Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005386.1 Hibiscus syriacus cultivar Beakdansim tig00012345_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: 69584
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:453 original size:18 final size:17
Alignment explanation
Indices: 425--476 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
415 ACTTGAACTG
*
425 AACCTTGAACCTAAACCT
1 AACC-TGAACCCAAACCT
443 AAACCTGAACCCAAACCCT
1 -AACCTGAACCCAAA-CCT
462 AA-CTGAACCCAAACC
1 AACCTGAACCCAAACC
477 CGAATGAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 2 0.06
17 11 0.35
18 11 0.35
19 7 0.23
ACGTcount: A:0.42, C:0.38, G:0.06, T:0.13
Consensus pattern (17 bp):
AACCTGAACCCAAACCT
Found at i:469 original size:17 final size:17
Alignment explanation
Indices: 447--552 Score: 82
Period size: 18 Copynumber: 6.4 Consensus size: 17
437 AAACCTAAAC
447 CTGAACCCAAACCCTAA
1 CTGAACCCAAACCCTAA
*
464 CTGAACCCAAACCCGAA
1 CTGAACCCAAACCCTAA
481 -TGAACCCAAACCC--A
1 CTGAACCCAAACCCTAA
* *
495 ---AACCCAAAACCAAA
1 CTGAACCCAAACCCTAA
* *
509 CCGAAAACCAAA-CCTGAA
1 CTG-AACCCAAACCCT-AA
527 CTCGAACCCAAACCCTAA
1 CT-GAACCCAAACCCTAA
545 TCTGAACC
1 -CTGAACC
553 TGAACCCAAC
Statistics
Matches: 73, Mismatches: 6, Indels: 19
0.74 0.06 0.19
Matches are distributed among these distances:
12 10 0.14
14 2 0.03
16 13 0.18
17 18 0.25
18 24 0.33
19 6 0.08
ACGTcount: A:0.44, C:0.40, G:0.08, T:0.08
Consensus pattern (17 bp):
CTGAACCCAAACCCTAA
Found at i:492 original size:6 final size:6
Alignment explanation
Indices: 483--541 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
473 AACCCGAATG
* * * ** * *
483 AACCCA AACCCA AACCCA AAACCA AACCGA AAACCA AACCTG AACTCG
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
531 AACCCA AACCC
1 AACCCA AACCC
542 TAATCTGAAC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.49, C:0.42, G:0.05, T:0.03
Consensus pattern (6 bp):
AACCCA
Found at i:574 original size:24 final size:24
Alignment explanation
Indices: 481--576 Score: 63
Period size: 24 Copynumber: 4.0 Consensus size: 24
471 CAAACCCGAA
* **
481 TGAACCCAAACCCAAACCCAAAACC
1 TGAACCCAAACCCAAA-ACTGAACC
* * * *
506 -AAACCGAAAACCAAACCTGAA-C
1 TGAACCCAAACCCAAAACTGAACC
* *
528 TCGAACCCAAACCCTAATCTGAACC
1 T-GAACCCAAACCCAAAACTGAACC
553 TGAACCC-AACCCAAAACTTGAACC
1 TGAACCCAAACCCAAAAC-TGAACC
577 CAAACCCTAA
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
22 1 0.02
23 12 0.22
24 40 0.73
25 2 0.04
ACGTcount: A:0.45, C:0.39, G:0.07, T:0.09
Consensus pattern (24 bp):
TGAACCCAAACCCAAAACTGAACC
Found at i:1031 original size:98 final size:98
Alignment explanation
Indices: 858--1057 Score: 307
Period size: 98 Copynumber: 2.0 Consensus size: 98
848 TGATTCGTTT
*
858 TACTGTGATTTATTTGCGTGTTGGTTGTTCATTCGGATGCTTTATAAGGTTGTTAGCTGCCTTTA
1 TACTGTGATTTATTTGCGTGTTGGTTGTTCATTCAGATGCTTTATAAGGTTGTTAGCTGCCTTTA
*
923 TTTACAGTTTAAATAAACTGTTTAA-TTGTAGC
66 TTTACAGTTTAAATAAACTATTTAATTTGTAGC
* * *
955 TACTGTGATTTGTTTGTGTTGTTGG-TGTTCATTCAGATTGATTTTATAAGGTTGTTAG-TGCCT
1 TACTGTGATTTATTTGCG-TGTTGGTTGTTCATTCAGA-TG-CTTTATAAGGTTGTTAGCTGCCT
1018 TTATTTACAGTTTAAATAAACTATTTAATTTGTAGC
63 TTATTTACAGTTTAAATAAACTATTTAATTTGTAGC
1054 TACT
1 TACT
1058 ATTGAGTTGT
Statistics
Matches: 94, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
97 27 0.29
98 40 0.43
99 27 0.29
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.48
Consensus pattern (98 bp):
TACTGTGATTTATTTGCGTGTTGGTTGTTCATTCAGATGCTTTATAAGGTTGTTAGCTGCCTTTA
TTTACAGTTTAAATAAACTATTTAATTTGTAGC
Found at i:1086 original size:83 final size:82
Alignment explanation
Indices: 982--1173 Score: 275
Period size: 83 Copynumber: 2.3 Consensus size: 82
972 GTTGTTGGTG
*
982 TTCATTCAGATTGA-TTTTATAAGGTTGTTAG-TGCCTTTATTTACAGTTTAAATAAACTATTTA
1 TTCATTCGGATT-ACTTTTATAAGGTTGTTAGCTGCCTTTA-TTACAGTTTAAATAAACTATTTA
1045 ATTTGTAGCTACTATTGAGTT
64 A-TTGTAGCTACTATTGA-TT
* *
1066 GTTCA-TCGGATTGC-TTTATAAGGTTGTTAGCTGCCTTTATTACAGTTTAAATAAACTGTTTAA
1 -TTCATTCGGATTACTTTTATAAGGTTGTTAGCTGCCTTTATTACAGTTTAAATAAACTATTTAA
*
1129 TTGTAGCTACTGTTGATT
65 TTGTAGCTACTATTGATT
1147 TTCATTCGGATTACTTTTATAAGGTTG
1 TTCATTCGGATTACTTTTATAAGGTTG
1174 GTTGCTAACC
Statistics
Matches: 98, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
80 4 0.04
81 10 0.10
82 27 0.28
83 39 0.40
84 14 0.14
85 4 0.04
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (82 bp):
TTCATTCGGATTACTTTTATAAGGTTGTTAGCTGCCTTTATTACAGTTTAAATAAACTATTTAAT
TGTAGCTACTATTGATT
Found at i:4495 original size:16 final size:16
Alignment explanation
Indices: 4474--4515 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
4464 TGTCATGTTA
4474 AAAACAGGTCAGGTTC
1 AAAACAGGTCAGGTTC
* *
4490 ATAACAGGTCAGGTTG
1 AAAACAGGTCAGGTTC
4506 AAAACAGGTC
1 AAAACAGGTC
4516 GGATAATACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (16 bp):
AAAACAGGTCAGGTTC
Found at i:6410 original size:2 final size:2
Alignment explanation
Indices: 6403--6433 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6393 TTAAATTTCA
6403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6434 AATGTTAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6596 original size:18 final size:18
Alignment explanation
Indices: 6575--6617 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6565 GTTTTTTTTA
6575 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAATAATT
6593 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
*
6611 CAATAAA
1 AAATAAA
6618 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:8058 original size:42 final size:42
Alignment explanation
Indices: 8012--8145 Score: 103
Period size: 42 Copynumber: 3.1 Consensus size: 42
8002 GCTGATTATA
8012 ATTCTTTAGATGACTCCCCTTCACGGGAAAGCCAAGTGGTAT
1 ATTCTTTAGATGACTCCCCTTCACGGGAAAGCCAAGTGGTAT
* * ** * * *
8054 ATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA-CCAGGTGAG-AT
1 ATTCTTTAGATGACTCCCCTTCACGGG---AAAGCCAAGTG-GTAT
* * *
8098 GA-TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTAT
1 -ATTCTTTAGATGACTCCCCTTCACGGGAAAGCCAAGTGGTAT
*
8140 GTTCTT
1 ATTCTT
8146 CATGTGGTTC
Statistics
Matches: 67, Mismatches: 17, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
41 3 0.04
42 33 0.49
44 27 0.40
45 4 0.06
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.31
Consensus pattern (42 bp):
ATTCTTTAGATGACTCCCCTTCACGGGAAAGCCAAGTGGTAT
Found at i:8215 original size:86 final size:86
Alignment explanation
Indices: 8014--8231 Score: 366
Period size: 86 Copynumber: 2.5 Consensus size: 86
8004 TGATTATAAT
* * * *
8014 TCTTTAGATGACTCCCCTTCACGGGAAAGCCAAGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATGTTCTTCAGGTGGTTCCCCTTCGCG
8079 GGTCTGAACCAGGTGAGATGA
66 GGTCTGAACCAGGTGAGATGA
*
8100 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATGTTCTTCATGTGGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATGTTCTTCAGGTGGTTCCCCTTCGCG
*
8165 GGTCTGAACCAGGTGAGATTA
66 GGTCTGAACCAGGTGAGATGA
8186 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGAG-ATGTTCTT
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTG-GTATGTTCTT
8232 TAAGTGACTC
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
86 124 0.99
87 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.31
Consensus pattern (86 bp):
TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATGTTCTTCAGGTGGTTCCCCTTCGCG
GGTCTGAACCAGGTGAGATGA
Found at i:8242 original size:42 final size:42
Alignment explanation
Indices: 8091--8232 Score: 123
Period size: 42 Copynumber: 3.3 Consensus size: 42
8081 TCTGAACCAG
*
8091 GTGAGATGATCTTTGGATGACTCCCCTTCACGGGAAAGTCAT
1 GTGAGATGTTCTTTGGATGACTCCCCTTCACGGGAAAGTCAT
** * * * *
8133 GTG-GTATGTTCTTCAT-G-TGGTTCCCCTTCGCGGGTCTGAA-CCAG
1 GTGAG-ATGTTCTT--TGGATGACTCCCCTTCACGGG---AAAGTCAT
8177 GTGAGAT-TATCTTTGGATGACTCCCCTTCACGGGAAAGTCAT
1 GTGAGATGT-TCTTTGGATGACTCCCCTTCACGGGAAAGTCAT
8219 GTGAGATGTTCTTT
1 GTGAGATGTTCTTT
8233 AAGTGACTCC
Statistics
Matches: 75, Mismatches: 13, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
41 3 0.04
42 39 0.52
43 4 0.05
44 26 0.35
45 3 0.04
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (42 bp):
GTGAGATGTTCTTTGGATGACTCCCCTTCACGGGAAAGTCAT
Found at i:16104 original size:5 final size:5
Alignment explanation
Indices: 16094--16160 Score: 66
Period size: 5 Copynumber: 12.8 Consensus size: 5
16084 GTTAAAAGAG
*
16094 AAAAT AAAAT AGAAT AAAAT AAAAT AAAA- AAAAGT AGGAAAAT AAAGAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T ---AAAAT AAA-AT
16143 AAAA- AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
16161 AAGGGAAACA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
4 8 0.15
5 35 0.66
6 5 0.09
8 1 0.02
9 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:16163 original size:23 final size:23
Alignment explanation
Indices: 16087--16182 Score: 68
Period size: 23 Copynumber: 4.0 Consensus size: 23
16077 AAAAAATGTT
*
16087 AAAAGAGAAAATAAAATAGAATAA
1 AAAAGAGAAAA-AAAATAAAATAA
* * *
16111 AATAAAATAAAAAAAAGTAGGAA-AA
1 AA-AAGAGAAAAAAAA-TA-AAATAA
* *
16136 TAAAGATAAAAAAAATAAAATAA
1 AAAAGAGAAAAAAAATAAAATAA
* * *
16159 AAAAGGGAAACATAATAAAATAA
1 AAAAGAGAAAAAAAATAAAATAA
16182 A
1 A
16183 TAATAATAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
22 2 0.03
23 23 0.40
24 18 0.31
25 12 0.21
26 3 0.05
ACGTcount: A:0.75, C:0.01, G:0.10, T:0.14
Consensus pattern (23 bp):
AAAAGAGAAAAAAAATAAAATAA
Found at i:16724 original size:13 final size:13
Alignment explanation
Indices: 16706--16744 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
16696 AGCATAACTA
16706 TTGAAAACAAAAT
1 TTGAAAACAAAAT
16719 TTGAAAACAAAAT
1 TTGAAAACAAAAT
* *
16732 TTAAAAAGAAAAT
1 TTGAAAACAAAAT
16745 AAAAAAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (13 bp):
TTGAAAACAAAAT
Found at i:16772 original size:12 final size:12
Alignment explanation
Indices: 16757--16787 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16747 AAAAGTATGC
16757 GAAAAATAGAGA
1 GAAAAATAGAGA
*
16769 GAAAGATAGAGA
1 GAAAAATAGAGA
16781 GAAAAAT
1 GAAAAAT
16788 TAGATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.10
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:18360 original size:75 final size:75
Alignment explanation
Indices: 18251--18437 Score: 207
Period size: 75 Copynumber: 2.5 Consensus size: 75
18241 AATATTTTTC
* * *
18251 TAGACTTAATATTATGGTTTGAGTCTT-AAGATTTGACACTCTAATATTAT-GATTTAATTATGT
1 TAGACTTAATATTGTGGTTTGAATCTTGAA-ATTTGACACTCTAATATTATAG-TTTAATTATGG
*
18314 ATTTTATTATTA
64 ATTTTACTATTA
* * * * **
18326 TAGAGTTAATATTGTAGTTTGAATCTTGAAATTTGACATTTTAATATTATAGTTTGTTTATGGAT
1 TAGACTTAATATTGTGGTTTGAATCTTGAAATTTGACACTCTAATATTATAGTTTAATTATGGAT
* *
18391 TTTACTGTTC
66 TTTACTATTA
* * *
18401 TAAACTTAATATTGTGGTTTGAATATTGATATTTGAC
1 TAGACTTAATATTGTGGTTTGAATCTTGAAATTTGAC
18438 TTTATTTATG
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
75 90 0.97
76 3 0.03
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.49
Consensus pattern (75 bp):
TAGACTTAATATTGTGGTTTGAATCTTGAAATTTGACACTCTAATATTATAGTTTAATTATGGAT
TTTACTATTA
Found at i:19142 original size:25 final size:24
Alignment explanation
Indices: 19113--19160 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
19103 ATATTATTTT
*
19113 TATATTAATTAAATTTAATATTTAA
1 TATATTAACTAAATTTAA-ATTTAA
* *
19138 TATATTTACTAATTTTAAATTTA
1 TATATTAACTAAATTTAAATTTA
19161 TGATTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TATATTAACTAAATTTAAATTTAA
Found at i:26100 original size:200 final size:198
Alignment explanation
Indices: 25729--26121 Score: 583
Period size: 200 Copynumber: 2.0 Consensus size: 198
25719 TCTTTGAATG
** * * * * * *
25729 TTAGGTAATTAAATGTTTTTTAAGGATCATGATTATAGGCCTTTGTCAAGTGAAGAGATTAGACA
1 TTAGGTAACGAAATGTCTTTTAAGGAACATGATTATAGACCTTTGACAAGGGAAGAGACTAGACA
* * **
25794 TTTTATATCTCATCCTAAGTCGAAATACAATCCCTTGATTTTTCACTTGAAATTGTCTACGATCA
66 TTTCATATCTCATCCTAAGTCAAAATACAATCCCTTGATTTTTCACTTGAAATCATCTACGATCA
*
25859 ACATCAAAAGACTCAACCTTGACATTTTTCGTTTATGAGGTATCAAAAGCTTACCCTTACATTTA
131 ACATCAAAAGACCCAACCTTGACATTTTTCGTTTATGAGGTATCAAAAGCTTA-CCTTACATTTA
25924 AACA
195 AACA
*
25928 TTAGGTAACGAAATGTCCTTTTAAGGAACATGGTTATAGACCTTTTGACAAGGGAAGAGACTAGA
1 TTAGGTAACGAAATGT-CTTTTAAGGAACATGATTATAGACC-TTTGACAAGGGAAGAGACTAGA
25993 CATTTCATATC-C-TACCTAAGTCAAAATACAATCCCTTGATTTTTCACTTGAAATCATCTACGA
64 CATTTCATATCTCAT-CCTAAGTCAAAATACAATCCCTTGATTTTTCACTTGAAATCATCTACGA
* * *
26056 TCAATATCAAAAGACCCAACCTTGACATTTTTCTTTTCTGAGGTATCAAAAGCTTACCTTACATT
128 TCAACATCAAAAGACCCAACCTTGACATTTTTCGTTTATGAGGTATCAAAAGCTTACCTTACATT
26121 T
193 T
26122 GTAGTCAACC
Statistics
Matches: 174, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
199 25 0.14
200 120 0.69
201 29 0.17
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (198 bp):
TTAGGTAACGAAATGTCTTTTAAGGAACATGATTATAGACCTTTGACAAGGGAAGAGACTAGACA
TTTCATATCTCATCCTAAGTCAAAATACAATCCCTTGATTTTTCACTTGAAATCATCTACGATCA
ACATCAAAAGACCCAACCTTGACATTTTTCGTTTATGAGGTATCAAAAGCTTACCTTACATTTAA
ACA
Found at i:38311 original size:18 final size:19
Alignment explanation
Indices: 38273--38311 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
38263 TTTCCCCACT
38273 AACATCCTTGGTTTCTATCC
1 AACATCCTT-GTTTCTATCC
*
38293 AACATCCTT-TTTCTCTCC
1 AACATCCTTGTTTCTATCC
38311 A
1 A
38312 TTACTCTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.41
Consensus pattern (19 bp):
AACATCCTTGTTTCTATCC
Found at i:42625 original size:19 final size:20
Alignment explanation
Indices: 42601--42638 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
42591 ACTATTATAT
*
42601 TACTTGCATTG-ATTGTGTA
1 TACTTGCATAGAATTGTGTA
42620 TACTTGCATAGAATTGTGT
1 TACTTGCATAGAATTGTGT
42639 GCCGCAACGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.45
Consensus pattern (20 bp):
TACTTGCATAGAATTGTGTA
Found at i:45849 original size:31 final size:31
Alignment explanation
Indices: 45814--45880 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
45804 AAAATATATA
* *
45814 TCTAATGTTTTCTCGGTTATGCTTTTAGGTG
1 TCTAACGTTTTCTCGGTTATACTTTTAGGTG
* *
45845 TCTAACGTTTTCTCTGTTATACTTTTATGTG
1 TCTAACGTTTTCTCGGTTATACTTTTAGGTG
*
45876 CCTAA
1 TCTAA
45881 ACAATAACAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (31 bp):
TCTAACGTTTTCTCGGTTATACTTTTAGGTG
Found at i:52874 original size:21 final size:20
Alignment explanation
Indices: 52835--52892 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
52825 ATGTAAAATT
*
52835 TAATAT-TAATATTAATTAAAA
1 TAATATATAATA-T-ATTTAAA
52856 TAATATATAATATATTTAAA
1 TAATATATAATATATTTAAA
52876 TAATCA-AGTAATATATT
1 TAAT-ATA-TAATATATT
52893 ATCGATGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.33
21 17 0.52
22 5 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TAATATATAATATATTTAAA
Found at i:54658 original size:38 final size:37
Alignment explanation
Indices: 54555--54675 Score: 138
Period size: 38 Copynumber: 3.2 Consensus size: 37
54545 AGTGTAATCT
* * *
54555 AAAATATTAGATTTTTTACTAATATTTTTATTG-AACAG
1 AAAATATTACA-TTTTCA-TAATATTTTTATTGCAACCG
54593 AAAATATTACATTTTCATAATATTTTTATTAGCAACCG
1 AAAATATTACATTTTCATAATATTTTTATT-GCAACCG
* *
54631 AAAATATTACATTCTTCGTAATATTTTAAATT-CAACCG
1 AAAATATTACATT-TTCATAATATTTT-TATTGCAACCG
54669 AAAATAT
1 AAAATAT
54676 CAAAAAAAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
36 13 0.18
37 6 0.08
38 40 0.54
39 12 0.16
40 3 0.04
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (37 bp):
AAAATATTACATTTTCATAATATTTTTATTGCAACCG
Found at i:59327 original size:21 final size:21
Alignment explanation
Indices: 59301--59373 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
59291 CACCAAAGTG
59301 CCACATAATTATCCCGAAAGA
1 CCACATAATTATCCCGAAAGA
* * * *
59322 CCACATAGTTTTGTACCG-AAGTG
1 CCACATA--ATTATCCCGAAAG-A
* *
59345 CCACATATTTATCCCAAAAGA
1 CCACATAATTATCCCGAAAGA
59366 CCACATAA
1 CCACATAA
59374 AACCCCGACT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
21 20 0.51
22 6 0.15
23 13 0.33
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.23
Consensus pattern (21 bp):
CCACATAATTATCCCGAAAGA
Found at i:59359 original size:44 final size:44
Alignment explanation
Indices: 59287--59372 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
59277 TAGCTCGTAA
*
59287 TTTGCACCAAAGTGCCACATAATTATCCCGAAAGACCACATAGT
1 TTTGCACCAAAGTGCCACATAATTATCCCAAAAGACCACATAGT
* * *
59331 TTTGTACCGAAGTGCCACATATTTATCCCAAAAGACCACATA
1 TTTGCACCAAAGTGCCACATAATTATCCCAAAAGACCACATA
59373 AAACCCCGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (44 bp):
TTTGCACCAAAGTGCCACATAATTATCCCAAAAGACCACATAGT
Found at i:59522 original size:21 final size:21
Alignment explanation
Indices: 59496--59546 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
59486 CATAGAGTCT
59496 GTTCACATTCACTGGTTCAAA
1 GTTCACATTCACTGGTTCAAA
*
59517 GTTCACATTCACTTGTTCAAA
1 GTTCACATTCACTGGTTCAAA
*
59538 GTTTACATT
1 GTTCACATT
59547 TTCATAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (21 bp):
GTTCACATTCACTGGTTCAAA
Found at i:65943 original size:2 final size:2
Alignment explanation
Indices: 65936--65971 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
65926 AAGATATACC
65936 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65972 TTCACTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65961 original size:17 final size:17
Alignment explanation
Indices: 65939--65971 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
65929 ATATACCTAT
65939 ATATATATATATATATA
1 ATATATATATATATATA
65956 ATATATATATATATAT
1 ATATATATATATATAT
65972 TTCACTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:66144 original size:24 final size:24
Alignment explanation
Indices: 66112--66158 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
66102 GATGGACCAA
66112 TTTTTGCACTGAAGTACCACATAG
1 TTTTTGCACTGAAGTACCACATAG
*
66136 TTTTTGCACTGAAGTGCCACATA
1 TTTTTGCACTGAAGTACCACATA
66159 TTTGTCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
TTTTTGCACTGAAGTACCACATAG
Found at i:66380 original size:21 final size:21
Alignment explanation
Indices: 66341--66380 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
66331 TTTACATTTC
66341 CATAATTGTATAATCATAAAA
1 CATAATTGTATAATCATAAAA
66362 CATAACTTGTATAAT-ATAA
1 CATAA-TTGTATAATCATAA
66381 CTTTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (21 bp):
CATAATTGTATAATCATAAAA
Found at i:66836 original size:21 final size:21
Alignment explanation
Indices: 66812--66884 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
66802 ACTATCCCCT
66812 AGTATCGATACTACCCCTTTC
1 AGTATCGATACTACCCCTTTC
*
66833 AGTATCGATAC--CCTCCTTAAC
1 AGTATCGATACTACC-CCTT-TC
* *
66854 TGTATCGATACTA-CCCTCTC
1 AGTATCGATACTACCCCTTTC
66874 AGTATCGATAC
1 AGTATCGATAC
66885 CCTCCTCGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 2 0.05
20 15 0.35
21 25 0.58
22 1 0.02
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (21 bp):
AGTATCGATACTACCCCTTTC
Found at i:66886 original size:41 final size:42
Alignment explanation
Indices: 66813--66907 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 42
66803 CTATCCCCTA
* *
66813 GTATCGATACTACCCCTTTCAGTATCGATACCCTCCTTAACT-
1 GTATCGATACTACCCCTCTCAGTATCGATACCCTCCTCAA-TG
*
66855 GTATCGATACTA-CCCTCTCAGTATCGATACCCTCCTCGATG
1 GTATCGATACTACCCCTCTCAGTATCGATACCCTCCTCAATG
66896 GTATCGATACTA
1 GTATCGATACTA
66908 GCCTTAAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
40 1 0.02
41 36 0.73
42 12 0.24
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.32
Consensus pattern (42 bp):
GTATCGATACTACCCCTCTCAGTATCGATACCCTCCTCAATG
Done.