Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001202.1 Hibiscus syriacus cultivar Beakdansim tig00002377_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: 92766
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:14822 original size:35 final size:35
Alignment explanation
Indices: 14775--14879 Score: 174
Period size: 35 Copynumber: 3.0 Consensus size: 35
14765 GATTGCCAGA
* *
14775 GGGAACAGATTCCTCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTACCGATTCCCC
*
14810 GGGAACAAATTCCCCCCAGGGGGTACCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTACCGATTCCCC
*
14845 GGGAACAGATTCCCCCCAAGGGGTACCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTACCGATTCCCC
14880 CTAGGTTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTACCGATTCCCC
Found at i:14843 original size:20 final size:19
Alignment explanation
Indices: 14818--14880 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
14808 CCGGGAACAA
14818 ATTCCCCCCAGGGGGTACCG
1 ATTCCCCCCA-GGGGTACCG
* *
14838 ATT--CCCC--GGGAACAG
1 ATTCCCCCCAGGGGTACCG
14853 ATTCCCCCCAAGGGGTACCG
1 ATTCCCCCC-AGGGGTACCG
14873 ATTCCCCC
1 ATTCCCCC
14881 TAGGTTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
15 9 0.26
17 4 0.12
18 4 0.12
20 17 0.50
ACGTcount: A:0.19, C:0.41, G:0.24, T:0.16
Consensus pattern (19 bp):
ATTCCCCCCAGGGGTACCG
Found at i:14955 original size:22 final size:21
Alignment explanation
Indices: 14913--14955 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
14903 AACAAAATGT
14913 CCAGAGGGTACCGATTCCCCC
1 CCAGAGGGTACCGATTCCCCC
* *
14934 CCAGGGGGTACCGATTTCCCC
1 CCAGAGGGTACCGATTCCCCC
14955 C
1 C
14956 TGTGTAACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.42, G:0.26, T:0.16
Consensus pattern (21 bp):
CCAGAGGGTACCGATTCCCCC
Found at i:21651 original size:18 final size:18
Alignment explanation
Indices: 21609--21651 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
21599 TATAAGGTAG
*
21609 TATTTATTTAAATATTTT
1 TATTTATTTAAATATTTA
*
21627 TAATTATTT-AATATTTAA
1 TATTTATTTAAATATTT-A
21645 TATTTAT
1 TATTTAT
21652 ATTTTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTATTTAAATATTTA
Found at i:28577 original size:23 final size:23
Alignment explanation
Indices: 28510--28570 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
28500 AATTTAATAA
*
28510 ATTAT-ACATGTGTCAGCACATG
1 ATTATAACACGTGTCAGCACATG
28532 ATTATAACACGTGTCAGCACATG
1 ATTATAACACGTGTCAGCACATG
28555 ATTATAACACGTGTCA
1 ATTATAACACGTGTCA
28571 ATACATGTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 5 0.14
23 32 0.86
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (23 bp):
ATTATAACACGTGTCAGCACATG
Found at i:30521 original size:21 final size:20
Alignment explanation
Indices: 30435--30592 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
30425 AAATGACCAA
**
30435 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
30454 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
30474 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
30494 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
30515 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
30536 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
30556 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
30577 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
30593 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:30621 original size:20 final size:20
Alignment explanation
Indices: 30559--30828 Score: 251
Period size: 20 Copynumber: 13.5 Consensus size: 20
30549 CGATTTTCCA
* ** *
30559 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
30579 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
30599 AAATCGCAACGCCTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30619 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30639 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30659 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30679 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30699 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
30719 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
30739 AAATCGCAACG-ATAATCCAT
1 AAATCGCAACGCGT-ATCCGT
* * *
30759 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
30779 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
30799 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
30819 AAATCACAAC
1 AAATCGCAAC
30829 ACTGAAATTT
Statistics
Matches: 206, Mismatches: 36, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 202 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:31549 original size:24 final size:24
Alignment explanation
Indices: 31510--31556 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31500 AAATTTGGTC
31510 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
31534 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
31557 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:34087 original size:33 final size:34
Alignment explanation
Indices: 34036--34284 Score: 242
Period size: 33 Copynumber: 7.2 Consensus size: 34
34026 CGGAAATTAC
* *
34036 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
34069 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
34103 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
34141 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* * *
34174 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
34213 AAT-GCGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* * *
34245 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
34278 AATCGCA
1 AATCGCA
34285 TATCTCTTCC
Statistics
Matches: 181, Mismatches: 18, Indels: 34
0.78 0.08 0.15
Matches are distributed among these distances:
31 1 0.01
32 7 0.04
33 97 0.54
34 17 0.09
35 1 0.01
36 2 0.01
37 1 0.01
38 32 0.18
39 22 0.12
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:34119 original size:19 final size:19
Alignment explanation
Indices: 34050--34284 Score: 276
Period size: 19 Copynumber: 13.4 Consensus size: 19
34040 GCAACGAGAG
34050 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
34069 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
34083 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
34103 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
34122 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
34141 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
34155 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
34174 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
34193 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
34207 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
34226 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
34245 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
34259 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
34278 AATCGCA
1 AATCGCA
34285 TATCTCTTCC
Statistics
Matches: 186, Mismatches: 9, Indels: 42
0.78 0.04 0.18
Matches are distributed among these distances:
14 42 0.23
15 3 0.02
16 7 0.04
17 7 0.04
18 3 0.02
19 108 0.58
20 16 0.09
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:34177 original size:52 final size:52
Alignment explanation
Indices: 34036--34284 Score: 382
Period size: 52 Copynumber: 4.8 Consensus size: 52
34026 CGGAAATTAC
*
34036 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
34083 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
34141 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
34193 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
34245 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
34285 TATCTCTTCC
Statistics
Matches: 187, Mismatches: 4, Indels: 17
0.90 0.02 0.08
Matches are distributed among these distances:
47 8 0.04
49 1 0.01
50 1 0.01
52 132 0.71
53 29 0.16
55 2 0.01
56 1 0.01
58 13 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:34782 original size:33 final size:33
Alignment explanation
Indices: 34740--34810 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
34730 AATACTAACT
*
34740 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
34773 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
34806 TGAAA
1 TGAAA
34811 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:35044 original size:22 final size:22
Alignment explanation
Indices: 34992--35046 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
34982 TGGTTGTGAG
**
34992 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
35014 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
35036 GGATTTCTTCG
1 GGATTTCTTCG
35047 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:35218 original size:20 final size:20
Alignment explanation
Indices: 35193--35346 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
35183 CTTTAAATAT
35193 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
35213 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
35235 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
35254 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
35274 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
35294 GGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
35314 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
35334 CGCGTTGCGATTT
1 CGCGTTGCGATTT
35347 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.83
21 15 0.14
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:35320 original size:40 final size:40
Alignment explanation
Indices: 35192--35346 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
35182 GCTTTAAATA
*
35192 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
35233 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* * *
35273 ACACGTTGCGATTTACGGATAGGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
35313 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
35347 TGGAAAATCG
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
40 64 0.68
41 30 0.32
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:35363 original size:21 final size:21
Alignment explanation
Indices: 35333--35415 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
35323 ATTTTCATAT
*
35333 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
35354 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
35375 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
35396 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
35416 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:35406 original size:42 final size:43
Alignment explanation
Indices: 35313--35411 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
35303 ATTTATGTGT
* *
35313 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
35354 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
35396 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
35412 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:39701 original size:13 final size:14
Alignment explanation
Indices: 39678--39769 Score: 59
Period size: 14 Copynumber: 6.9 Consensus size: 14
39668 TGGCAATCCA
39678 TTCATTTATGTTCG
1 TTCATTTATGTTCG
39692 TTCA-TTA---T-G
1 TTCATTTATGTTCG
* * *
39701 TTCAATTATCTTCA
1 TTCATTTATGTTCG
* * *
39715 TTCGTTTATGTCCA
1 TTCATTTATGTTCG
* *
39729 TTCATTTATATTTG
1 TTCATTTATGTTCG
* *
39743 TCCATTTATGTCCG
1 TTCATTTATGTTCG
39757 TTCATTTATGTTC
1 TTCATTTATGTTC
39770 TCTAGCCAAT
Statistics
Matches: 57, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
9 5 0.09
10 4 0.07
13 4 0.07
14 44 0.77
ACGTcount: A:0.18, C:0.17, G:0.10, T:0.54
Consensus pattern (14 bp):
TTCATTTATGTTCG
Found at i:39737 original size:28 final size:28
Alignment explanation
Indices: 39701--39765 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
39691 GTTCATTATG
* * * *
39701 TTCAATTATCTTCATTCGTTTATGTCCA
1 TTCATTTATATTCATCCATTTATGTCCA
** *
39729 TTCATTTATATTTGTCCATTTATGTCCG
1 TTCATTTATATTCATCCATTTATGTCCA
39757 TTCATTTAT
1 TTCATTTAT
39766 GTTCTCTAGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.20, C:0.18, G:0.08, T:0.54
Consensus pattern (28 bp):
TTCATTTATATTCATCCATTTATGTCCA
Found at i:39865 original size:21 final size:22
Alignment explanation
Indices: 39841--39885 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
39831 AACATAATTA
39841 ATTTAAA-CAA-AAATAGAAAAT
1 ATTTAAATCAATAAA-AGAAAAT
*
39862 ATTTAAATCAATTAAAGAAAAT
1 ATTTAAATCAATAAAAGAAAAT
39884 AT
1 AT
39886 AAATCCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 12 0.57
23 2 0.10
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (22 bp):
ATTTAAATCAATAAAAGAAAAT
Found at i:41839 original size:23 final size:23
Alignment explanation
Indices: 41805--41865 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
41795 CTCATATAAA
*
41805 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
41828 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
41851 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
41866 TATAATAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:43458 original size:21 final size:21
Alignment explanation
Indices: 43434--43478 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43424 TTTTGTTCGT
* *
43434 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
43455 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
43476 TTG
1 TTG
43479 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:44411 original size:16 final size:16
Alignment explanation
Indices: 44370--44412 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
44360 ATCATCAGTT
*
44370 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
44386 ATTAATCAATCAAAGTC
1 CTT-ATCAATCAAAATC
44403 CTTATCAATC
1 CTTATCAATC
44413 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.33
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:48368 original size:21 final size:21
Alignment explanation
Indices: 48344--48388 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
48334 TTTTGTTCGT
* *
48344 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
**
48365 TTGACTGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
48386 TTG
1 TTG
48389 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.27, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:57234 original size:13 final size:14
Alignment explanation
Indices: 57210--57239 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
57200 TTTAGTAATT
57210 TTAAGATTTTGAAA
1 TTAAGATTTTGAAA
57224 TTAAG-TTTTGAAA
1 TTAAGATTTTGAAA
57237 TTA
1 TTA
57240 CTCCCCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TTAAGATTTTGAAA
Found at i:59476 original size:23 final size:22
Alignment explanation
Indices: 59424--59506 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 22
59414 CAGAACCCTC
* *
59424 AGGGGGTATCGATTCCCCTATA
1 AGGGGGAATCGATTCCCCTTTA
*
59446 A-GGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGATTCCCCTTT-A
*
59468 AGGGGGAATC-AGTTCCCCTTCA
1 AGGGGGAATCGA-TTCCCCTTTA
*
59490 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
59507 TCTGTACTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
21 16 0.31
22 18 0.35
23 17 0.33
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTTA
Found at i:59934 original size:13 final size:13
Alignment explanation
Indices: 59860--59933 Score: 121
Period size: 13 Copynumber: 5.7 Consensus size: 13
59850 TGCGTCATAA
59860 ATTTATGACACAC
1 ATTTATGACACAC
59873 ATTTATGACACAC
1 ATTTATGACACAC
59886 ATTTATGACACAC
1 ATTTATGACACAC
*
59899 ATTTATGACGCAC
1 ATTTATGACACAC
* *
59912 ATTTATGACGCGC
1 ATTTATGACACAC
59925 ATTTATGAC
1 ATTTATGAC
59934 GTTCATTGAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 59 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (13 bp):
ATTTATGACACAC
Found at i:60004 original size:85 final size:85
Alignment explanation
Indices: 59912--60077 Score: 210
Period size: 85 Copynumber: 2.0 Consensus size: 85
59902 TATGACGCAC
* * * **
59912 ATTTATGACGCGCATTTATGACGTT-CATTGAGCGTCATTGAAGC-CACCGTCATAAATTAAGAT
1 ATTTATGACACGCATGTATGAC-TTACATTGAGCGTCATTGAAGCACA-CGCCATAAACAAAGAT
59975 GACACACATTTGTGTGTCATAA
64 GACACACATTTGTGTGTCATAA
* * * * *
59997 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACATGCCATTAACAAATATGA
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACGCCATAAACAAAGATGA
60062 CACACATTTGTGTGTC
66 CACACATTTGTGTGTC
60078 GTGATTGTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 2 0.03
85 65 0.94
86 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACGCCATAAACAAAGATGA
CACACATTTGTGTGTCATAA
Found at i:60110 original size:2 final size:2
Alignment explanation
Indices: 60103--60133 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60093 AAATTATTGT
60103 TA TA TA 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 TA TA TA T
60134 TGTAGATCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68314 original size:19 final size:19
Alignment explanation
Indices: 68290--68335 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
68280 TTCTTGAGTA
68290 TAGCCTTGAGCAACAAGTC
1 TAGCCTTGAGCAACAAGTC
68309 TAGCCTTGAGCAACAAGTC
1 TAGCCTTGAGCAACAAGTC
68328 TAGCCTTG
1 TAGCCTTG
68336 TTTCTCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (19 bp):
TAGCCTTGAGCAACAAGTC
Found at i:78551 original size:21 final size:21
Alignment explanation
Indices: 78520--78579 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
78510 ACTGCTCAAG
*
78520 ACAAAGAGTATCGGTACTCCT
1 ACAAGGAGTATCGGTACTCCT
* *
78541 ACAGGGAGTATCGATACTCCT
1 ACAAGGAGTATCGGTACTCCT
** *
78562 TTAATGAGTATCGGTACT
1 ACAAGGAGTATCGGTACT
78580 ACCTTTGTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (21 bp):
ACAAGGAGTATCGGTACTCCT
Found at i:80175 original size:17 final size:18
Alignment explanation
Indices: 80155--80193 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
80145 ATGTTTTGTT
80155 ATTTTAAATAAAA-AATA
1 ATTTTAAATAAAACAATA
*
80172 ATTTTAATTAAAACAATA
1 ATTTTAAATAAAACAATA
80190 ATTT
1 ATTT
80194 GTGGTATGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTAAATAAAACAATA
Found at i:83745 original size:20 final size:20
Alignment explanation
Indices: 83716--83788 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
83706 AATCACTTTG
* *
83716 GGTATTGATACCAAGGCTTC
1 GGTATGGATACCAAGCCTTC
* **
83736 GGTATGGATATCTAA-TTTTC
1 GGTATGGATA-CCAAGCCTTC
83756 GGTATGGATACC-AGTCCTTC
1 GGTATGGATACCAAG-CCTTC
83776 GGTATGGATACCA
1 GGTATGGATACCA
83789 TTTTATTTGG
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 37 0.88
21 3 0.07
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
GGTATGGATACCAAGCCTTC
Found at i:88199 original size:17 final size:17
Alignment explanation
Indices: 88177--88210 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
88167 TAAAAGGGTT
88177 TATTAGTCTT-TTAAATA
1 TATTAGT-TTATTAAATA
88194 TATTAGTTTATTAAATA
1 TATTAGTTTATTAAATA
88211 GATATGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTAGTTTATTAAATA
Found at i:88812 original size:21 final size:21
Alignment explanation
Indices: 88786--88834 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
88776 GACTTAACGA
88786 TGGTATCGACACCTCACCCTT
1 TGGTATCGACACCTCACCCTT
88807 TGGTATCGACACCTCACCCTT
1 TGGTATCGACACCTCACCCTT
88828 TGGTATC
1 TGGTATC
88835 ATACTTAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.35, G:0.16, T:0.31
Consensus pattern (21 bp):
TGGTATCGACACCTCACCCTT
Found at i:89395 original size:16 final size:16
Alignment explanation
Indices: 89374--89406 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
89364 TACAATCCTC
89374 GGTATCGATACCAAAG
1 GGTATCGATACCAAAG
89390 GGTATCGATACCAAAG
1 GGTATCGATACCAAAG
89406 G
1 G
89407 ACTGATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (16 bp):
GGTATCGATACCAAAG
Found at i:90893 original size:288 final size:285
Alignment explanation
Indices: 90346--90924 Score: 1052
Period size: 288 Copynumber: 2.0 Consensus size: 285
90336 AGTTTGATAT
*
90346 TCATTTAAACAAGTTTCAAGTTCGAGTCCTTCTATATGCAGAAAATCCCCACTGGAGATTCACTC
1 TCATTTAAACAAGTTTCAAGTTCGAGTCCTTATATATGCAGAAAATCCCCACTGGAGATTCACTC
* *
90411 ACCAAAGCTAGAAGTGCGACCTAGGTCGGTCTGGATTAATTAAGGCAGAAGCCTTGGGAACCTAA
66 ACCAAAGCTAGAAGTGCGACCTAGGTCGGTCTGAATTAATCAAGGCAGAAGCCTTGGGAACCTAA
90476 AGGTAAAAAAAGGACAAAGCACTCTAGGGGAAAAAGGTTGCTTTAGTGGAAATGTACAACCCAAT
131 AGGTAAAAAAAGGACAAAGCACTCTAGGGGAAAAAGGTTGCTTTAGTGGAAATGTACAACCCAAT
*
90541 AACCAAGCTTGGTTGAGTTTCAAAACCACACCCGCCTTTAAATTTGAACTATTAACAATTCACTC
196 AACCAAGCTTGGTTGAGTTTCAAAACCACACCCACCTTTAAATTTGAACTATTAACAATTCACTC
90606 CCCCTCCCTTGTAAAAATTTATAGA
261 CCCCTCCCTTGTAAAAATTTATAGA
90631 TCATTTAAACAAGTTTCAAGTTCGAGTCCTTATATATGCAGAAAATCCCCACTGGAGATTCACTC
1 TCATTTAAACAAGTTTCAAGTTCGAGTCCTTATATATGCAGAAAATCCCCACTGGAGATTCACTC
* *
90696 ACCAAA-ATCAGAAGTGCGACCTAGGTCGGTCTGAATTAATCAAGGTAGAAGCCTTGGGAACCTA
66 ACCAAAGCT-AGAAGTGCGACCTAGGTCGGTCTGAATTAATCAAGGCAGAAGCCTTGGGAACCTA
90760 AAGGTAAAAAAAAAAGGACAAAGCACTCTAGGGGAAAAAGGTTGCTTTAGTGGAAATGTACAACC
130 AAGGT---AAAAAAAGGACAAAGCACTCTAGGGGAAAAAGGTTGCTTTAGTGGAAATGTACAACC
*
90825 CAATAACCAAGCTTGGTTGAGTTTCAAACCCACACCCACCTTTAAATTTGAACTATTAACAATTC
192 CAATAACCAAGCTTGGTTGAGTTTCAAAACCACACCCACCTTTAAATTTGAACTATTAACAATTC
90890 ACTCCCCCTCCCTTGTAAAAATTTATAGA
257 ACTCCCCCTCCCTTGTAAAAATTTATAGA
90919 TCATTT
1 TCATTT
90925 GAGGACCAAA
Statistics
Matches: 283, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
284 1 0.00
285 127 0.45
288 155 0.55
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (285 bp):
TCATTTAAACAAGTTTCAAGTTCGAGTCCTTATATATGCAGAAAATCCCCACTGGAGATTCACTC
ACCAAAGCTAGAAGTGCGACCTAGGTCGGTCTGAATTAATCAAGGCAGAAGCCTTGGGAACCTAA
AGGTAAAAAAAGGACAAAGCACTCTAGGGGAAAAAGGTTGCTTTAGTGGAAATGTACAACCCAAT
AACCAAGCTTGGTTGAGTTTCAAAACCACACCCACCTTTAAATTTGAACTATTAACAATTCACTC
CCCCTCCCTTGTAAAAATTTATAGA
Done.