Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005767.1 Hibiscus syriacus cultivar Beakdansim tig00013501_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: 207275
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6074 original size:13 final size:11
Alignment explanation
Indices: 6033--6117 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
6023 ACAATCTGTC
6033 CATCACCATTAT
1 CATCACCA-TAT
*
6045 CA-CGCCTATAT
1 CATCACC-ATAT
6056 CATCACCATAGT
1 CATCACCATA-T
6068 CCATCACCATTAT
1 -CATCACCA-TAT
*
6081 CA-CGCCTATAT
1 CATCACC-ATAT
6092 CATCACCATATT
1 CATCACCATA-T
6104 CCATCACCATAT
1 -CATCACCATAT
6116 CA
1 CA
6118 CGCATATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6077 original size:36 final size:36
Alignment explanation
Indices: 6030--6134 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
6020 GATACAATCT
6030 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6066 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6102 TTCCATCACCA-TATCACGCATATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6135 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6539 original size:17 final size:19
Alignment explanation
Indices: 6506--6549 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
6496 AAAGTGCTGC
*
6506 AAGAA-AAAGCAACAAGA-
1 AAGAAGAAAACAACAAGAG
6523 AAGAAGAAAACAA-AAGAG
1 AAGAAGAAAACAACAAGAG
6541 AA-AAGAAAA
1 AAGAAGAAAA
6550 AGACTCCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAACAACAAGAG
Found at i:9790 original size:13 final size:11
Alignment explanation
Indices: 9749--9833 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
9739 ATAATCTGTC
9749 CATCACCATTAT
1 CATCACCA-TAT
*
9761 CATGC-CTATAT
1 CAT-CACCATAT
9772 CATCACCATAGT
1 CATCACCATA-T
9784 CCATCACCATTAT
1 -CATCACCA-TAT
*
9797 CATGC-CTATAT
1 CAT-CACCATAT
9808 CATCACCATATT
1 CATCACCATA-T
9820 CCATCACCATAT
1 -CATCACCATAT
9832 CA
1 CA
9834 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 2 0.03
11 22 0.37
12 13 0.22
13 21 0.35
14 2 0.03
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.31
Consensus pattern (11 bp):
CATCACCATAT
Found at i:9793 original size:36 final size:36
Alignment explanation
Indices: 9746--9850 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
9736 GATATAATCT
9746 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCATGCCTATATCATCACCATA
9782 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCATGCCTATATCATCACCATA
* * *
9818 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCATGCCTATATCATCACCA
9851 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.34, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCATGCCTATATCATCACCATA
Found at i:16876 original size:91 final size:91
Alignment explanation
Indices: 16721--16903 Score: 303
Period size: 91 Copynumber: 2.0 Consensus size: 91
16711 CCTAGAACAC
* *
16721 CCATGTGCCTTGCATGTGACCAGCCCCCATGTGCCTTGTATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATGTGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
16786 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * *
16812 CCATGTGTTTTGCATGTGATCATCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATGTGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
16877 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
16903 C
1 C
16904 ATCAACTACC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATGTGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:20331 original size:91 final size:91
Alignment explanation
Indices: 20176--20358 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 91
20166 CCTAGAACAC
* *
20176 CCATGTGCCTTGCATTTGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATGTGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
*
20241 AAGAGTTCTCTCCCTATTCGTCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
** * * * * *
20267 CCATGTGTTTTGCATGTGATCATCCCCTATGTGCCTTGTATGTGGTTCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATGTGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
20332 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGGCCAAG
20358 C
1 C
20359 ATCAACTACC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (91 bp):
CCATGTGCCTTGCATGTGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
AAGAGTTCTCTCCCTATTCGGCCAAG
Found at i:35129 original size:19 final size:20
Alignment explanation
Indices: 35088--35138 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
35078 GAAACCCCTT
*
35088 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
35108 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
35127 TGAAGATACATG
1 TGAAAATACATG
35139 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:39180 original size:19 final size:20
Alignment explanation
Indices: 39139--39189 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
39129 GAAACCCCTT
*
39139 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
39159 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
39178 TGAAGATACATG
1 TGAAAATACATG
39190 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:43338 original size:16 final size:16
Alignment explanation
Indices: 43317--43351 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
43307 TTTGATAACA
43317 TTTTC-TATCCATTTCC
1 TTTTCTTAT-CATTTCC
43333 TTTTCTTATCATTTCC
1 TTTTCTTATCATTTCC
43349 TTT
1 TTT
43352 CTTCTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTCTTATCATTTCC
Found at i:49685 original size:19 final size:20
Alignment explanation
Indices: 49661--49711 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
49651 CGGCCAAGAG
* *
49661 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
49680 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
49700 CATGTATTTTCA
1 CATGTATTTTCA
49712 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:50148 original size:23 final size:22
Alignment explanation
Indices: 50121--50170 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
50111 CTCTATTTTT
*
50121 TTATTTA-TTTCATTTCATTATTA
1 TTATTTATTTTCATTAC-TTA-TA
50144 TTATTTATTTTCATTACTTATA
1 TTATTTATTTTCATTACTTATA
50166 TTATT
1 TTATT
50171 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:53880 original size:19 final size:20
Alignment explanation
Indices: 53856--53906 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
53846 CGGCCAAGAG
* *
53856 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
53875 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
53895 CATGTATTTTCA
1 CATGTATTTTCA
53907 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:54344 original size:23 final size:22
Alignment explanation
Indices: 54317--54366 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
54307 TCTATTTTTT
*
54317 TTATTTA-TTTCATTTCATTATTA
1 TTATTTATTTTCATTAC-TTA-TA
54340 TTATTTATTTTCATTACTTATA
1 TTATTTATTTTCATTACTTATA
54362 TTATT
1 TTATT
54367 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:55876 original size:11 final size:13
Alignment explanation
Indices: 55844--55869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55834 TGGAAAAAGA
55844 TGAAAAGGTATGT
1 TGAAAAGGTATGT
55857 TGAAAAGGTATGT
1 TGAAAAGGTATGT
55870 AAAAGGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:65221 original size:14 final size:14
Alignment explanation
Indices: 65202--65230 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
65192 AGCATGCTTA
65202 ATCATTCATTTGTT
1 ATCATTCATTTGTT
65216 ATCATTCATTTGTT
1 ATCATTCATTTGTT
65230 A
1 A
65231 GCTCATATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (14 bp):
ATCATTCATTTGTT
Found at i:65253 original size:20 final size:22
Alignment explanation
Indices: 65218--65257 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
65208 CATTTGTTAT
65218 CATTCATTTGTTAGCTCATATG
1 CATTCATTTGTTAGCTCATATG
65240 CATTCA-TT-TTAGCTCATA
1 CATTCATTTGTTAGCTCATA
65258 GGTCTTACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (22 bp):
CATTCATTTGTTAGCTCATATG
Found at i:66781 original size:23 final size:25
Alignment explanation
Indices: 66755--66809 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
66745 AAATCCAGCA
66755 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
66778 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
66803 AAGAAAA
1 AAGAAAA
66810 AGAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:79843 original size:16 final size:15
Alignment explanation
Indices: 79787--79843 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
79777 AAGATATGGT
*
79787 AATGAAATAAGAAAA
1 AATGAAATAATAAAA
* *
79802 GATGAAAGAATAAAGA
1 AATGAAATAATAAA-A
79818 AATGAAATAATAAAA
1 AATGAAATAATAAAA
79833 AATGAAGATAA
1 AATGAA-ATAA
79844 CTTACAACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 18 0.51
16 17 0.49
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (15 bp):
AATGAAATAATAAAA
Found at i:80476 original size:13 final size:12
Alignment explanation
Indices: 80456--80520 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
80446 ATATAGGTGT
80456 GATATGGTGATG
1 GATATGGTGATG
80468 GACTATGGTGAT-
1 GA-TATGGTGATG
*
80480 GATATAGGCG-T-
1 GATAT-GGTGATG
80491 GATAATGGTGATG
1 GAT-ATGGTGATG
80504 GAATATGGTGAT-
1 G-ATATGGTGATG
80516 GATAT
1 GATAT
80521 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 11 0.24
13 18 0.40
14 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:80511 original size:36 final size:36
Alignment explanation
Indices: 80438--80541 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
80428 ATTTAGAAGT
* * *
80438 TGGTGATAATATAGGTGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
80473 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
80509 TGGTGATGATATAGGCGTGATAATGATGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
80542 CAGATTGTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:85544 original size:16 final size:15
Alignment explanation
Indices: 85488--85544 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
85478 AAGATATGGT
*
85488 AATGAAATAAGAAAA
1 AATGAAATAATAAAA
* *
85503 GATGAAAGAATAAAGA
1 AATGAAATAATAAA-A
85519 AATGAAATAATAAAA
1 AATGAAATAATAAAA
85534 AATGAAGATAA
1 AATGAA-ATAA
85545 CTTACAACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 18 0.51
16 17 0.49
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (15 bp):
AATGAAATAATAAAA
Found at i:86179 original size:13 final size:12
Alignment explanation
Indices: 86159--86223 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
86149 ATATAGGCGT
86159 GATATGGTGATG
1 GATATGGTGATG
86171 GACTATGGTGAT-
1 GA-TATGGTGATG
*
86183 GATATAGGCG-T-
1 GATAT-GGTGATG
86194 GATAATGGTGATG
1 GAT-ATGGTGATG
86207 GAATATGGTGAT-
1 G-ATATGGTGATG
86219 GATAT
1 GATAT
86224 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 11 0.24
13 18 0.40
14 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:86214 original size:36 final size:36
Alignment explanation
Indices: 86141--86244 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
86131 ATTTAGAAGT
* *
86141 TGGTGATAATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
86176 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
86212 TGGTGATGATATAGGCGTGATAATGATGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
86245 CAGATTGTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:92456 original size:19 final size:21
Alignment explanation
Indices: 92432--92476 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
92422 TCTTTTTTAT
92432 TTATTTCA-TTTCATTA-T-TA
1 TTATTT-ATTTTCATTACTATA
92451 TTATTTATTTTCATTACTATA
1 TTATTTATTTTCATTACTATA
92472 TTATT
1 TTATT
92477 ACCCTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.04
19 14 0.61
20 1 0.04
21 7 0.30
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTTATTTTCATTACTATA
Found at i:92473 original size:24 final size:23
Alignment explanation
Indices: 92428--92477 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
92418 TCTATCTTTT
*
92428 TTATTTATTTCATTTCATTATTA
1 TTATTTATTTCATTACATTATTA
92451 TTATTTATTTTCATTAC-TATATTA
1 TTATTTA-TTTCATTACAT-TATTA
92475 TTA
1 TTA
92478 CCCTTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATTTATTTCATTACATTATTA
Found at i:92760 original size:18 final size:18
Alignment explanation
Indices: 92737--92789 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
92727 AATTGGAGTG
92737 CAAAAAG-AAAGAAAACGA
1 CAAAAAGAAAAGAAAA-GA
92755 CAAAAAGAAGAAGAAAAGA
1 CAAAAAGAA-AAGAAAAGA
92774 -AGAAAAGAAAAGAAAA
1 CA-AAAAGAAAAGAAAA
92790 AGAATTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 15 0.47
19 10 0.31
20 7 0.22
ACGTcount: A:0.75, C:0.06, G:0.19, T:0.00
Consensus pattern (18 bp):
CAAAAAGAAAAGAAAAGA
Found at i:98060 original size:23 final size:22
Alignment explanation
Indices: 98033--98082 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
98023 TCTATCTTTT
*
98033 TTATTTA-TTTCATTTCATTATTA
1 TTATTTATTTTCATTAC-TTA-TA
98056 TTATTTATTTTCATTACTTATA
1 TTATTTATTTTCATTACTTATA
98078 TTATT
1 TTATT
98083 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:99564 original size:76 final size:76
Alignment explanation
Indices: 99438--99594 Score: 269
Period size: 76 Copynumber: 2.1 Consensus size: 76
99428 GGGTGGTATG
* * *
99438 AAGTACTTTGACCCACTAGTTATAAAAAATTAGGAACTAGAAGTATCAAGGTGAAAAGAGAAGGG
1 AAGTACTTTGACCCACTAGCTATAAAAAACTAGGAACCAGAAGTATCAAGGTGAAAAGAGAAGGG
*
99503 GTTGATGCCAC
66 GTTGACGCCAC
99514 AAGTACTTTGACCCACTAGCTATAAAAAACTAGGAACCAGAAGTATCAAGGTGAAAAGAGAAGGG
1 AAGTACTTTGACCCACTAGCTATAAAAAACTAGGAACCAGAAGTATCAAGGTGAAAAGAGAAGGG
*
99579 GTTGACGCCAT
66 GTTGACGCCAC
99590 AAGTA
1 AAGTA
99595 TAAATTATAC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (76 bp):
AAGTACTTTGACCCACTAGCTATAAAAAACTAGGAACCAGAAGTATCAAGGTGAAAAGAGAAGGG
GTTGACGCCAC
Found at i:100892 original size:11 final size:11
Alignment explanation
Indices: 100870--100936 Score: 66
Period size: 11 Copynumber: 5.8 Consensus size: 11
100860 AAATGGAATT
100870 TGGTGATGATA
1 TGGTGATGATA
100881 TAGGTG-TGATA
1 T-GGTGATGATA
100892 TGGTGATGGACTA
1 TGGTGAT-GA-TA
100905 TGGTGATGATA
1 TGGTGATGATA
*
100916 TAGGCG-TGATAA
1 T-GGTGATGAT-A
100928 TGGTGATGA
1 TGGTGATGA
100937 AAGATGGTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 4 0.09
11 18 0.38
12 16 0.34
13 9 0.19
ACGTcount: A:0.27, C:0.03, G:0.37, T:0.33
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:100895 original size:22 final size:24
Alignment explanation
Indices: 100870--100916 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
100860 AAATGGAATT
100870 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
100892 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
100916 T
1 T
100917 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:100909 original size:35 final size:36
Alignment explanation
Indices: 100870--100949 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 36
100860 AAATGGAATT
* * **
100870 TGGTGATGATATAGGTGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGAAAGA
100905 TGGTGATGATATAGGCGTGATAATGGTGATGAAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGAAAGA
100941 TGGTGATGA
1 TGGTGATGA
100950 ACATATTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 20 0.50
36 20 0.50
ACGTcount: A:0.29, C:0.03, G:0.38, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGAAAGA
Found at i:109625 original size:33 final size:33
Alignment explanation
Indices: 109583--109651 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
109573 GTTGATGAAT
*
109583 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGAG-TGAAATGGTAATG
* * *
109616 GAAGGATGATGTTATTGGAGTGATATGGTGATG
1 GAAGGATGATGTTAATGGAGTGAAATGGTAATG
109649 GAA
1 GAA
109652 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:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGAGTGAAATGGTAATG
Found at i:109656 original size:13 final size:12
Alignment explanation
Indices: 109637--109701 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
109627 TTATTGGAGT
109637 GATATGGTGATG
1 GATATGGTGATG
109649 GAATATGGTGAT-
1 G-ATATGGTGATG
*
109661 GATATAGGCG-T-
1 GATAT-GGTGATG
109672 GATAATGGTGATG
1 GAT-ATGGTGATG
109685 GACTATGGTGAT-
1 GA-TATGGTGATG
109697 GATAT
1 GATAT
109702 AGGAGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:109686 original size:36 final size:36
Alignment explanation
Indices: 109622--109734 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
109612 AATGGAAGGA
* *
109622 TGATGTTATTGGAGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGAGTGATAATGGTGATGGAATATGG
* *
109657 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGAGTGATAATGGTGATGGAATATGG
* * *
109693 TGATGATATAGGAGTGATAATTGAGATGGATTATGG
1 TGATGATATAGGAGTGATAATGGTGATGGAATATGG
109729 TGATGA
1 TGATGA
109735 AAATAGTATC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 15 0.22
36 54 0.78
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGAGTGATAATGGTGATGGAATATGG
Found at i:114857 original size:25 final size:23
Alignment explanation
Indices: 114811--114858 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
114801 TGTAGGAGTC
* *
114811 TTTTTCTTTTCTTTTTGTTTTTT
1 TTTTTCTTTTCTTGTTGCTTTTT
114834 TTTTTCTTCTTTCTTGTTGCTTTTT
1 TTTTTC-T-TTTCTTGTTGCTTTTT
114859 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 1 0.05
25 14 0.67
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (23 bp):
TTTTTCTTTTCTTGTTGCTTTTT
Found at i:115243 original size:33 final size:33
Alignment explanation
Indices: 115201--115269 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
115191 GTTGATGAAT
*
115201 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCGA-GAAATGGTAATG
* * *
115234 GAAGGATGATGTTATTGGCGAGATATGGTGATG
1 GAAGGATGATGTTAATGGCGAGAAATGGTAATG
115267 GAA
1 GAA
115270 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 23 0.74
34 8 0.26
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.29
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGAGAAATGGTAATG
Found at i:115274 original size:13 final size:12
Alignment explanation
Indices: 115255--115351 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
115245 TTATTGGCGA
115255 GATATGGTGATG
1 GATATGGTGATG
115267 GAATATGGTGAT-
1 G-ATATGGTGATG
*
115279 GATATAGGCG-T-
1 GATAT-GGTGATG
115290 GATAATGGTGATG
1 GAT-ATGGTGATG
115303 GACTATGGTGAT-
1 GA-TATGGTGATG
*
115315 GATATAGGCG-T-
1 GATAT-GGTGATG
*
115326 GATAATGGAGATG
1 GAT-ATGGTGATG
115339 GATTATGGTGATG
1 GA-TATGGTGATG
115352 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:115299 original size:36 final size:36
Alignment explanation
Indices: 115240--115352 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
115230 AATGGAAGGA
* * *
115240 TGATGTTATTGGCGAGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
115275 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
115311 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
115347 TGATGA
1 TGATGA
115353 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 15 0.21
36 56 0.79
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:116830 original size:16 final size:15
Alignment explanation
Indices: 116809--116842 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
116799 TGTGTCGGTT
116809 TAGAAATGGCTATGGA
1 TAGAAATGGCTAT-GA
*
116825 TAGAAATGGTTATGA
1 TAGAAATGGCTATGA
116840 TAG
1 TAG
116843 GGTAGAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.03, G:0.29, T:0.29
Consensus pattern (15 bp):
TAGAAATGGCTATGA
Found at i:117569 original size:35 final size:36
Alignment explanation
Indices: 117530--117609 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
117520 AAATGGAATT
* **
117530 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
117565 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
117601 TGGTGATGA
1 TGGTGATGA
117610 ACAGATTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 20 0.49
36 21 0.51
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCATGATAATGGTGATGGAAGA
Found at i:117987 original size:19 final size:20
Alignment explanation
Indices: 117949--117991 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
117939 GAAACCCCTT
*
117949 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
117969 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
117988 TGAA
1 TGAA
117992 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:121598 original size:19 final size:21
Alignment explanation
Indices: 121574--121625 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
121564 CGGCCAAGAG
121574 CATGTATCTTCA-TTAAAA-T
1 CATGTATCTTCATTTAAAAGT
*
121593 CATGTATTTTCATTTAAAAGT
1 CATGTATCTTCATTTAAAAGT
* *
121614 CATATATTTTCA
1 CATGTATCTTCA
121626 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 6 0.21
21 12 0.41
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATCTTCATTTAAAAGT
Found at i:122061 original size:19 final size:20
Alignment explanation
Indices: 122037--122086 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
122027 TATCCTTTAT
122037 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
122056 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
122076 -TATTATTATTT
1 TTATT-TTATTT
122087 TTATTAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.44
20 8 0.30
21 3 0.11
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:122377 original size:34 final size:31
Alignment explanation
Indices: 122335--122406 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 31
122325 GTACAAAAAG
* *
122335 AAAGAAAAGATA-AAAATAAGAAGAAAATTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTC--AA
122369 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
122400 AAAGAAA
1 AAAGAAA
122407 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 9 0.26
33 7 0.20
34 19 0.54
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.08
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:125554 original size:19 final size:21
Alignment explanation
Indices: 125530--125581 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
125520 CGGCCAAGAA
*
125530 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
125549 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
125570 CATGTATTTTCA
1 CATGTATTTTCA
125582 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:125974 original size:23 final size:25
Alignment explanation
Indices: 125947--125999 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
125937 TCTCTATCCT
*
125947 TTATTTATTTT-ATTTCAT-TATTA
1 TTATTTATTTTCATTACATATATTA
*
125970 TTATTTATTTTCATTACTTATATTA
1 TTATTTATTTTCATTACATATATTA
125995 TTATT
1 TTATT
126000 ACCTTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 11 0.42
24 5 0.19
25 10 0.38
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (25 bp):
TTATTTATTTTCATTACATATATTA
Found at i:125975 original size:19 final size:20
Alignment explanation
Indices: 125951--125999 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
125941 TATCCTTTAT
125951 TTATTTTATTTCATTA-TTA
1 TTATTTTATTTCATTACTTA
125970 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
125990 -TATTATTATT
1 TTATT-TTATT
126000 ACCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 6 0.23
21 3 0.12
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:126580 original size:52 final size:51
Alignment explanation
Indices: 126517--126677 Score: 218
Period size: 52 Copynumber: 3.1 Consensus size: 51
126507 AATTATAATT
*
126517 AAATGAAAAACACGCTGTTATGTGAATGTGAGTGCACGTAAATTAACAAAAC
1 AAATGATAAACA-GCTGTTATGTGAATGTGAGTGCACGTAAATTAACAAAAC
*
126569 AAATGATAAACATGCTGTTATGTGAATGTGAGTGCACGTGAATTAACAAAAC
1 AAATGATAAACA-GCTGTTATGTGAATGTGAGTGCACGTAAATTAACAAAAC
* * * *
126621 AAATGATAGACA--TGTTGATCTGAATGTGAATGCTCGTGAAATTAACAAAAC
1 AAATGATAAACAGCTGTT-ATGTGAATGTGAGTGCACGT-AAATTAACAAAAC
126672 AAATGA
1 AAATGA
126678 ATTCAAATAT
Statistics
Matches: 99, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
49 4 0.04
50 17 0.17
51 18 0.18
52 60 0.61
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (51 bp):
AAATGATAAACAGCTGTTATGTGAATGTGAGTGCACGTAAATTAACAAAAC
Found at i:137771 original size:24 final size:23
Alignment explanation
Indices: 137715--137774 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
137705 AGAACTTTTC
**
137715 TTCTTTTTTTTTAATTTTTGGAA
1 TTCTTTTTTTTTAATTTTCAGAA
137738 TT-TGTATTTTTTTAAATTTTCAGAA
1 TTCT-T-TTTTTTT-AATTTTCAGAA
137763 TTCTTTTTTTTT
1 TTCTTTTTTTTT
137775 CAAGATGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 1 0.03
23 3 0.10
24 14 0.45
25 12 0.39
26 1 0.03
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (23 bp):
TTCTTTTTTTTTAATTTTCAGAA
Found at i:137772 original size:25 final size:25
Alignment explanation
Indices: 137712--137774 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
137702 ACAAGAACTT
* **
137712 TTCTTCTTTTTTTTTAATTTTTGGAA
1 TTCTT-TTTTTTTTAAATTTTCAGAA
*
137738 TT-TGTATTTTTTTAAATTTTCAGAA
1 TTCT-TTTTTTTTTAAATTTTCAGAA
137763 TTCTTTTTTTTT
1 TTCTTTTTTTTT
137775 CAAGATGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.70
Consensus pattern (25 bp):
TTCTTTTTTTTTTAAATTTTCAGAA
Found at i:139272 original size:52 final size:52
Alignment explanation
Indices: 139215--139367 Score: 204
Period size: 52 Copynumber: 3.0 Consensus size: 52
139205 ATTAAATAAA
* *
139215 AAACATGTTGTTATGTGAATGTGAGTGCACGTAAATTAACAAAATAAATGAT
1 AAACATGATGTTATGTGAATGTGAGTGCACGTAAATTAACAAAACAAATGAT
*
139267 AAACATGATGTTATGTGAATGTGAGTGCACGTGAATTAACAAAACAAATGAT
1 AAACATGATGTTATGTGAATGTGAGTGCACGTAAATTAACAAAACAAATGAT
* * ** *
139319 AGA-ATGCTACTA--TGAATGTGAATGCACGTGAAATTAACAAAACAAATGA
1 AAACATGATGTTATGTGAATGTGAGTGCACGT-AAATTAACAAAACAAATGA
139368 ATTCAAATAT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
49 16 0.18
50 18 0.20
51 6 0.07
52 51 0.56
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.27
Consensus pattern (52 bp):
AAACATGATGTTATGTGAATGTGAGTGCACGTAAATTAACAAAACAAATGAT
Found at i:139704 original size:23 final size:23
Alignment explanation
Indices: 139659--139704 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
139649 TTATACCTAT
*
139659 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
139682 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
139705 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:141331 original size:17 final size:16
Alignment explanation
Indices: 141308--141360 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
141298 ATTGGAGTGC
141308 AAAAAAGAAAGAAAAG
1 AAAAAAGAAAGAAAAG
141324 ACAAAAAG-AAGAAAAG
1 A-AAAAAGAAAGAAAAG
*
141340 AAGAAAAGAAGGAAAAG
1 AA-AAAAGAAAGAAAAG
141357 AAAA
1 AAAA
141361 GAAAAAGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.03
16 17 0.52
17 15 0.45
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAGAAAAG
Found at i:141332 original size:8 final size:8
Alignment explanation
Indices: 141308--141360 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
141298 ATTGGAGTGC
141308 AAAAAAGA
1 AAAAAAGA
141316 AAGAAAAGA
1 AA-AAAAGA
*
141325 CAAAAAGA
1 AAAAAAGA
*
141333 AGAAAAGA
1 AAAAAAGA
*
141341 AGAAAAGA
1 AAAAAAGA
*
141349 AGGAAAAGA
1 A-AAAAAGA
141358 AAA
1 AAA
141361 GAAAAAGAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 24 0.62
9 15 0.38
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:141340 original size:5 final size:5
Alignment explanation
Indices: 141310--141365 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
141300 TGGAGTGCAA
*
141310 AAAAG -AAAG AAAAG ACAAA- AAGAAG AAAAG --AAG AAAAG -AAGG AAAAG
1 AAAAG AAAAG AAAAG A-AAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG
141357 AAAAG AAAA
1 AAAAG AAAA
141366 AGAGAAGTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
3 3 0.07
4 8 0.19
5 26 0.62
6 5 0.12
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:147039 original size:23 final size:23
Alignment explanation
Indices: 147013--147071 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
147003 AAAAATCATA
* *
147013 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
147036 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
147060 -AAGAAAAATCAA
1 AAAG-AAAATCAA
147072 AGAAAAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.61, C:0.15, G:0.15, T:0.08
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:147054 original size:24 final size:23
Alignment explanation
Indices: 147024--147069 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
147014 AAGAAAGTGA
147024 AGCACTCAAAAGAAAGAAAAATCC
1 AGCACTCAAAAG-AAGAAAAATCC
147048 AGCACTCAAAAGAAGAAAAATC
1 AGCACTCAAAAGAAGAAAAATC
147070 AAAGAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.59, C:0.20, G:0.13, T:0.09
Consensus pattern (23 bp):
AGCACTCAAAAGAAGAAAAATCC
Found at i:154117 original size:72 final size:73
Alignment explanation
Indices: 154014--154172 Score: 220
Period size: 73 Copynumber: 2.2 Consensus size: 73
154004 TAAATCCATC
* * * *
154014 CATTCATGCA-AGAAGCCAAATAGACATGTTCACAC-AAG-GGGAAAGAATTTCAGCCAAGATAC
1 CATTCATCCATAGAAGACAAATAGACAAGTTCACACGAAGTGGG-AAGAATCTCAGCCAAGATAC
154076 ATTCATGAA
65 ATTCATGAA
*
154085 CATTCATCCATAGAAGACAAATCA-ACAAGTTCACACGATGTGGGAAGAATCTCAGCCAAGATAC
1 CATTCATCCATAGAAGACAAAT-AGACAAGTTCACACGAAGTGGGAAGAATCTCAGCCAAGATAC
154149 ATTCATGAA
65 ATTCATGAA
154158 CATTCATCCAT-GAAG
1 CATTCATCCATAGAAG
154173 GTTCACTCAT
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
71 9 0.11
72 25 0.32
73 42 0.53
74 3 0.04
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (73 bp):
CATTCATCCATAGAAGACAAATAGACAAGTTCACACGAAGTGGGAAGAATCTCAGCCAAGATACA
TTCATGAA
Found at i:155572 original size:11 final size:13
Alignment explanation
Indices: 155540--155569 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
155530 TGGCCAAAGA
155540 TGAAAAGGTATGT
1 TGAAAAGGTATGT
155553 TGAAAAGGTATG-
1 TGAAAAGGTATGT
155565 TGAAA
1 TGAAA
155570 GGTGTTTAAT
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:158474 original size:71 final size:71
Alignment explanation
Indices: 158399--158535 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 71
158389 TATAGGTGTT
* * * *
158399 AAATGGTGATAGAAGATGGTAATGATATAGGCGTG-CAATGGTAATGGAATATGGTGATGTTATA
1 AAATGGTGAGAGAAGATGATAATGATATAGGCGTGAAAATGGTAATGGAAGATGGTGATGTT-TA
158463 GGCGTGA
65 GGCGTGA
* * * *
158470 AAATGGTGAGGGAAGATGATGATGTTATAGGCGTGAAAATGGTGATGGAAGATGGTGATGTTTAG
1 AAATGGTGAGAGAAGATGATAATGATATAGGCGTGAAAATGGTAATGGAAGATGGTGATGTTTAG
158535 G
66 G
158536 TAGTATCTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 34 0.60
72 23 0.40
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (71 bp):
AAATGGTGAGAGAAGATGATAATGATATAGGCGTGAAAATGGTAATGGAAGATGGTGATGTTTAG
GCGTGA
Found at i:158493 original size:36 final size:36
Alignment explanation
Indices: 158399--158535 Score: 188
Period size: 36 Copynumber: 3.9 Consensus size: 36
158389 TATAGGTGTT
* * *
158399 AAATGGTGATAGAAGATGGTAATGATATAGGCGTG-
1 AAATGGTGATGGAAGATGGTGATGTTATAGGCGTGA
* * *
158434 CAATGGTAATGGAATATGGTGATGTTATAGGCGTGA
1 AAATGGTGATGGAAGATGGTGATGTTATAGGCGTGA
* *
158470 AAATGGTGAGGGAAGATGATGATGTTATAGGCGTGA
1 AAATGGTGATGGAAGATGGTGATGTTATAGGCGTGA
158506 AAATGGTGATGGAAGATGGTGATGTT-TAGG
1 AAATGGTGATGGAAGATGGTGATGTTATAGG
158536 TAGTATCTTA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 33 0.38
36 55 0.62
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.28
Consensus pattern (36 bp):
AAATGGTGATGGAAGATGGTGATGTTATAGGCGTGA
Found at i:158911 original size:19 final size:20
Alignment explanation
Indices: 158873--158915 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
158863 GAAACCCATT
158873 TGAAAACACAAGATTTTTAA
1 TGAAAACACAAGATTTTTAA
158893 TGAAAACACATA-A-TTTTAA
1 TGAAAACACA-AGATTTTTAA
158912 TGAA
1 TGAA
158916 GATAAATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.45
20 11 0.50
21 1 0.05
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (20 bp):
TGAAAACACAAGATTTTTAA
Found at i:164323 original size:19 final size:20
Alignment explanation
Indices: 164301--164362 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
164291 TGAACTTCTC
164301 TTTTTCTT-TTCTTT-TCTTG
1 TTTTTCTTATT-TTTCTCTTG
164320 -TTTTCTTATTTTTCTCTTG
1 TTTTTCTTATTTTTCTCTTG
* * *
164339 -TTTTCTGATTTTTGTCTTC
1 TTTTTCTTATTTTTCTCTTG
164358 TTTTT
1 TTTTT
164363 GCACTCCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.27
19 23 0.62
20 4 0.11
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (20 bp):
TTTTTCTTATTTTTCTCTTG
Found at i:168215 original size:19 final size:20
Alignment explanation
Indices: 168168--168218 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
168158 GAAACCCCTT
**
168168 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
168188 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
168207 TGAAGATACATG
1 TGAAAATACATG
168219 CTCTTGGCCG
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:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:170025 original size:19 final size:21
Alignment explanation
Indices: 170001--170052 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
169991 CGGCCAAGAG
*
170001 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
170020 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
170041 CATGTATTTTCA
1 CATGTATTTTCA
170053 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:170488 original size:19 final size:20
Alignment explanation
Indices: 170464--170512 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
170454 TATCCTTTCT
170464 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
170483 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
170503 -TATTATTATT
1 TTATT-TTATT
170513 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:173666 original size:19 final size:21
Alignment explanation
Indices: 173642--173693 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
173632 CAGCCAAGAG
*
173642 CATGTATCTTCATT-AAA-AT
1 CATGTATTTTCATTAAAACAT
173661 CATGTATTTTCATTAAAACAT
1 CATGTATTTTCATTAAAACAT
173682 CATGTATTTTCA
1 CATGTATTTTCA
173694 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (21 bp):
CATGTATTTTCATTAAAACAT
Found at i:181395 original size:24 final size:25
Alignment explanation
Indices: 181349--181396 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
181339 CACCATGATC
* * *
181349 TGCATTTTCTTCAGTTTCTTCGTCT
1 TGCATTGTCTTCAGGTTCCTCGTCT
181374 TGCATTGT-TTCAGGTTCCTCGTC
1 TGCATTGTCTTCAGGTTCCTCGTC
181397 AAAAATAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.08, C:0.25, G:0.17, T:0.50
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCGTCT
Found at i:183771 original size:33 final size:33
Alignment explanation
Indices: 183729--183797 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
183719 GTTGATGAAT
*
183729 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGG-CATGAAATGGTAATG
* * *
183762 GAAGGATGATGTTATTGGCATGATATGGTGATG
1 GAAGGATGATGTTAATGGCATGAAATGGTAATG
183795 GAA
1 GAA
183798 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCATGAAATGGTAATG
Found at i:188278 original size:33 final size:33
Alignment explanation
Indices: 188236--188304 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
188226 GTTGATGAAT
*
188236 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGG-CATGAAATGGTAATG
* * *
188269 GAAGGATGATGTTATTGGCATGATATGGTGATG
1 GAAGGATGATGTTAATGGCATGAAATGGTAATG
188302 GAA
1 GAA
188305 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCATGAAATGGTAATG
Found at i:191266 original size:19 final size:19
Alignment explanation
Indices: 191222--191276 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
191212 GAAATCCCTT
* *
191222 TGAAAATACATGATTTTTAA
1 TGAAAATACATGA-CTCTAA
191242 TGAAAATACATGACTCTAA
1 TGAAAATACATGACTCTAA
*
191261 TTAAAATACATG-CTCT
1 TGAAAATACATGACTCT
191277 TGGCCGAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 4 0.12
19 15 0.47
20 13 0.41
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.35
Consensus pattern (19 bp):
TGAAAATACATGACTCTAA
Found at i:200299 original size:24 final size:21
Alignment explanation
Indices: 200265--200307 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
200255 TGCACAAGAT
*
200265 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
200287 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
200308 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:204986 original size:22 final size:22
Alignment explanation
Indices: 204961--205012 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
204951 TAATAAAGGG
204961 TAATAATAAT-AATGAAAATAAA
1 TAATAATAATAAATG-AAATAAA
*
204983 TAAT-AGAATGAAATGAAATAAA
1 TAATAATAAT-AAATGAAATAAA
*
205005 TAAAAATA
1 TAATAATA
205013 GAGAGATGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (22 bp):
TAATAATAATAAATGAAATAAA
Found at i:205456 original size:19 final size:20
Alignment explanation
Indices: 205411--205457 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
205401 ACCCCTTTGA
205411 AAATACATGATTTTTAAATG
1 AAATACATGATTTTTAAATG
205431 AAA-ACATGA-TTTT-AATG
1 AAATACATGATTTTTAAATG
205448 AAGATACATG
1 AA-ATACATG
205458 CTCTTGGCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.24
18 5 0.20
19 11 0.44
20 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (20 bp):
AAATACATGATTTTTAAATG
Done.