Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000125.1 Hibiscus syriacus cultivar Beakdansim tig00000224_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: 98074
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3592 original size:34 final size:33
Alignment explanation
Indices: 3551--3614 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
3541 AAATAATAAT
*
3551 TTTTGTTCATTATGTATAGGGTTTACGCTAAGAA
1 TTTTGTTCATTATGTATA-GGTTTACACTAAGAA
3585 TTTTGTTCATTATGTATAGGTTTACACTAA
1 TTTTGTTCATTATGTATAGGTTTACACTAA
3615 TTAGGGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (33 bp):
TTTTGTTCATTATGTATAGGTTTACACTAAGAA
Found at i:4762 original size:21 final size:20
Alignment explanation
Indices: 4736--4776 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
4726 CTTTGCTTTC
*
4736 CTATGCTCTTTTCTTGTTTTT
1 CTATGCTCTTTT-TTCTTTTT
4757 CTATGCTCTTTTTTCTTTTT
1 CTATGCTCTTTTTTCTTTTT
4777 AGAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.05, C:0.20, G:0.07, T:0.68
Consensus pattern (20 bp):
CTATGCTCTTTTTTCTTTTT
Found at i:11914 original size:143 final size:145
Alignment explanation
Indices: 11560--11922 Score: 345
Period size: 143 Copynumber: 2.5 Consensus size: 145
11550 AGCAAGTAAC
* * * * * * * *
11560 AACATTTCAACATTCCATAATTCAGAATATCAGTGGTACCTAAAAGTGATTGACTACTCAAGCTA
1 AACAATTCAACAATCAACAATTCAGAATACCACTGGTTCCTAAAGGTGATTGACTACTCAAGCTA
*
11625 TTGGAGAATTAGCATACTCAGAGTGACATCCAAAAGACAAAAGCCCTTAAAAGTTCATATGATTT
66 TT-G-GAATTAGCATACTCAGAGTGACATCCAAAAGACAAAAGCCCTTAAAAGTTCATACGATTT
* * *
11690 ATCTTTCACATGCTAGC
129 ATCTATCACATCCTAGA
* * * ** * * * * **
11707 AACATTTTAACAATCCACAATTCAGAATAGTACTGATTTCGAAAGGGGATTGACTACTTGAGCTA
1 AACAATTCAACAATCAACAATTCAGAATACCACTGGTTCCTAAAGGTGATTGACTACTCAAGCTA
* *** ** * **
11772 TTGGAATTAGCATACTCGGAGTGGTGTTTAGAAGA-AAAAGGTCTTAAAAGTTCATACGATTTAT
66 TTGGAATTAGCATACTCAGAGTGACATCCAAAAGACAAAAGCCCTTAAAAGTTCATACGATTTAT
11836 C-ATCACATCCTAGA
131 CTATCACATCCTAGA
* * * * *
11850 AACAATTCAAGATAT-AACTATTCAAAATACCATTGGTTCCTAAAGGTGATTGACAACTCAAGCT
1 AACAATTCAACA-ATCAACAATTCAGAATACCACTGGTTCCTAAAGGTGATTGACTACTCAAGCT
11914 ATTGGAATT
65 ATTGGAATT
11923 TGCAGACACA
Statistics
Matches: 172, Mismatches: 43, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
143 64 0.37
144 29 0.17
145 25 0.15
146 1 0.01
147 53 0.31
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (145 bp):
AACAATTCAACAATCAACAATTCAGAATACCACTGGTTCCTAAAGGTGATTGACTACTCAAGCTA
TTGGAATTAGCATACTCAGAGTGACATCCAAAAGACAAAAGCCCTTAAAAGTTCATACGATTTAT
CTATCACATCCTAGA
Found at i:13666 original size:24 final size:25
Alignment explanation
Indices: 13610--13672 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
13600 AATATGGTAC
13610 TTATTTTTTTAAATGTAATTAACTATA
1 TTATTTTTTT--ATGTAATTAACTATA
* *
13637 TAATTTTTTTATGTAATTAAGTA-A
1 TTATTTTTTTATGTAATTAACTATA
13661 TTATTTTTTTAT
1 TTATTTTTTTAT
13673 TTGATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.36
25 12 0.36
27 9 0.27
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (25 bp):
TTATTTTTTTATGTAATTAACTATA
Found at i:14999 original size:31 final size:31
Alignment explanation
Indices: 14932--14991 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
14922 ACGAAAGCAT
* *
14932 AAAATTAAAATAAGGGATAAAATTTAAAAAA
1 AAAATCAAAATAAGGGATAAAATATAAAAAA
14963 AAAATCAAAATAAGGGATACAAA-ATAAAA
1 AAAATCAAAATAAGGGATA-AAATATAAAA
14992 CCAAAATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.18
Consensus pattern (31 bp):
AAAATCAAAATAAGGGATAAAATATAAAAAA
Found at i:20502 original size:16 final size:16
Alignment explanation
Indices: 20469--20502 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20459 AGTTTGTAAA
*
20469 CAGTAAATCAATACAT
1 CAGTAAATCAAAACAT
*
20485 CAGTAAATCAAAATAT
1 CAGTAAATCAAAACAT
20501 CA
1 CA
20503 ACAATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.24
Consensus pattern (16 bp):
CAGTAAATCAAAACAT
Found at i:21752 original size:48 final size:48
Alignment explanation
Indices: 21681--21779 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
21671 GGGCAAGGGT
21681 ATTGGTATCGGATGAACAGTACCGATACTCCAAAGCAAAAATATGTGA
1 ATTGGTATCGGATGAACAGTACCGATACTCCAAAGCAAAAATATGTGA
21729 ATTGGTATCGGATGAACAGTACCGATACTCCAAAGCAAAAATATGTGA
1 ATTGGTATCGGATGAACAGTACCGATACTCCAAAGCAAAAATATGTGA
21777 ATT
1 ATT
21780 CTGGGTTTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (48 bp):
ATTGGTATCGGATGAACAGTACCGATACTCCAAAGCAAAAATATGTGA
Found at i:24841 original size:43 final size:46
Alignment explanation
Indices: 24793--24903 Score: 156
Period size: 47 Copynumber: 2.5 Consensus size: 46
24783 GTAAGTATGT
24793 AAATAAGCTTACGAGCTTATG-AA-T-AATGGAAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGAAATTAAATGGAAAGTATATTGATA
* * * *
24836 AAATAAGCTTACGAGCTTACGAAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGAAA-TTAAATGGAAAGTATATTGATA
24883 AAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
24904 GGATAAATGG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
43 20 0.34
44 2 0.03
46 1 0.02
47 36 0.61
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGAAATTAAATGGAAAGTATATTGATA
Found at i:29486 original size:56 final size:55
Alignment explanation
Indices: 29426--29663 Score: 249
Period size: 55 Copynumber: 4.3 Consensus size: 55
29416 TCCTTCAGGA
* *
29426 AGTATAAGACTCGAACAATCTTCATA-AAACGGGTTCGCTCCTTCTTTCTTTCAG-G
1 AGTATAAGACTCGAACAATCTTCA-ACAATCGTGTTCGCTCC-TCTTTCTTTCAGAG
* *
29481 AAGTAT-AGAACTCGAATAATCTTCAACAATCGTG-TCTGATCC-CTATTCTTTCAGAG
1 -AGTATAAG-ACTCGAACAATCTTCAACAATCGTGTTC-GCTCCTCT-TTCTTTCAGAG
* * *
29537 AGTATAAGACTCGGACAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTT-AGAG
1 AGTATAAGACTCGAACAATCTTCAACAATCGTGTTCGCT-CCTCTTTCTTTCAGAG
* * *
29592 AGTATAAGACTCGAATAATCTTCAACAATCGTG-TCTACTCC-CTATTCCTTCAGAG
1 AGTATAAGACTCGAACAATCTTCAACAATCGTGTTC-GCTCCTCT-TTCTTTCAGAG
29647 AGTATAAGACTCGAACA
1 AGTATAAGACTCGAACA
29664 TATTCTCTTA
Statistics
Matches: 154, Mismatches: 16, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
53 1 0.01
54 10 0.06
55 101 0.66
56 41 0.27
57 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (55 bp):
AGTATAAGACTCGAACAATCTTCAACAATCGTGTTCGCTCCTCTTTCTTTCAGAG
Found at i:29549 original size:55 final size:55
Alignment explanation
Indices: 29471--29661 Score: 273
Period size: 55 Copynumber: 3.5 Consensus size: 55
29461 CGCTCCTTCT
29471 TTCTTTCAG-GAAGTAT-AGAACTCGAATAATCTTCAACAATCGTGTCTGATCCCTA
1 TTCTTTCAGAG-AGTATAAG-ACTCGAATAATCTTCAACAATCGTGTCTGATCCCTA
* * * *
29526 TTCTTTCAGAGAGTATAAGACTCGGACAATCTTCAACAATCGTGTTTGCTCCCTA
1 TTCTTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGTGTCTGATCCCTA
29581 TTTCTTT-AGAGAGTATAAGACTCGAATAATCTTCAACAATCGTGTCT-ACTCCCTA
1 -TTCTTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGTGTCTGA-TCCCTA
*
29636 TTCCTTCAGAGAGTATAAGACTCGAA
1 TTCTTTCAGAGAGTATAAGACTCGAA
29662 CATATTCTCT
Statistics
Matches: 122, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
54 5 0.04
55 108 0.89
56 9 0.07
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.32
Consensus pattern (55 bp):
TTCTTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGTGTCTGATCCCTA
Found at i:29724 original size:110 final size:108
Alignment explanation
Indices: 29416--29714 Score: 363
Period size: 110 Copynumber: 2.7 Consensus size: 108
29406 CGGTCCGTAC
* *
29416 TCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAACGGGTTCGCTCCTTCTTTCTTTCAG
1 TCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAT-CAACGGGTTCGCTCCCTCTTTCTTT-AG
*
29480 GAAGTATAGAACTCGAATAATCTTCAACAATCGTGTCTGATCCCTAT
63 GGAGTAT-GAACTCGAATAATCTTCAACAATCGTGTCTGATCCCTAT
* * * * * * *
29527 TCTTTCAGAGAGTATAAGACTCGGACAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTTAGAG
1 TCCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAA-CGGGTTCGCTCCCTCTTTCTTTAGGG
*
29592 AGTATAAGACTCGAATAATCTTCAACAATCGTGTCT-ACTCCCTAT
65 AGTATGA-ACTCGAATAATCTTCAACAATCGTGTCTGA-TCCCTAT
* * *
29637 TCCTTCAGAGAGTATAAGACTCGAAC-ATATTC-TCTTACGGGTTCGCTCCCTCTTTCTTTTGGG
1 TCCTTCAGAGAGTATAAGACTCGAACAATCTTCATC-AACGGGTTCGCTCCCTCTTTCTTTAGGG
29700 AGTATGGAACTCGAA
65 AGTAT-GAACTCGAA
29715 CATCTTCTTC
Statistics
Matches: 160, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
108 34 0.21
109 9 0.06
110 68 0.43
111 48 0.30
112 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (108 bp):
TCCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAACGGGTTCGCTCCCTCTTTCTTTAGGGA
GTATGAACTCGAATAATCTTCAACAATCGTGTCTGATCCCTAT
Found at i:30179 original size:36 final size:37
Alignment explanation
Indices: 30112--30225 Score: 158
Period size: 37 Copynumber: 3.1 Consensus size: 37
30102 ATTCTTCCGA
* * * *
30112 GAAGGCTTAAAAAGGATATGCTTCATTACTCTTCGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
* *
30149 GAAGGCTTAAAATGG-TTTTCTTCACTACTCTTTAGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
*
30185 GAAGGCTCAAAATGGATTTGCTTCACTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
30222 GAAG
1 GAAG
30226 ACTTGACTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 30 0.45
37 37 0.55
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (37 bp):
GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
Found at i:31710 original size:125 final size:125
Alignment explanation
Indices: 31488--31736 Score: 358
Period size: 125 Copynumber: 2.0 Consensus size: 125
31478 AAATGCCGTA
* *
31488 ACATTATCTTATTCAGGTAAGAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTT
1 ACATTATCTCATACAGGTAAGAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTT
* * *
31553 CAATGCCTTCTTGGTCTGAATCTTATCATCTCAACATGATGTGGGTTCAGTCGTGCCCCG
66 CAATGACTTCTTGGTCTAAATCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCCG
* * * * *
31613 ACATTATCTCATACTGGTACGAGCCTTCAAAATGCCCCATCACCTCAATTTGTAAGGCTCATTCT
1 ACATTATCTCATACAGGTAAGAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATT-T
* *
31678 TC-ATGAC-TCATTGGTCTAAATCTTGTCATCTCAACATGATGTGGGTTTAGTCATGCCCC
65 TCAATGACTTC-TTGGTCTAAATCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCC
31737 AATGTGGGTA
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
124 2 0.02
125 105 0.95
126 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (125 bp):
ACATTATCTCATACAGGTAAGAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTT
CAATGACTTCTTGGTCTAAATCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCCG
Found at i:35257 original size:72 final size:72
Alignment explanation
Indices: 35139--35287 Score: 244
Period size: 72 Copynumber: 2.1 Consensus size: 72
35129 CCCTAACATG
* * * *
35139 TTCTTGATCAGTTGCTATCATCATATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTCT
1 TTCTTAATCAGTTGCTATAATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCT
35204 TCATATT
66 TCATATT
* *
35211 TTCTTAATCATTTGCTATAATCACATTGGCTGCACCACTAATATTCAGATTCTCACCCGAAGTCT
1 TTCTTAATCAGTTGCTATAATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCT
35276 TCATATT
66 TCATATT
35283 TTCTT
1 TTCTT
35288 GTGTAATAGG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.39
Consensus pattern (72 bp):
TTCTTAATCAGTTGCTATAATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCT
TCATATT
Found at i:36043 original size:55 final size:55
Alignment explanation
Indices: 35972--36079 Score: 189
Period size: 55 Copynumber: 2.0 Consensus size: 55
35962 TGTGGATCAG
*
35972 TCTTCAATCAGTTTCAAATTTCTTCATTCATTGGATGTCCTTCTTCATGAATCGT
1 TCTTCAATCAGGTTCAAATTTCTTCATTCATTGGATGTCCTTCTTCATGAATCGT
* *
36027 TCTTCAGTCAGGTTCAAATTTTTTCATTCATTGGATGTCCTTCTTCATGAATC
1 TCTTCAATCAGGTTCAAATTTCTTCATTCATTGGATGTCCTTCTTCATGAATC
36080 ATCTGAACGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (55 bp):
TCTTCAATCAGGTTCAAATTTCTTCATTCATTGGATGTCCTTCTTCATGAATCGT
Found at i:36495 original size:46 final size:47
Alignment explanation
Indices: 36393--36516 Score: 178
Period size: 46 Copynumber: 2.7 Consensus size: 47
36383 CACAAAAAAT
* * * * * *
36393 CCTAACCGCATGATATCTAATTCGCATGCTTGTTCGAGAAAAATAAA
1 CCTAACCGCATGATTTCTAGTTCGCATACATGCTCGAAAAAAATAAA
*
36440 CCTAGCCGCATGATTTCTAGTTCGCATACATGCTC-AAAAAAATAAA
1 CCTAACCGCATGATTTCTAGTTCGCATACATGCTCGAAAAAAATAAA
36486 CCTAACCGCATGATTTCTAGTTCGCATACAT
1 CCTAACCGCATGATTTCTAGTTCGCATACAT
36517 TTATTCAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
46 40 0.58
47 29 0.42
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (47 bp):
CCTAACCGCATGATTTCTAGTTCGCATACATGCTCGAAAAAAATAAA
Found at i:36527 original size:46 final size:46
Alignment explanation
Indices: 36380--36527 Score: 135
Period size: 46 Copynumber: 3.2 Consensus size: 46
36370 TGCCTTTGTC
* * * *
36380 ATTCACAAAA-AATCCTAACCGCATGATATCTAATTCGCATGC--TT
1 ATTCA-AAAATAAACCTAACCGCATGATTTCTAGTTCGCATACATTT
* * *
36424 GTTCGAGAAAAATAAACCTAGCCGCATGATTTCTAGTTCGCATACATGCTC
1 ATTC---AAAAATAAACCTAACCGCATGATTTCTAGTTCGCATACAT--TT
*
36475 A--AAAAAATAAACCTAACCGCATGATTTCTAGTTCGCATACATTT
1 ATTCAAAAATAAACCTAACCGCATGATTTCTAGTTCGCATACATTT
36519 ATTCAAAAA
1 ATTCAAAAA
36528 ACGAAATTAA
Statistics
Matches: 82, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
44 5 0.06
46 48 0.59
47 28 0.34
51 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.28
Consensus pattern (46 bp):
ATTCAAAAATAAACCTAACCGCATGATTTCTAGTTCGCATACATTT
Found at i:43933 original size:18 final size:18
Alignment explanation
Indices: 43898--43946 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
43888 TTTTAAGGGT
43898 ATTCTAGTCATTTTATTTA
1 ATTC-AGTCATTTTATTTA
43917 ATTCAGTC-TTTTCATTTA
1 ATTCAGTCATTTT-ATTTA
* *
43935 TTTCAATCATTT
1 ATTCAGTCATTT
43947 CAAACAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 15 0.58
19 7 0.27
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.57
Consensus pattern (18 bp):
ATTCAGTCATTTTATTTA
Found at i:52527 original size:24 final size:25
Alignment explanation
Indices: 52466--52548 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 25
52456 TGGGGATTTT
52466 ATTATTTCAAATTAATT-AAATCTATA
1 ATTATTT--AATTAATTAAAATCTATA
52492 ATTATTTAATTAATTAAAAT-TA-A
1 ATTATTTAATTAATTAAAATCTATA
52515 A-TATTTGAGATT-ATTAAAA-C-AT-
1 ATTATTT-A-ATTAATTAAAATCTATA
52537 A-TATTTAATTAA
1 ATTATTTAATTAA
52549 CTCTAGATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
20 3 0.06
21 2 0.04
22 12 0.24
23 10 0.20
24 13 0.25
25 4 0.08
26 7 0.14
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTATTTAATTAATTAAAATCTATA
Found at i:58851 original size:16 final size:17
Alignment explanation
Indices: 58830--58862 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
58820 TTACTGTTCA
58830 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
58846 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
58863 TGTCGGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:63323 original size:98 final size:98
Alignment explanation
Indices: 63154--63350 Score: 376
Period size: 98 Copynumber: 2.0 Consensus size: 98
63144 AATATTAGAG
*
63154 AGTTTTTTTGTGAGTAGTGAGTATTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCT
1 AGTTTTCTTGTGAGTAGTGAGTATTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCT
63219 GCAGCAGTCCGGAGACATAAGCAAATTGGCTGA
66 GCAGCAGTCCGGAGACATAAGCAAATTGGCTGA
63252 AGTTTTCTTGTGAGTAGTGAGTATTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCT
1 AGTTTTCTTGTGAGTAGTGAGTATTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCT
*
63317 GCAGCAGTCCGGAGACGTAAGCAAATTGGCTGA
66 GCAGCAGTCCGGAGACATAAGCAAATTGGCTGA
63350 A
1 A
63351 TTCTGTTATC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (98 bp):
AGTTTTCTTGTGAGTAGTGAGTATTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCT
GCAGCAGTCCGGAGACATAAGCAAATTGGCTGA
Found at i:63951 original size:26 final size:26
Alignment explanation
Indices: 63915--63967 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
63905 GAATTTTCCA
63915 TACTCTCAAAGTTCTCGATCAAAATT
1 TACTCTCAAAGTTCTCGATCAAAATT
63941 TACTCTCAAAGTTCTCGATCAAAATT
1 TACTCTCAAAGTTCTCGATCAAAATT
63967 T
1 T
63968 GCTTCATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.36
Consensus pattern (26 bp):
TACTCTCAAAGTTCTCGATCAAAATT
Found at i:66273 original size:2 final size:2
Alignment explanation
Indices: 66266--66312 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
66256 TGTATCATGC
66266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66308 AT AT A
1 AT AT A
66313 ATAGTATGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:74294 original size:11 final size:11
Alignment explanation
Indices: 74278--74317 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
74268 ATCCACGAAT
74278 AATAAAAATAA
1 AATAAAAATAA
74289 AATAAAAATAA
1 AATAAAAATAA
74300 ATATAAAAGA-AA
1 A-ATAAAA-ATAA
74312 AATAAA
1 AATAAA
74318 TTTGTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 17 0.63
12 9 0.33
13 1 0.04
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:74318 original size:17 final size:17
Alignment explanation
Indices: 74278--74318 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
74268 ATCCACGAAT
* *
74278 AATAAAAATAAAATAAA
1 AATAAATATAAAAGAAA
74295 AATAAATATAAAAGAAA
1 AATAAATATAAAAGAAA
74312 AATAAAT
1 AATAAAT
74319 TTGTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AATAAATATAAAAGAAA
Found at i:89402 original size:24 final size:24
Alignment explanation
Indices: 89361--89414 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
89351 AATGAAGAAC
89361 AATGAGATAGGCTCTCAAAGGAAA
1 AATGAGATAGGCTCTCAAAGGAAA
*
89385 AATGAGATGGGCGT-TCAAAGGAAA
1 AATGAGATAGGC-TCTCAAAGGAAA
89409 AA-GAGA
1 AATGAGA
89415 GTTTTGAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 4 0.14
24 23 0.82
25 1 0.04
ACGTcount: A:0.46, C:0.09, G:0.30, T:0.15
Consensus pattern (24 bp):
AATGAGATAGGCTCTCAAAGGAAA
Found at i:93953 original size:17 final size:18
Alignment explanation
Indices: 93922--93961 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
93912 ATACAAGAAA
93922 AAAAACAACTCAAATAAT
1 AAAAACAACTCAAATAAT
93940 AAAAACAACT-AAATAAT
1 AAAAACAACTCAAATAAT
93957 AAAAA
1 AAAAA
93962 TAATTCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAACAACTCAAATAAT
Found at i:93962 original size:26 final size:26
Alignment explanation
Indices: 93933--93987 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
93923 AAAACAACTC
93933 AAATAATAAAAACAACTAAATAATAA
1 AAATAATAAAAACAACTAAATAATAA
** *
93959 AAATAATTCAAACAATTAAATAATAA
1 AAATAATAAAAACAACTAAATAATAA
93985 AAA
1 AAA
93988 CTAACAAACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (26 bp):
AAATAATAAAAACAACTAAATAATAA
Found at i:96068 original size:15 final size:17
Alignment explanation
Indices: 96048--96084 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
96038 AAACTAATAC
96048 TAAAAATT-A-AATAAA
1 TAAAAATTCACAATAAA
*
96063 TAAAAATTCACAATAAT
1 TAAAAATTCACAATAAA
96080 TAAAA
1 TAAAA
96085 TTACAACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAATTCACAATAAA
Found at i:96614 original size:58 final size:58
Alignment explanation
Indices: 96504--96614 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
96494 TACGTGACGT
* * * *
96504 CAGCTCGGATAGAACTCCGAAGGCACGGATGACGATTCACGCCTTTTCTTACTGGTGC
1 CAGCTCGGACAGAACCCCGAAGGCACGGATGACGATCCACGCCTTTTATTACTGGTGC
* *
96562 CAGCTCGGACAGAACCCCTTGAAGGCGCGGATGACGATCCATG-C-TTTATTACT
1 CAGCTCGGACAGAACCCC--GAAGGCACGGATGACGATCCACGCCTTTTATTACT
96615 ACCGTGTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 24 0.53
59 1 0.02
60 20 0.44
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (58 bp):
CAGCTCGGACAGAACCCCGAAGGCACGGATGACGATCCACGCCTTTTATTACTGGTGC
Done.