Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001887.1 Hibiscus syriacus cultivar Beakdansim tig00003830_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: 101052
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:8416 original size:35 final size:34
Alignment explanation
Indices: 8331--8417 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
8321 AATATAATTT
*
8331 TAAATACAACAAACTTACAATAAGAATTAAATAG
1 TAAATACAACAAAATTACAATAAGAATTAAATAG
* * *
8365 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATAG
8403 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
8418 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATAG
Found at i:9024 original size:18 final size:18
Alignment explanation
Indices: 9001--9035 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8991 AGGCGGCGGT
* *
9001 ATCATATATGGTTGTGGC
1 ATCATAAATGGCTGTGGC
9019 ATCATAAATGGCTGTGG
1 ATCATAAATGGCTGTGG
9036 TGGCTGCTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (18 bp):
ATCATAAATGGCTGTGGC
Found at i:10721 original size:17 final size:18
Alignment explanation
Indices: 10701--10741 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
10691 AAATTATATT
10701 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
10718 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
10736 ATTAAA
1 AGTAAA
10742 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:10952 original size:50 final size:52
Alignment explanation
Indices: 10894--11013 Score: 165
Period size: 50 Copynumber: 2.3 Consensus size: 52
10884 CCCCTGTACC
10894 GCGCTATACCCCACGTGTCAGATAAAC-AG-ATATAGCGCGGATCAGGGGCT
1 GCGCTATACCCCACGTGTCAGATAAACGAGCATATAGCGCGGATCAGGGGCT
* * * *
10944 GCGCTATACCCCACGTGTCAGATAAACGTGGCGTATAGCGCTGATCAGGGGGT
1 GCGCTATACCCCACGTGTCAGATAAACG-AGCATATAGCGCGGATCAGGGGCT
*
10997 GTGCTATA-CCCACGTGT
1 GCGCTATACCCCACGTGT
11014 AAGCCATGTC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 27 0.44
52 10 0.16
53 25 0.40
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (52 bp):
GCGCTATACCCCACGTGTCAGATAAACGAGCATATAGCGCGGATCAGGGGCT
Found at i:11560 original size:29 final size:29
Alignment explanation
Indices: 11502--11569 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
11492 GTATTAGTAG
*
11502 TATATATATTTTTTATCATAAATTATATT
1 TATACATATTTTTTATCATAAATTATATT
*
11531 TA-ACATATTTTTT-TTATAAATTAATAATT
1 TATACATATTTTTTATCATAAATT-AT-ATT
11560 TATAC-TATTT
1 TATACATATTT
11570 ACATTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 8 0.24
28 12 0.35
29 12 0.35
30 2 0.06
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (29 bp):
TATACATATTTTTTATCATAAATTATATT
Found at i:16109 original size:12 final size:12
Alignment explanation
Indices: 16081--16113 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16071 GTTGGAGGCT
16081 AGTTGGTTATGAG
1 AGTT-GTTATGAG
16094 -GTTGTTATGAG
1 AGTTGTTATGAG
16105 AGTTGTTAT
1 AGTTGTTAT
16114 ACAGCTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45
Consensus pattern (12 bp):
AGTTGTTATGAG
Found at i:20965 original size:6 final size:6
Alignment explanation
Indices: 20954--20982 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
20944 CATTACTACT
20954 GCTAGG GCTAGG GCTAGG GCTAGG GCTAG
1 GCTAGG GCTAGG GCTAGG GCTAGG GCTAG
20983 TTAGGGCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.17
Consensus pattern (6 bp):
GCTAGG
Found at i:27644 original size:29 final size:29
Alignment explanation
Indices: 27585--27645 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
27575 TAAATATTTA
* * *
27585 TATTTTTATAATTCAAATTGAATAAATAT
1 TATTTTTATAATTAAAAATGAATAAAAAT
*
27614 TATTTTTATTATTAAAAAT-AATAATAAAT
1 TATTTTTATAATTAAAAATGAATAA-AAAT
27643 TAT
1 TAT
27646 AGCTGACTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (29 bp):
TATTTTTATAATTAAAAATGAATAAAAAT
Found at i:31904 original size:2 final size:2
Alignment explanation
Indices: 31897--31921 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31887 CATATACATT
31897 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
31922 CCGGTCTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33125 original size:41 final size:41
Alignment explanation
Indices: 33080--33262 Score: 330
Period size: 41 Copynumber: 4.5 Consensus size: 41
33070 ATTCGCGTTG
33080 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
33121 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
33162 TATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
33203 CATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
33244 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
33263 CTACAGTTGT
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 135 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:33130 original size:20 final size:20
Alignment explanation
Indices: 33081--33259 Score: 133
Period size: 20 Copynumber: 8.8 Consensus size: 20
33071 TTCGCGTTGC
* *
33081 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
** *
33102 AAATCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCA
* *
33122 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
** * *
33143 AAATCGCATTGCGATTTTCT
1 ATTTCGCGTTGCGATTTTCA
* *
33163 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
* *
33184 AATTCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCA
* *
33204 ATTTCGCGTTGCGATAGTTGA
1 ATTTCGCGTTGCGAT-TTTCA
** * *
33225 AAATCACGTTGCGATTTTCC
1 ATTTCGCGTTGCGATTTTCA
33245 ATTTCGCGTTGCGAT
1 ATTTCGCGTTGCGAT
33260 AGTCTACAGT
Statistics
Matches: 116, Mismatches: 39, Indels: 7
0.72 0.24 0.04
Matches are distributed among these distances:
20 59 0.51
21 57 0.49
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTTCGCGTTGCGATTTTCA
Found at i:33294 original size:22 final size:21
Alignment explanation
Indices: 33231--33294 Score: 51
Period size: 22 Copynumber: 3.0 Consensus size: 21
33221 TTGAAAATCA
33231 CGTTGCGATTTTCC-ATTTCG-
1 CGTTGCGATTTTCCAATTT-GT
** * *
33251 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCA-ATTTGT
33273 CGTTGCGATTTTCCAAATTTGT
1 CGTTGCGATTTTCC-AATTTGT
33295 TGTGATAGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
20 11 0.34
21 1 0.03
22 19 0.59
23 1 0.03
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (21 bp):
CGTTGCGATTTTCCAATTTGT
Found at i:33302 original size:82 final size:79
Alignment explanation
Indices: 33080--33309 Score: 284
Period size: 82 Copynumber: 2.8 Consensus size: 79
33070 ATTCGCGTTG
*
33080 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTG-AAATTGCGTTGCGATTTTCCATTT--CGTTGCGATAGTTGAAA
*
33145 ATCGCATTGCGATTTTC
63 ATCACATTGCGATTTTC
*
33162 TATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAATT-GCGTTGCGATTTTCCATTT--CGTTGCGATAGTTGAAA
*
33227 ATCACGTTGCGATTTTC
63 ATCACATTGCGATTTTC
* * *
33244 CATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATTT-GTTGTGATAGTTAA
1 CATTTCGCGTTGCGATAGT-TGA-AATTG-CGTTGCGATTTTCC--ATTTCGTTGCGATAGTTGA
33307 AAA
61 AAA
33310 AAAAGATTTT
Statistics
Matches: 134, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
81 4 0.03
82 108 0.81
83 18 0.13
85 4 0.03
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (79 bp):
CATTTCGCGTTGCGATAGTTGAAATTGCGTTGCGATTTTCCATTTCGTTGCGATAGTTGAAAATC
ACATTGCGATTTTC
Found at i:33392 original size:6 final size:6
Alignment explanation
Indices: 33381--33411 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
33371 GACACGTATT
33381 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
33412 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:33447 original size:22 final size:22
Alignment explanation
Indices: 33421--33492 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
33411 AATTTGGAAA
33421 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
33443 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
33462 ATCGCAACGACAACTGCAGACT
1 ATCGCAACGACAACTGTAGACT
33484 ATCGCAACG
1 ATCGCAACG
33493 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:33467 original size:19 final size:19
Alignment explanation
Indices: 33408--33471 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
33398 GACCACGACC
33408 ACGAATTTGGAAAATCGCA
1 ACGAATTTGGAAAATCGCA
* * **
33427 ACGACAACTGTAGACTATCGCA
1 ACG--AA-TTTGGAAAATCGCA
33449 ACGAATTTGGAAAATCGCA
1 ACGAATTTGGAAAATCGCA
33468 ACGA
1 ACGA
33472 CAACTGCAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 17 0.50
20 2 0.06
21 2 0.06
22 13 0.38
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (19 bp):
ACGAATTTGGAAAATCGCA
Found at i:33572 original size:41 final size:40
Alignment explanation
Indices: 33415--33746 Score: 264
Period size: 41 Copynumber: 8.1 Consensus size: 40
33405 ACCACGAATT
* * * *
33415 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATT
1 TGGAAAATCGCAACG-CGATTTTA-ACTATCGCAACGCGAA-A
* * **
33456 TGGAAAATCGCAACGACAACTGCAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTTTA-ACTATCGCAACGCGAAA
* *
33498 TGGAAAATCACAATGCG-----AACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTAACTATCGCAACGCGAAA
33533 TGGAAAATCGCAACGCGAATTTTAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCG-ATTTTAACTATCGCAACGCGAAA
* *
33574 TGGAAAATCGCAATGCGAATTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCG-ATTTTAACTATCGCAACGCGAAA
* * *
33615 TGGAAAATCGCAACACGATTTTCAACTATCGTAACGCGAATT
1 TGGAAAATCGCAACGCGATTTT-AACTATCGCAACGCGAA-A
*** *
33657 TGCGATAGTGGAGATCGCGTTGCGATTTCAACTATCGCAACGCGAAA
1 TG-GA-A----A-ATCGCAACGCGATTTTAACTATCGCAACGCGAAA
* * *
33704 TGGAAAAACGCAATGCGATTTTCAACTATCGCAATGCGAAA
1 TGGAAAATCGCAACGCGATTTT-AACTATCGCAACGCGAAA
33745 TG
1 TG
33747 CAACGTGAAT
Statistics
Matches: 247, Mismatches: 26, Indels: 36
0.80 0.08 0.12
Matches are distributed among these distances:
35 32 0.13
36 1 0.00
40 16 0.06
41 143 0.58
42 15 0.06
43 6 0.02
44 1 0.00
45 1 0.00
46 2 0.01
47 2 0.01
48 17 0.07
49 11 0.04
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (40 bp):
TGGAAAATCGCAACGCGATTTTAACTATCGCAACGCGAAA
Found at i:33642 original size:82 final size:81
Alignment explanation
Indices: 33481--33746 Score: 319
Period size: 89 Copynumber: 3.2 Consensus size: 81
33471 ACAACTGCAG
*
33481 ACTATCGCAACGCGAAATGGAAAATCACAATGCG-----AACTATCGCAACGCGAAATGGAAAAT
1 ACTATCGCAACGCGAAATGGAAAATCGCAATGCGATTTCAACTATCGCAACGCGAAATGGAAAAT
33541 CGCAACGCGAATTTT-A
66 CGCAACGCG-ATTTTCA
33557 ACTATCGCAACGCGAAATGGAAAATCGCAATGCGAATTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAATGCG-ATTTCAACTATCGCAACGCGAAATGGAAAA
*
33622 TCGCAACACGATTTTCA
65 TCGCAACGCGATTTTCA
* * **
33639 ACTATCGTAACGCGAATTTGCGATAGTGGAGATCGCGTTGCGATTTCAACTATCGCAACGCGAAA
1 ACTATCGCAACGCGAA-ATG-GA-A----A-ATCGCAATGCGATTTCAACTATCGCAACGCGAAA
* *
33704 TGGAAAAACGCAATGCGATTTTCA
58 TGGAAAATCGCAACGCGATTTTCA
*
33728 ACTATCGCAATGCGAAATG
1 ACTATCGCAACGCGAAATG
33747 CAACGTGAAT
Statistics
Matches: 163, Mismatches: 12, Indels: 18
0.84 0.06 0.09
Matches are distributed among these distances:
76 33 0.20
81 5 0.03
82 50 0.31
83 2 0.01
84 2 0.01
85 1 0.01
88 2 0.01
89 59 0.36
90 9 0.06
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (81 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAATGCGATTTCAACTATCGCAACGCGAAATGGAAAAT
CGCAACGCGATTTTCA
Found at i:33750 original size:21 final size:21
Alignment explanation
Indices: 33685--33750 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
33675 GTTGCGATTT
*
33685 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAATGCGAAATG
* * * ** *
33706 GAA-AAACGCAATGCGATTTT
1 CAACTATCGCAATGCGAAATG
33726 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAATGCGAAATG
33747 CAAC
1 CAAC
33751 GTGAATTTGC
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (21 bp):
CAACTATCGCAATGCGAAATG
Found at i:34145 original size:2 final size:2
Alignment explanation
Indices: 34138--34167 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34128 TTAGTTTTTC
34138 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
34168 GTAATTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36520 original size:22 final size:23
Alignment explanation
Indices: 36479--36524 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
36469 GAGGTGGAGC
36479 AAAGAGGAAAAGAAAGTCGAAGG
1 AAAGAGGAAAAGAAAGTCGAAGG
36502 AAAGAGGAAAAG-AAGTCGAAGG
1 AAAGAGGAAAAGAAAGTCGAAGG
36524 A
1 A
36525 CCATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.57, C:0.04, G:0.35, T:0.04
Consensus pattern (23 bp):
AAAGAGGAAAAGAAAGTCGAAGG
Found at i:43222 original size:28 final size:28
Alignment explanation
Indices: 43185--43240 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
43175 TGGATTAAGG
43185 TTTGAACAAATATTTATGAATGAATGGT
1 TTTGAACAAATATTTATGAATGAATGGT
43213 TTTGAACAAATATTTATGAATGAATGGT
1 TTTGAACAAATATTTATGAATGAATGGT
43241 ATCTTACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (28 bp):
TTTGAACAAATATTTATGAATGAATGGT
Found at i:46786 original size:39 final size:38
Alignment explanation
Indices: 46713--46837 Score: 128
Period size: 39 Copynumber: 3.2 Consensus size: 38
46703 CTTATTGGTC
* * * *
46713 TGAAGAAGCCATGCA-CTCTGGGGTCTTCTCCATTTGAT
1 TGAAGACGCCATGCAGTTGTGGGGTCTTCTTCATTTG-T
*
46751 TGAAGACGCCATGCAGTTGTGGGGTATTCTTCATTTGT
1 TGAAGACGCCATGCAGTTGTGGGGTCTTCTTCATTTGT
* * *
46789 CTGAAGACGCCATGCAGTCGTGGAGTCTTCAT-ATTTAGCT
1 -TGAAGACGCCATGCAGTTGTGGGGTCTTCTTCATTT-G-T
46829 TGAAGACGC
1 TGAAGACGC
46838 GTGGATCACC
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
38 19 0.26
39 54 0.73
40 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (38 bp):
TGAAGACGCCATGCAGTTGTGGGGTCTTCTTCATTTGT
Found at i:59520 original size:24 final size:24
Alignment explanation
Indices: 59475--59524 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
59465 TGGTGGTTGG
59475 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
59499 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
59523 TT
1 TT
59525 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:62771 original size:13 final size:14
Alignment explanation
Indices: 62753--62782 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
62743 TTTGTTTGTT
62753 TTTCTTTA-TTTTA
1 TTTCTTTATTTTTA
62766 TTTCTTTATTTTTA
1 TTTCTTTATTTTTA
62780 TTT
1 TTT
62783 TTAATATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCTTTATTTTTA
Found at i:63958 original size:20 final size:20
Alignment explanation
Indices: 63929--63973 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
63919 GTAGCAGCGT
*
63929 AAAAAATGAAAAAGTAA-AA
1 AAAAAATGAAAAAATAAGAA
63948 AAAAAAGTGAAAAAATAAGAA
1 AAAAAA-TGAAAAAATAAGAA
63969 AAAAA
1 AAAAA
63974 TGTGTACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (20 bp):
AAAAAATGAAAAAATAAGAA
Found at i:68573 original size:36 final size:36
Alignment explanation
Indices: 68522--68661 Score: 194
Period size: 36 Copynumber: 3.9 Consensus size: 36
68512 TGAATAAGAA
* *
68522 GAACGAAAGGAAGCATCAGCACTTTCGGTTCAAAAT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
* *
68558 AAACGGAAGGAAGCATCGGCACTTTCGATTCAAGAA-
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA-AAT
*
68594 GAACGAAAGGAAGCATCGGCACTTTCGATTC-AAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
* *
68629 GAACGGAAGGAAGCATCCGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA
68662 TTGTTCATCT
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
34 1 0.01
35 30 0.33
36 59 0.64
37 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
Found at i:76180 original size:15 final size:15
Alignment explanation
Indices: 76160--76192 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
76150 TGAAAGTTAC
76160 ATTTAAATCAATGAT
1 ATTTAAATCAATGAT
76175 ATTTAAATCAATGAT
1 ATTTAAATCAATGAT
76190 ATT
1 ATT
76193 CTTTGTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
ATTTAAATCAATGAT
Found at i:76592 original size:20 final size:20
Alignment explanation
Indices: 76567--76616 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
76557 GACCAACAAA
76567 TTCGCAACGCAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
*
76587 TTCGCAACGTAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
76607 TTCGCAACGC
1 TTCGCAACGC
76617 GAATATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.34, G:0.12, T:0.22
Consensus pattern (20 bp):
TTCGCAACGCAAACTCCAAT
Found at i:76841 original size:22 final size:22
Alignment explanation
Indices: 76796--76841 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
76786 GCGACATCCG
* **
76796 TCCCCATCTCCTACGAAATTCA
1 TCCCCATCTCCGACGAAACCCA
76818 TCCCCATCTCCGACGAAACCCA
1 TCCCCATCTCCGACGAAACCCA
76840 TC
1 TC
76842 TATCTCCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.46, G:0.07, T:0.22
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAACCCA
Found at i:77237 original size:20 final size:20
Alignment explanation
Indices: 77212--77251 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
77202 GAAAATCGCA
77212 CGATTTTCATTTTCGCGTTG
1 CGATTTTCATTTTCGCGTTG
*
77232 CGATTTTCATTTTCGTGTTG
1 CGATTTTCATTTTCGCGTTG
77252 TGAATTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.17, G:0.20, T:0.53
Consensus pattern (20 bp):
CGATTTTCATTTTCGCGTTG
Found at i:79227 original size:4 final size:4
Alignment explanation
Indices: 79218--79263 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
79208 TTTTTCGGCA
* * * *
79218 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
79264 TTAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:79426 original size:21 final size:21
Alignment explanation
Indices: 79400--79505 Score: 92
Period size: 21 Copynumber: 5.0 Consensus size: 21
79390 GAAGCCCGAT
79400 GCACCTATCATCGTTCAAGAG
1 GCACCTATCATCGTTCAAGAG
*
79421 GCACCT-TCTATCTTTCAAGAG
1 GCACCTATC-ATCGTTCAAGAG
*
79442 GC-CTCTATCATC-ATCGAAGAG
1 GCAC-CTATCATCGTTC-AAGAG
* ** *
79463 GCCCCTCCCACCGTTCAAGAG
1 GCACCTATCATCGTTCAAGAG
* *
79484 GCCCCTGTCATCGTTCAAGAG
1 GCACCTATCATCGTTCAAGAG
79505 G
1 G
79506 TCCGAGACCG
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.07
21 60 0.86
22 5 0.07
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (21 bp):
GCACCTATCATCGTTCAAGAG
Found at i:79451 original size:42 final size:42
Alignment explanation
Indices: 79403--79505 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
79393 GCCCGATGCA
* * * *
79403 CCTATCATCGTTCAAGAGGCACCTTCTATCTTTCAAGAGGCC
1 CCTATCATCGTTCAAGAGGCACCTCCCACCGTTCAAGAGGCC
* * *
79445 TCTATCATC-ATCGAAGAGGCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCGTTC-AAGAGGCACCTCCCACCGTTCAAGAGGCC
*
79487 CCTGTCATCGTTCAAGAGG
1 CCTATCATCGTTCAAGAGG
79506 TCCGAGACCG
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.04
42 45 0.92
43 2 0.04
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (42 bp):
CCTATCATCGTTCAAGAGGCACCTCCCACCGTTCAAGAGGCC
Found at i:81003 original size:66 final size:65
Alignment explanation
Indices: 80844--81019 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
80834 TGGGGTATAC
80844 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAA
1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAA
80908 GAATTA
60 GAATTA
* *
80914 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT
80978 A
65 A
80979 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
81020 GTTTTAAATT
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 17 0.17
65 19 0.19
66 40 0.40
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:81138 original size:20 final size:20
Alignment explanation
Indices: 81113--81183 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
81103 TTGTAATTTT
* * *
81113 GTCAAATTCGAAATGCAAAA
1 GTCAAATTCGCAACGCGAAA
81133 GTCAAATTCGCAACGCGAAA
1 GTCAAATTCGCAACGCGAAA
*
81153 GTCAAATTTGCAACGCGAAA
1 GTCAAATTCGCAACGCGAAA
81173 GTCAAATTCGC
1 GTCAAATTCGC
81184 GTTACGATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (20 bp):
GTCAAATTCGCAACGCGAAA
Found at i:81529 original size:6 final size:6
Alignment explanation
Indices: 81520--81555 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
81510 TTGTGATTAA
**
81520 GATTTT GATTTT GATTGC GATTTT GATTTT GATTTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT
81556 CTTTTGCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.17, C:0.03, G:0.19, T:0.61
Consensus pattern (6 bp):
GATTTT
Found at i:83197 original size:64 final size:65
Alignment explanation
Indices: 83018--83177 Score: 259
Period size: 65 Copynumber: 2.5 Consensus size: 65
83008 GATTTAATTG
* * *
83018 AACATCGAATGCATTTTATGCATCGATGTACATACCATGAATCGATGCACTCAGGGTTTTATAAA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
* *
83083 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTT-TCAA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
*
83147 AACATCGAATGCATTTTATGTATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
83178 TCTTAGTGCA
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
64 32 0.36
65 56 0.64
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
Found at i:89026 original size:24 final size:23
Alignment explanation
Indices: 88998--89077 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
88988 CACTTAACAA
88998 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CCTTTGAATG
* *
89022 TGCATCGATTCATCATGTTG-A--
1 TGCATCGATGCATCCT-TTGAATG
* *
89043 TGCACCGATGCAAGCC-TTGAATG
1 TGCATCGATGC-ATCCTTTGAATG
89066 TGCATCGATGCA
1 TGCATCGATGCA
89078 CAGGGTCATG
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
20 3 0.07
21 10 0.23
22 3 0.07
23 13 0.30
24 15 0.34
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (23 bp):
TGCATCGATGCATCCTTTGAATG
Found at i:91962 original size:64 final size:65
Alignment explanation
Indices: 91783--91942 Score: 277
Period size: 65 Copynumber: 2.5 Consensus size: 65
91773 GATTTAATTG
*
91783 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGGTTTTATAAA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
* * *
91848 AACATCGAATGCATTTGATGCATCAATGCACATACCATGCATCGATGCACTCAGGCTTTT-TCAA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
91912 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
91943 TCTTAGTGCA
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 32 0.36
65 57 0.64
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
Found at i:92761 original size:40 final size:40
Alignment explanation
Indices: 92712--92800 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
92702 TTTTCATTCA
92712 ATATTCATTTTGCTTTCAAGAACACTTATTGTGCTCAATT
1 ATATTCATTTTGCTTTCAAGAACACTTATTGTGCTCAATT
92752 ATATTCATTTTGCTTTCAAGAACACTTATTGTGCTCAATT
1 ATATTCATTTTGCTTTCAAGAACACTTATTGTGCTCAATT
*
92792 GTATTCATT
1 ATATTCATT
92801 CTTGAGTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (40 bp):
ATATTCATTTTGCTTTCAAGAACACTTATTGTGCTCAATT
Found at i:92770 original size:21 final size:21
Alignment explanation
Indices: 92711--92773 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
92701 TTTTTCATTC
92711 AATATTCATTTTGCTTTCAAG
1 AATATTCATTTTGCTTTCAAG
* * *
92732 AACACTT-ATTGTGC--TCAAT
1 AATA-TTCATTTTGCTTTCAAG
*
92751 TATATTCATTTTGCTTTCAAG
1 AATATTCATTTTGCTTTCAAG
92772 AA
1 AA
92774 CACTTATTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
18 2 0.07
19 12 0.40
21 14 0.47
22 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (21 bp):
AATATTCATTTTGCTTTCAAG
Found at i:92786 original size:21 final size:21
Alignment explanation
Indices: 92722--92786 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
92712 ATATTCATTT
92722 TGCTTTCAAGAACACTTATTG
1 TGCTTTCAAGAACACTTATTG
** * *
92743 TGC--TCAATTATA-TTCATTT
1 TGCTTTCAAGAACACTT-ATTG
92762 TGCTTTCAAGAACACTTATTG
1 TGCTTTCAAGAACACTTATTG
92783 TGCT
1 TGCT
92787 CAATTGTATT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
18 2 0.06
19 12 0.38
21 16 0.50
22 2 0.06
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.43
Consensus pattern (21 bp):
TGCTTTCAAGAACACTTATTG
Found at i:94297 original size:24 final size:24
Alignment explanation
Indices: 94263--94316 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
94253 CCATCACATC
94263 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
94287 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
94311 ATCAAA
1 ATCAAA
94317 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:94330 original size:24 final size:24
Alignment explanation
Indices: 94263--94330 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
94253 CCATCACATC
* * *
94263 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
94287 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
94311 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
94331 TAGTACTTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:95319 original size:20 final size:21
Alignment explanation
Indices: 95231--95320 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 21
95221 CCAAAACATT
*
95231 TGTGTTGCGAAATT-AAATTC
1 TGTGTTGCGAATTTGAAATTC
*
95251 -GTGTTGCGAATTTGAAAATC
1 TGTGTTGCGAATTTGAAATTC
* * *
95271 T-AGATGCGAATTTGAAATTT
1 TGTGTTGCGAATTTGAAATTC
* *
95291 TGCGTTGCGAATTTG-ACTTC
1 TGTGTTGCGAATTTGAAATTC
95311 TGTGTTGCGA
1 TGTGTTGCGA
95321 TTTACATATT
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 12 0.21
20 33 0.59
21 11 0.20
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (21 bp):
TGTGTTGCGAATTTGAAATTC
Found at i:95377 original size:20 final size:19
Alignment explanation
Indices: 95328--95381 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
95318 CGATTTACAT
95328 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
95347 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
95367 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
95382 TTTGTTAGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Done.