGAC-AATACGTAAAATCGCAATGCGTATCCGT
1 AAATCGCAACG-CGAATACGT-AAATCGCAACGCGTATCCGT
* *
1035116 AAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGT
1 AAATCGCAACGCGAATACGTAAATCGCAACGCGTATCCGT
* *
1035156 AAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGTAAATCGCAACGCGTATCCGT
1035196 AAATCGCAACGAC-AATACGTAAAATCGCAACGCG-ATTCCGT
1 AAATCGCAACG-CGAATACGT-AAATCGCAACGCGTA-TCCGT
* *
1035237 AAATCGCAACGCGATTACGTAAATCGCAACGCG-ATTACGT
1 AAATCGCAACGCGAATACGTAAATCGCAACGCGTA-TCCGT
*
1035277 AAATCGCAACGCGAATACGTAAATCGCAACGCG-ATTACGT
1 AAATCGCAACGCGAATACGTAAATCGCAACGCGTA-TCCGT
*
1035317 AAATCGCAATGCGAAT-CTGTAAATCGCAACG
1 AAATCGCAACGCGAATAC-GTAAATCGCAACG
1035348 AGATTCTGAC
Statistics
Matches: 319, Mismatches: 24, Indels: 23
0.87 0.07 0.06
Matches are distributed among these distances:
39 2 0.01
40 210 0.66
41 102 0.32
42 4 0.01
43 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGAATACGTAAATCGCAACGCGTATCCGT
Found at i:1035177 original size:121 final size:121
Alignment explanation
Indices: 1034974--1035325 Score: 498
Period size: 121 Copynumber: 2.9 Consensus size: 121
1034964 GCGAACATAT
* * * * *
1034974 AAATCGCAACGCGATTCTG-ACTATCGCAACGAGTATCCGTTAAATCGCAACGCGTATCCGTAAA
1 AAATCGCAACGCGATTCCGTA-AATCGCAACGAGAATACG-TAAATCGCAACGCGTATCTGTAAA
* *
1035038 TCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
64 TCGCAACGCGAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
*
1035096 AAATCGCAATGCG-TATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAAT
1 AAATCGCAACGCGAT-TCCGTAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAAT
* *
1035160 CGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTA
65 CGCAACGCGAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
* *
1035217 AAATCGCAACGCGATTCCGTAAATCGCAACGCGATTACGTAAATCGCAACGCG-AT-TACGTAAA
1 AAATCGCAACGCGATTCCGTAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCT--GTAAA
*
1035280 TCGCAACGCGAATACGTAAATCGCAACGCG-ATTACGTAAATCGCAA
64 TCGCAACGCGAATACGTAAATCGCAACGCGTA-TCCGTAAATCGCAA
1035326 TGCGAATCTG
Statistics
Matches: 208, Mismatches: 16, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
119 1 0.00
120 3 0.01
121 172 0.83
122 31 0.15
123 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (121 bp):
AAATCGCAACGCGATTCCGTAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATC
GCAACGCGAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA
Found at i:1036231 original size:24 final size:24
Alignment explanation
Indices: 1036204--1036257 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1036194 GTATTTGAAA
1036204 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1036228 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1036252 TTTGAT
1 TTTGAT
1036258 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1039747 original size:42 final size:42
Alignment explanation
Indices: 1039668--1039760 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1039658 CATCTTCAAT
* * *
1039668 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
1039710 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
1039752 GATGACAGG
1 GATGACAGG
1039761 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1040261 original size:20 final size:20
Alignment explanation
Indices: 1040238--1040306 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
1040228 GAAACTTAAA
1040238 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1040258 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1040278 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
1040298 ATCGCAACG
1 ATCGCAACG
1040307 AGAGAATCGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1040363 original size:19 final size:19
Alignment explanation
Indices: 1040339--1040382 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1040329 AAATTGCAAC
1040339 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
1040358 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
1040377 GCGATT
1 GCGATT
1040383 CTCTCATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:1040411 original size:19 final size:17
Alignment explanation
Indices: 1040368--1040430 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
1040358 GCGATTTTGG
*
1040368 TTTCGCGTTGCGATTC-
1 TTTCTCGTTGCGATTCA
*
1040384 --TCTCATTGCGATTTTCA
1 TTTCTCGTTGCGA--TTCA
1040401 TTTCTCGTTGCGATTCA
1 TTTCTCGTTGCGATTCA
*
1040418 TTTCGCGTTGCGA
1 TTTCTCGTTGCGA
1040431 CAGTCATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
14 9 0.24
16 3 0.08
17 16 0.42
19 10 0.26
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (17 bp):
TTTCTCGTTGCGATTCA
Found at i:1040419 original size:17 final size:17
Alignment explanation
Indices: 1040349--1040430 Score: 62
Period size: 19 Copynumber: 4.8 Consensus size: 17
1040339 GCGATTATAG
**
1040349 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGA--TTCA
1040368 TTTCGCGTTGCGATTC-
1 TTTCGCGTTGCGATTCA
* *
1040384 --TCTCATTGCGATTTTCA
1 TTTCGCGTTGCGA--TTCA
*
1040401 TTTCTCGTTGCGATTCA
1 TTTCGCGTTGCGATTCA
1040418 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
1040431 CAGTCATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
14 9 0.17
16 3 0.06
17 18 0.34
19 23 0.43
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.45
Consensus pattern (17 bp):
TTTCGCGTTGCGATTCA
Found at i:1040688 original size:93 final size:94
Alignment explanation
Indices: 1040519--1040897 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
1040509 ATGGATTGCA
1040519 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
1040583 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1040612 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCA-CGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
*
1040676 TTAGCAGGATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1040705 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
*
1040770 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
1040799 TTAC-TTCAACCAAAAGACAAAATAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAA-CAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAG
* *
1040863 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1040893 TTACT
1 TTACT
1040898 AAGCAATCTA
Statistics
Matches: 273, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
93 113 0.41
94 160 0.59
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1040838 original size:187 final size:188
Alignment explanation
Indices: 1040519--1040897 Score: 674
Period size: 187 Copynumber: 2.0 Consensus size: 188
1040509 ATGGATTGCA
1040519 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
*
1040583 TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
66 TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAAAAAGACAAATAC
*
1040648 TAACTTCAC-GTGTTAAAGAATACACAGTTTAGCAGGATTGGCAGCAACCGAACAAAT
131 TAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGGATTGGCAGCAACCGAACAAAT
*
1040705 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
*
1040770 TTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAATAAAAGACAAATA
66 TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA-AAAAGACAAATA
* *
1040834 CTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATAAAT
130 CTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGGATTGGCAGCAACCGAACAAAT
1040893 TTACT
1 TTACT
1040898 AAGCAATCTA
Statistics
Matches: 184, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
186 22 0.12
187 112 0.61
188 50 0.27
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (188 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAAAAAGACAAATAC
TAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGGATTGGCAGCAACCGAACAAAT
Found at i:1042672 original size:33 final size:33
Alignment explanation
Indices: 1042622--1042749 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
1042612 GAGAATGACT
* ** *
1042622 ATCGCAATGCGGAAATGACTATCGCAATGGGAGA
1 ATCGCAACGC-GAAATGAAAATCGCAATGAGAGA
1042656 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
* * *
1042689 ATCGCAACGCGAAATTAAAATCGCAACGAGAAA
1 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
*
1042722 ATCTCAACGCGAAATGAAAATCGCAATG
1 ATCGCAACGCGAAATGAAAATCGCAATG
1042750 CGATTTTGGT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 75 0.89
34 9 0.11
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
Found at i:1042679 original size:19 final size:19
Alignment explanation
Indices: 1042655--1042752 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1042645 GCAATGGGAG
1042655 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
1042674 AATCGCAA--TG--A-GAG
1 AATCGCAACGCGAAATGAA
*
1042688 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATGAA
1042707 AATCGCAA--CG--A-GAA
1 AATCGCAACGCGAAATGAA
*
1042721 AATCTCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1042740 AATCGCAATGCGA
1 AATCGCAACGCGA
1042753 TTTTGGTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 31 0.52
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1042781 original size:19 final size:20
Alignment explanation
Indices: 1042759--1042869 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 20
1042749 GCGATTTTGG
*
1042759 TTTCGCGTTGCGATTTTCA-
1 TTTCACGTTGCGATTTTCAT
1042778 TTTCACGTTGCGA--TTC--
1 TTTCACGTTGCGATTTTCAT
*
1042794 --TCTCGTTGCGATTTTCAT
1 TTTCACGTTGCGATTTTCAT
* **
1042812 TTCTCTCGTTGCGATAGTCAT
1 TT-TCACGTTGCGATTTTCAT
**
1042833 TTTCGTGTTGCGATTTTCAT
1 TTTCACGTTGCGATTTTCAT
*
1042853 TTTCATGTTGCGATTTT
1 TTTCACGTTGCGATTTT
1042870 AAGTTTAGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 12 0.16
20 30 0.39
21 18 0.24
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.50
Consensus pattern (20 bp):
TTTCACGTTGCGATTTTCAT
Found at i:1043452 original size:20 final size:20
Alignment explanation
Indices: 1043427--1043599 Score: 186
Period size: 20 Copynumber: 8.6 Consensus size: 20
1043417 CTTTAAAAAT
1043427 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1043447 CGCGTTGCAATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1043467 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
1043488 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
1043508 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
1043528 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
1043548 CTCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1043568 CGCATTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1043589 CTCGTTGCGAT
1 CGCGTTGCGAT
1043600 AGTCAGAATC
Statistics
Matches: 122, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
20 88 0.72
21 34 0.28
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1043513 original size:40 final size:41
Alignment explanation
Indices: 1043429--1043599 Score: 256
Period size: 40 Copynumber: 4.2 Consensus size: 41
1043419 TTAAAAATCG
* * *
1043429 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
1043470 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
* *
1043510 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
* * *
1043550 CGTTGTGATTTACGGATACGCATTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
1043591 CGTTGCGAT
1 CGTTGCGAT
1043600 AGTCAGAATC
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 74 0.63
41 44 0.37
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
Found at i:1043583 original size:81 final size:80
Alignment explanation
Indices: 1043429--1043641 Score: 277
Period size: 81 Copynumber: 2.6 Consensus size: 80
1043419 TTAAAAATCG
* * *
1043429 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCATT
* *
1043494 GCGATTTACGTATTCT
65 GCGATTTACGGATACT
*
1043510 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGTGATTTACGGATACGCATTG
1 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTG
1043575 CGATTTTACGGATACT
66 CGA-TTTACGGATACT
* ** * *
1043591 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCGCGTTGCGATTT
1 CGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACGTATTCTCGTTGCGATTT
1043642 TCATATTCGC
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
80 39 0.33
81 77 0.66
82 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (80 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTG
CGATTTACGGATACT
Found at i:1043631 original size:20 final size:20
Alignment explanation
Indices: 1043608--1043660 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1043598 ATAGTCAGAA
*
1043608 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1043628 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1043648 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1043661 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1044475 original size:24 final size:25
Alignment explanation
Indices: 1044438--1044484 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1044428 GTCTAAGGTA
*
1044438 TATTTTATTATATTTTAA-TATTTTG
1 TATTTAATTATA-TTTAAGTATTTTG
1044463 TATTTAATT-TATTTAAGTATTT
1 TATTTAATTATATTTAAGTATTT
1044485 AATTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (25 bp):
TATTTAATTATATTTAAGTATTTTG
Found at i:1044477 original size:9 final size:9
Alignment explanation
Indices: 1044463--1044496 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1044453 TAATATTTTG
1044463 TATTTAATT
1 TATTTAATT
*
1044472 TATTTAA-G
1 TATTTAATT
1044480 TATTTAATT
1 TATTTAATT
1044489 TATTTAAT
1 TATTTAAT
1044497 ATTTTATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:1044502 original size:17 final size:17
Alignment explanation
Indices: 1044462--1044500 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1044452 TTAATATTTT
1044462 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1044479 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1044496 -TATTT
1 GTATTT
1044501 TATCTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Done.