Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007333.1 Hibiscus syriacus cultivar Beakdansim tig00019621_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: 125671
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:488 original size:14 final size:14
Alignment explanation
Indices: 469--498 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
459 AATTTTAAGG
*
469 TATGATTTAGGGTT
1 TATGATTTAAGGTT
483 TATGATTTAAGGTT
1 TATGATTTAAGGTT
497 TA
1 TA
499 AAAGTTATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (14 bp):
TATGATTTAAGGTT
Found at i:1702 original size:59 final size:60
Alignment explanation
Indices: 1616--1751 Score: 152
Period size: 59 Copynumber: 2.3 Consensus size: 60
1606 TAAATGTTCC
** * * * *
1616 ATTTCATCCTTAAACTATGATTATCATTTTAAATCAATCCTC-AACTTTTTGAACATTTAA
1 ATTTCATCCCCAAACTATGACTATCATTCTAAATCAATCCTCAAAATTTTT-AACATTCAA
** *
1676 ATTTCATCCCCAAACTATGACT-TCATTCTAAATTGATCCTCAAAATTTTTAACATTCCA
1 ATTTCATCCCCAAACTATGACTATCATTCTAAATCAATCCTCAAAATTTTTAACATTCAA
*
1735 ATTTTAT-CCCAAACTAT
1 ATTTCATCCCCAAACTAT
1752 ATGTATACTA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 10 0.15
59 29 0.45
60 26 0.40
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (60 bp):
ATTTCATCCCCAAACTATGACTATCATTCTAAATCAATCCTCAAAATTTTTAACATTCAA
Found at i:3136 original size:2 final size:2
Alignment explanation
Indices: 3129--3158 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3119 TGCAAACATA
*
3129 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3159 TATTATGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7216 original size:24 final size:24
Alignment explanation
Indices: 7189--7235 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
7179 GATTTGGGAA
7189 TGGAGAAAGGAGGG-TTAGGGATTT
1 TGGAG-AAGGAGGGATTAGGGATTT
* *
7213 TGGAGGATGAGGGATTAGGGATT
1 TGGAGAAGGAGGGATTAGGGATT
7236 CACGAGAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.26
Consensus pattern (24 bp):
TGGAGAAGGAGGGATTAGGGATTT
Found at i:9102 original size:26 final size:26
Alignment explanation
Indices: 9066--9118 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
9056 ACTGCTAGAT
9066 GCAATAAAGTAGAGTGGCAAATGCAG
1 GCAATAAAGTAGAGTGGCAAATGCAG
9092 GCAATAAAGTAGAGTGGCAAATGCAG
1 GCAATAAAGTAGAGTGGCAAATGCAG
9118 G
1 G
9119 GACATACTTT
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:0.42, C:0.11, G:0.32, T:0.15
Consensus pattern (26 bp):
GCAATAAAGTAGAGTGGCAAATGCAG
Found at i:14322 original size:18 final size:18
Alignment explanation
Indices: 14299--14334 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
14289 TTTGCCAAGG
*
14299 ATTTTATTTTCTTTAGGT
1 ATTTTATTTTCGTTAGGT
14317 ATTTTATTTTCGTTAGGT
1 ATTTTATTTTCGTTAGGT
14335 TTTCTCACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.14, T:0.64
Consensus pattern (18 bp):
ATTTTATTTTCGTTAGGT
Found at i:22456 original size:23 final size:23
Alignment explanation
Indices: 22424--22482 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
22414 TGAATAAATT
*
22424 TAAACAAATGAATATAAACAACA
1 TAAACGAATGAATATAAACAACA
*
22447 TAAACGAATGAATATAAATAACA
1 TAAACGAATGAATATAAACAACA
*
22470 TAAACGAACGAAT
1 TAAACGAATGAAT
22483 TATCGAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.61, C:0.12, G:0.08, T:0.19
Consensus pattern (23 bp):
TAAACGAATGAATATAAACAACA
Found at i:29104 original size:19 final size:17
Alignment explanation
Indices: 29064--29097 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29054 AGAATCATAC
29064 ACTTGAGATATATTAAT
1 ACTTGAGATATATTAAT
29081 ACTTGAGATATATTAAT
1 ACTTGAGATATATTAAT
29098 GGACTTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
ACTTGAGATATATTAAT
Found at i:31052 original size:17 final size:18
Alignment explanation
Indices: 31025--31067 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
31015 AATCGGTAAA
* *
31025 TATTCAATATTTAAT-TT
1 TATTAAATATTAAATATT
*
31042 TTTTAAATATTAAATATT
1 TATTAAATATTAAATATT
31060 TATTAAAT
1 TATTAAAT
31068 TATAAGATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTAAATATTAAATATT
Found at i:32656 original size:21 final size:21
Alignment explanation
Indices: 32630--32671 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
32620 AAACCTAATA
*
32630 AATTTAGAATAAATCGCAACG
1 AATTTAAAATAAATCGCAACG
*
32651 AATTTAAAATAAATCGTAACG
1 AATTTAAAATAAATCGCAACG
32672 CGAACTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (21 bp):
AATTTAAAATAAATCGCAACG
Found at i:32718 original size:42 final size:42
Alignment explanation
Indices: 32642--32732 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
32632 TTTAGAATAA
** * *
32642 ATCGCAACGAATTTAAAATAAATCGTAACGCGAACTTCGATT
1 ATCGCAACGAATTTAAAATAAATCACAACACGAACTTCGACT
* * *
32684 ATCGCAACGAATTTGAAATAAATCACAATACGAACTTGGACT
1 ATCGCAACGAATTTAAAATAAATCACAACACGAACTTCGACT
32726 ATCGCAA
1 ATCGCAA
32733 TGCGAATATG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (42 bp):
ATCGCAACGAATTTAAAATAAATCACAACACGAACTTCGACT
Found at i:34181 original size:19 final size:20
Alignment explanation
Indices: 34157--34195 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34147 CAAAACATGG
34157 CCATTTC-TCCTTCGGTATC
1 CCATTTCTTCCTTCGGTATC
*
34176 CCATTTCTTCGTTCGGTATC
1 CCATTTCTTCCTTCGGTATC
34196 TGTCTGGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.10, C:0.33, G:0.13, T:0.44
Consensus pattern (20 bp):
CCATTTCTTCCTTCGGTATC
Found at i:35872 original size:21 final size:20
Alignment explanation
Indices: 35848--35912 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 20
35838 AACTTTGAAA
35848 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
35869 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
35883 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
35904 AAATGTTTT
1 AAATGTTTT
35913 TTTGAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
19 4 0.11
20 8 0.23
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:35886 original size:35 final size:36
Alignment explanation
Indices: 35840--35961 Score: 158
Period size: 35 Copynumber: 3.4 Consensus size: 36
35830 TGGTAACCAA
35840 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
35877 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* * * *
35912 TTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGCTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
35949 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
35962 AATGGGATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 35 0.46
36 14 0.18
37 27 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:40491 original size:21 final size:20
Alignment explanation
Indices: 40467--40527 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
40457 AACTTTGAAA
40467 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTT-GT
*
40488 AAAT-G-TTTC----TTTGA
1 AAATGGTTTTCAAAGTTTGT
40502 AAATGGTTTTCAAAGTTTTGT
1 AAATGGTTTTCAAAG-TTTGT
40523 AAATG
1 AAATG
40528 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 1 0.03
21 13 0.42
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (20 bp):
AAATGGTTTTCAAAGTTTGT
Found at i:40573 original size:36 final size:36
Alignment explanation
Indices: 40459--40578 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
40449 TGGTACCCAA
40459 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
40496 CTTTG-AAAATGGTTTTCAAAGTTTTGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
40531 CTTTGAAAAATAGTTTTTTAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
40568 -GTTGAAAAATG
1 CTTTGAAAAATG
40579 ATAACGAGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 35 0.46
36 14 0.18
37 27 0.36
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:41996 original size:22 final size:23
Alignment explanation
Indices: 41959--42001 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
41949 AATGACATCA
41959 ATTCACTTAAAAAATATTTATGG
1 ATTCACTTAAAAAATATTTATGG
41982 ATTCACTT-AAAAATATTTAT
1 ATTCACTTAAAAAATATTTAT
42002 TTGTGTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (23 bp):
ATTCACTTAAAAAATATTTATGG
Found at i:50667 original size:14 final size:14
Alignment explanation
Indices: 50650--50683 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
50640 TCCTCCACAG
50650 TAAACATATATATA
1 TAAACATATATATA
*
50664 TAAATATATATATA
1 TAAACATATATATA
*
50678 AAAACA
1 TAAACA
50684 CAAATAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAACATATATATA
Found at i:50672 original size:12 final size:12
Alignment explanation
Indices: 50655--50679 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50645 CACAGTAAAC
50655 ATATATATATAA
1 ATATATATATAA
50667 ATATATATATAA
1 ATATATATATAA
50679 A
1 A
50680 AACACAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATATAA
Found at i:50935 original size:29 final size:29
Alignment explanation
Indices: 50874--51014 Score: 101
Period size: 29 Copynumber: 4.9 Consensus size: 29
50864 TTAGGACGGG
* * * *
50874 GATACAATCCCATGTAGAATCAAGACT-GG
1 GATATAATCCCATGCAGAATCAGGA-TAGA
50903 GATATAATCCCATGCAGAATCAGGATAGA
1 GATATAATCCCATGCAGAATCAGGATAGA
* * *
50932 GATATAATTCCATACAGAATCA-GA-ACGG
1 GATATAATCCCATGCAGAATCAGGATA-GA
* * * *
50960 GATATAATCTCACGCAGAACCAGGA-CGAA
1 GATATAATCCCATGCAGAATCAGGATAG-A
** *
50989 GATATAATCTTATGCAGAGTCAGGAT
1 GATATAATCCCATGCAGAATCAGGAT
51015 GGGAAACATA
Statistics
Matches: 89, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
27 1 0.01
28 22 0.25
29 66 0.74
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (29 bp):
GATATAATCCCATGCAGAATCAGGATAGA
Found at i:52679 original size:21 final size:22
Alignment explanation
Indices: 52645--52689 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
52635 ATATTTTTAA
*
52645 TTTTAAAATTTTTAATAGTTTT
1 TTTTAAAATATTTAATAGTTTT
52667 TTTTAAAA-ATTTAATAGTTTT
1 TTTTAAAATATTTAATAGTTTT
52688 TT
1 TT
52690 ATGAACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTAAAATATTTAATAGTTTT
Found at i:53462 original size:23 final size:23
Alignment explanation
Indices: 53436--53481 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53426 GTTAAACGAT
*
53436 TGAAAATGTGACATAAAAACATA
1 TGAAAACGTGACATAAAAACATA
* *
53459 TGAAAACGTGTCATAAAGACATA
1 TGAAAACGTGACATAAAAACATA
53482 ATTATTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (23 bp):
TGAAAACGTGACATAAAAACATA
Found at i:53516 original size:16 final size:16
Alignment explanation
Indices: 53495--53532 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
53485 ATTAAAAATA
*
53495 AAAAATA-AAATACGAT
1 AAAAATAGAAA-ACAAT
53511 AAAAATAGAAAACAAT
1 AAAAATAGAAAACAAT
53527 AAAAAT
1 AAAAAT
53533 GTTGAAGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (16 bp):
AAAAATAGAAAACAAT
Found at i:54966 original size:26 final size:27
Alignment explanation
Indices: 54937--54987 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
54927 GTCTCTTGTT
54937 TATTTAATATTATTT-ATGTTTAATGA
1 TATTTAATATTATTTCATGTTTAATGA
* * *
54963 TATTTGATATTTTTTCATTTTTAAT
1 TATTTAATATTATTTCATGTTTAAT
54988 TGGACTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (27 bp):
TATTTAATATTATTTCATGTTTAATGA
Found at i:55154 original size:3 final size:3
Alignment explanation
Indices: 55146--55242 Score: 185
Period size: 3 Copynumber: 32.3 Consensus size: 3
55136 ATTGTGATAC
55146 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
55194 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
55242 A
1 A
55243 CCGATGGATC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:55559 original size:31 final size:30
Alignment explanation
Indices: 55492--55559 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 30
55482 ATAATATCTG
*
55492 GTCACTTTCGTTTTTATTTAATTAAGATTT
1 GTCACTTTCGTTTTTATTTAATTAAGATTA
55522 GATCACTTTCGTTTTTATTTAATTAAGATGTA
1 G-TCACTTTCGTTTTTATTTAATTAAGAT-TA
55554 GTCACT
1 GTCACT
55560 GAAGCCTAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 1 0.03
31 32 0.91
32 2 0.06
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (30 bp):
GTCACTTTCGTTTTTATTTAATTAAGATTA
Found at i:57186 original size:59 final size:59
Alignment explanation
Indices: 57120--57255 Score: 200
Period size: 59 Copynumber: 2.3 Consensus size: 59
57110 TTATATCATT
* * * **
57120 GACCACCTAATTATTTGACCCTTTTACTTTTGTCATTGATCTCTCAATTTTGTCAATTA
1 GACCACCTAACTATTTAAACCTTTTACTTTTGTCATTGATCTCTCAATTTTACCAATTA
* * *
57179 GACCACCTAACTATTAAAACCTTTTAGTTTTTTCATTGATCTCTCAATTTTACCAATTA
1 GACCACCTAACTATTTAAACCTTTTACTTTTGTCATTGATCTCTCAATTTTACCAATTA
57238 GACCACCTAACTATTTAA
1 GACCACCTAACTATTTAA
57256 TTATTATCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.42
Consensus pattern (59 bp):
GACCACCTAACTATTTAAACCTTTTACTTTTGTCATTGATCTCTCAATTTTACCAATTA
Found at i:58310 original size:2 final size:2
Alignment explanation
Indices: 58276--58300 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58266 TCGAAAGAAT
58276 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 T
58301 CAAAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62846 original size:74 final size:75
Alignment explanation
Indices: 62766--62929 Score: 197
Period size: 82 Copynumber: 2.1 Consensus size: 75
62756 ATTTTATAAC
* *
62766 TTTTAATAGTCGAGT-GACCTAAAAATAATATTTTATAATCAGATAATCATTTTATAATTTTTAA
1 TTTTAATACTCGA-TAGACCTAAAAATAATACTTTATAATCAGATAATCATTTTATAATTTTTAA
*
62830 TAACCGAATAA
65 TAACCGAAGAA
* *
62841 TTTAATAAAATAATACTCTATAGTCCTAAAAATAATACTTTATAATCAGATAATCATTTTATAAT
1 -TT--T----TAATACTCGATAGACCTAAAAATAATACTTTATAATCAGATAATCATTTTATAAT
62906 TTTTAATAACCGAAGAA
59 TTTTAATAACCGAAGAA
62923 -TTTAATA
1 TTTTAATA
62930 AAATAATACT
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
74 5 0.07
76 2 0.03
78 2 0.03
80 1 0.01
81 1 0.01
82 65 0.86
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.40
Consensus pattern (75 bp):
TTTTAATACTCGATAGACCTAAAAATAATACTTTATAATCAGATAATCATTTTATAATTTTTAAT
AACCGAAGAA
Found at i:62874 original size:82 final size:82
Alignment explanation
Indices: 62783--62947 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
62773 AGTCGAGTGA
* *
62783 CCTAAAAATAATATTTTATAATCAGATAATCATTTTATAATTTTTAATAACCGAATAATTTAATA
1 CCTAAAAATAATACTTTATAATCAGATAATCATTTTATAATTTTTAATAACCGAAGAATTTAATA
62848 AAATAATACTCTATAGT
66 AAATAATACTCTATAGT
62865 CCTAAAAATAATACTTTATAATCAGATAATCATTTTATAATTTTTAATAACCGAAGAATTTAATA
1 CCTAAAAATAATACTTTATAATCAGATAATCATTTTATAATTTTTAATAACCGAAGAATTTAATA
62930 AAATAATACTCTATAGT
66 AAATAATACTCTATAGT
62947 C
1 C
62948 AGAGACCATT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (82 bp):
CCTAAAAATAATACTTTATAATCAGATAATCATTTTATAATTTTTAATAACCGAAGAATTTAATA
AAATAATACTCTATAGT
Found at i:66543 original size:2 final size:2
Alignment explanation
Indices: 66538--66580 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
66528 ACACACACAC
66538 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
66580 A
1 A
66581 AGTGGGTGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:72026 original size:11 final size:11
Alignment explanation
Indices: 72002--72052 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
71992 AATTTTAAAT
*
72002 AATTGGTGTAC
1 AATTGGTGTCC
*
72013 AATCGGTGTCC
1 AATTGGTGTCC
*
72024 AATTGGTGTGC
1 AATTGGTGTCC
72035 AATTGGTGTCC
1 AATTGGTGTCC
72046 AAGTTGG
1 AA-TTGG
72053 ATTAGTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 30 0.88
12 4 0.12
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (11 bp):
AATTGGTGTCC
Found at i:72028 original size:22 final size:22
Alignment explanation
Indices: 72002--72052 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
71992 AATTTTAAAT
72002 AATTGGTGTACAATCGGTGTCC
1 AATTGGTGTACAATCGGTGTCC
* *
72024 AATTGGTGTGCAATTGGTGTCC
1 AATTGGTGTACAATCGGTGTCC
72046 AAGTTGG
1 AA-TTGG
72053 ATTAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (22 bp):
AATTGGTGTACAATCGGTGTCC
Found at i:73986 original size:2 final size:2
Alignment explanation
Indices: 73969--74019 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
73959 CCATGTCAGT
* *
73969 TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74011 TA TA TA TA T
1 TA TA TA TA T
74020 GACACGCATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:76709 original size:2 final size:2
Alignment explanation
Indices: 76702--76756 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
76692 AGTATAAATG
76702 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
76744 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
76757 ACTTCTTAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76931 original size:2 final size:2
Alignment explanation
Indices: 76924--76951 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
76914 AAAGAGATTC
76924 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
76952 GAATAAGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89160 original size:10 final size:10
Alignment explanation
Indices: 89145--89184 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
89135 TACATTTTTA
89145 TTTTTTTATT
1 TTTTTTTATT
89155 TTTTTTTATT
1 TTTTTTTATT
*
89165 TTTTGTTTAAT
1 TTTT-TTTATT
*
89176 TTTATTTAT
1 TTTTTTTAT
89185 CTCCATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:89166 original size:17 final size:17
Alignment explanation
Indices: 89138--89182 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
89128 AATATATTAC
89138 ATTTTTATTTTTTTATTT
1 ATTTTTA-TTTTTTATTT
* *
89156 TTTTTTATTTTTTGTTT
1 ATTTTTATTTTTTATTT
*
89173 AATTTTATTT
1 ATTTTTATTT
89183 ATCTCCATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (17 bp):
ATTTTTATTTTTTATTT
Found at i:89178 original size:18 final size:18
Alignment explanation
Indices: 89132--89182 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
89122 CTAATAAATA
89132 TATTACATTTTTATTTTTT
1 TATTA-ATTTTTATTTTTT
**
89151 TATTTTTTTTTATTTTTT
1 TATTAATTTTTATTTTTT
89169 GT-TTAA-TTTTATTT
1 -TATTAATTTTTATTT
89183 ATCTCCATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 8 0.30
18 14 0.52
19 5 0.19
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (18 bp):
TATTAATTTTTATTTTTT
Found at i:89178 original size:21 final size:20
Alignment explanation
Indices: 89145--89184 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
89135 TACATTTTTA
* *
89145 TTTTTTTATTTTTTTTTATT
1 TTTTTTTAATTTTATTTATT
89165 TTTTGTTTAATTTTATTTAT
1 TTTT-TTTAATTTTATTTAT
89185 CTCCATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTTTTAATTTTATTTATT
Found at i:89297 original size:24 final size:24
Alignment explanation
Indices: 89219--89286 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
89209 ATATATATAT
*
89219 ATTATTTTCATAGGTAGTGGTTTG
1 ATTATTTTAATAGGTAGTGGTTTG
89243 ATTATTTTAATAGGTAGTGGTTTG
1 ATTATTTTAATAGGTAGTGGTTTG
*
89267 ATTATTTTAATAAGTAGTGG
1 ATTATTTTAATAGGTAGTGG
89287 GTTATTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (24 bp):
ATTATTTTAATAGGTAGTGGTTTG
Found at i:93416 original size:105 final size:105
Alignment explanation
Indices: 93233--94296 Score: 1860
Period size: 105 Copynumber: 10.1 Consensus size: 105
93223 GAGAGTAAAT
* *
93233 AACAAACATTTCTCAGATTTCAGAGCCAATTTCAAATTCACAACGAAGGATATTGGACTCCAGAC
1 AACAAACATTTCTC-GATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
* * * *
93298 AACACAAGCTCAACTTCATGACGAAGGGGCCGCTGGTTGTC
65 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
93339 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
1 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
93404 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
66 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
*
93444 AACAAACATTTATCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
1 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
93509 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
66 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
93549 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
1 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
* *
93614 GCGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTC
66 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
93654 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
1 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
*
93719 ACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTC
66 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
93759 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
1 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
93824 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
66 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
* *
93864 AACAAACATTTATCGATTTCAGAGTCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACA
1 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
**
93929 ACATAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
66 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
*
93969 AACAAACATTTATCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
1 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
**
94034 ACATAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
66 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
* *
94074 AACAAACATTTCCCAATTTCAGAG-CTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
1 AACAAACATTTCTCGATTTCAGAGTC-AATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
*
94138 AACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTC
65 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
* * * * *
94179 AATAAACATTTCCCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACA
1 AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
*
94244 ACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
66 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
94284 AACAAACAATTTC
1 AACAAAC-ATTTC
94297 CCAGTTCCAG
Statistics
Matches: 925, Mismatches: 30, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
104 1 0.00
105 904 0.98
106 20 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (105 bp):
AACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
Found at i:96227 original size:10 final size:9
Alignment explanation
Indices: 96208--96237 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
96198 ATATATTACA
96208 TTTTTATTT
1 TTTTTATTT
96217 TTTTTATTT
1 TTTTTATTT
96226 TTTTTATTT
1 TTTTTATTT
96235 TTT
1 TTT
96238 GTTTAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:96246 original size:12 final size:10
Alignment explanation
Indices: 96208--96253 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
96198 ATATATTACA
96208 TTTTTA-TTT
1 TTTTTATTTT
96217 TTTTTA-TTT
1 TTTTTATTTT
96226 TTTTTATTTT
1 TTTTTATTTT
*
96236 TTGTTTAATTT
1 TT-TTTATTTT
*
96247 TATTTAT
1 TTTTTAT
96254 CTCCATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 15 0.47
10 9 0.28
11 8 0.25
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:96364 original size:24 final size:24
Alignment explanation
Indices: 96286--96353 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
96276 ATATATATAT
*
96286 ATTATTTTCATAGGTAGTGGTTTG
1 ATTATTTTAATAGGTAGTGGTTTG
96310 ATTATTTTAATAGGTAGTGGTTTG
1 ATTATTTTAATAGGTAGTGGTTTG
*
96334 ATTATTTTAATAAGTAGTGG
1 ATTATTTTAATAGGTAGTGG
96354 GTTATTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.26, C:0.01, G:0.24, T:0.49
Consensus pattern (24 bp):
ATTATTTTAATAGGTAGTGGTTTG
Found at i:97926 original size:12 final size:13
Alignment explanation
Indices: 97909--97938 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
97899 CATTTATATT
97909 TTTTAAAA-AATA
1 TTTTAAAATAATA
97921 TTTTAAAATAATA
1 TTTTAAAATAATA
97934 TTTTA
1 TTTTA
97939 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAATAATA
Found at i:105198 original size:58 final size:60
Alignment explanation
Indices: 105088--105208 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 60
105078 TTAAATATTG
105088 ATGGTCCCTCGACTATAGAATATTATTTTATTAAGTCCTCTGACTATTAAAAGTTACAAA
1 ATGGTCCCTCGACTATAGAATATTATTTTATTAAGTCCTCTGACTATTAAAAGTTACAAA
* * * *
105148 ATGGTCCC-CGACTATAGGATGTTGCTTTT-TTAAGT-CTCTGACTATTAAAAGTTATAAA
1 ATGGTCCCTCGACTATAGAATATT-ATTTTATTAAGTCCTCTGACTATTAAAAGTTACAAA
105206 ATG
1 ATG
105209 ATCACTCAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
58 25 0.45
59 19 0.34
60 12 0.21
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (60 bp):
ATGGTCCCTCGACTATAGAATATTATTTTATTAAGTCCTCTGACTATTAAAAGTTACAAA
Found at i:105225 original size:174 final size:171
Alignment explanation
Indices: 104917--105252 Score: 460
Period size: 174 Copynumber: 1.9 Consensus size: 171
104907 AAATATGCAA
* * * *
104917 ATGGTCCCTCAACTATAGAGTATTACTTTATTAAGTCCTTTAACTATTAAAAGTTATAAAATGAT
1 ATGGTCCCTCAACTATAGAATATTACTTTATTAAGTCCTCTAACTATTAAAAGTTACAAAATGAG
** * *
104982 TCTTCGACTATAGAATGTTTTTTAAGTCCCTGACTATTAAAAGTTACAAAATGATCATCCGATTA
66 TCCCCGACTATAGAATGTTTTTTAAGTCCCTGACTATTAAAAGTTACAAAATGATCATCCAACTA
*
105047 TTCATTATGTTCCAAACTCGTCCTTTTCTTTTTAAATATTG
131 TTCATTATGTTCCAAACTCGTCATTTTCTTTTTAAATATTG
* * *
105088 ATGGTCCCTCGACTATAGAATATTATTTTATTAAGTCCTCTGACTATTAAAAGTTACAAAATG-G
1 ATGGTCCCTCAACTATAGAATATTACTTTATTAAGTCCTCTAACTATTAAAAGTTACAAAATGAG
* * *
105152 TCCCCGACTATAGGATGTTGCTTTTTTAAGTCTCTGACTATTAAAAGTTATAAAATGATCA-CTC
66 TCCCCGACTATA-GA--ATG-TTTTTTAAGTCCCTGACTATTAAAAGTTACAAAATGATCATC-C
* *
105216 AACTATTCATTGTGTTTCAAACTCGTCATTTTCTTTT
126 AACTATTCATTATGTTCCAAACTCGTCATTTTCTTTT
105253 AAAAATTTAT
Statistics
Matches: 143, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
170 10 0.07
171 59 0.41
173 3 0.02
174 71 0.50
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (171 bp):
ATGGTCCCTCAACTATAGAATATTACTTTATTAAGTCCTCTAACTATTAAAAGTTACAAAATGAG
TCCCCGACTATAGAATGTTTTTTAAGTCCCTGACTATTAAAAGTTACAAAATGATCATCCAACTA
TTCATTATGTTCCAAACTCGTCATTTTCTTTTTAAATATTG
Found at i:105698 original size:22 final size:21
Alignment explanation
Indices: 105668--105712 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
105658 AAATTTGTAG
*
105668 AATTTAAATAATTTATATGTTA
1 AATTAAAATAATTTATAT-TTA
* *
105690 AATTAAAATTATTTTTATTTA
1 AATTAAAATAATTTATATTTA
105711 AA
1 AA
105713 AAATAAATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTAAAATAATTTATATTTA
Found at i:105783 original size:28 final size:29
Alignment explanation
Indices: 105752--105806 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
105742 CAATTAGACC
*
105752 CACAAATTTTCTAAAA-TATCAATTACGT
1 CACAAATTTTCTAAAAGAATCAATTACGT
105780 CACAAATTTTCTAAAAGAATCAATTAC
1 CACAAATTTTCTAAAAGAATCAATTAC
105807 TTCTATATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (29 bp):
CACAAATTTTCTAAAAGAATCAATTACGT
Found at i:105801 original size:29 final size:28
Alignment explanation
Indices: 105725--105806 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 28
105715 ATAAATACTT
* *
105725 AAATTTTCTTTAAAAATCAATTA-GACCCAC
1 AAATTTTC-TAAAAAATCAATTACG--TCAC
*
105755 AAATTTTCTAAAATATCAATTACGTCAC
1 AAATTTTCTAAAAAATCAATTACGTCAC
105783 AAATTTTCTAAAAGAATCAATTAC
1 AAATTTTCTAAAA-AATCAATTAC
105807 TTCTATATAC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 16 0.35
29 21 0.46
30 9 0.20
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (28 bp):
AAATTTTCTAAAAAATCAATTACGTCAC
Found at i:108822 original size:25 final size:26
Alignment explanation
Indices: 108770--108824 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
108760 TGTTAAGATG
* * *
108770 ATAATAAAATATATTTTAAAATTAAA
1 ATAAGAAAAAATATTTTAAAATAAAA
108796 ATAAGAAAAAATATTTT-AAATAAAA
1 ATAAGAAAAAATATTTTAAAATAAAA
108821 ATAA
1 ATAA
108825 ATATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAAGAAAAAATATTTTAAAATAAAA
Found at i:108832 original size:21 final size:19
Alignment explanation
Indices: 108794--108833 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
108784 TTTAAAATTA
*
108794 AAATAAGAAAAAATATTTT
1 AAATAAAAAAAAATATTTT
108813 AAATAAAAATAAATATATTTT
1 AAATAAAAA-AAA-ATATTTT
108834 TTTCTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
AAATAAAAAAAAATATTTT
Found at i:112554 original size:28 final size:28
Alignment explanation
Indices: 112514--112570 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
112504 CTGAAACTTA
112514 AAAAAGAAAAACTATTATATTTTCCAGC
1 AAAAAGAAAAACTATTATATTTTCCAGC
112542 AAAAAGAAAAACTATTATATTTTCCAGC
1 AAAAAGAAAAACTATTATATTTTCCAGC
112570 A
1 A
112571 CAAGCCACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAAAGAAAAACTATTATATTTTCCAGC
Found at i:119776 original size:31 final size:31
Alignment explanation
Indices: 119699--119777 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
119689 TTGTTTCTCT
* ** * *
119699 CAATGTGATCCTCCAACTCAGAAAATAAGTT
1 CAATGTGACCCTTTAACTCACAAAATAAGTC
**
119730 CAATGTGACTTTTTAACTCACAAAATAAGTC
1 CAATGTGACCCTTTAACTCACAAAATAAGTC
119761 CAATGTGACCCTTTAAC
1 CAATGTGACCCTTTAAC
119778 CTATGTTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (31 bp):
CAATGTGACCCTTTAACTCACAAAATAAGTC
Found at i:120327 original size:21 final size:21
Alignment explanation
Indices: 120301--120360 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
120291 TACAGCCCTA
* *
120301 GTCTACGGTGCTAACGTGATG
1 GTCTACGGTGCTGACGTGACG
120322 GTCTACGGTGCTGACGTGACG
1 GTCTACGGTGCTGACGTGACG
*
120343 GTCTACGATGCTGACGTG
1 GTCTACGGTGCTGACGTG
120361 GCAGTCCATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.35, T:0.27
Consensus pattern (21 bp):
GTCTACGGTGCTGACGTGACG
Found at i:121215 original size:11 final size:11
Alignment explanation
Indices: 121195--121250 Score: 73
Period size: 10 Copynumber: 5.4 Consensus size: 11
121185 AGTAACCAAC
121195 AACT-ATAACA
1 AACTAATAACA
121205 AACTAATAAC-
1 AACTAATAACA
121215 AACTAATAACA
1 AACTAATAACA
*
121226 AGCTAATAACA
1 AACTAATAACA
*
121237 AAC-CATAACA
1 AACTAATAACA
121247 AACT
1 AACT
121251 CTAACATTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
10 23 0.57
11 17 0.43
ACGTcount: A:0.59, C:0.21, G:0.02, T:0.18
Consensus pattern (11 bp):
AACTAATAACA
Found at i:121225 original size:21 final size:20
Alignment explanation
Indices: 121192--121250 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
121182 CCAAGTAACC
121192 AACAACTATAACAAACTAAT
1 AACAACTATAACAAACTAAT
*
121212 AACAACTAATAACAAGCTAAT
1 AACAACT-ATAACAAACTAAT
*
121233 AACAAACCATAACAAACT
1 AAC-AACTATAACAAACT
121251 CTAACATTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 24 0.71
22 3 0.09
ACGTcount: A:0.59, C:0.22, G:0.02, T:0.17
Consensus pattern (20 bp):
AACAACTATAACAAACTAAT
Found at i:122844 original size:11 final size:11
Alignment explanation
Indices: 122824--122867 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
122814 AGTAACCAAC
122824 AACT-ATAACA
1 AACTAATAACA
122834 AACTAATAAC-
1 AACTAATAACA
122844 -ACTAATAACA
1 AACTAATAACA
*
122854 AGCTAATAACA
1 AACTAATAACA
122865 AAC
1 AAC
122868 CATAACAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 9 0.31
10 4 0.14
11 16 0.55
ACGTcount: A:0.59, C:0.20, G:0.02, T:0.18
Consensus pattern (11 bp):
AACTAATAACA
Done.