Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000347.1 Hibiscus syriacus cultivar Beakdansim tig00000640_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: 70833
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:8864 original size:25 final size:26
Alignment explanation
Indices: 8814--8864 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
8804 GTTTCAATTT
8814 TTTTCGGTTATCGGTTTTTTGAATCGA
1 TTTTCGGTTATC-GTTTTTTGAATCGA
* *
8841 TTTTCGGTTAT-TTTTTTTGGATCG
1 TTTTCGGTTATCGTTTTTTGAATCG
8865 TTTGGATCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
27 11 0.50
ACGTcount: A:0.12, C:0.10, G:0.22, T:0.57
Consensus pattern (26 bp):
TTTTCGGTTATCGTTTTTTGAATCGA
Found at i:16123 original size:13 final size:13
Alignment explanation
Indices: 16105--16148 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
16095 ATGATAAATA
*
16105 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
16118 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
16131 AAACAACTACAAT
1 AAAAAACTACAAT
16144 AAAAA
1 AAAAA
16149 GTACTAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:16629 original size:36 final size:36
Alignment explanation
Indices: 16573--16642 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
16563 GCATCCAGGA
* * *
16573 GGGGTCATAAAACTCTGTGAAGGCGGCGGCGGCGGC
1 GGGGTCATAAAACTCAGTGAAGGCGACAGCGGCGGC
16609 GGGGTCATAAAAC-CAAGTGAAGGCGACAGCGGCG
1 GGGGTCATAAAACTC-AGTGAAGGCGACAGCGGCG
16643 ACATCTGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.26, C:0.21, G:0.41, T:0.11
Consensus pattern (36 bp):
GGGGTCATAAAACTCAGTGAAGGCGACAGCGGCGGC
Found at i:20606 original size:17 final size:17
Alignment explanation
Indices: 20584--20651 Score: 61
Period size: 16 Copynumber: 4.1 Consensus size: 17
20574 TTTATTTTTA
20584 AATTATCTATTTAAATT
1 AATTATCTATTTAAATT
*
20601 AATTATCTA-TTCAATT
1 AATTATCTATTTAAATT
* * *
20617 ATTTATTTATTTGAAATA
1 AATTATCTATTT-AAATT
20635 ATATTAT-T-TTTAAATT
1 A-ATTATCTATTTAAATT
20651 A
1 A
20652 TCTATTTAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
16 18 0.44
17 14 0.34
18 5 0.12
19 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (17 bp):
AATTATCTATTTAAATT
Found at i:23615 original size:24 final size:23
Alignment explanation
Indices: 23588--23632 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
23578 AGTTTAACAT
23588 TTTTAATCTTAGTTATTTTTTTCC
1 TTTTAATCTTAG-TATTTTTTTCC
* *
23612 TTTTAATTTTTGTATTTTTTT
1 TTTTAATCTTAGTATTTTTTT
23633 ATTTGTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTAATCTTAGTATTTTTTTCC
Found at i:27497 original size:106 final size:106
Alignment explanation
Indices: 27351--28675 Score: 2023
Period size: 106 Copynumber: 12.6 Consensus size: 106
27341 CTCGAGAGTA
* * * * * * *
27351 AATTTCAACTTCTCAATGAAGGATCTT-GAATCCAAGACAACACAAGCTCAACTTCATGACGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
27415 GGGCGGCTGATTGTCAACAAACAACTTCTCAATTTCAGAGCC
65 GGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
* *
27457 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
27522 GACCGTTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
* * *
27563 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAGTTCGACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
27628 GACCGCTGGTTGTCAA-CAACAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
27668 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
27733 GACCGCTGCTTGTCAA-CAACAACTTCTCAATTTCAGAGTC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
* *
27773 AATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCATGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
27838 GACCGCTGGTTGTCAAT--A-AA-----CAATTTC----CC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
27867 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
27932 GACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAAAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
27973 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
28038 GACCACTGGTTGTCAATAACCAACTTCTCAAATTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
28079 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
28144 GACCACTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
28185 GATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
28250 GACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
*
28291 AATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
** * * *
28356 GACCGCTGGTTGTCAATAAACAGTTTCCCAATCTCAGGGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
* *
28397 GATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
** * * *
28462 GACCGCTGGTTGTCAATAAACAGTTTCCCAATCTCAGGGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
* *
28503 GATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
** * *
28568 GACCGCTGGTTGTCAATAAACAGTTTCTCAATCTCAGGGCC
66 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
* * * *
28609 GATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
28674 GA
66 GA
28676 ATCGTGCACA
Statistics
Matches: 1152, Mismatches: 53, Indels: 28
0.93 0.04 0.02
Matches are distributed among these distances:
94 80 0.07
97 2 0.00
98 7 0.01
102 7 0.01
103 2 0.00
104 1 0.00
105 201 0.17
106 847 0.74
107 5 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCC
Found at i:27824 original size:43 final size:43
Alignment explanation
Indices: 27776--27931 Score: 116
Period size: 43 Copynumber: 3.4 Consensus size: 43
27766 CAGAGTCAAT
27776 TTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
** *** * * * *
27819 TTCAACTTCATGACGAAGGGACCGCTGG-TTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGGACT-TC---AGACAA---CGCAAG
* *
27870 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
*
27913 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
27932 GACCGCTGGT
Statistics
Matches: 82, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
43 36 0.44
44 4 0.05
45 5 0.06
46 5 0.06
48 5 0.06
49 4 0.05
50 4 0.05
51 19 0.23
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
Found at i:31682 original size:24 final size:23
Alignment explanation
Indices: 31655--31699 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
31645 AGTTTAACAT
31655 TTTTAATCTTAGTTATTTTTTTCC
1 TTTTAATCTTAG-TATTTTTTTCC
* *
31679 TTTTAATTTTTGTATTTTTTT
1 TTTTAATCTTAGTATTTTTTT
31700 ATTTGTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTAATCTTAGTATTTTTTTCC
Found at i:32527 original size:16 final size:16
Alignment explanation
Indices: 32505--32551 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
32495 AAAAGAACTT
32505 TTATTTTTTAAAAAA-
1 TTATTTTTTAAAAAAG
**
32520 TATATTTTAAAAAAAAG
1 T-TATTTTTTAAAAAAG
*
32537 TTTTTTTTTAAAAAA
1 TTATTTTTTAAAAAA
32552 AAGAAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TTATTTTTTAAAAAAG
Found at i:42571 original size:21 final size:21
Alignment explanation
Indices: 42542--42720 Score: 215
Period size: 21 Copynumber: 8.7 Consensus size: 21
42532 ATTCTGACTA
* *
42542 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTACCTAAT
* *
42563 TCGCGTTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
*
42583 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
* *
42604 TCGTATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACCTAAT
*
42624 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
*
42645 TCGCATTGCGATTTACGTAAT
1 TCGCATTGCGATTTACCTAAT
*
42666 T-GCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACCTAAT
*
42686 TCGCACTT-CGATTTACGTAA-
1 TCGCA-TTGCGATTTACCTAAT
42706 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
42721 GTAAATCGCA
Statistics
Matches: 134, Mismatches: 19, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
19 2 0.01
20 64 0.48
21 66 0.49
22 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTACCTAAT
Found at i:42575 original size:41 final size:41
Alignment explanation
Indices: 42541--42719 Score: 297
Period size: 41 Copynumber: 4.4 Consensus size: 41
42531 GATTCTGACT
* * *
42541 ATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTACGTA
1 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
*
42582 ATCGCATTGCGATTTTCCTAATTCGTATTGCGATTTACGTA
1 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
42623 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
*
42664 ATTGCATTGCGATTTTCCTAATTCGCACTT-CGATTTACGTA
1 ATCGCATTGCGATTTTCCTAATTCGCA-TTGCGATTTACGTA
42705 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
42720 AGTAAATCGC
Statistics
Matches: 130, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
41 128 0.98
42 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
Found at i:42591 original size:20 final size:20
Alignment explanation
Indices: 42541--42730 Score: 204
Period size: 20 Copynumber: 9.3 Consensus size: 20
42531 GATTCTGACT
* **
42541 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACGTA
*
42561 ATTCGCGTTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
* *
42582 ATCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
*
42602 ATTCGTATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
* *
42623 ATCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
42643 ATTCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
* * *
42664 ATTGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
42684 ATTCGCACTT-CGATTTACGTA
1 A-TCGCA-TTGCGATTTACGTA
42705 ATCGCATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACGT-A
42725 ATCGCA
1 ATCGCA
42731 ATGAGATTCT
Statistics
Matches: 142, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.03
20 71 0.50
21 65 0.46
22 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
ATCGCATTGCGATTTACGTA
Found at i:46184 original size:20 final size:19
Alignment explanation
Indices: 46156--46210 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
46146 CAATCATCTT
*
46156 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
46176 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
46195 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
46211 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:46198 original size:19 final size:17
Alignment explanation
Indices: 46163--46266 Score: 76
Period size: 19 Copynumber: 6.1 Consensus size: 17
46153 CTTAATGTCT
*
46163 ATCGCAACGCGGAAATGA
1 ATCGCAATGC-GAAATGA
46181 CTATCGCAATGCGAAATGAAA
1 --ATCGCAATGCGAAATG--A
*
46202 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
46216 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
46235 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
46249 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
46266 A
1 A
46267 AATCACAACG
Statistics
Matches: 69, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
14 16 0.23
16 10 0.14
17 12 0.17
19 21 0.30
20 9 0.13
21 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:46220 original size:14 final size:14
Alignment explanation
Indices: 46201--46255 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
46191 GCGAAATGAA
46201 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
46215 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
46234 AATCGCAACGAGAG
1 AATCGCAACGAGAG
46248 AATCGCAA
1 AATCGCAA
46256 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:46225 original size:33 final size:33
Alignment explanation
Indices: 46183--46309 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
46173 GGAAATGACT
46183 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
46216 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
46249 ATCGCAATGCGAAATGAAAATCACAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
46282 ATCGTAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
46310 TGAATTTAGT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:46331 original size:19 final size:19
Alignment explanation
Indices: 46309--46371 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
46299 AAATCGCAAC
*
46309 GTGAATTTAGTTTCGCGTT
1 GTGATTTTAGTTTCGCGTT
46328 GTGATTTTAGTTTCGCGTT
1 GTGATTTTAGTTTCGCGTT
*
46347 GCGATTTTCA-TTTCGCGTT
1 GTGATTTT-AGTTTCGCGTT
*
46366 GCGATT
1 GTGATT
46372 CTCTCGTTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 40 0.98
20 1 0.02
ACGTcount: A:0.13, C:0.14, G:0.25, T:0.48
Consensus pattern (19 bp):
GTGATTTTAGTTTCGCGTT
Found at i:46529 original size:14 final size:14
Alignment explanation
Indices: 46510--46546 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
46500 CATCAATTAA
46510 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
46524 ACAAATCATCTTTT
1 ACAAATCAACTTTT
46538 ACAAATCAA
1 ACAAATCAA
46547 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:47959 original size:21 final size:21
Alignment explanation
Indices: 47894--47959 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
47884 GTGAATCGGG
*
47894 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
47914 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA
47935 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
47956 CTCT
1 CTCT
47960 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:47978 original size:42 final size:41
Alignment explanation
Indices: 47894--48015 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 41
47884 GTGAATCGGG
* * * *
47894 CTCTTGAATGGTGGGA-GGGACTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGATGACAGGGGC
*
47935 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
47977 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
48016 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 19 0.28
42 46 0.69
43 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:48452 original size:19 final size:19
Alignment explanation
Indices: 48412--48533 Score: 84
Period size: 19 Copynumber: 6.8 Consensus size: 19
48402 TCTGGAACTT
*
48412 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
48433 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
48452 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
48466 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
48485 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAATG
**
48499 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAA-TG
48519 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
48534 TTATAGTTTC
Statistics
Matches: 81, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.25
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 23 0.28
20 15 0.19
21 11 0.14
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:48478 original size:33 final size:33
Alignment explanation
Indices: 48436--48530 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
48426 AAAAATGACT
* *
48436 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
48469 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
**
48502 ATCGCAACGCGAAACCAAAAATCGCAACG
1 ATCGCAACGCGAAA-TGAAAATCGCAACG
48531 CGATTATAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 45 0.79
34 12 0.21
ACGTcount: A:0.46, C:0.25, G:0.20, T:0.08
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:48614 original size:19 final size:19
Alignment explanation
Indices: 48592--48648 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
48582 GTGATTCTCT
*
48592 CGTTGCGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCG
*
48611 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
*
48631 CATTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
48649 AACCAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:48850 original size:94 final size:93
Alignment explanation
Indices: 48737--49014 Score: 385
Period size: 94 Copynumber: 3.1 Consensus size: 93
48727 ATGGATTGCA
* *
48737 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
48801 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAAACGAA-AAAT
48830 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
48895 TTAGCAGAATTGACAGCAATCG---AAT
66 TTAGCAGAATTGGCAGCAAACGAAAAAT
* * *
48920 ATACTTT-AACCAAAAGACAAAACAAAAGATAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
48980 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAAACGAA-AAAT
49010 TTACT
1 TTACT
49015 AAGCAATCTA
Statistics
Matches: 168, Mismatches: 11, Indels: 15
0.87 0.06 0.08
Matches are distributed among these distances:
86 28 0.17
89 16 0.10
90 42 0.25
93 4 0.02
94 78 0.46
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAAACGAAAAAT
Found at i:49837 original size:21 final size:22
Alignment explanation
Indices: 49795--49837 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
49785 AATAACAAAC
*
49795 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
49817 ATTA-TAATT-TTAAAAATATTA
1 ATTAGTAATTGTTAAAAA-ATTA
49838 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:50706 original size:20 final size:20
Alignment explanation
Indices: 50681--50718 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50671 TCTTTTGGTT
50681 GAAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAACGCG
**
50701 GAAATGACTATCGCAACG
1 GAAATGAAAATCGCAACG
50719 AGAGAATCGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (20 bp):
GAAATGAAAATCGCAACGCG
Found at i:50729 original size:14 final size:14
Alignment explanation
Indices: 50710--50763 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
50700 GGAAATGACT
50710 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
50724 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
50743 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
50757 ATCGCAA
1 ATCGCAA
50764 TGCGATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 15 0.45
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.24
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:50747 original size:33 final size:34
Alignment explanation
Indices: 50689--50763 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
50679 TTGAAATGAA
* **
50689 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACACGGAAATGAAAATCGCAACGAGAG
50723 AATCGCAACAC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAACACGGAAATGAAAATCGCAACGAGAG
50756 AATCGCAA
1 AATCGCAA
50764 TGCGATTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 28 0.74
34 10 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (34 bp):
AATCGCAACACGGAAATGAAAATCGCAACGAGAG
Found at i:50816 original size:19 final size:20
Alignment explanation
Indices: 50794--50848 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
50784 GCGATTATCT
*
50794 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATATTCATTTCCG
*
50813 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATATTCATTTCCG
50833 CGTTGCGATATTCATT
1 CGTTGCGATATTCATT
50849 CTCGAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATATTCATTTCCG
Found at i:51508 original size:21 final size:21
Alignment explanation
Indices: 51393--51505 Score: 149
Period size: 21 Copynumber: 5.4 Consensus size: 21
51383 CGATAGTCAG
51393 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
51414 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
*
51435 ATTCGCATTTCGATTTTCCTA
1 ATTCGCATTGCGATTTTCCTA
* *
51456 ATTCGCATTGCG-GTTT-ATA
1 ATTCGCATTGCGATTTTCCTA
* * *
51475 TATTCGCGTTACGATTTTCATA
1 -ATTCGCATTGCGATTTTCCTA
51497 ATTCGCATT
1 ATTCGCATT
51506 ACGTATTCGC
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
19 2 0.02
20 13 0.16
21 63 0.78
22 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.44
Consensus pattern (21 bp):
ATTCGCATTGCGATTTTCCTA
Found at i:51524 original size:34 final size:34
Alignment explanation
Indices: 51475--51539 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
51465 GCGGTTTATA
*
51475 TATTCGCGTTACGATTTTCATAATTCGCATTACG
1 TATTCGCATTACGATTTTCATAATTCGCATTACG
* *
51509 TATTCGCATTGCGATTTTCGTAATTCGCATT
1 TATTCGCATTACGATTTTCATAATTCGCATT
51540 GCGAATTAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (34 bp):
TATTCGCATTACGATTTTCATAATTCGCATTACG
Found at i:51557 original size:21 final size:21
Alignment explanation
Indices: 51540--51606 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
51530 AATTCGCATT
51540 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
51561 GCGAATTAGGAAAATCGCATC
1 GCGAATTAGGAAAATCGCAAC
* * *
51582 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
51603 GCGA
1 GCGA
51607 TAGTCAGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:52571 original size:16 final size:18
Alignment explanation
Indices: 52547--52581 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
52537 TATTGAATGA
52547 AAATAATATTT-TTTTAT
1 AAATAATATTTATTTTAT
52564 AAAT-ATATTTATTTTAT
1 AAATAATATTTATTTTAT
52581 A
1 A
52582 TCAAATTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AAATAATATTTATTTTAT
Found at i:53832 original size:20 final size:20
Alignment explanation
Indices: 53807--53846 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
53797 CACAATTTTC
53807 TAATTATTGTGATTTTCTTG
1 TAATTATTGTGATTTTCTTG
53827 TAATTATTGTGATTTTCTTG
1 TAATTATTGTGATTTTCTTG
53847 GTCTACGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.15, T:0.60
Consensus pattern (20 bp):
TAATTATTGTGATTTTCTTG
Found at i:61870 original size:12 final size:12
Alignment explanation
Indices: 61833--61878 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
61823 GGTGTGTTCG
61833 GTTCGTTTATGA
1 GTTCGTTTATGA
*
61845 GCTCGTTTATGA
1 GTTCGTTTATGA
61857 GTTCGTTTATGA
1 GTTCGTTTATGA
*
61869 GTTCATTTAT
1 GTTCGTTTAT
61879 CAACTCGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (12 bp):
GTTCGTTTATGA
Found at i:61886 original size:24 final size:24
Alignment explanation
Indices: 61835--61887 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
61825 TGTGTTCGGT
* * **
61835 TCGTTTATGAGCTCGTTTATGAGT
1 TCGTTTATGAGCTCATTTATCAAC
*
61859 TCGTTTATGAGTTCATTTATCAAC
1 TCGTTTATGAGCTCATTTATCAAC
61883 TCGTT
1 TCGTT
61888 CATTTATGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (24 bp):
TCGTTTATGAGCTCATTTATCAAC
Found at i:62192 original size:36 final size:36
Alignment explanation
Indices: 62133--62227 Score: 93
Period size: 36 Copynumber: 2.7 Consensus size: 36
62123 ACGAACACTA
* * * * *
62133 ATGAACGT-TAAACGAACTTGTTCATAAACACTTTT
1 ATGAACATATAAACAAACATGTTCATAAACACATTC
* * * *
62168 GTGAACATATAAATAAACATGTTCATGAATACATTC
1 ATGAACATATAAACAAACATGTTCATAAACACATTC
*
62204 ATGAACATATAAACGAACATGTTC
1 ATGAACATATAAACAAACATGTTC
62228 GCTAGGGGTG
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
35 6 0.13
36 41 0.87
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.31
Consensus pattern (36 bp):
ATGAACATATAAACAAACATGTTCATAAACACATTC
Done.