Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004736.1 Hibiscus syriacus cultivar Beakdansim tig00010692_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: 65135
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7154 original size:18 final size:18
Alignment explanation
Indices: 7131--7172 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
7121 TCAACTCCCA
*
7131 TCGATCCTGAACCTGTCG
1 TCGATCCTGAACCTATCG
7149 TCGATCCTGAACCTATCG
1 TCGATCCTGAACCTATCG
7167 TCGATC
1 TCGATC
7173 TCCCTCCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.29
Consensus pattern (18 bp):
TCGATCCTGAACCTATCG
Found at i:22329 original size:36 final size:35
Alignment explanation
Indices: 22232--22330 Score: 126
Period size: 36 Copynumber: 2.8 Consensus size: 35
22222 GTAACATAGT
*
22232 CATCAATTACATTCTAAACCCTAAATTCCAAAATA
1 CATCAATTACATTCTAAACCCAAAATTCCAAAATA
* * *
22267 CTTAAATTACATTCTAAACCTAAAATTCCAAAAATA
1 CATCAATTACATTCTAAACCCAAAATTCC-AAAATA
* * *
22303 CATCAATTACATGCTCAACCCCAAATTC
1 CATCAATTACATTCTAAACCCAAAATTC
22331 ATAATCTATT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
35 25 0.47
36 28 0.53
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.28
Consensus pattern (35 bp):
CATCAATTACATTCTAAACCCAAAATTCCAAAATA
Found at i:22962 original size:37 final size:37
Alignment explanation
Indices: 22849--22962 Score: 96
Period size: 37 Copynumber: 3.2 Consensus size: 37
22839 CTCACATGCC
22849 ACATCATCTTCTACTGACGGCAATAAAACGGACGGTT
1 ACATCATCTTCTACTGACGGCAATAAAACGGACGGTT
* * *** * *
22886 ACATCA-CATTCTA--AAC-G-AACT-AAATGTTTGATG
1 ACATCATC-TTCTACTGACGGCAA-TAAAACGGACGGTT
22919 ACCATCATCTTCTACTGACGGCAATAAAACGGACGGTT
1 A-CATCATCTTCTACTGACGGCAATAAAACGGACGGTT
22957 ACATCA
1 ACATCA
22963 CACATTCTAA
Statistics
Matches: 54, Mismatches: 14, Indels: 18
0.63 0.16 0.21
Matches are distributed among these distances:
33 9 0.17
34 12 0.22
35 3 0.06
36 3 0.06
37 18 0.33
38 9 0.17
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (37 bp):
ACATCATCTTCTACTGACGGCAATAAAACGGACGGTT
Found at i:27550 original size:2 final size:2
Alignment explanation
Indices: 27543--27570 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27533 ATGTGAAGGC
27543 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
27571 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35126 original size:29 final size:29
Alignment explanation
Indices: 35083--35165 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
35073 CTCACCTAAC
35083 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
35113 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
35142 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
35166 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:39893 original size:29 final size:29
Alignment explanation
Indices: 39850--39932 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
39840 CTCACCTAAC
39850 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
39880 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
39909 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
39933 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:42086 original size:23 final size:23
Alignment explanation
Indices: 42059--42103 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
42049 AATCGAACAC
42059 TGAACTTTCTCCTCTCACGTAAG
1 TGAACTTTCTCCTCTCACGTAAG
*
42082 TGAACTTTCTCCTTTCACGTAA
1 TGAACTTTCTCCTCTCACGTAA
42104 TTATTTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.38
Consensus pattern (23 bp):
TGAACTTTCTCCTCTCACGTAAG
Found at i:45967 original size:3 final size:3
Alignment explanation
Indices: 45959--45996 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
45949 TGTTTCCTAT
45959 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
45997 TCAATTGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47406 original size:14 final size:15
Alignment explanation
Indices: 47295--47412 Score: 148
Period size: 15 Copynumber: 7.5 Consensus size: 15
47285 TAATAAAGTT
47295 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
47310 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
47325 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
47340 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
47355 ATTTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
47374 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
47392 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
47406 ATTTATT
1 ATTTATT
47413 AGTATGGATT
Statistics
Matches: 92, Mismatches: 4, Indels: 15
0.83 0.04 0.14
Matches are distributed among these distances:
14 12 0.13
15 59 0.64
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 7 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:47430 original size:32 final size:32
Alignment explanation
Indices: 47392--47601 Score: 177
Period size: 32 Copynumber: 7.4 Consensus size: 32
47382 TTTTAAAATA
47392 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
47424 ATTTATTTT--A-AA---A-TA-T-T-GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
47446 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
47478 ATTTA--TT--AT--TGTAGTT-GTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
*
47504 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
47536 ATTTATTTT--A-AA---A-TA-TA--GATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
**
47558 ATTTATTTTAAATAATTTATTAGTATAAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
47590 ATTTATTTTAAA
1 ATTTATTTTAAA
47602 ATATGGATTG
Statistics
Matches: 144, Mismatches: 6, Indels: 56
0.70 0.03 0.27
Matches are distributed among these distances:
22 27 0.19
23 1 0.01
24 5 0.03
25 8 0.06
26 20 0.14
27 2 0.01
28 6 0.04
29 8 0.06
30 9 0.06
31 3 0.02
32 55 0.38
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:47431 original size:22 final size:22
Alignment explanation
Indices: 47415--47457 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
47405 AATTTATTAG
47415 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
47437 TATTGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
47458 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:47447 original size:69 final size:67
Alignment explanation
Indices: 47310--47467 Score: 212
Period size: 69 Copynumber: 2.3 Consensus size: 67
47300 TTTTAAAATA
47310 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
47375 TG
66 TG
* ** * * * *
47377 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAATTTATTATAAAATATG
47441 GATTG
63 GATTG
47446 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
47468 GTATGGATTG
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
66 13 0.16
67 22 0.28
68 13 0.16
69 32 0.40
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGGAT
TG
Found at i:47458 original size:54 final size:54
Alignment explanation
Indices: 47392--47618 Score: 337
Period size: 54 Copynumber: 4.1 Consensus size: 54
47382 TTTTAAAATA
* *
47392 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
* ***
47446 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTA-T-TT-TA-AAATATGGATTG
* *
47504 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
*
47558 ATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
47612 ATTTATT
1 ATTTATT
47619 ATTGTAGTTG
Statistics
Matches: 156, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
54 102 0.65
55 3 0.02
56 4 0.03
57 3 0.02
58 44 0.28
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
Found at i:47518 original size:112 final size:112
Alignment explanation
Indices: 47392--47596 Score: 365
Period size: 112 Copynumber: 1.8 Consensus size: 112
47382 TTTTAAAATA
* * *
47392 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTAATTTATTTTAA
**
47457 ATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGGATTG
66 ATAATTTATTAGTATAAATTGATTTATTATTGTAGTTGTATGGATTG
47504 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTAATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTAATTTATTTTAA
47569 ATAATTTATTAGTATAAATTGATTTATT
66 ATAATTTATTAGTATAAATTGATTTATT
47597 TTAAAATATG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 88 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (112 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTAATTTATTTTAA
ATAATTTATTAGTATAAATTGATTTATTATTGTAGTTGTATGGATTG
Found at i:47575 original size:14 final size:15
Alignment explanation
Indices: 47554--47601 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
47544 TAAAATATAG
47554 ATTAATTTATTTTAA
1 ATTAATTTATTTTAA
47569 A-TAATTTATTAGTATAA
1 ATTAATTTATT--T-TAA
*
47586 ATTGATTTATTTTAA
1 ATTAATTTATTTTAA
47601 A
1 A
47602 ATATGGATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 9 0.32
15 5 0.18
16 2 0.07
17 4 0.14
18 8 0.29
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (15 bp):
ATTAATTTATTTTAA
Found at i:47579 original size:22 final size:22
Alignment explanation
Indices: 47527--47569 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
47517 AATTTATTAG
*
47527 TATAGATTGATTTATTTTAAAA
1 TATAGATTAATTTATTTTAAAA
47549 TATAGATTAATTTATTTTAAA
1 TATAGATTAATTTATTTTAAA
47570 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TATAGATTAATTTATTTTAAAA
Found at i:47595 original size:18 final size:18
Alignment explanation
Indices: 47518--47596 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
47508 ATTTTAAATA
*
47518 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAAATTG
*
47536 ATTTATT-TTA-AAATATAG
1 ATTTATTAGTATAAAT-T-G
* * * *
47554 ATTAATTTATTTTAAA-TA
1 ATTTA-TTAGTATAAATTG
47572 ATTTATTAGTATAAATTG
1 ATTTATTAGTATAAATTG
47590 ATTTATT
1 ATTTATT
47597 TTAAAATATG
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
16 3 0.07
17 11 0.24
18 24 0.52
19 3 0.07
20 2 0.04
21 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
ATTTATTAGTATAAATTG
Found at i:47657 original size:14 final size:14
Alignment explanation
Indices: 47638--47690 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
47628 GTATGGATTG
47638 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
47652 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
47670 ATTTATTTTAAATA
1 ATTTATTTTAAATA
47684 ATTTATT
1 ATTTATT
47691 ATTGTAGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 17 0.55
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:47670 original size:32 final size:32
Alignment explanation
Indices: 47628--47691 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
47618 TATTGTAGTT
*
47628 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
47660 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
47692 TTGTAGATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
GTATGAATTGATTTATTTTAAATAATTTATTA
Found at i:47763 original size:31 final size:31
Alignment explanation
Indices: 47705--47764 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
47695 TAGATGTATG
* **
47705 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATATCAGTATTACAAAACTAA
47736 AATTATTTAAATATCAGTATTACAAAACT
1 AATTATTTAAATATCAGTATTACAAAACT
47765 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATATCAGTATTACAAAACTAA
Found at i:48432 original size:20 final size:20
Alignment explanation
Indices: 48407--48646 Score: 96
Period size: 20 Copynumber: 11.7 Consensus size: 20
48397 AAATGACCAA
48407 CAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGTGATAGT
**
48427 CAAATTCGCAACACAGA-AGT
1 CAAATTCGCAAC-GTGATAGT
* *
48447 CAAATTCGTAACGCGATAGT
1 CAAATTCGCAACGTGATAGT
* **** * *
48467 CAAATTTGCAATACAAAAAT
1 CAAATTCGCAACGTGATAGT
* * *
48487 TAAATTCACAACGCAAACGCGAAAGT
1 CAAATT-----CGC-AACGTGATAGT
*
48513 CAAATTCGCAACGTGA-ACT
1 CAAATTCGCAACGTGATAGT
*
48532 CCAATTTCGCAACGTGAATAGT
1 -CAAATTCGCAACGTG-ATAGT
* * *
48554 -AAAATCGCAACGCGA-ACTT
1 CAAATTCGCAACGTGATA-GT
* *
48573 CAATTTCGCAATGTGAATAGT
1 CAAATTCGCAACGTG-ATAGT
* *
48594 AAAAATCGCAACGTGAATAGT
1 CAAATTCGCAACGTG-ATAGT
*
48615 GAAA-TCGCAACGTGAATAGT
1 CAAATTCGCAACGTG-ATAGT
*
48635 -AAAATCGCAACG
1 CAAATTCGCAACG
48647 AATATATGTA
Statistics
Matches: 167, Mismatches: 37, Indels: 32
0.71 0.16 0.14
Matches are distributed among these distances:
18 1 0.01
19 9 0.05
20 112 0.67
21 28 0.17
22 3 0.02
25 2 0.01
26 12 0.07
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGTGATAGT
Found at i:48492 original size:40 final size:40
Alignment explanation
Indices: 48407--48500 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 40
48397 AAATGACCAA
* * *
48407 CAAATTCGCAACGTGATAGTCAAATTCGCAACACAGAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAAT
* * *
48447 CAAATTCGTAACGCGATAGTCAAATTTGCAATACAAAAAT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAAT
* *
48487 TAAATTCACAACGC
1 CAAATTCGCAACGC
48501 AAACGCGAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAAT
Found at i:48562 original size:40 final size:40
Alignment explanation
Indices: 48518--48646 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
48508 AAAGTCAAAT
*
48518 TCGCAACGTGAACTCCAATTTCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAACTTCAATTTCGCAACGTGAATAGTAAAA
* *
48558 TCGCAACGCGAACTTCAATTTCGCAATGTGAATAGTAAAAA
1 TCGCAACGTGAACTTCAATTTCGCAACGTGAATAGT-AAAA
* *
48599 TCGCAACGTGAA-TAGTGAA-ATCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAACT--TCAATTTCGCAACGTGAATAGTAAAA
48639 TCGCAACG
1 TCGCAACG
48647 AATATATGTA
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
40 46 0.58
41 30 0.38
42 3 0.04
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (40 bp):
TCGCAACGTGAACTTCAATTTCGCAACGTGAATAGTAAAA
Found at i:48604 original size:21 final size:20
Alignment explanation
Indices: 48538--48646 Score: 132
Period size: 20 Copynumber: 5.4 Consensus size: 20
48528 AACTCCAATT
48538 TCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
* **
48558 TCGCAACGCGAACT--TCAATT
1 TCGCAACGTGAA-TAGT-AAAA
*
48578 TCGCAATGTGAATAGTAAAAA
1 TCGCAACGTGAATAGT-AAAA
*
48599 TCGCAACGTGAATAGTGAAA
1 TCGCAACGTGAATAGTAAAA
48619 TCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
48639 TCGCAACG
1 TCGCAACG
48647 AATATATGTA
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
19 2 0.03
20 53 0.72
21 19 0.26
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAACGTGAATAGTAAAA
Found at i:48997 original size:21 final size:19
Alignment explanation
Indices: 48973--49022 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
48963 AATTCGCAAC
48973 GCGATTTTTTAAATTCGCGTT
1 GCGATTTTTT--ATTCGCGTT
48994 GCGATTTTATTATTCGCGTT
1 GCGATTTT-TTATTCGCGTT
49014 GCGATTTTT
1 GCGATTTTT
49023 ATTATTCACG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.04
20 17 0.61
21 8 0.29
22 2 0.07
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (19 bp):
GCGATTTTTTATTCGCGTT
Found at i:49008 original size:20 final size:21
Alignment explanation
Indices: 48985--49029 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
48975 GATTTTTTAA
48985 ATTCGCGTTGCGA-TTTTATT
1 ATTCGCGTTGCGATTTTTATT
49005 ATTCGCGTTGCGATTTTTATT
1 ATTCGCGTTGCGATTTTTATT
49026 ATTC
1 ATTC
49030 ACGCTACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (21 bp):
ATTCGCGTTGCGATTTTTATT
Found at i:49039 original size:21 final size:21
Alignment explanation
Indices: 48998--49042 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
48988 CGCGTTGCGA
* * *
48998 TTTTATTATTCGCGTTGCGAT
1 TTTTATTATTCACGCTACGAT
49019 TTTTATTATTCACGCTACGAT
1 TTTTATTATTCACGCTACGAT
49040 TTT
1 TTT
49043 GGAAATTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (21 bp):
TTTTATTATTCACGCTACGAT
Found at i:52163 original size:30 final size:30
Alignment explanation
Indices: 52127--52195 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
52117 AGTGGTCTAG
52127 ACGTCTTCCCAAAGACATTAGGTAATTCAC
1 ACGTCTTCCCAAAGACATTAGGTAATTCAC
* *
52157 ACGTCTTCCCAAATATATTAGGTAATTCAC
1 ACGTCTTCCCAAAGACATTAGGTAATTCAC
*
52187 ATGTCTTCC
1 ACGTCTTCC
52196 TACCGTCACC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (30 bp):
ACGTCTTCCCAAAGACATTAGGTAATTCAC
Found at i:57784 original size:35 final size:35
Alignment explanation
Indices: 57738--57807 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
57728 TAGGCTTTAT
57738 AAACTTACATTAGATAATTCAAGTCAATCTCAACC
1 AAACTTACATTAGATAATTCAAGTCAATCTCAACC
57773 AAACTTACATTAGATAATTCAAGTCAATCTCAACC
1 AAACTTACATTAGATAATTCAAGTCAATCTCAACC
57808 TACCTTGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (35 bp):
AAACTTACATTAGATAATTCAAGTCAATCTCAACC
Found at i:64680 original size:21 final size:21
Alignment explanation
Indices: 64642--64682 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
64632 TATTAAAGTT
* * *
64642 TAAAATATTCAAATTAAAATC
1 TAAAATACTAAAAATAAAATC
64663 TAAAATACTAAAAATAAAAT
1 TAAAATACTAAAAATAAAAT
64683 AAATTATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAATACTAAAAATAAAATC
Done.