Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007787.1 Hibiscus syriacus cultivar Beakdansim tig00110073_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: 146544
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:10399 original size:14 final size:14
Alignment explanation
Indices: 10380--10409 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10370 GGTGATGAAC
10380 TATGGTAATGGAAA
1 TATGGTAATGGAAA
*
10394 TATGGTGATGGAAA
1 TATGGTAATGGAAA
10408 TA
1 TA
10410 GTATCTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (14 bp):
TATGGTAATGGAAA
Found at i:18991 original size:19 final size:21
Alignment explanation
Indices: 18948--18999 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
18938 GAAACCCCTT
18948 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
18969 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
18988 TGAAGATACATG
1 TGAAAATACATG
19000 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:23177 original size:19 final size:21
Alignment explanation
Indices: 23134--23185 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
23124 GAAACCCCTT
23134 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
23155 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
23174 TGAAGATACATG
1 TGAAAATACATG
23186 CTCTTAGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:30912 original size:15 final size:16
Alignment explanation
Indices: 30875--30931 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
30865 CAAATAAGGT
30875 AATGAAAT-AAGA-AA
1 AATGAAATAAAGAGAA
* *
30889 AGATAAAATAAA-AGGA
1 A-ATGAAATAAAGAGAA
30905 AATGAAATAAAGAGAA
1 AATGAAATAAAGAGAA
30921 AATGAAGATAA
1 AATGAA-ATAA
30932 CTTACAACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 1 0.03
15 16 0.47
16 13 0.38
17 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (16 bp):
AATGAAATAAAGAGAA
Found at i:31938 original size:20 final size:19
Alignment explanation
Indices: 31913--31955 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
31903 GAAACCCCTT
31913 TGAAAACACA-AGATTTTTAA
1 TGAAAACACATA-A-TTTTAA
*
31933 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
31952 TGAA
1 TGAA
31956 GATAAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 10 0.48
21 1 0.05
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:37522 original size:11 final size:13
Alignment explanation
Indices: 37491--37519 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
37481 GGCCAAAGAA
37491 GAAAAGGTATGTT
1 GAAAAGGTATGTT
37504 GAAAAGGTATG-T
1 GAAAAGGTATGTT
37516 GAAA
1 GAAA
37520 GGTGTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (13 bp):
GAAAAGGTATGTT
Found at i:50616 original size:15 final size:15
Alignment explanation
Indices: 50580--50609 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
50570 GTGCTTCAAC
50580 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
50594 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
50609 T
1 T
50610 GTTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:51589 original size:16 final size:16
Alignment explanation
Indices: 51540--51581 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
51530 GTGTTCTAGG
51540 TGGATGATGGAAGAGA
1 TGGATGATGGAAGAGA
51556 TGGATGATGGAAGAGA
1 TGGATGATGGAAGAGA
51572 TGGATGATGG
1 TGGATGATGG
51582 TGATGATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.45, T:0.21
Consensus pattern (16 bp):
TGGATGATGGAAGAGA
Found at i:56804 original size:17 final size:15
Alignment explanation
Indices: 56761--56812 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
56751 TTTGAATTTC
56761 TTTTTC-TTTTCTTT
1 TTTTTCTTTTTCTTT
**
56775 TTTTTCTGATTCTTCT
1 TTTTTCTTTTTCTT-T
56791 TTTTGTCTTTTTCTTT
1 TTTT-TCTTTTTCTTT
56807 TCTTTT
1 T-TTTT
56813 TGCACTCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 6 0.20
15 5 0.17
16 8 0.27
17 11 0.37
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:61070 original size:24 final size:24
Alignment explanation
Indices: 61043--61096 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
61033 ATCAGCAAAT
*
61043 AAAAGTCAAGCATTCCAAAAGAAG
1 AAAAGTCAAGCATTCAAAAAGAAG
* *
61067 AAAAATCCAGCATTCAAAAAGAAG
1 AAAAGTCAAGCATTCAAAAAGAAG
61091 AAAAGT
1 AAAAGT
61097 AAAGAAAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (24 bp):
AAAAGTCAAGCATTCAAAAAGAAG
Found at i:62399 original size:24 final size:25
Alignment explanation
Indices: 62353--62407 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
62343 ACAATTATGC
*
62353 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
62377 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
62402 CA-TTGA
1 CACTTGA
62408 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:68274 original size:8 final size:8
Alignment explanation
Indices: 68253--68303 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
68243 TATTTTTGGA
68253 TTTCTTC-
1 TTTCTTCT
68260 TTT-TTCT
1 TTTCTTCT
68267 TTTCTTCT
1 TTTCTTCT
68275 TTTCTTCT
1 TTTCTTCT
*
68283 TTTTTGTCT
1 TTTCT-TCT
68292 TTTCTTTCT
1 TTTC-TTCT
68301 TTT
1 TTT
68304 TTTGTACTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 3 0.08
7 6 0.16
8 16 0.42
9 12 0.32
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTCTTCT
Found at i:68282 original size:25 final size:26
Alignment explanation
Indices: 68254--68303 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
68244 ATTTTTGGAT
68254 TTCTTCTTTT-TCTTTTC-TTCTTTTC
1 TTCTT-TTTTGTCTTTTCTTTCTTTTC
68279 TTCTTTTTTGTCTTTTCTTTCTTTT
1 TTCTTTTTTGTCTTTTCTTTCTTTT
68304 TTTGTACTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 7 0.30
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (26 bp):
TTCTTTTTTGTCTTTTCTTTCTTTTC
Found at i:68286 original size:17 final size:17
Alignment explanation
Indices: 68253--68304 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
68243 TATTTTTGGA
68253 TTTCTTC-TTT-TTC-T
1 TTTCTTCTTTTCTTCTT
68267 TTTCTTCTTTTCTTCTT
1 TTTCTTCTTTTCTTCTT
68284 TTT-TGTCTTTTCTTTCTT
1 TTTCT-TCTTTTC-TTCTT
68302 TTT
1 TTT
68305 TTGTACTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.21
15 3 0.09
16 4 0.12
17 11 0.33
18 8 0.24
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTCTTCTTTTCTTCTT
Found at i:68296 original size:22 final size:21
Alignment explanation
Indices: 68253--68306 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
68243 TATTTTTGGA
68253 TTTCTTCTTTTTCTTTTCTTC
1 TTTCTTCTTTTTCTTTTCTTC
68274 TTTTCTTCTTTTT-TGTCTT-TTC
1 -TTTCTTCTTTTTCT-T-TTCTTC
68296 TTTCTT-TTTTT
1 TTTCTTCTTTTT
68307 GTACTCCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.17
21 7 0.23
22 16 0.53
23 2 0.07
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTCTTCTTTTTCTTTTCTTC
Found at i:76203 original size:24 final size:24
Alignment explanation
Indices: 76171--76219 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
76161 TCATCCTAAC
*
76171 ACCCTTGACGCCTAGACAAGTCCA
1 ACCCTTGACACCTAGACAAGTCCA
76195 ACCCTTGACACCTAGACAAGTCCA
1 ACCCTTGACACCTAGACAAGTCCA
76219 A
1 A
76220 ATTGATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.37, G:0.14, T:0.16
Consensus pattern (24 bp):
ACCCTTGACACCTAGACAAGTCCA
Found at i:79781 original size:8 final size:8
Alignment explanation
Indices: 79755--79801 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
79745 TTGGAGTGCA
79755 AAAAGAAAG
1 AAAAG-AAG
*
79764 AAAAATAAG
1 -AAAAGAAG
79773 AAAAGAAG
1 AAAAGAAG
79781 AAAAGAAG
1 AAAAGAAG
*
79789 AAAAAAAG
1 AAAAGAAG
79797 AAAAG
1 AAAAG
79802 GAAAGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 26 0.79
9 3 0.09
10 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:79785 original size:26 final size:26
Alignment explanation
Indices: 79755--79810 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
79745 TTGGAGTGCA
79755 AAAAGAAAGAAAAATAAGAAAA-G-AAG
1 AAAAG-AAGAAAAA-AAGAAAAGGAAAG
79781 AAAAGAAGAAAAAAAGAAAAGGAAAG
1 AAAAGAAGAAAAAAAGAAAAGGAAAG
79807 AAAA
1 AAAA
79811 AGAGAAGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.25
25 9 0.32
26 12 0.43
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (26 bp):
AAAAGAAGAAAAAAAGAAAAGGAAAG
Found at i:79795 original size:11 final size:12
Alignment explanation
Indices: 79754--79799 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
79744 ATTGGAGTGC
79754 AAAAAGAAAGAA
1 AAAAAGAAAGAA
79766 AAATAAGAAAAGAA
1 AAA-AAG-AAAGAA
*
79780 GAAAAG-AAGAA
1 AAAAAGAAAGAA
79791 AAAAAGAAA
1 AAAAAGAAA
79800 AGGAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 10 0.34
12 5 0.17
13 6 0.21
14 8 0.28
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAGAA
Found at i:79806 original size:29 final size:29
Alignment explanation
Indices: 79757--79817 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
79747 GGAGTGCAAA
*
79757 AAGAAAGAAAAATAAGAAAAGAAGAAA-AG
1 AAGAAAGAAAAAAAAGAAAAGAA-AAAGAG
*
79786 AAGAAA-AAAAGAAAAGGAAAGAAAAAGAG
1 AAGAAAGAAAA-AAAAGAAAAGAAAAAGAG
79815 AAG
1 AAG
79818 TTCAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (29 bp):
AAGAAAGAAAAAAAAGAAAAGAAAAAGAG
Found at i:79810 original size:16 final size:16
Alignment explanation
Indices: 79755--79816 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
79745 TTGGAGTGCA
*
79755 AAAAGAAAGAAAAATAAG
1 AAAA-AAAG-AAAAGAAG
*
79773 AAAAGAAGAAAAGAAG
1 AAAAAAAGAAAAGAAG
79789 AAAAAAAGAAAAGGAAAG
1 AAAAAAAGAAAA-G-AAG
*
79807 AAAAAGAGAA
1 AAAAAAAGAA
79817 GTTCAAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
16 18 0.47
17 4 0.11
18 16 0.42
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAG
Found at i:98132 original size:18 final size:18
Alignment explanation
Indices: 98109--98150 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
98099 TAGTTTGATT
98109 AATGAAATAACATTATTC
1 AATGAAATAACATTATTC
* *
98127 AATGAAATAACTTTATTT
1 AATGAAATAACATTATTC
98145 AATGAA
1 AATGAA
98151 CTAAATGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (18 bp):
AATGAAATAACATTATTC
Found at i:98230 original size:17 final size:17
Alignment explanation
Indices: 98210--98251 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
98200 ACTACTTCCC
98210 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
98227 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
98244 TTAATGAA
1 TAAATGAA
98252 CAACATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:104309 original size:11 final size:11
Alignment explanation
Indices: 104295--104350 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
104285 TCTTTTTGAA
104295 TTCTTTTTCTT
1 TTCTTTTTCTT
104306 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
104319 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
104332 TGTCTTTTTC-T
1 T-TCTTTTTCTT
104343 TTCTTTTT
1 TTCTTTTT
104351 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:104319 original size:19 final size:18
Alignment explanation
Indices: 104295--104350 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
104285 TCTTTTTGAA
104295 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
104313 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
104332 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
104350 T
1 T
104351 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:129747 original size:17 final size:17
Alignment explanation
Indices: 129706--129777 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
129696 ATTCATGCAT
129706 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
129723 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
129741 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
129758 CTAGTTCATTTATTAGA
1 CTAGTTCATTAATTAAA
129775 CTA
1 CTA
129778 ACTCTTAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
17 33 0.72
18 13 0.28
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:130391 original size:22 final size:21
Alignment explanation
Indices: 130365--130405 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
130355 TTGTGAAAAT
130365 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
130387 TGATGGTTTTGATGATGAA
1 TGATGGTCTTGATGATGAA
130406 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.34, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:132062 original size:18 final size:18
Alignment explanation
Indices: 132034--132068 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
132024 CATTGATTCA
132034 TGAAAGGTGATG-ACTCT
1 TGAAAGGTGATGTACTCT
132051 TGAAATGGTGATGTACTC
1 TGAAA-GGTGATGTACTC
132069 ATAAGTCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (18 bp):
TGAAAGGTGATGTACTCT
Found at i:134907 original size:22 final size:21
Alignment explanation
Indices: 134881--134921 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
134871 CTGCGAAAAT
134881 TGATGG-TCTTGATGGATGAAGA
1 TGATGGCT-TTGAT-GATGAAGA
134903 TGATGGCTTTGATGATGAA
1 TGATGGCTTTGATGATGAA
134922 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 11 0.61
23 1 0.06
ACGTcount: A:0.27, C:0.05, G:0.34, T:0.34
Consensus pattern (21 bp):
TGATGGCTTTGATGATGAAGA
Found at i:135824 original size:10 final size:11
Alignment explanation
Indices: 135801--135839 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
135791 GATGATGGTA
135801 TAGCTCCAATT
1 TAGCTCCAATT
135812 TAGCTCC-ATT
1 TAGCTCCAATT
*
135822 TAGCTCCAATG
1 TAGCTCCAATT
135833 TAGCTCC
1 TAGCTCC
135840 CAAGTGTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (11 bp):
TAGCTCCAATT
Found at i:137092 original size:91 final size:91
Alignment explanation
Indices: 136937--137119 Score: 278
Period size: 91 Copynumber: 2.0 Consensus size: 91
136927 CCTAGAACAC
*
136937 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
137002 AAGAGTTCTCTCCCTATTC-AGCCAAG
66 AAGAGTTCTCTCCCTATTCGA-CCAAG
** * * * *
137028 CCATGTGTTTTGCATGTGATCAGCCCCCATGTTCCTTGCATGTGGTTCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
*
137093 AAGGGTTCTCTCCCTATTCGACCAAG
66 AAGAGTTCTCTCCCTATTCGACCAAG
137119 C
1 C
137120 ATCAACTACC
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 82 0.99
92 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTCGACCAAG
Found at i:140335 original size:48 final size:48
Alignment explanation
Indices: 140243--140335 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 48
140233 CACACTCCAA
* * *
140243 TTTGCCTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATTTATCATG
1 TTTGCCTTTCATCGCGACTAGGAGGGTTGGATAGAGACACTTATCATG
*
140291 TTTGCCTTTTCATTGCGACTAGGAGGGCTT-GATAG-GACACTTATC
1 TTTGCC-TTTCATCGCGACTAGGAGGG-TTGGATAGAGACACTTATC
140336 CATCTATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 14 0.36
49 23 0.59
50 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (48 bp):
TTTGCCTTTCATCGCGACTAGGAGGGTTGGATAGAGACACTTATCATG
Found at i:140859 original size:20 final size:19
Alignment explanation
Indices: 140808--140859 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
140798 ATTTTAAAAA
**
140808 AAAAAACCAAAAAAAGGGC
1 AAAAAACCAAAAAAAAAGC
*
140827 AAAAAACAAAAAAAAAAAGC
1 AAAAAAC-CAAAAAAAAAGC
140847 AAAAAATCCAAAA
1 AAAAAA-CCAAAA
140860 TTTCAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 19 0.70
21 1 0.04
ACGTcount: A:0.77, C:0.13, G:0.08, T:0.02
Consensus pattern (19 bp):
AAAAAACCAAAAAAAAAGC
Done.