Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009262.1 Hibiscus syriacus cultivar Beakdansim tig00112913_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: 63965
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:7277 original size:47 final size:46
Alignment explanation
Indices: 7200--7289 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 46
7190 AGAAAATATT
*
7200 AAAATATATATGATAATTTTAAATAAATTAAAATATTAAAAAATTAA
1 AAAATATATATAATAATTTTAAATAAATTAAAA-ATTAAAAAATTAA
* ** *
7247 AAAATATATA-AATATTTTTATAATTTATTAAAAATTATAAAAT
1 AAAATATATATAATAATTTTA-AATAAATTAAAAATTAAAAAAT
7290 AATTGAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 17 0.46
47 20 0.54
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (46 bp):
AAAATATATATAATAATTTTAAATAAATTAAAAATTAAAAAATTAA
Found at i:7285 original size:29 final size:30
Alignment explanation
Indices: 7246--7329 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 30
7236 TAAAAAATTA
* *
7246 AAAAATATATAAATATTTTTATAA-TTTATT
1 AAAAAT-TATAAATATTTTGAAAATTTTATT
*
7276 AAAAATTATAAA-ATAATTGAAAATTTTATT
1 AAAAATTATAAATAT-TTTGAAAATTTTATT
* *
7306 AAAAA-TATAAA-ATATTCAAAATTT
1 AAAAATTATAAATATTTTGAAAATTT
7330 CAAAAATTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.25
29 19 0.40
30 17 0.35
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (30 bp):
AAAAATTATAAATATTTTGAAAATTTTATT
Found at i:7290 original size:30 final size:30
Alignment explanation
Indices: 7246--7321 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
7236 TAAAAAATTA
* *
7246 AAAAATATATAAATATTTTTATAA-TTTATT
1 AAAAATATA-AAATATTTTGAAAATTTTATT
*
7276 AAAAATTATAAAATA-ATTGAAAATTTTATT
1 AAAAA-TATAAAATATTTTGAAAATTTTATT
7306 AAAAATATAAAATATT
1 AAAAATATAAAATATT
7322 CAAAATTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 14 0.36
30 21 0.54
31 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
AAAAATATAAAATATTTTGAAAATTTTATT
Found at i:11250 original size:17 final size:17
Alignment explanation
Indices: 11228--11264 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
11218 TTTGTATTTC
11228 CATAATGAATCCAAAAA
1 CATAATGAATCCAAAAA
11245 CATAATGAATCCAAAAA
1 CATAATGAATCCAAAAA
11262 CAT
1 CAT
11265 TCATTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19
Consensus pattern (17 bp):
CATAATGAATCCAAAAA
Found at i:11848 original size:17 final size:17
Alignment explanation
Indices: 11822--11869 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
11812 TGAAAAACAT
*
11822 AAAATATGACTTTTCAA
1 AAAATTTGACTTTTCAA
11839 AAAATTTGACTTTTCAA
1 AAAATTTGACTTTTCAA
11856 AAAATTTGACTTTT
1 AAAATTTGACTTTT
11870 TGGTCAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (17 bp):
AAAATTTGACTTTTCAA
Found at i:15376 original size:26 final size:27
Alignment explanation
Indices: 15347--15399 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
15337 AGGTTATGAG
15347 ATTAAAA-TTTAATCATATCCTAGTAA
1 ATTAAAATTTTAATCATATCCTAGTAA
15373 ATTAAAATTTTAATCATATCCTAGTAA
1 ATTAAAATTTTAATCATATCCTAGTAA
15400 GCATATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (27 bp):
ATTAAAATTTTAATCATATCCTAGTAA
Found at i:17450 original size:2 final size:2
Alignment explanation
Indices: 17377--17436 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
17367 ATGTATCAAA
17377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
17418 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
17437 ACCTAATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23536 original size:34 final size:34
Alignment explanation
Indices: 23493--23562 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
23483 ATATCTTATA
*
23493 GTCGAGGGATTAGATGTGTCTACAAGGTATATGT
1 GTCGAGGGATCAGATGTGTCTACAAGGTATATGT
* * *
23527 GTCGAGGGATCGGCTGTGTCTACAAGGTATGTGT
1 GTCGAGGGATCAGATGTGTCTACAAGGTATATGT
23561 GT
1 GT
23563 TGTCAATGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.31
Consensus pattern (34 bp):
GTCGAGGGATCAGATGTGTCTACAAGGTATATGT
Found at i:24347 original size:21 final size:21
Alignment explanation
Indices: 24321--24395 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
24311 ATTCTGACTA
24321 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
24342 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* ** *
24363 TCGCAATGCGATAGTCCAAAA
1 TCGCATTGCGATTTTCCAAAT
24384 TCGCATTGCGAT
1 TCGCATTGCGAT
24396 AGCACTGTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:24413 original size:21 final size:21
Alignment explanation
Indices: 24389--24542 Score: 213
Period size: 21 Copynumber: 7.4 Consensus size: 21
24379 CAAAATCGCA
24389 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
* *
24410 TTGCGATATCATTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
24431 TTGCGATAGCACTGTTTA-CG
1 TTGCGATAGCACTGTTCACCG
24451 TTGCGATAGCACTGTTCA-CG
1 TTGCGATAGCACTGTTCACCG
* * *
24471 ATGCGATAGTACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
* *
24492 TTACGATAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
*
24513 TTGCGATAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
24534 TTGCGATAG
1 TTGCGATAG
24543 TGATCAAAAT
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
20 37 0.31
21 82 0.69
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:24486 original size:82 final size:83
Alignment explanation
Indices: 24390--24542 Score: 227
Period size: 82 Copynumber: 1.9 Consensus size: 83
24380 AAAATCGCAT
* * * * * * *
24390 TGCGATAGCACTGTTCACCGTTGCGATATCATTGTTCACCGTTGCGATAGCACTGTTTA-CGTTG
1 TGCGATAGCACTGTTCACCATTACGATAGCACTGTTCACCATTGCGATAGCACTGTTCACCATTG
24454 CGATAGCACTGTTCACGA
66 CGATAGCACTGTTCACGA
*
24472 TGCGATAGTACTGTTCACCATTACGATAGCACTGTTCACCATTGCGATAGCACTGTTCACCATTG
1 TGCGATAGCACTGTTCACCATTACGATAGCACTGTTCACCATTGCGATAGCACTGTTCACCATTG
24537 CGATAG
66 CGATAG
24543 TGATCAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
82 52 0.84
83 10 0.16
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.31
Consensus pattern (83 bp):
TGCGATAGCACTGTTCACCATTACGATAGCACTGTTCACCATTGCGATAGCACTGTTCACCATTG
CGATAGCACTGTTCACGA
Found at i:30454 original size:48 final size:46
Alignment explanation
Indices: 30386--30501 Score: 133
Period size: 46 Copynumber: 2.5 Consensus size: 46
30376 ATTATACTTA
* * *
30386 TAGCACGTGTCTGACATCTGTGTGACGGTGGTGCTACTGTATGATACT
1 TAGCACGTGTATGACATC--TGTGACAGTGGTGCTACTATATGATACT
* * *
30434 TAGCACGTGTATGTCGTCTGTGACAGTGGTGCTACTATATGGTACT
1 TAGCACGTGTATGACATCTGTGACAGTGGTGCTACTATATGATACT
* * *
30480 TAGCACATGTCTGACATTTGTG
1 TAGCACGTGTATGACATCTGTG
30502 TGATAGTAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 42 0.74
48 15 0.26
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (46 bp):
TAGCACGTGTATGACATCTGTGACAGTGGTGCTACTATATGATACT
Found at i:30741 original size:27 final size:27
Alignment explanation
Indices: 30706--30795 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 27
30696 ACGAAATGAA
*
30706 AAAGTGAAT-AGTATATGATATGAAATG
1 AAAGTGAATGA-TACATGATATGAAATG
*
30733 AAAGTGAATGATACATGCTATGAAATG
1 AAAGTGAATGATACATGATATGAAATG
* *
30760 AATTAAATGAATGATACATGCTATGAAAT-
1 -A--AAGTGAATGATACATGATATGAAATG
30789 AAA-TGAA
1 AAAGTGAA
30796 ATGAATGGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
25 4 0.07
26 2 0.04
27 23 0.41
28 3 0.05
30 24 0.43
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (27 bp):
AAAGTGAATGATACATGATATGAAATG
Found at i:30773 original size:30 final size:30
Alignment explanation
Indices: 30719--30821 Score: 136
Period size: 30 Copynumber: 3.4 Consensus size: 30
30709 GTGAATAGTA
*
30719 TATGATATGAAATGAAAGTGAATGATACATGC
1 TATGAAATG-AATGAAA-TGAATGATACATGC
*
30751 TATGAAATGAATTAAATGAATGATACATGC
1 TATGAAATGAATGAAATGAATGATACATGC
* *
30781 TATGAAATAAATGAAATGAATGGA-AGATGC
1 TATGAAATGAATGAAATGAAT-GATACATGC
30811 TATGAAATGAA
1 TATGAAATGAA
30822 CAAAGTGAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
30 48 0.75
31 8 0.12
32 8 0.12
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (30 bp):
TATGAAATGAATGAAATGAATGATACATGC
Found at i:30838 original size:60 final size:62
Alignment explanation
Indices: 30719--30852 Score: 152
Period size: 60 Copynumber: 2.2 Consensus size: 62
30709 GTGAATAGTA
* * *
30719 TATGATATGAAATGAAAGTGAATGATACATGCTATGAAATGAATTAAATGAATGATACATGC
1 TATGAAATGAAATGAAAGTGAATGATACATGCTATGAAATGAATCAAATGAAAGATACATGC
* *
30781 TATGAAAT-AAATGAAA-TGAATGGA-AGATGCTATGAAATGAA-CAAAGTGAAAGGTACATG-
1 TATGAAATGAAATGAAAGTGAAT-GATACATGCTATGAAATGAATCAAA-TGAAAGATACATGC
* *
30840 TTTGATATGAAAT
1 TATGAAATGAAAT
30853 AAAAATGTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
59 9 0.15
60 36 0.58
61 10 0.16
62 7 0.11
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (62 bp):
TATGAAATGAAATGAAAGTGAATGATACATGCTATGAAATGAATCAAATGAAAGATACATGC
Found at i:37486 original size:21 final size:21
Alignment explanation
Indices: 37460--37523 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
37450 TTTTGGTGCA
*
37460 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
37481 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
37502 GAAGGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATCCCCCCCA
37524 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:37530 original size:21 final size:21
Alignment explanation
Indices: 37462--37542 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
37452 TTGGTGCAGA
*
37462 GGGAATCGA-TCCCCCC-CATG
1 GGGAACCGATTCCCCCCACA-G
*
37482 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
37506 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
37527 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
37543 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 1 0.02
21 24 0.49
22 6 0.12
23 16 0.33
24 1 0.02
25 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:39824 original size:32 final size:32
Alignment explanation
Indices: 39787--39857 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
39777 GGAGAAGAAT
39787 AAGTGTTTAATGTTTTACATGATAAATTGAAG
1 AAGTGTTTAATGTTTTACATGATAAATTGAAG
39819 AAGTGTTTAATGTTTTACATGATAAATTGAAG
1 AAGTGTTTAATGTTTTACATGATAAATTGAAG
39851 AAGTGTT
1 AAGTGTT
39858 AAAGTAAGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.41
Consensus pattern (32 bp):
AAGTGTTTAATGTTTTACATGATAAATTGAAG
Found at i:45730 original size:76 final size:76
Alignment explanation
Indices: 45626--45843 Score: 222
Period size: 76 Copynumber: 2.9 Consensus size: 76
45616 ATTTTCATAG
* * * *
45626 AAACCTCAATCTTGAATATCTTAGGACTTATATCTTAGAAAGTTTAGTTTAATGTTTCTAAAGTT
1 AAACCTCAATCTTGAATTTCTTAGGACTTGTATCATAGAAAGTTTAGTTTAATGTTTCTAAAGAT
*
45691 TGTTCCCTGAG
66 TGTTCCCTGAA
* * * * * ** * *
45702 GAACCTCATTCTTGATTTTCTTAGGACTTGTCTCCTAGAAAACTTAGTTTAATGTTCCTTAAGAT
1 AAACCTCAATCTTGAATTTCTTAGGACTTGTATCATAGAAAGTTTAGTTTAATGTTTCTAAAGAT
* *
45767 TGTTTCCTTAA
66 TGTTCCCTGAA
* * * * * *
45778 AAACCTCAATCTT-AGCTTTCTTAAGATTTGTATCATAGAAAGTTCAATTTAGTGTTTCTAAAGA
1 AAACCTCAATCTTGA-ATTTCTTAGGACTTGTATCATAGAAAGTTTAGTTTAATGTTTCTAAAGA
45842 TT
65 TT
45844 ATTTTCCAAA
Statistics
Matches: 112, Mismatches: 29, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
75 1 0.01
76 111 0.99
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (76 bp):
AAACCTCAATCTTGAATTTCTTAGGACTTGTATCATAGAAAGTTTAGTTTAATGTTTCTAAAGAT
TGTTCCCTGAA
Found at i:45865 original size:39 final size:38
Alignment explanation
Indices: 45821--45932 Score: 100
Period size: 38 Copynumber: 2.9 Consensus size: 38
45811 CATAGAAAGT
*
45821 TCAATTTAGTGTTTCTAAAGATTATTTTCCAAAGAAAAC
1 TCAATTTAGTCTTTCTAAAGA-TATTTTCCAAAGAAAAC
* * * * * *
45860 TCAATTTAGTTTTTCTTAAGACCA-TTTCCTAATAAAAT
1 TCAATTTAGTCTTTCTAAAGA-TATTTTCCAAAGAAAAC
* * * *
45898 TTAATTTGGTCTTTCTAAAGATGTTCTCCAAAGAA
1 TCAATTTAGTCTTTCTAAAGATATTTTCCAAAGAA
45933 CCTTATTCTT
Statistics
Matches: 56, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
38 36 0.64
39 20 0.36
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (38 bp):
TCAATTTAGTCTTTCTAAAGATATTTTCCAAAGAAAAC
Found at i:51180 original size:31 final size:29
Alignment explanation
Indices: 51130--51219 Score: 74
Period size: 31 Copynumber: 3.0 Consensus size: 29
51120 TTAAAACATG
* * *
51130 TAAAATCATAAAATAATTTAATAATAAAA
1 TAAAATTAAAAAATTATTTAATAATAAAA
*
51159 TAAAAGTTCAAAAAATTATTTATATATTAAAAA
1 TAAAA-TT-AAAAAATTATTTA-ATAAT-AAAA
* **
51192 TAGAATTAAAAAA-TATCCAATAATAAAA
1 TAAAATTAAAAAATTATTTAATAATAAAA
51220 CAAGTTAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
28 4 0.08
29 9 0.18
30 5 0.10
31 17 0.35
32 6 0.12
33 8 0.16
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (29 bp):
TAAAATTAAAAAATTATTTAATAATAAAA
Found at i:53332 original size:3 final size:3
Alignment explanation
Indices: 53319--53353 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
53309 TAATGGGCCT
53319 ATA ATA A-A ATA ATA AT- ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53354 AAGATCTGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:53333 original size:11 final size:11
Alignment explanation
Indices: 53319--53353 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
53309 TAATGGGCCT
53319 ATAATAAAATA
1 ATAATAAAATA
*
53330 ATAATATAATA
1 ATAATAAAATA
53341 ATAATAATAATA
1 ATAATAA-AATA
53353 A
1 A
53354 AAGATCTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:53839 original size:15 final size:16
Alignment explanation
Indices: 53821--53851 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53811 GATTTCTTAC
53821 TTTTC-GAAAATTTTA
1 TTTTCTGAAAATTTTA
53836 TTTTCTGAAAATTTTA
1 TTTTCTGAAAATTTTA
53852 ATGAGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTTCTGAAAATTTTA
Found at i:53956 original size:256 final size:258
Alignment explanation
Indices: 53467--54420 Score: 1312
Period size: 256 Copynumber: 3.8 Consensus size: 258
53457 AAACAACTCT
* *
53467 GAAGGA-TT-ATCATCTTGCTCGAAAGACTTACTGATGGCCTAAAG-GACTTACCAATTTTGAAA
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTAAAGTGACTTACCAATTTTGGAA
** * * *
53529 ATAGTTTACTA-GCCAGAAACTTTGGAAATCG-CTT-TTACTTTTCACAAATTTCATTTTTTGAA
66 ATAGTTTACTAGGTAAGAAACTTTGGAAATCGATTTCTTACTTTTCAAAAATTTCATTTTCTGAA
* * *
53591 AA-TTTAA-AAGAAACTTTGAAAATCAATTTCTTATTTTTCAAATTATAATATGAAAGCATCTTG
131 AATTTTAATGAGAAACTTTGAAAATCACTTTCTTATTTTTCAAATTATCATATGAAAGCATCTTG
*
53654 CCGAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGACTGACAGATGACCC
196 CCGAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTACTCGAAAGACTGACAGATGACCC
* * * * **
53717 GAAGGATTTAATTATGA-GCTCAAAAGATTTACTGATGATCTAAAGTG-CTTACCAATTTTGGAA
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTAAAGTGACTTACCAATTTTGGAA
* *
53780 ATAGTTTACTAGGTAAGAAACTTTGGAAATCGATTTCTTACTTTTCGAAAATTTTATTTTCTGAA
66 ATAGTTTACTAGGTAAGAAACTTTGGAAATCGATTTCTTACTTTTCAAAAATTTCATTTTCTGAA
* * * *
53845 AATTTTAATGAGAAATTTTGAAAATCGCTTTCTTAGTTTTCAGATTATCATATGAAAGCATCTTG
131 AATTTTAATGAGAAACTTTGAAAATCACTTTCTTATTTTTCAAATTATCATATGAAAGCATCTTG
* * * *
53910 TCCGAAGGTCTTATAGATGGCTCGAAGGACTTATAATCTT-CTCGAAAGACTGACAGATGGCCC
196 -CCGAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTACTCGAAAGACTGACAGATGACCC
** *
53973 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCC-CGA-TGACTTACCTATTTTGGAA
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTAAAGTGACTTACCAATTTTGGAA
* * * *
54036 ATAGTTTACTAGGTAAGAAACTTTGGAAATTGATTTCTTATTTTTCAAAAATTTTATTTTTTGAA
66 ATAGTTTACTAGGTAAGAAACTTTGGAAATCGATTTCTTACTTTTCAAAAATTTCATTTTCTGAA
* * ** *
54101 AATTTTAATGAGAAACTTTGAAAATC-GTTTC-TCTTTTTCAAATTATCATATTCAAGAATCTTG
131 AATTTTAATGAGAAACTTTGAAAATCACTTTCTTATTTTTCAAATTATCATATGAAAGCATCTTG
54164 CCCGAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTACTCGAAAGACTGACAGATGACCC
196 -CCGAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTACTCGAAAGACTGACAGATGACCC
* ** *
54228 GAATGATTTAATCATCATGCTCGAAAGAC-TACTGATGGCCTGTAGCG-CTTACCAATTTTGGAA
1 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTAAAGTGACTTACCAATTTTGGAA
*
54291 ATAGTTTACTAGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCTGAA
66 ATAGTTTACTAGGTAAGAAACTTTGGAAATCGATTTCTTACTTTTCAAAAATTTCATTTTCTGAA
* * * * * *
54356 AATACTAAATGAGAAACTTTGAAAACCACTTTCTCATTTTTCAAATTGTCATATGAAATCATCTT
131 AAT-TTTAATGAGAAACTTTGAAAATCACTTTCTTATTTTTCAAATTATCATATGAAAGCATCTT
54421 AATGTTCTGG
Statistics
Matches: 614, Mismatches: 73, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
250 6 0.01
251 52 0.08
252 23 0.04
253 2 0.00
254 99 0.16
255 140 0.23
256 209 0.34
257 59 0.10
258 24 0.04
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (258 bp):
GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTAAAGTGACTTACCAATTTTGGAA
ATAGTTTACTAGGTAAGAAACTTTGGAAATCGATTTCTTACTTTTCAAAAATTTCATTTTCTGAA
AATTTTAATGAGAAACTTTGAAAATCACTTTCTTATTTTTCAAATTATCATATGAAAGCATCTTG
CCGAAGGTCTTATAGATGGCCCGAATGACTTATCATCTTACTCGAAAGACTGACAGATGACCC
Found at i:53968 original size:40 final size:42
Alignment explanation
Indices: 53924--54016 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
53914 AAGGTCTTAT
* *
53924 AGATGGCTCGAAGGACTT-ATAATC-TTCTCGAAAGACTGAC
1 AGATGGCCCGAAGGACTTAATAATCATGCTCGAAAGACTGAC
* * *
53964 AGATGGCCCGAAGGATTTAATCATCATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTTAATAATCATGCTCGAAAGACTGAC
*
54006 TGATGGCCCGA
1 AGATGGCCCGA
54017 TGACTTACCT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 16 0.36
41 5 0.11
42 24 0.53
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (42 bp):
AGATGGCCCGAAGGACTTAATAATCATGCTCGAAAGACTGAC
Found at i:54094 original size:16 final size:16
Alignment explanation
Indices: 54073--54107 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54063 AATTGATTTC
54073 TTATTTTTCAAAAATT
1 TTATTTTTCAAAAATT
**
54089 TTATTTTTTGAAAATT
1 TTATTTTTCAAAAATT
54105 TTA
1 TTA
54108 ATGAGAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TTATTTTTCAAAAATT
Found at i:54223 original size:41 final size:41
Alignment explanation
Indices: 54178--54267 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
54168 AAGGTCTTAT
*
54178 AGATGGCCCGAATGACTT-ATCATCTTACTCGAAAGACTGAC
1 AGATGGCCCGAATGACTTAATCATCATACTCGAAAGACT-AC
* * *
54219 AGATGACCCGAATGATTTAATCATCATGCTCGAAAGACTAC
1 AGATGGCCCGAATGACTTAATCATCATACTCGAAAGACTAC
*
54260 TGATGGCC
1 AGATGGCC
54268 TGTAGCGCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 24 0.57
42 18 0.43
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
AGATGGCCCGAATGACTTAATCATCATACTCGAAAGACTAC
Found at i:54254 original size:42 final size:41
Alignment explanation
Indices: 54178--54257 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
54168 AAGGTCTTAT
* *
54178 AGATGGCCCGAATGACTTATCATCTTACTCGAAAGACTGAC
1 AGATGACCCGAATGACTTATCATCATACTCGAAAGACTGAC
* *
54219 AGATGACCCGAATGATTTAATCATCATGCTCGAAAGACT
1 AGATGACCCGAATGACTT-ATCATCATACTCGAAAGACT
54258 ACTGATGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 16 0.47
42 18 0.53
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (41 bp):
AGATGACCCGAATGACTTATCATCATACTCGAAAGACTGAC
Found at i:56458 original size:14 final size:14
Alignment explanation
Indices: 56435--56475 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
56425 ATTCTTCTTT
56435 TTCT-TTTTTTTTC
1 TTCTATTTTTTTTC
56448 -TCTAATTTTTTTTC
1 TTCT-ATTTTTTTTC
56462 TTCTATTTTTTTTC
1 TTCTATTTTTTTTC
56476 ACTTTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
14 19 0.76
15 3 0.12
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTATTTTTTTTC
Found at i:56458 original size:15 final size:15
Alignment explanation
Indices: 56438--56474 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
56428 CTTCTTTTTC
56438 TTTTTTTTTC-TCTA
1 TTTTTTTTTCTTCTA
*
56452 ATTTTTTTTCTTCTA
1 TTTTTTTTTCTTCTA
56467 TTTTTTTT
1 TTTTTTTT
56475 CACTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTTTCTTCTA
Done.