Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008878.1 Hibiscus syriacus cultivar Beakdansim tig00112117_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: 84504
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3294 original size:14 final size:14
Alignment explanation
Indices: 3275--3304 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3265 CGAGTCTTTC
3275 CTTGACTACGATCT
1 CTTGACTACGATCT
3289 CTTGACTACGATCT
1 CTTGACTACGATCT
3303 CT
1 CT
3305 AATTGGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (14 bp):
CTTGACTACGATCT
Found at i:6207 original size:5 final size:5
Alignment explanation
Indices: 6197--6249 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
6187 AACGGTCAAT
* *
6197 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
6246 GGTC
1 GGTC
6250 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:6212 original size:17 final size:17
Alignment explanation
Indices: 6190--6250 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 17
6180 AACGGTCAAC
6190 GGTCAATGGTCGGGTCG
1 GGTCAATGGTCGGGTCG
6207 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA---T--GGTCGGGTCG
*
6229 GGTCAACGGTCGGGTCG
1 GGTCAATGGTCGGGTCG
6246 GGTCA
1 GGTCA
6251 GACCGGTCAG
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 21 0.55
20 1 0.03
22 16 0.42
ACGTcount: A:0.11, C:0.21, G:0.48, T:0.20
Consensus pattern (17 bp):
GGTCAATGGTCGGGTCG
Found at i:6225 original size:22 final size:22
Alignment explanation
Indices: 6183--6249 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
6173 GAAAGTCAAC
*
6183 GGTCAACGGTCAATGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
6207 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
6229 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
6250 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.22, G:0.46, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:6260 original size:9 final size:9
Alignment explanation
Indices: 6246--6285 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
6236 GGTCGGGTCG
6246 GGTCAGACC
1 GGTCAGACC
6255 GGTCAGACC
1 GGTCAGACC
6264 GGTTCAGACC
1 GG-TCAGACC
*
6274 GGTCAAACC
1 GGTCAGACC
6283 GGT
1 GGT
6286 TCGAACCGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.23, C:0.30, G:0.33, T:0.15
Consensus pattern (9 bp):
GGTCAGACC
Found at i:6270 original size:19 final size:19
Alignment explanation
Indices: 6248--6305 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
6238 TCGGGTCGGG
*
6248 TCAGACCGGTCAGACCGGT
1 TCAGACCGGTCAAACCGGT
6267 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
6286 TC-GAACCGGTTAAACCGGT
1 TCAG-ACCGGTCAAACCGGT
6305 T
1 T
6306 TCCAGCAGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 1 0.03
19 35 0.97
ACGTcount: A:0.24, C:0.29, G:0.28, T:0.19
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:6272 original size:10 final size:10
Alignment explanation
Indices: 6248--6305 Score: 61
Period size: 9 Copynumber: 6.1 Consensus size: 10
6238 TCGGGTCGGG
6248 TCAGACCGG-
1 TCAGACCGGT
6257 TCAGACCGGT
1 TCAGACCGGT
6267 TCAGACCGG-
1 TCAGACCGGT
*
6276 TCAAACCGGT
1 TCAGACCGGT
6286 TC-GAACCGGT
1 TCAG-ACCGGT
*
6296 T-AAACCGGT
1 TCAGACCGGT
6305 T
1 T
6306 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 24 0.57
10 18 0.43
ACGTcount: A:0.24, C:0.29, G:0.28, T:0.19
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:8200 original size:21 final size:21
Alignment explanation
Indices: 8176--8226 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
8166 TATTAGTATC
*
8176 AAATCATTAAATATTAATAAT
1 AAATTATTAAATATTAATAAT
8197 AAATTATTAAATATTAATAAT
1 AAATTATTAAATATTAATAAT
8218 AAATTATTA
1 AAATTATTA
8227 TTATCAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTATTAAATATTAATAAT
Found at i:8272 original size:12 final size:12
Alignment explanation
Indices: 8257--8302 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
8247 CATTATCATC
*
8257 ATTATTATAATG
1 ATTATTATAATA
8269 ATTATTACTAAATA
1 ATTATTA-T-AATA
8283 ATTATTATAATA
1 ATTATTATAATA
8295 ATTATTAT
1 ATTATTAT
8303 CAAATCATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 19 0.61
13 2 0.06
14 10 0.32
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (12 bp):
ATTATTATAATA
Found at i:8321 original size:63 final size:61
Alignment explanation
Indices: 8223--8361 Score: 74
Period size: 61 Copynumber: 2.3 Consensus size: 61
8213 ATAATAAATT
* * *
8223 ATTATTATCAAATCATTACTAAATCATTATCAT--CATTATTAT-AATGATTATTACTAAATA
1 ATTATTATCAAATCATTACTAAATCATTATTATAATATTATTATAAATAATTATTA-T-AATA
* * * * * * * * * *
8283 ATTATTATAATAATTATTA-TCAAATCATTACTA-AATCATCA-AATCATTAAATATTAAAATC
1 ATTATTATCA-AATCATTACT-AAATCATTATTATAAT-ATTATTATAAATAATTATTATAATA
8344 ATTATTATCAAATCATTA
1 ATTATTATCAAATCATTA
8362 TTATCAAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
60 17 0.29
61 29 0.49
62 2 0.03
63 11 0.19
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.42
Consensus pattern (61 bp):
ATTATTATCAAATCATTACTAAATCATTATTATAATATTATTATAAATAATTATTATAATA
Found at i:8358 original size:14 final size:14
Alignment explanation
Indices: 8218--8375 Score: 88
Period size: 14 Copynumber: 10.6 Consensus size: 14
8208 TATTAATAAT
*
8218 AAATTATTATTATC
1 AAATCATTATTATC
*
8232 AAATCATTACTAAATC
1 AAATCATTA-T-TATC
* * *
8248 ATTATCATCATTATT
1 A-AATCATTATTATC
*
8263 ATAATGATTATTA-C
1 A-AATCATTATTATC
*
8277 TAAATAATTATTAT-
1 -AAATCATTATTATC
*
8291 -AATAATTATTATC
1 AAATCATTATTATC
8304 AAATCATTACTAAATCATC
1 AAATCATTA-T---T-ATC
* *
8323 AAATCATTAAATATTA
1 AAATCATT-ATTA-TC
8339 AAATCATTATTATC
1 AAATCATTATTATC
8353 AAATCATTATTATC
1 AAATCATTATTATC
*
8367 AAATTATTA
1 AAATCATTA
8376 CTAAATTATA
Statistics
Matches: 113, Mismatches: 17, Indels: 28
0.72 0.11 0.18
Matches are distributed among these distances:
12 12 0.11
14 48 0.42
15 19 0.17
16 15 0.13
17 6 0.05
18 1 0.01
19 11 0.10
20 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (14 bp):
AAATCATTATTATC
Found at i:8362 original size:72 final size:72
Alignment explanation
Indices: 8173--8375 Score: 184
Period size: 72 Copynumber: 2.8 Consensus size: 72
8163 GATTATTAGT
* *
8173 ATCAAATCATTAAATATTAATAATA-AATTATTAAATATTAATAATAAATTATTATTATCAAATC
1 ATCAAATCATTAAATATTAA-AATATTATTATAAAATATT-ATAAT-AA-TATTATTATCAAATC
8237 ATTACTAAATC
62 ATTACTAAATC
* * * * *
8248 AT--TATCA-TCATTATTATAATGATTATTACT-AAATAATTATTATAATAATTATTATCAAATC
1 ATCAAATCATTAAATATTAAAAT-ATTATTA-TAAAAT-ATTATAATAAT-ATTATTATCAAATC
8309 ATTACTAAATC
62 ATTACTAAATC
* *
8320 ATCAAATCATTAAATATTAAAATCATTATTATCAAATCATTATTATCAA-ATTATTA
1 ATCAAATCATTAAATATTAAAAT-ATTATTATAAAAT-ATTATAAT-AATATTATTA
8376 CTAAATTATA
Statistics
Matches: 106, Mismatches: 12, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
71 4 0.04
72 37 0.35
73 16 0.15
74 16 0.15
75 31 0.29
76 2 0.02
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (72 bp):
ATCAAATCATTAAATATTAAAATATTATTATAAAATATTATAATAATATTATTATCAAATCATTA
CTAAATC
Found at i:8501 original size:21 final size:21
Alignment explanation
Indices: 8475--8519 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
8465 TTCGAATCTC
*
8475 TTAAATATTAATATTAAATAA
1 TTAAATATTAATAATAAATAA
*
8496 TTAAATATTAATAATAAATTA
1 TTAAATATTAATAATAAATAA
8517 TTA
1 TTA
8520 TTAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAATATTAATAATAAATAA
Found at i:8524 original size:38 final size:35
Alignment explanation
Indices: 8480--8557 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 35
8470 ATCTCTTAAA
* *
8480 TATTAATATTAAATAATTAAATATTAATAATAAATTAT
1 TATTAATAAT-AATAACTAAATATT--TAATAAATTAT
* *
8518 TATTAATAATAATTACTAAATATTTATTAAATTAT
1 TATTAATAATAATAACTAAATATTTAATAAATTAT
8553 TATTA
1 TATTA
8558 TCATTATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 15 0.42
37 12 0.33
38 9 0.25
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (35 bp):
TATTAATAATAATAACTAAATATTTAATAAATTAT
Found at i:8525 original size:14 final size:14
Alignment explanation
Indices: 8497--8648 Score: 50
Period size: 14 Copynumber: 11.9 Consensus size: 14
8487 ATTAAATAAT
*
8497 TAAA-TATTAATAA
1 TAAATTATTATTAA
8510 TAAATTATTATTAA
1 TAAATTATTATTAA
*
8524 T-AA-TA--ATTAC
1 TAAATTATTATTAA
*
8534 TAAA-TA-T-TTAT
1 TAAATTATTATTAA
8545 TAAATTATTATT-A
1 TAAATTATTATTAA
*
8558 T-CATTATTA-T--
1 TAAATTATTATTAA
* *
8568 CAAATCATTATT-A
1 TAAATTATTATTAA
* *
8581 TCAAATCATTATTAT
1 T-AAATTATTATTAA
*
8596 TAAATCATTATT-A
1 TAAATTATTATTAA
*
8609 TCAAATCATTATT-A
1 T-AAATTATTATTAA
* *
8623 T-AATGATTATTAC
1 TAAATTATTATTAA
*
8636 TAAATCATTATTA
1 TAAATTATTATTA
8649 TAATAATCAT
Statistics
Matches: 111, Mismatches: 14, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
10 5 0.05
11 18 0.16
12 21 0.19
13 10 0.09
14 56 0.50
15 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.47
Consensus pattern (14 bp):
TAAATTATTATTAA
Found at i:8599 original size:51 final size:51
Alignment explanation
Indices: 8541--8757 Score: 197
Period size: 51 Copynumber: 4.4 Consensus size: 51
8531 TACTAAATAT
* * *
8541 TTATTAAATTATTATTATCATTATTATCAAATCATTATTATCAAATCATTA
1 TTATTAAATCATTATTATCATCATTATTAAATCATTATTATCAAATCATTA
*
8592 TTATTAAATCATTATTATCAAATCATTATTATAATGATTATTA-CTAAATCATTA
1 TTATTAAATCATTATTATC--ATCATTATTA-AATCATTATTATC-AAATCATTA
* * * *
8646 TTATAATAATCATTACTA-AATCATTGTTAAATCATTATTATCAAATC---A
1 TTATTA-AATCATTATTATCATCATTATTAAATCATTATTATCAAATCATTA
* *
8694 TTATTAAATCATCA-TATCATCAAATATTCAAATCATTA-T-T--AA--ATTA
1 TTATTAAATCATTATTATCATC-ATTATT-AAATCATTATTATCAAATCATTA
8740 TTATTAAATCATTATTAT
1 TTATTAAATCATTATTAT
8758 GGTTAATTGA
Statistics
Matches: 138, Mismatches: 15, Indels: 30
0.75 0.08 0.16
Matches are distributed among these distances:
45 2 0.01
46 16 0.12
47 14 0.10
48 11 0.08
49 9 0.07
51 33 0.24
52 10 0.07
53 9 0.07
54 24 0.17
55 10 0.07
ACGTcount: A:0.43, C:0.11, G:0.01, T:0.46
Consensus pattern (51 bp):
TTATTAAATCATTATTATCATCATTATTAAATCATTATTATCAAATCATTA
Found at i:8669 original size:11 final size:11
Alignment explanation
Indices: 8510--8756 Score: 111
Period size: 11 Copynumber: 20.2 Consensus size: 11
8500 ATATTAATAA
*
8510 TAAATTATTAT
1 TAAATCATTAT
* *
8521 TAATAATAATTAC
1 T-A-AATCATTAT
8534 TAAAT-ATTTAT
1 TAAATCA-TTAT
*
8545 TAAATTATTAT
1 TAAATCATTAT
* *
8556 TATCATTATTAT
1 TA-AATCATTAT
*
8568 CAAATCATTATT
1 TAAATCATTA-T
8580 ATCAAATCATTATTAT
1 -T-AAATC---ATTAT
8596 TAAATCATTATT
1 TAAATCATTA-T
8608 ATCAAATCATTAT
1 -T-AAATCATTAT
*
8621 TATAATGATTATT
1 TA-AATCATTA-T
8634 ACTAAATCATTATT
1 --TAAATCATTA-T
*
8648 ATAATAATCATTAC
1 -T-A-AATCATTAT
*
8662 TAAATCATTGT
1 TAAATCATTAT
8673 TAAATCATTATT
1 TAAATCATTA-T
8685 ATCAAATCATTAT
1 -T-AAATCATTAT
*
8698 TAAATCATCA-
1 TAAATCATTAT
* *
8708 TATCATCAAATAT
1 TA-AATC-ATTAT
8721 TCAAATCATTAT
1 T-AAATCATTAT
*
8733 TAAATTATTAT
1 TAAATCATTAT
8744 TAAATCATTAT
1 TAAATCATTAT
8755 TA
1 TA
8757 TGGTTAATTG
Statistics
Matches: 186, Mismatches: 23, Indels: 54
0.71 0.09 0.21
Matches are distributed among these distances:
10 3 0.02
11 77 0.41
12 32 0.17
13 19 0.10
14 39 0.21
15 11 0.06
16 1 0.01
17 4 0.02
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.45
Consensus pattern (11 bp):
TAAATCATTAT
Found at i:8693 original size:14 final size:14
Alignment explanation
Indices: 8557--8699 Score: 160
Period size: 14 Copynumber: 10.7 Consensus size: 14
8547 AATTATTATT
8557 ATCATTATTATCAA
1 ATCATTATTATCAA
8571 ATCATTATTATCAA
1 ATCATTATTATCAA
*
8585 ATCATTATTATTAA
1 ATCATTATTATCAA
8599 ATCATTATTATCAA
1 ATCATTATTATCAA
8613 ATCATTATTAT--A
1 ATCATTATTATCAA
*
8625 ATGATTATTA-CTAA
1 ATCATTATTATC-AA
8639 ATCATTATTAT--A
1 ATCATTATTATCAA
* *
8651 ATAATCATTA-CTAA
1 ATCATTATTATC-AA
*
8665 ATCATT-GT-T-AA
1 ATCATTATTATCAA
8676 ATCATTATTATCAA
1 ATCATTATTATCAA
8690 ATCATTATTA
1 ATCATTATTA
8700 AATCATCATA
Statistics
Matches: 108, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
11 8 0.07
12 20 0.19
13 2 0.02
14 78 0.72
ACGTcount: A:0.43, C:0.11, G:0.01, T:0.45
Consensus pattern (14 bp):
ATCATTATTATCAA
Found at i:8925 original size:21 final size:20
Alignment explanation
Indices: 8901--8992 Score: 50
Period size: 21 Copynumber: 4.7 Consensus size: 20
8891 TAGTAATAAT
8901 TATTAAATCATTACTATCAAA
1 TATTAAATCATTACTATC-AA
* *
8922 TATTTAATTATTA--AT-AA
1 TATTAAATCATTACTATCAA
** * *
8939 T-TTTCATTATTACTAATCAT
1 TATTAAATCATTACT-ATCAA
*
8959 TACTAAATCATTACTATCAAA
1 TATTAAATCATTACTATC-AA
8980 TAATTAAAT-ATTA
1 T-ATTAAATCATTA
8993 ATAATAATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
16 10 0.19
17 3 0.06
19 4 0.07
20 5 0.09
21 26 0.48
22 6 0.11
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAAATCATTACTATCAA
Found at i:8966 original size:58 final size:59
Alignment explanation
Indices: 8886--9047 Score: 224
Period size: 58 Copynumber: 2.8 Consensus size: 59
8876 TTATTCCATA
* * *
8886 ATTATTAGTAATAATTATTAAATCATTACTATCAAATATTTAATTATTAATAAT-TTTC
1 ATTATTACTAATCATTACTAAATCATTACTATCAAATATTTAATTATTAATAATATTTC
* *
8944 ATTATTACTAATCATTACTAAATCATTACTATCAAATAATTAAATATTAATAATAATTTC
1 ATTATTACTAATCATTACTAAATCATTACTATCAAATATTTAATTATTAATAAT-ATTTC
* *
9004 ATTATTACTAATCATTACTAAATAATTATTAT--AAT-TTTAATTAT
1 ATTATTACTAATCATTACTAAATCATTACTATCAAATATTTAATTAT
9048 AAAATCACTA
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
57 7 0.08
58 52 0.56
60 34 0.37
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.46
Consensus pattern (59 bp):
ATTATTACTAATCATTACTAAATCATTACTATCAAATATTTAATTATTAATAATATTTC
Found at i:9031 original size:21 final size:20
Alignment explanation
Indices: 8946--9027 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 20
8936 TAATTTTCAT
8946 TATTACTAATCATTACTAAA
1 TATTACTAATCATTACTAAA
* *
8966 TCATTACT-ATCAAATAATTAAA
1 T-ATTACTAATC--ATTACTAAA
* * * *
8988 TATTAATAATAATT--TCAT
1 TATTACTAATCATTACTAAA
9006 TATTACTAATCATTACTAAA
1 TATTACTAATCATTACTAAA
9026 TA
1 TA
9028 ATTATTATAA
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
18 14 0.31
20 10 0.22
21 11 0.24
22 10 0.22
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (20 bp):
TATTACTAATCATTACTAAA
Found at i:9060 original size:50 final size:50
Alignment explanation
Indices: 8957--9060 Score: 113
Period size: 50 Copynumber: 2.1 Consensus size: 50
8947 ATTACTAATC
* ** *
8957 ATTACTAAATCATTACTATCAAATAATTAAATATTAATAATAATTTCATT
1 ATTACTAAATCATTACTATAAAATAATTAAATATTAATAATAAAATCACT
* * *
9007 ATTACT-AATCATTACTA-AATAATTATTATAATTTTAATTATAAAATCACT
1 ATTACTAAATCATTACTATAA-AATAATTA-AATATTAATAATAAAATCACT
9057 ATTA
1 ATTA
9061 AATCATGATT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
48 1 0.02
49 18 0.40
50 26 0.58
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (50 bp):
ATTACTAAATCATTACTATAAAATAATTAAATATTAATAATAAAATCACT
Found at i:9077 original size:14 final size:14
Alignment explanation
Indices: 9060--9093 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9050 AATCACTATT
9060 AAATCATGATTATC
1 AAATCATGATTATC
* *
9074 AAATCATTATTATT
1 AAATCATGATTATC
9088 AAATCA
1 AAATCA
9094 AATCATGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (14 bp):
AAATCATGATTATC
Found at i:11908 original size:4 final size:4
Alignment explanation
Indices: 11899--11932 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
11889 ATCTAATATA
11899 AACT AACT AACT AACT AACT AACT AACT AACT AA
1 AACT AACT AACT AACT AACT AACT AACT AACT AA
11933 TTTACACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
AACT
Found at i:12395 original size:28 final size:27
Alignment explanation
Indices: 12358--12480 Score: 133
Period size: 28 Copynumber: 4.5 Consensus size: 27
12348 ATAATCTAAT
*
12358 ATATACCTTAAACTAACAAACTAATATA
1 ATATAACTTAAACTAACAAACTAA-ATA
12386 ATATAACTTAAACTAACAAACT-AATA
1 ATATAACTTAAACTAACAAACTAAATA
* * * **
12412 ATTTATACTAACAAACAAACTGACTAAATA
1 ATATA-ACT--TAAACTAACAAACTAAATA
*
12442 ATATAACTTAAACTAACAAACTAACTA
1 ATATAACTTAAACTAACAAACTAAATA
12469 A-ATAACTTAAAC
1 ATATAACTTAAAC
12481 CATAAACTAA
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
26 18 0.23
27 19 0.24
28 21 0.27
29 13 0.16
30 8 0.10
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.27
Consensus pattern (27 bp):
ATATAACTTAAACTAACAAACTAAATA
Found at i:12419 original size:56 final size:56
Alignment explanation
Indices: 12353--12499 Score: 156
Period size: 56 Copynumber: 2.5 Consensus size: 56
12343 TTTATATAAT
*
12353 CTAATATATACCTTAAACTAACAAACTAATATAATATAACTTAAACTAACAAACTAA
1 CTAATTTATACC-TAAACTAACAAACTAATATAATATAACTTAAACTAACAAACTAA
* *
12410 -TAATTTATA-CT-AACAAACAAACTGACTAAATAATATAACTTAAACTAACAAACTAA
1 CTAATTTATACCTAAACTAACAAACT-A--ATATAATATAACTTAAACTAACAAACTAA
*
12466 CTAAATAACTTAAACCATAAACTAACAAACTAAT
1 CT-AAT---TTATACC-TAAACTAACAAACTAAT
12500 TATTTCATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
53 11 0.15
54 2 0.03
55 1 0.01
56 36 0.49
57 1 0.01
58 3 0.04
61 5 0.07
62 1 0.01
63 2 0.03
64 11 0.15
ACGTcount: A:0.55, C:0.18, G:0.01, T:0.27
Consensus pattern (56 bp):
CTAATTTATACCTAAACTAACAAACTAATATAATATAACTTAAACTAACAAACTAA
Found at i:12421 original size:21 final size:21
Alignment explanation
Indices: 12388--12465 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
12378 CTAATATAAT
12388 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
12409 ATAATTTATACTAACAAAC--
1 ATAACTTAAACTAACAAACTA
*
12428 A-AAC-T-GACTAA-ATAA-T-
1 ATAACTTAAACTAACA-AACTA
12444 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
12465 A
1 A
12466 CTAAATAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 16
0.68 0.08 0.25
Matches are distributed among these distances:
15 1 0.02
16 8 0.18
17 4 0.09
18 3 0.07
19 8 0.18
20 2 0.05
21 18 0.41
ACGTcount: A:0.56, C:0.17, G:0.01, T:0.26
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:13019 original size:14 final size:14
Alignment explanation
Indices: 13000--13034 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12990 GGACGTGCAC
13000 GGCCTCGCTCGGAT
1 GGCCTCGCTCGGAT
*
13014 GGCCTCACTCGGAT
1 GGCCTCGCTCGGAT
*
13028 GCCCTCG
1 GGCCTCG
13035 GATGCCCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.40, G:0.31, T:0.20
Consensus pattern (14 bp):
GGCCTCGCTCGGAT
Found at i:15589 original size:137 final size:137
Alignment explanation
Indices: 15373--15626 Score: 323
Period size: 137 Copynumber: 1.9 Consensus size: 137
15363 TTGAGGATGT
* * * * * * *
15373 AATTTAATATTAAAATAATGATCTCACGTTATGTAGAAATTTAGATTCTTGTGATATTAAAACGT
1 AATTTAATATTAAAATAATAACCTCACGTTATGCAGAAAATAAAATTCATGTGATATTAAAACGT
* * * *
15438 CTCAAAAAATTTATCACGAGCACTATTTAATATATCTTACGTTTTTTAATACCTCATTTTTTTAG
66 CTCAAAAAATTTATCACGAGCAATATTTAACATATCTCACGTTTTTCAATACCTCATTTTTTTAG
15503 GGGGTGC
131 GGGGTGC
*
15510 AATTTAATATTAGAATTAATAACCTCACGTTATGCA-AAACATAAAATTCATGTGATATTAAAAC
1 AATTTAATATTA-AAATAATAACCTCACGTTATGCAGAAA-ATAAAATTCATGTGATATTAAAAC
** * * *
15574 G-CTTGAGAAATTTATCGCGAGTAATATTTAACATATCTCACGTTTTTCAATAC
64 GTCTCAAAAAATTTATCACGAGCAATATTTAACATATCTCACGTTTTTCAATAC
15627 GTGAGTTTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
137 58 0.59
138 40 0.41
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (137 bp):
AATTTAATATTAAAATAATAACCTCACGTTATGCAGAAAATAAAATTCATGTGATATTAAAACGT
CTCAAAAAATTTATCACGAGCAATATTTAACATATCTCACGTTTTTCAATACCTCATTTTTTTAG
GGGGTGC
Found at i:15648 original size:137 final size:136
Alignment explanation
Indices: 15367--15655 Score: 305
Period size: 137 Copynumber: 2.1 Consensus size: 136
15357 ACTTTTTTGA
* * * * * * * *
15367 GGATGTAATTTAATATTAAAATAATGATCTCACGTTATGTAGAAATTTAGATTCTTGTGATATTA
1 GGATGCAATTTAATATTAAAATAATAACCTCACGTTATGCAGAAAATAAAATTCATGTGATATTA
* * * * *
15432 AAACGTCTCAAAAAATTTATCACGAGCACTATTTAATATATCTTACGTTTTTTAATACCTCATTT
66 AAACGTCTCAAAAAATTTATCACGAGCAATATTTAACATATCTCACGTTTTTCAATACCTCA-TG
15497 TTTTAGG
130 TTTTAGG
* *
15504 GGGTGCAATTTAATATTAGAATTAATAACCTCACGTTATGCA-AAACATAAAATTCATGTGATAT
1 GGATGCAATTTAATATTA-AAATAATAACCTCACGTTATGCAGAAA-ATAAAATTCATGTGATAT
** * * * * *
15568 TAAAACG-CTTGAGAAATTTATCGCGAGTAATATTTAACATATCTCACGTTTTTCAATACGTGA-
64 TAAAACGTCTCAAAAAATTTATCACGAGCAATATTTAACATATCTCACGTTTTTCAATACCTCAT
15631 GTTTTACGG
129 GTTTTA-GG
*
15640 ATGATGCAATTTAATA
1 -GGATGCAATTTAATA
15656 GTGGAATTGA
Statistics
Matches: 124, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
135 5 0.04
136 2 0.02
137 77 0.62
138 40 0.32
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (136 bp):
GGATGCAATTTAATATTAAAATAATAACCTCACGTTATGCAGAAAATAAAATTCATGTGATATTA
AAACGTCTCAAAAAATTTATCACGAGCAATATTTAACATATCTCACGTTTTTCAATACCTCATGT
TTTAGG
Found at i:16595 original size:13 final size:14
Alignment explanation
Indices: 16570--16602 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
16560 AAAATAATAA
16570 ATTATATTTTTAAT
1 ATTATATTTTTAAT
16584 ATTATA-TTTTAAT
1 ATTATATTTTTAAT
*
16597 AATATA
1 ATTATA
16603 ATAATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTATATTTTTAAT
Found at i:16598 original size:32 final size:32
Alignment explanation
Indices: 16522--16600 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
16512 TGAGCTTGAA
*
16522 ATAATATTAATAATATATTACATTTTTAATATT
1 ATAAT-TTAATAATAAATTACATTTTTAATATT
** *
16555 ATAATAAAATAATAAATTATATTTTTAATATT
1 ATAATTTAATAATAAATTACATTTTTAATATT
*
16587 ATATTTTAATAATA
1 ATAATTTAATAATA
16601 TAATAATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 34 0.87
33 5 0.13
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
ATAATTTAATAATAAATTACATTTTTAATATT
Found at i:16805 original size:23 final size:23
Alignment explanation
Indices: 16779--16823 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16769 AATAATATTT
16779 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
16802 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
16824 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:16968 original size:28 final size:29
Alignment explanation
Indices: 16926--16982 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
16916 TTATAAAAAC
**
16926 AATATTTTAGTAATAAATAA-ATT-ATTTT
1 AATATTTTAAAAAT-AATAATATTAATTTT
16954 AATATTTTAAAAATAATAATATTAATTTT
1 AATATTTTAAAAATAATAATATTAATTTT
16983 TATGATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 15 0.60
29 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
AATATTTTAAAAATAATAATATTAATTTT
Found at i:28873 original size:20 final size:20
Alignment explanation
Indices: 28836--28874 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28826 TATTTATTAA
* * *
28836 ATTTTAATGAGATGTTTTTC
1 ATTTTAATAAAATATTTTTC
28856 ATTTTAATAAAATATTTTT
1 ATTTTAATAAAATATTTTT
28875 ATTAAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (20 bp):
ATTTTAATAAAATATTTTTC
Found at i:31528 original size:60 final size:59
Alignment explanation
Indices: 31456--31621 Score: 201
Period size: 60 Copynumber: 2.8 Consensus size: 59
31446 TCTGGATGAT
* * * * *
31456 TTTGGGATGAAATTAGAAGATTCAAAAGTTTAAGGGTTAATTTAAAACT-AG-AGCTATAG
1 TTTGGGATGAAATTAAAATATTTAAAAGTTTAAGGATTAATTTAAAA-TGAGAATC-ATAG
*
31515 TTTGGGAATGAAATTAAAATATTTAAAACTTTAAGGATTAATTTAAAATGAGAATCATAG
1 TTTGGG-ATGAAATTAAAATATTTAAAAGTTTAAGGATTAATTTAAAATGAGAATCATAG
* * *
31575 CTTGGGGATAAAATTAAAATATTTAAAAGTTTATGGATTAATTTAAA
1 -TTTGGGATGAAATTAAAATATTTAAAAGTTTAAGGATTAATTTAAA
31622 GTAAAGGTTA
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
59 7 0.08
60 79 0.85
61 7 0.08
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (59 bp):
TTTGGGATGAAATTAAAATATTTAAAAGTTTAAGGATTAATTTAAAATGAGAATCATAG
Found at i:31620 original size:29 final size:29
Alignment explanation
Indices: 31528--31621 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
31518 GGGAATGAAA
*
31528 TTAAAATATTTAAAACTTTAAGGATTAAT
1 TTAAAATATTTAAAAGTTTAAGGATTAAT
** * * * ** * *
31557 TTAAAATGAGAATCATAGCTTGGGGATAAAA
1 TTAAAAT-A-TTTAAAAGTTTAAGGATTAAT
*
31588 TTAAAATATTTAAAAGTTTATGGATTAAT
1 TTAAAATATTTAAAAGTTTAAGGATTAAT
31617 TTAAA
1 TTAAA
31622 GTAAAGGTTA
Statistics
Matches: 44, Mismatches: 19, Indels: 4
0.66 0.28 0.06
Matches are distributed among these distances:
29 24 0.55
30 2 0.05
31 18 0.41
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (29 bp):
TTAAAATATTTAAAAGTTTAAGGATTAAT
Found at i:36175 original size:28 final size:28
Alignment explanation
Indices: 36135--36198 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
36125 ATGCTATTAG
*
36135 GCAGCTACCGGAAGCGCTTGATCTTCAT
1 GCAGCAACCGGAAGCGCTTGATCTTCAT
36163 GCAGCAACCGGAAGCGCTTGATCTTCAT
1 GCAGCAACCGGAAGCGCTTGATCTTCAT
36191 GCAGCAAC
1 GCAGCAAC
36199 GATGACGGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (28 bp):
GCAGCAACCGGAAGCGCTTGATCTTCAT
Found at i:45735 original size:2 final size:2
Alignment explanation
Indices: 45726--45766 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
45716 GAAAGAAAAA
45726 AT AT -T AT 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 AT AT AT AT
45767 TTAAAACTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:48562 original size:2 final size:2
Alignment explanation
Indices: 48557--48603 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
48547 TTGTACACAC
48557 AT AT AT AT 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 AT AT AT AT
48599 AT AT A
1 AT AT A
48604 ATAACTAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65425 original size:37 final size:37
Alignment explanation
Indices: 65369--65507 Score: 192
Period size: 37 Copynumber: 3.8 Consensus size: 37
65359 ACATGTATTC
* * * *
65369 ATCACTCACACCCGAATCTGAATAACATCGGAAT-TGA
1 ATCATTCACACCTGAATCTGAGTAACATCGG-ATCCGA
*
65406 ATCATTCACACCT-ATATCTGAGTAACATCGGATCCAA
1 ATCATTCACACCTGA-ATCTGAGTAACATCGGATCCGA
*
65443 ATCATTCACACCTGAATCTGAGTAACATCAGATCCGA
1 ATCATTCACACCTGAATCTGAGTAACATCGGATCCGA
65480 ATCATTCACACCTGAATCTGAGTAACAT
1 ATCATTCACACCTGAATCTGAGTAACAT
65508 GGACGTGGAT
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
36 3 0.03
37 88 0.96
38 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (37 bp):
ATCATTCACACCTGAATCTGAGTAACATCGGATCCGA
Found at i:70332 original size:65 final size:65
Alignment explanation
Indices: 70228--70356 Score: 258
Period size: 65 Copynumber: 2.0 Consensus size: 65
70218 ATCAGAGTAT
70228 GAATAAATCAAAACAAACTTTATTTCTACATAAAATAATTTTAACATAAATATTTTTAAACTGAG
1 GAATAAATCAAAACAAACTTTATTTCTACATAAAATAATTTTAACATAAATATTTTTAAACTGAG
70293 GAATAAATCAAAACAAACTTTATTTCTACATAAAATAATTTTAACATAAATATTTTTAAACTGA
1 GAATAAATCAAAACAAACTTTATTTCTACATAAAATAATTTTAACATAAATATTTTTAAACTGA
70357 AGAAACTGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.36
Consensus pattern (65 bp):
GAATAAATCAAAACAAACTTTATTTCTACATAAAATAATTTTAACATAAATATTTTTAAACTGAG
Found at i:72309 original size:70 final size:71
Alignment explanation
Indices: 72184--72327 Score: 218
Period size: 70 Copynumber: 2.0 Consensus size: 71
72174 TCTCGGGTGC
* *
72184 AGCTGACAAAGAAGATGTAGATAACGAACTATTTAACAAAGAAAAATATTCTGCAACTGCATCAA
1 AGCTGACAAAGAAGATGTAGACAACGAACTATTTAACAAAGAAAAACATTCTGCAACTGCATCAA
72249 AAACAA
66 AAACAA
* * * * *
72255 AGCTG-CAAAGAAGGTGTAGACGACGAACTATTTAACAAAGGAAAACATTGTGCAACTGGATCAA
1 AGCTGACAAAGAAGATGTAGACAACGAACTATTTAACAAAGAAAAACATTCTGCAACTGCATCAA
72319 AAACAA
66 AAACAA
72325 AGC
1 AGC
72328 AAAAAGAACG
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
70 61 0.92
71 5 0.08
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (71 bp):
AGCTGACAAAGAAGATGTAGACAACGAACTATTTAACAAAGAAAAACATTCTGCAACTGCATCAA
AAACAA
Found at i:73104 original size:43 final size:43
Alignment explanation
Indices: 73050--73133 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
73040 GATATACAAA
73050 GGGTTAACTTATTCGAAGCACTAACCTTAGGGATCAATACATT
1 GGGTTAACTTATTCGAAGCACTAACCTTAGGGATCAATACATT
73093 GGGTTAACTTATTCGAAGCACTAACCTTAGGGATCAATACA
1 GGGTTAACTTATTCGAAGCACTAACCTTAGGGATCAATACA
73134 ATGTCGGTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (43 bp):
GGGTTAACTTATTCGAAGCACTAACCTTAGGGATCAATACATT
Done.