Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000753.1 Hibiscus syriacus cultivar Beakdansim tig00001456_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: 138665
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6844 original size:23 final size:23
Alignment explanation
Indices: 6818--6872 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
6808 AACGATTGAG
*
6818 AAAGA-AAACAAAAAACGTGTTAC
1 AAAGACAAA-AAAAAACGTGTCAC
* *
6841 AAAGACATATAAAAACGTGTCAC
1 AAAGACAAAAAAAAACGTGTCAC
*
6864 AAAGGCAAA
1 AAAGACAAA
6873 TTATTCTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.13
Consensus pattern (23 bp):
AAAGACAAAAAAAAACGTGTCAC
Found at i:8162 original size:21 final size:22
Alignment explanation
Indices: 8129--8169 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
8119 GGTTAAAATA
8129 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
8151 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
8170 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:8968 original size:76 final size:75
Alignment explanation
Indices: 8816--8979 Score: 231
Period size: 76 Copynumber: 2.2 Consensus size: 75
8806 TAAAAATAAT
* * *
8816 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGTTA
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
8881 AAATATAAAA
66 AAATATAAAA
*
8891 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1 ATAATATCCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
* * *
8955 ATAATGTTTAAA
65 AAAAT-ATAAAA
*
8967 ATATTATCCTAAA
1 ATAATATCCTAAA
8980 TTTGAGTTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 31 0.39
76 48 0.61
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.30
Consensus pattern (75 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
AAATATAAAA
Found at i:14222 original size:22 final size:21
Alignment explanation
Indices: 14197--14239 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
14187 TAGGTTGATT
*
14197 TTAAAATATACACATATAAATA
1 TTAAAATATAAACATA-AAATA
* *
14219 TTAAGATTTAAACATAAAATA
1 TTAAAATATAAACATAAAATA
14240 ATACCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Found at i:29490 original size:22 final size:23
Alignment explanation
Indices: 29465--29545 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 23
29455 ACACAATAAA
29465 TAATATTATTTATCATAAAAT-T
1 TAATATTATTTATCATAAAATAT
*
29487 TAATATTA-TTATTTATAAAATAT
1 TAATATTATTTA-TCATAAAATAT
* *
29510 TAAAATAATTTATTTATTATTAAATAT
1 T--AAT-A-TTATTTATCATAAAATAT
*
29537 TAATTTTAT
1 TAATATTAT
29546 ATTTTTATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
21 3 0.06
22 16 0.33
23 6 0.12
25 6 0.12
26 1 0.02
27 14 0.29
28 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATATTATTTATCATAAAATAT
Found at i:29516 original size:25 final size:25
Alignment explanation
Indices: 29461--29526 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
29451 TTAAACACAA
29461 TAAATAATATTATTTATCATAAAAT
1 TAAATAATATTATTTATCATAAAAT
* *
29486 TTAATATTATTATTTAT-A-AAATAT
1 TAAATAATATTATTTATCATAAA-AT
29510 TAAAATAAT-TTATTTAT
1 T-AAATAATATTATTTAT
29527 TATTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.09
24 12 0.34
25 20 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAATAATATTATTTATCATAAAAT
Found at i:29706 original size:19 final size:18
Alignment explanation
Indices: 29642--29708 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 18
29632 TTAAATATCT
29642 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATT--A
29661 TTATTAGATTAATATTA--A
1 TTATTA-A-TAATATTATTA
* *
29679 ATATAAATAATATTATTCA
1 TTATTAATAATATTATT-A
29698 TTATTAATAAT
1 TTATTAATAAT
29709 TTAATAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 8 0.21
17 1 0.03
18 5 0.13
19 16 0.42
20 1 0.03
22 7 0.18
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (18 bp):
TTATTAATAATATTATTA
Found at i:29760 original size:24 final size:23
Alignment explanation
Indices: 29673--29782 Score: 55
Period size: 27 Copynumber: 4.5 Consensus size: 23
29663 ATTAGATTAA
29673 TATT-AAAT-ATAAATAATATTAT
1 TATTAAAATAATAAATAATA-TAT
* *
29695 TCATTATTAATAATTTAATAATAATAT
1 T-ATTA-AAATAA-TAAATAAT-ATAT
29722 T-TCTACGAAATTAATAAATAATATAAT
1 TAT-TA--AAA-TAATAAATAATAT-AT
* ** *
29749 TTTTAAAATAATTTATTATATAT
1 TATTAAAATAATAAATAATATAT
29772 TATTAAAATAA
1 TATTAAAATAA
29783 AACTATAATA
Statistics
Matches: 68, Mismatches: 9, Indels: 21
0.69 0.09 0.21
Matches are distributed among these distances:
22 1 0.01
23 15 0.22
24 10 0.15
25 7 0.10
26 5 0.07
27 25 0.37
28 5 0.07
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (23 bp):
TATTAAAATAATAAATAATATAT
Found at i:29793 original size:24 final size:23
Alignment explanation
Indices: 29739--29798 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
29729 AAATTAATAA
* **
29739 ATAATATAATTTTTAAAATAATTT
1 ATAATAT-ATTATTAAAATAAACT
*
29763 ATTATATATTATTAAAATAAAACT
1 ATAATATATTATTAAAAT-AAACT
*
29787 ATAATATCTTAT
1 ATAATATATTAT
29799 ATTATTATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATATATTATTAAAATAAACT
Found at i:29852 original size:22 final size:23
Alignment explanation
Indices: 29824--29870 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
29814 TTGATTATTT
29824 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
29846 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
29869 TA
1 TA
29871 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:29875 original size:22 final size:22
Alignment explanation
Indices: 29832--29875 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
29822 TTTATTATAA
*
29832 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
29854 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
29876 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:31167 original size:58 final size:58
Alignment explanation
Indices: 31098--31215 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 58
31088 AGAACAACAA
* * *
31098 TAATTTCTTTATCACTGAAGTCATTTGATTTAAGTAAAAATATATACCATTTTAACGT
1 TAATTTCTTTATCACCGAAGTCATTTGATTTAAGTAAAAATATATACCAATTTAAAGT
31156 TAATTTCTTTATCACCGAAGTCATTTGATTTAAGTAAAAATATATACCAATTTAAAGT
1 TAATTTCTTTATCACCGAAGTCATTTGATTTAAGTAAAAATATATACCAATTTAAAGT
31214 TA
1 TA
31216 GTTGGGTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (58 bp):
TAATTTCTTTATCACCGAAGTCATTTGATTTAAGTAAAAATATATACCAATTTAAAGT
Found at i:31798 original size:2 final size:2
Alignment explanation
Indices: 31793--31825 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31783 TATATGTTAT
31793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31826 GCTTTAGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43738 original size:14 final size:15
Alignment explanation
Indices: 43719--43772 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
43709 TTTTTAAAAA
43719 AATAAT-AATATAAT
1 AATAATGAATATAAT
43733 AATAATGAATA-AA-
1 AATAATGAATATAAT
*
43746 AA-AATGAAAATAAT
1 AATAATGAATATAAT
*
43760 AAAAAT-AATATAA
1 AATAATGAATATAA
43773 AGTTATAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 7 0.21
13 4 0.12
14 16 0.47
15 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
AATAATGAATATAAT
Found at i:44050 original size:18 final size:17
Alignment explanation
Indices: 44027--44069 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
44017 ATATATACAT
44027 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
44045 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
44062 ATAA-AATA
1 ATAATAATA
44070 TCCACATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:44476 original size:37 final size:37
Alignment explanation
Indices: 44426--44529 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
44416 GTGCTTGTGG
* * * * *
44426 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* * *
44463 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
44500 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
44530 TGACGAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:45477 original size:105 final size:105
Alignment explanation
Indices: 45073--45803 Score: 1016
Period size: 105 Copynumber: 7.0 Consensus size: 105
45063 GAATTGTTTC
* * * *
45073 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGTGAAGTTG-TTGTTGACA
* * * * *
45137 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
45179 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A---TGAAATT-TTGTTAACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
* * * *
45239 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
45279 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A---TGAAATT-TTATTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
*
45339 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
45379 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
45444 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
45484 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
*
45549 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
45589 AAGTCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGATAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
45654 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
45694 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTG-TTGTTGACAA
* * * * * *
45759 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
45800 GAGT
1 GAGT
45804 GTCACGATAT
Statistics
Matches: 580, Mismatches: 38, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
100 181 0.31
101 1 0.00
102 6 0.01
104 6 0.01
105 302 0.52
106 84 0.14
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:46050 original size:36 final size:36
Alignment explanation
Indices: 46003--46078 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
45993 TGTTTGGAGA
* * *
46003 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
46039 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
46075 GAAA
1 GAAA
46079 TGTTTATGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:46131 original size:39 final size:40
Alignment explanation
Indices: 46076--46157 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 40
46066 ATTTCAAGGG
* * *
46076 AAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACA
1 AAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAA
* *
46116 AAAT-TTTCTGTTTCAAGGGAAACTATCTCAAGAGAGAAA
1 AAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAA
46155 AAA
1 AAA
46158 AATCATTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 33 0.89
40 4 0.11
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (40 bp):
AAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAA
Found at i:46200 original size:105 final size:104
Alignment explanation
Indices: 46077--46287 Score: 377
Period size: 105 Copynumber: 2.0 Consensus size: 104
46067 TTTCAAGGGA
*
46077 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCAAGGGAAACTAT
1 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTCTGTTTCAAGGGAAACTAT
*
46142 CTCAAGAGAGAAAAAAAATCATTTCAAGGGAAATGTTTTC
66 CTCAAGAGAG-AAAAAAATAATTTCAAGGGAAATGTTTTC
*
46182 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTCTGTTTCGAGGGAAACTAT
1 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTCTGTTTCAAGGGAAACTAT
*
46247 CTCAAGAGAGAAAAAATTAATTTCAAGGGAAATGTTTTC
66 CTCAAGAGAGAAAAAAATAATTTCAAGGGAAATGTTTTC
46286 AA
1 AA
46288 GAGAAACTGT
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 29 0.28
105 73 0.72
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (104 bp):
AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTCTGTTTCAAGGGAAACTAT
CTCAAGAGAGAAAAAAATAATTTCAAGGGAAATGTTTTC
Found at i:46495 original size:72 final size:75
Alignment explanation
Indices: 46372--46533 Score: 199
Period size: 72 Copynumber: 2.2 Consensus size: 75
46362 AAACAACAGC
* *
46372 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAA-TCTTGTTTT
1 CTTGAGTGAAAT-AAAT-CCTTCTTTCGAGAGAAAACGGTCTCAAGCGAGACAAAGT-ATGTTTT
*
46436 AAG-AAAAACAAT
63 AAGAAAAAAAAAT
** *
46448 CTTGAGTGAAATAAAT-CTTCTTTCGAGAG-AAATTGTCTCAAGTGAGACAAAGTATGTTTTAAG
1 CTTGAGTGAAATAAATCCTTCTTTCGAGAGAAAACGGTCTCAAGCGAGACAAAGTATGTTTTAAG
46511 AAAAAAAAAT
66 AAAAAAAAAT
*
46521 -TTGAGTGAGATAA
1 CTTGAGTGAAATAA
46534 TCATCTGCAT
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
72 40 0.52
73 21 0.27
75 4 0.05
76 12 0.16
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.29
Consensus pattern (75 bp):
CTTGAGTGAAATAAATCCTTCTTTCGAGAGAAAACGGTCTCAAGCGAGACAAAGTATGTTTTAAG
AAAAAAAAAT
Found at i:47886 original size:183 final size:183
Alignment explanation
Indices: 47674--48210 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
47664 ATCAGGTTTA
** *
47674 ACTGAAGGGTTCATCTCATCACAAAGTCTTTAACCTGACAAAAGCAGTGGAGCAAATACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* ** *
47739 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATATATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
47803 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
47857 ATTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
47922 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCAAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
47987 TCCTCTACAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
48040 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTAACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
48105 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
48170 CCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
48211 CGGATTTAAT
Statistics
Matches: 336, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
183 335 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:49800 original size:18 final size:16
Alignment explanation
Indices: 49761--49790 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49751 TGGACTATCT
49761 TCAT-TTGATCTTCTA
1 TCATCTTGATCTTCTA
49776 TCATCTTGATCTTCT
1 TCATCTTGATCTTCT
49791 CTTCCATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.23, G:0.07, T:0.53
Consensus pattern (16 bp):
TCATCTTGATCTTCTA
Found at i:52484 original size:23 final size:23
Alignment explanation
Indices: 52440--52485 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
52430 GGTTTTTTTT
**
52440 AAAATAATAATAATAATGAATAA
1 AAAATAATAATAATAAAAAATAA
52463 AAAATGAA-AATAATAAAAAATAA
1 AAAAT-AATAATAATAAAAAATAA
52486 TATAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAATAATAATAATAAAAAATAA
Found at i:52493 original size:16 final size:15
Alignment explanation
Indices: 52448--52490 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
52438 TTAAAATAAT
52448 AATAATAATGAATAAAA
1 AATAAT-AT-AATAAAA
*
52465 AATGAAAATAATAAAA
1 AAT-AATATAATAAAA
52481 AATAATATAA
1 AATAATATAA
52491 ATATATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.26
16 10 0.43
17 5 0.22
18 2 0.09
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (15 bp):
AATAATATAATAAAA
Found at i:52725 original size:34 final size:33
Alignment explanation
Indices: 52657--52725 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 33
52647 TATTAGACTT
* * * *
52657 ATAAGTAAAATATTAAAGAAATATATATATATA
1 ATAAGTAAAATATTAAAAAAATAAATAAAAATA
52690 ATAA-TAAAATATAGTAAAAAAATAAATAAAAATA
1 ATAAGTAAAATAT--TAAAAAAATAAATAAAAATA
52724 AT
1 AT
52726 TTAATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
32 8 0.27
33 4 0.13
34 18 0.60
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (33 bp):
ATAAGTAAAATATTAAAAAAATAAATAAAAATA
Found at i:52766 original size:52 final size:52
Alignment explanation
Indices: 52676--52799 Score: 127
Period size: 52 Copynumber: 2.5 Consensus size: 52
52666 ATATTAAAGA
* *
52676 AATATATATATATA-ATAATAA-AATATAGTAAAAAAATAAATAAAAATAATTT
1 AATATATATATATACAT-ATAATAATATAGTAAAAAAAT-AATAAAAATAAATG
**
52728 AATATATATATATACATATAATAATA-A-TAACATGAATAATAAAAATAAATG
1 AATATATATATATACATATAATAATATAGTAA-AAAAATAATAAAAATAAATG
*
52779 AATA-A-A-ATATCCATATAATAA
1 AATATATATATATACATATAATAA
52800 ATAAAGGGAC
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
48 14 0.22
49 1 0.02
50 1 0.02
51 19 0.30
52 23 0.36
53 6 0.09
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (52 bp):
AATATATATATATACATATAATAATATAGTAAAAAAATAATAAAAATAAATG
Found at i:52768 original size:18 final size:17
Alignment explanation
Indices: 52745--52787 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
52735 ATATATACAT
52745 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
52763 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
52780 ATAA-AATA
1 ATAATAATA
52788 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:53186 original size:37 final size:38
Alignment explanation
Indices: 53136--53240 Score: 124
Period size: 37 Copynumber: 2.8 Consensus size: 38
53126 GTGCTTGTGG
* * * * *
53136 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACT-CT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAAATACT
* *
53173 ATCCTATTTTTAGGAGTTTGAATCATAGCA-AAATATT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAAATACT
*
53210 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
53241 GACGAAAATG
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 3 0.05
37 54 0.95
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (38 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAAATACT
Found at i:54187 original size:105 final size:105
Alignment explanation
Indices: 53783--54500 Score: 990
Period size: 105 Copynumber: 6.9 Consensus size: 105
53773 GCATTGTTCC
* * * *
53783 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGTGAAGTTG-TTGTTGACA
* * * * *
53847 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTC
64 AGCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
53889 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A---TGAAATT-TTGTTAACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
* * *
53949 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
53989 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A---TGAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
* * *
54049 TAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
54089 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
*
54154 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
54194 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTAACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
*
54259 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
54299 AAGTCCAATATCATTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
*
54364 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
54404 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTG-TTGTTGACAA
* **
54469 CCAGCCGTCCCTTCGTTATGAAGTTGAACTTG
65 GCAGCCGTCCCTTCGTCGTGAAGTTGAACTTG
54501 TGTTATCTCG
Statistics
Matches: 566, Mismatches: 39, Indels: 14
0.91 0.06 0.02
Matches are distributed among these distances:
100 180 0.32
101 1 0.00
102 6 0.01
104 6 0.01
105 299 0.53
106 74 0.13
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGTGAAGTTGTTGTTGACAAG
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:54760 original size:36 final size:36
Alignment explanation
Indices: 54713--54893 Score: 126
Period size: 36 Copynumber: 5.1 Consensus size: 36
54703 TGTTTGGAGA
*
54713 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGGGAGACAAAATTCGTTTCAAGG
* * *
54749 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGGGAGACAAAATTCGTTTCAAGG
* * * ** *
54785 GAAA-TGTTTTCAA---TG-C-TTA-T-GTTTCAAGA
1 GAAACT-ATCTCAAGGGAGACAAAATTCGTTTCAAGG
*
54814 GAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCAAGG
1 GAAACTATCTCAAGGGAGACAAAA--TTC-GTTTCAAGG
* * * *
54853 GAAACTATCTCAAGAGAGAAAAAAAATCTTTTCAAGG
1 GAAACTATCTCAAGGGAG-ACAAAATTCGTTTCAAGG
54890 GAAA
1 GAAA
54894 TGTTTTCAAT
Statistics
Matches: 109, Mismatches: 23, Indels: 25
0.69 0.15 0.16
Matches are distributed among these distances:
29 16 0.15
30 2 0.02
31 1 0.01
32 1 0.01
33 2 0.02
34 1 0.01
35 1 0.01
36 41 0.38
37 13 0.12
38 2 0.02
39 24 0.22
40 5 0.05
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
GAAACTATCTCAAGGGAGACAAAATTCGTTTCAAGG
Found at i:54911 original size:105 final size:104
Alignment explanation
Indices: 54688--55005 Score: 500
Period size: 105 Copynumber: 3.1 Consensus size: 104
54678 TTCGTTAAAT
* **
54688 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCAAGGG
* *
54750 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
*
54789 TGTTTTCAATGCTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCAAGGG
* *
54854 AAACTATCTCAAGAGAGAAAAAAAATCTTTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
* *
54894 TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTCTG-TTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCAAGGG
*
54958 AAACTATCTCAAGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
54997 TGTTTTCAA
1 TGTTTTCAA
55006 GAGAAACTGT
Statistics
Matches: 199, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
101 45 0.23
103 31 0.16
104 50 0.25
105 73 0.37
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCAAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:55213 original size:72 final size:74
Alignment explanation
Indices: 55090--55251 Score: 204
Period size: 72 Copynumber: 2.2 Consensus size: 74
55080 AAACAACAGC
* * * *
55090 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAA-TCTTGTTTT
1 CTTGAGTGAAAT-AAAT-CCTTCATTCGAGAGAAAACAGTCTCAAGCGAGACAAAGT-ATGTTTT
*
55154 AAGAAAAACAAT
63 AAGAAAAAAAAT
*
55166 CTTGAGTGAAATAAAT-CTTCATTCGAGAG-AAACAGTCTCAAGTGAGACAAAGTATGTTTTAAG
1 CTTGAGTGAAATAAATCCTTCATTCGAGAGAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAG
55229 AAAAAAAAT
66 AAAAAAAAT
* *
55238 TTTGAGTGAGATAA
1 CTTGAGTGAAATAA
55252 TCATCTGCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
72 49 0.64
73 12 0.16
75 4 0.05
76 12 0.16
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (74 bp):
CTTGAGTGAAATAAATCCTTCATTCGAGAGAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAG
AAAAAAAAT
Found at i:56741 original size:183 final size:183
Alignment explanation
Indices: 56392--56927 Score: 950
Period size: 183 Copynumber: 2.9 Consensus size: 183
56382 ATCAGGTTTA
* * * *
56392 ACTGAAGGGTTCATCTCATCACACAGTCTTTGACCTGACAAAAGTAGTGGACCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * **
56457 GCCAAGTGTCCGAGCAATGTTAT-GATTTG-ATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
56520 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
56574 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
56639 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
56704 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
56757 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTAGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
56822 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
56887 TCCTCTATAACCAATTGCCTTAGTGAAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
56928 CGGATTTAAT
Statistics
Matches: 340, Mismatches: 12, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
182 85 0.25
183 255 0.75
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:61389 original size:2 final size:2
Alignment explanation
Indices: 61382--61421 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
61372 TATTAAAGAA
*
61382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61422 GTAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:62399 original size:27 final size:28
Alignment explanation
Indices: 62341--62399 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
62331 TTAATATAAT
*
62341 TTATACTAATAATTATATTTGAATAAAA
1 TTATAATAATAATTATATTTGAATAAAA
*
62369 -TATAATAAT-ATTAATATTT-TATAAAA
1 TTATAATAATAATT-ATATTTGAATAAAA
62395 TTATA
1 TTATA
62400 GAATACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
TTATAATAATAATTATATTTGAATAAAA
Found at i:62759 original size:32 final size:32
Alignment explanation
Indices: 62709--62777 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
62699 CCGTGTCTCG
* * *
62709 ACCCGGATGTTACAGGTACCTGGTAATCTGGT
1 ACCCGGATGTTACAGGTACCCGATAATCGGGT
* * *
62741 ACCCGGATTTTGCGGGTACCCGATAATCGGGT
1 ACCCGGATGTTACAGGTACCCGATAATCGGGT
62773 ACCCG
1 ACCCG
62778 ATACCCGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.26, G:0.29, T:0.25
Consensus pattern (32 bp):
ACCCGGATGTTACAGGTACCCGATAATCGGGT
Found at i:64328 original size:10 final size:10
Alignment explanation
Indices: 64313--64349 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
64303 CAATGTGAAG
64313 TATAAAAAAA
1 TATAAAAAAA
*
64323 TATAAAAAAT
1 TATAAAAAAA
64333 TA-AAAAAAA
1 TATAAAAAAA
64342 TATAAAAA
1 TATAAAAA
64350 CTAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:64354 original size:18 final size:19
Alignment explanation
Indices: 64316--64357 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
64306 TGTGAAGTAT
*
64316 AAAAAAATATAAAAAATTA
1 AAAAAAATATAAAAAACTA
64335 AAAAAAATAT-AAAAACTA
1 AAAAAAATATAAAAAACTA
64353 AAAAA
1 AAAAA
64358 TTAATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAAAATATAAAAAACTA
Found at i:64356 original size:19 final size:19
Alignment explanation
Indices: 64316--64357 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
64306 TGTGAAGTAT
*
64316 AAAAAAATATAAAAAATTA
1 AAAAAAATATAAAAAATAA
*
64335 AAAAAAATATAAAAACTAA
1 AAAAAAATATAAAAAATAA
64354 AAAA
1 AAAA
64358 TTAATTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAAAATATAAAAAATAA
Found at i:65125 original size:60 final size:60
Alignment explanation
Indices: 65031--65167 Score: 211
Period size: 60 Copynumber: 2.3 Consensus size: 60
65021 CTTTGCAATG
*
65031 AAAGTTACAAAATGATCCCTTAACTATAGAGAGTTGCTTTGTTGAGTCCCTTAACTATTA
1 AAAGTTACAAAATGATCCCTTAACTATAGAGAGTTGCTTTGTTGAGTCCCTCAACTATTA
*** * * *
65091 AAAGTTACAAAATGATCCCTTGTTTATAGGGAGTTGTTTTGTTGAGTCCCTCGACTATTA
1 AAAGTTACAAAATGATCCCTTAACTATAGAGAGTTGCTTTGTTGAGTCCCTCAACTATTA
65151 AAAGTTACAAAATGATC
1 AAAGTTACAAAATGATC
65168 GCTCGACTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (60 bp):
AAAGTTACAAAATGATCCCTTAACTATAGAGAGTTGCTTTGTTGAGTCCCTCAACTATTA
Found at i:69349 original size:16 final size:16
Alignment explanation
Indices: 69328--69358 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
69318 TCCCTCTTTT
69328 ATATTTATTACTATAA
1 ATATTTATTACTATAA
*
69344 ATATTTATTATTATA
1 ATATTTATTACTATA
69359 TTATTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTTATTACTATAA
Found at i:69694 original size:2 final size:2
Alignment explanation
Indices: 69687--69755 Score: 97
Period size: 2 Copynumber: 35.5 Consensus size: 2
69677 TCGGGCCGGG
* * *
69687 TA TA TA TA TT TA AA T- TA AA TA TA TA -A 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
69727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69756 TTTAATTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:70735 original size:2 final size:2
Alignment explanation
Indices: 70728--70759 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
70718 ATCTGAGACA
70728 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
70760 TATTAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73657 original size:16 final size:16
Alignment explanation
Indices: 73634--73712 Score: 133
Period size: 16 Copynumber: 4.9 Consensus size: 16
73624 TTTAATAAAT
73634 AAACGAACATAAAC-A
1 AAACGAACATAAACGA
73649 AACACGAACATAAACGA
1 AA-ACGAACATAAACGA
73666 AAACGAACATAAACGA
1 AAACGAACATAAACGA
73682 AAACGAACATAAACGA
1 AAACGAACATAAACGA
*
73698 ACACGAACATAAACG
1 AAACGAACATAAACG
73713 TTGGAGACCC
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
15 2 0.03
16 56 0.92
17 3 0.05
ACGTcount: A:0.61, C:0.22, G:0.11, T:0.06
Consensus pattern (16 bp):
AAACGAACATAAACGA
Found at i:74810 original size:14 final size:14
Alignment explanation
Indices: 74791--74833 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
74781 AGATTGGGTT
*
74791 GAACATAAATGAAC
1 GAACATAAACGAAC
* *
74805 GAACATGACCGAAC
1 GAACATAAACGAAC
*
74819 GAACATAACCGAAC
1 GAACATAAACGAAC
74833 G
1 G
74834 TTCACGAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.23, G:0.19, T:0.09
Consensus pattern (14 bp):
GAACATAAACGAAC
Found at i:75976 original size:23 final size:21
Alignment explanation
Indices: 75942--75984 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
75932 TGGAACTAAT
75942 ATTTTATTTTAAATAATTTAC
1 ATTTTATTTTAAATAATTTAC
*
75963 ATTTGTATCTTTAACTAATTTA
1 ATTT-TAT-TTTAAATAATTTA
75985 TAATTACAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTATTTTAAATAATTTAC
Found at i:86496 original size:41 final size:41
Alignment explanation
Indices: 86430--86507 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
86420 AACATTTTTA
86430 GATTTTATTATTTAATTAATTAGGA-TTCTAGTTTGCCAAG
1 GATTTTATTATTTAATTAATTAGGATTTCTAGTTTGCCAAG
* *
86470 GATTTTAATTATTT-ATTTATTAAGGATTTTTAGTTTGC
1 GATTTT-ATTATTTAATTAATT-AGGATTTCTAGTTTGC
86508 TATGACTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 12 0.36
41 11 0.33
42 10 0.30
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (41 bp):
GATTTTATTATTTAATTAATTAGGATTTCTAGTTTGCCAAG
Found at i:87709 original size:18 final size:18
Alignment explanation
Indices: 87686--87755 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
87676 TTCAGTATTC
*
87686 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
*
87704 GTCCCGAAGGACAACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
87726 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
87744 GTCCCGAAGGAC
1 GTCCCGAAGGAC
87756 TAATCCTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 27 0.63
22 16 0.37
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:89395 original size:64 final size:62
Alignment explanation
Indices: 89262--89422 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 62
89252 TAATGAAGGT
* * *
89262 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
89327 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
89391 ATGCATCGATGCACTACATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
89423 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:94227 original size:15 final size:16
Alignment explanation
Indices: 94198--94227 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
94188 GAGCCAAAGG
94198 TGAGTTTTCTGATTAT
1 TGAGTTTTCTGATTAT
94214 TGAGTTTT-TGATTA
1 TGAGTTTTCTGATTA
94228 AATTTAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.03, G:0.20, T:0.57
Consensus pattern (16 bp):
TGAGTTTTCTGATTAT
Found at i:98469 original size:19 final size:20
Alignment explanation
Indices: 98447--98485 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
98437 TTATTGCTTT
*
98447 AATTTATTTTATT-TTATTC
1 AATTTATTTAATTATTATTC
98466 AATTTATTTAATTATTATTC
1 AATTTATTTAATTATTATTC
98486 TTAACCCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTTATTTAATTATTATTC
Found at i:100313 original size:17 final size:17
Alignment explanation
Indices: 100291--100334 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
100281 TTGCCATCTT
100291 TTTTCTTCCTCTGCTGA
1 TTTTCTTCCTCTGCTGA
*
100308 TTTTCTTCCTCTTCTGA
1 TTTTCTTCCTCTGCTGA
100325 TTTTCTTCCT
1 TTTTCTTCCT
100335 ATGGTCATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.05, C:0.30, G:0.07, T:0.59
Consensus pattern (17 bp):
TTTTCTTCCTCTGCTGA
Found at i:104038 original size:21 final size:21
Alignment explanation
Indices: 104014--104059 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
104004 CTTAACGTCT
*
104014 ATAACAACAAAGTTAAAATCC
1 ATAACAACAAACTTAAAATCC
* * *
104035 ATAACGACCAACTTGAAATCC
1 ATAACAACAAACTTAAAATCC
104056 ATAA
1 ATAA
104060 TAATAAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.22, G:0.07, T:0.20
Consensus pattern (21 bp):
ATAACAACAAACTTAAAATCC
Found at i:104829 original size:41 final size:41
Alignment explanation
Indices: 104755--104858 Score: 104
Period size: 41 Copynumber: 2.5 Consensus size: 41
104745 TATTATGGAA
* * * *
104755 TTTT-TATACAAACGCCACTAAAGAACTATTCTGTCACG-G
1 TTTTGTATAAAAACACCGCTAAAGAACTACTCTGTCACGAG
* *
104794 TGTTTGTATAAAAACACCGCTAAAGTACTACTCTGTCGCGACG
1 T-TTTGTATAAAAACACCGCTAAAGAACTACTCTGTCACGA-G
**
104837 TTTTGTATAAAAATGCCGCTAA
1 TTTTGTATAAAAACACCGCTAA
104859 TGTTATCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
39 1 0.02
40 3 0.06
41 28 0.53
42 19 0.36
43 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (41 bp):
TTTTGTATAAAAACACCGCTAAAGAACTACTCTGTCACGAG
Found at i:106309 original size:17 final size:18
Alignment explanation
Indices: 106228--106310 Score: 51
Period size: 19 Copynumber: 4.3 Consensus size: 18
106218 ATTGATTTAC
*
106228 TATTTATTTATATATTTA
1 TATTTATTTATATAGTTA
* *
106246 TTTATTTATAACTATATAATTTA
1 --TATTTAT--TTATAT-AGTTA
*
106269 CTATTTATTTATATATTTA
1 -TATTTATTTATATAGTTA
*
106288 CTATTTTTTTATATAGTT-
1 -TATTTATTTATATAGTTA
106306 TATTT
1 TATTT
106311 GGAGGTCGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.09
19 21 0.38
20 12 0.22
22 12 0.22
23 5 0.09
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (18 bp):
TATTTATTTATATAGTTA
Found at i:107273 original size:34 final size:32
Alignment explanation
Indices: 107220--107301 Score: 137
Period size: 34 Copynumber: 2.5 Consensus size: 32
107210 AAATTATATT
107220 ATATTAAAATAAAAATTAAAGATTTAATTTAA
1 ATATTAAAATAAAAATTAAAGATTTAATTTAA
*
107252 ATATTAAAAATAGAAAATTAAAGATTTCATTTAA
1 ATATT-AAAATA-AAAATTAAAGATTTAATTTAA
107286 ATATTAAAATAAAAAT
1 ATATTAAAATAAAAAT
107302 ATTAAATAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
32 10 0.21
33 12 0.26
34 25 0.53
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (32 bp):
ATATTAAAATAAAAATTAAAGATTTAATTTAA
Found at i:107626 original size:14 final size:14
Alignment explanation
Indices: 107571--107738 Score: 77
Period size: 14 Copynumber: 11.9 Consensus size: 14
107561 TAATCATTGG
*
107571 TATTAAATTATTAA
1 TATTAAATCATTAA
*
107585 TCATTATAATTTCATTAT
1 T-ATTA-AA--TCATTAA
*
107603 TAGT-AATCATTAA
1 TATTAAATCATTAA
*
107616 CATTAAATCATTAAA
1 TATTAAATCATT-AA
* *
107631 CCATTAAATTATTATTA
1 -TATTAAATCATTA--A
*
107648 TTATTAAATCATTAG
1 -TATTAAATCATTAA
107663 TATTAAATC-----
1 TATTAAATCATTAA
*
107672 -ATTAAAT-ATTAT
1 TATTAAATCATTAA
107684 TATTAAATCATTAA
1 TATTAAATCATTAA
107698 TATTAAATCATTAAA
1 TATTAAATCATT-AA
*
107713 TATT--ATTATTAAA
1 TATTAAATCATT-AA
107726 TCATTAAATCATT
1 T-ATTAAATCATT
107739 TAAAAACATT
Statistics
Matches: 120, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
8 7 0.06
13 24 0.20
14 36 0.30
15 15 0.12
16 18 0.15
17 14 0.12
18 6 0.05
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (14 bp):
TATTAAATCATTAA
Found at i:107629 original size:8 final size:8
Alignment explanation
Indices: 107607--107738 Score: 108
Period size: 8 Copynumber: 17.9 Consensus size: 8
107597 CATTATTAGT
107607 AATCATT-
1 AATCATTA
107614 AA-CATTA
1 AATCATTA
107621 AATCATTA
1 AATCATTA
*
107629 AACCATTA
1 AATCATTA
*
107637 AATTATTA
1 AATCATTA
* *
107645 TTATTATTA
1 -AATCATTA
107654 AATCATT-
1 AATCATTA
*
107661 AGT-ATTA
1 AATCATTA
107668 AATCATTA
1 AATCATTA
107676 AAT-ATT-
1 AATCATTA
*
107682 -ATTATTA
1 AATCATTA
107689 AATCATT-
1 AATCATTA
107696 AAT-ATTA
1 AATCATTA
107703 AATCATTA
1 AATCATTA
107711 AAT-ATT-
1 AATCATTA
*
107717 -ATTATTA
1 AATCATTA
107724 AATCATTA
1 AATCATTA
107732 AATCATT
1 AATCATT
107739 TAAAAACATT
Statistics
Matches: 102, Mismatches: 10, Indels: 25
0.74 0.07 0.18
Matches are distributed among these distances:
5 4 0.04
6 16 0.16
7 20 0.20
8 55 0.54
9 7 0.07
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (8 bp):
AATCATTA
Found at i:107689 original size:35 final size:35
Alignment explanation
Indices: 107643--107732 Score: 171
Period size: 35 Copynumber: 2.6 Consensus size: 35
107633 ATTAAATTAT
*
107643 TATTATTATTAAATCATTAGTATTAAATCATTAAA
1 TATTATTATTAAATCATTAATATTAAATCATTAAA
107678 TATTATTATTAAATCATTAATATTAAATCATTAAA
1 TATTATTATTAAATCATTAATATTAAATCATTAAA
107713 TATTATTATTAAATCATTAA
1 TATTATTATTAAATCATTAA
107733 ATCATTTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.47
Consensus pattern (35 bp):
TATTATTATTAAATCATTAATATTAAATCATTAAA
Found at i:107733 original size:21 final size:22
Alignment explanation
Indices: 107607--107738 Score: 96
Period size: 21 Copynumber: 6.0 Consensus size: 22
107597 CATTATTAGT
*
107607 AATCATTAACATTAAATCATTA
1 AATCATTAATATTAAATCATTA
* * *
107629 AACCATTAAATTATTATTATTATTA
1 AATCATT-AA-TATTA-AATCATTA
*
107654 AATCATTAGTATTAAATCATTA
1 AATCATTAATATTAAATCATTA
*
107676 AAT-ATTATTATTAAATCATT-
1 AATCATTAATATTAAATCATTA
107696 AAT-ATTAAATCATTAAAT-ATT-
1 AATCATT-AAT-ATTAAATCATTA
*
107717 -ATTATTAAATCATTAAATCATT
1 AATCATT-AAT-ATTAAATCATT
107739 TAAAAACATT
Statistics
Matches: 93, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
20 8 0.09
21 36 0.39
22 25 0.27
23 7 0.08
24 5 0.05
25 12 0.13
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (22 bp):
AATCATTAATATTAAATCATTA
Found at i:107771 original size:31 final size:31
Alignment explanation
Indices: 107736--107795 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
107726 TCATTAAATC
* *
107736 ATTTAAAAACATTCATTTAAATATAAATAAT
1 ATTTAAAAACATTCATTCAAATACAAATAAT
*
107767 ATTTACAAACATTCATTCAAATACAAATA
1 ATTTAAAAACATTCATTCAAATACAAATA
107796 CAAATATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (31 bp):
ATTTAAAAACATTCATTCAAATACAAATAAT
Found at i:112061 original size:25 final size:25
Alignment explanation
Indices: 112027--112081 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
112017 AATCGCAACT
*
112027 GATAATTTGAGAAAATAAAAATGAA
1 GATAACTTGAGAAAATAAAAATGAA
112052 GATAACTTGAGAAAATAAAAATGAA
1 GATAACTTGAGAAAATAAAAATGAA
112077 GATAA
1 GATAA
112082 AAGAGACACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.60, C:0.02, G:0.16, T:0.22
Consensus pattern (25 bp):
GATAACTTGAGAAAATAAAAATGAA
Found at i:128870 original size:21 final size:21
Alignment explanation
Indices: 128822--128863 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
128812 CCTAGTACAG
*
128822 AGGGTATCGGTATTCCTATAA
1 AGGGTATCGGTACTCCTATAA
*
128843 AGGGTATCGGTACTCGTATAA
1 AGGGTATCGGTACTCCTATAA
128864 GGAGTATTAG
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:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (21 bp):
AGGGTATCGGTACTCCTATAA
Found at i:135458 original size:48 final size:49
Alignment explanation
Indices: 135379--135472 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 49
135369 GGTTATTTCC
* ** *
135379 AGTTCGGGTCAATATCGGATCGGTTG-CTTTTTGGATCAGGTCAATATCG
1 AGTTCGGGTCAATATCAGATCAATTGATTTTTTGG-TCAGGTCAATATCG
* *
135428 AGTT-GGGTTAATATCAGATCAATTGATTTTTTGGTCGGGTCAATA
1 AGTTCGGGTCAATATCAGATCAATTGATTTTTTGGTCAGGTCAATA
135473 CAGGATCGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
48 27 0.71
49 11 0.29
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (49 bp):
AGTTCGGGTCAATATCAGATCAATTGATTTTTTGGTCAGGTCAATATCG
Found at i:135497 original size:32 final size:31
Alignment explanation
Indices: 135432--135521 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 31
135422 ATATCGAGTT
* * * *
135432 GGGTTAATATCAGATCAATTGATTTTTTGGTC
1 GGGTCAATATCGGATCGATTGA-TTTTGGGTC
135464 GGGTCAATA-CAGGATCGATTAGATTTTGGGTC
1 GGGTCAATATC-GGATCGATT-GATTTTGGGTC
*
135496 GGGTCAATATCGGATCGGTTGATTTT
1 GGGTCAATATCGGATCGATTGATTTT
135522 CGGTTTAGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
31 7 0.14
32 40 0.80
33 3 0.06
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (31 bp):
GGGTCAATATCGGATCGATTGATTTTGGGTC
Found at i:136321 original size:16 final size:16
Alignment explanation
Indices: 136238--136359 Score: 66
Period size: 16 Copynumber: 7.6 Consensus size: 16
136228 TTTCGGGTTT
* *
136238 GGTTAAATTCAGTTCG
1 GGTTAATTTCGGTTCG
* * * *
136254 AGTTACTTTTGGATCG
1 GGTTAATTTCGGTTCG
136270 GGTTAAAATTT-GGTTCG
1 GGTT--AATTTCGGTTCG
** * *
136287 GGTTGCTTTCAGCTCG
1 GGTTAATTTCGGTTCG
*
136303 GGTTAATTTCGGTTTG
1 GGTTAATTTCGGTTCG
** **
136319 GGTTGTTTTTTGTTCG
1 GGTTAATTTCGGTTCG
*
136335 GGTTAATTTCGGTTCT
1 GGTTAATTTCGGTTCG
*
136351 GGTTGATTT
1 GGTTAATTT
136360 TTATTTCGCT
Statistics
Matches: 74, Mismatches: 29, Indels: 6
0.68 0.27 0.06
Matches are distributed among these distances:
15 3 0.04
16 58 0.78
17 9 0.12
18 4 0.05
ACGTcount: A:0.14, C:0.11, G:0.29, T:0.47
Consensus pattern (16 bp):
GGTTAATTTCGGTTCG
Found at i:136336 original size:32 final size:32
Alignment explanation
Indices: 136300--136361 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
136290 TGCTTTCAGC
*
136300 TCGGGTTAATTTCGGTT-TGGGTTGTTTTTTGT
1 TCGGGTTAATTTCGGTTCT-GGTTGATTTTTGT
136332 TCGGGTTAATTTCGGTTCTGGTTGATTTTT
1 TCGGGTTAATTTCGGTTCTGGTTGATTTTT
136362 ATTTCGCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.08, C:0.08, G:0.29, T:0.55
Consensus pattern (32 bp):
TCGGGTTAATTTCGGTTCTGGTTGATTTTTGT
Found at i:136649 original size:20 final size:20
Alignment explanation
Indices: 136578--136651 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 20
136568 ATTAAATAAT
136578 TATTTATATATATTTATAAAAA
1 TATTTATA-ATA-TTATAAAAA
*
136600 T-TTATATTAAATTATTCTAAAAGTA
1 TATT-TA-T-AA-TATTATAAAA--A
136625 TATTTATAATATTATAAAAA
1 TATTTATAATATTATAAAAA
136645 TATTTAT
1 TATTTAT
136652 TTAATTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
20 8 0.19
21 2 0.05
22 12 0.28
23 11 0.26
24 4 0.09
25 4 0.09
26 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (20 bp):
TATTTATAATATTATAAAAA
Found at i:136684 original size:19 final size:19
Alignment explanation
Indices: 136662--136717 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 19
136652 TTAATTTTTA
136662 AAATCATATTATTTATTTG
1 AAATCATATTATTTATTTG
136681 AAATGACATTGATTATTTATTTG
1 AAAT--CA-T-ATTATTTATTTG
*
136704 AAATAATATTATTT
1 AAATCATATTATTT
136718 TTAAATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 11 0.34
20 1 0.03
21 3 0.09
22 1 0.03
23 16 0.50
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (19 bp):
AAATCATATTATTTATTTG
Found at i:136745 original size:18 final size:18
Alignment explanation
Indices: 136694--136747 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
136684 TGACATTGAT
*
136694 TATTT-ATTTGAAATA-A
1 TATTTAATTTTAAATATA
*
136710 TA-TTATTTTTAAATTATA
1 TATTTAATTTTAAA-TATA
136728 TATTTAATTTTAAATATA
1 TATTTAATTTTAAATATA
136746 TA
1 TA
136748 CATAGCTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.06
16 8 0.26
17 2 0.06
18 9 0.29
19 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTTAATTTTAAATATA
Done.