Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005451.1 Hibiscus syriacus cultivar Beakdansim tig00012487_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: 72352
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:879 original size:3 final size:3
Alignment explanation
Indices: 866--899 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
856 ACAATTTTGT
*
866 TAA TAAA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
900 ATGTAGAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5099 original size:41 final size:43
Alignment explanation
Indices: 5053--5145 Score: 131
Period size: 41 Copynumber: 2.2 Consensus size: 43
5043 ATGTACGGAC
5053 TTTAATTAATATTTTACCT-AA-ATTATTTTTACACATATTT-T
1 TTTAATTAAT-TTTTACCTAAATATTATTTTTACACATATTTAT
*
5094 TTTAATT-ATTTTTTCCTAAATATTATTTTTACACATATTTAT
1 TTTAATTAATTTTTACCTAAATATTATTTTTACACATATTTAT
5136 TTTAAATTAA
1 TTT-AATTAA
5146 CAATATAAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
39 7 0.15
40 4 0.09
41 26 0.57
42 4 0.09
43 4 0.09
44 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (43 bp):
TTTAATTAATTTTTACCTAAATATTATTTTTACACATATTTAT
Found at i:7130 original size:31 final size:30
Alignment explanation
Indices: 7095--7207 Score: 127
Period size: 31 Copynumber: 3.7 Consensus size: 30
7085 AAAAATTTAG
*
7095 GTACTAAAATGAAATAAAAAGTTAACAATA
1 GTACTAAAATGAAACAAAAAGTTAACAATA
* * * **
7125 TGTACTAAAATGAAATAAAAAATTAATAGAGG
1 -GTACTAAAATGAAACAAAAAGTTAACA-ATA
* *
7157 GTACTAAAATGAAACAAAATGTTAACGATGA
1 GTACTAAAATGAAACAAAAAGTTAACAAT-A
7188 GTACTAAAATGAAACAAAAA
1 GTACTAAAATGAAACAAAAA
7208 TAAATATTAG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.01
31 66 0.97
32 1 0.01
ACGTcount: A:0.58, C:0.07, G:0.13, T:0.22
Consensus pattern (30 bp):
GTACTAAAATGAAACAAAAAGTTAACAATA
Found at i:10241 original size:37 final size:37
Alignment explanation
Indices: 10191--10261 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
10181 ACCACTTTCC
10191 TAAGACTATATAAAGAGCTACTTTAGATATTAACACA
1 TAAGACTATATAAAGAGCTACTTTAGATATTAACACA
10228 TAAGACTATATAAAGAGCTACTTTAGATATTAAC
1 TAAGACTATATAAAGAGCTACTTTAGATATTAAC
10262 GCGGATTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (37 bp):
TAAGACTATATAAAGAGCTACTTTAGATATTAACACA
Found at i:13634 original size:64 final size:64
Alignment explanation
Indices: 13533--13662 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
13523 CTTTCAAAAG
*
13533 AAATTGTGATCAACCTTGCACTTGTTGTTTTTATTAGCTATATCTATTCCTGAGACAATGAACT
1 AAATTGTGATCAACCTTGCACTTGCTGTTTTTATTAGCTATATCTATTCCTGAGACAATGAACT
13597 AAATTGTGATCAACCTTGCACTTGCTGTTTTTATTAGCTATATCTATTCCTGAGACAATGAACT
1 AAATTGTGATCAACCTTGCACTTGCTGTTTTTATTAGCTATATCTATTCCTGAGACAATGAACT
13661 AA
1 AA
13663 TTACTGCCGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (64 bp):
AAATTGTGATCAACCTTGCACTTGCTGTTTTTATTAGCTATATCTATTCCTGAGACAATGAACT
Found at i:14985 original size:2 final size:2
Alignment explanation
Indices: 14978--15012 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
14968 TTATTTTTGT
14978 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
15013 ATTGAGGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21545 original size:83 final size:83
Alignment explanation
Indices: 21375--21723 Score: 326
Period size: 83 Copynumber: 4.2 Consensus size: 83
21365 ACTCGACAAT
* * * * * * * * *
21375 TTTGATGGCAGATAACCATTCTCGTCTTGAGTTATGCTGTAAATTTGATTTGCCTCTGAGTTGAA
1 TTTGATGACAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCTCGGAGCT-AA
*
21440 -TGTAATCGAACTCGAAGGTC
63 GTGTAATCAAACTCGAAGGTC
* * * *
21460 TTTGATGACAGATCA-CCCTTCTAGCCTTGAGTTATGCTGCAAATAATATGCCTCGGAGTTAAGC
1 TTTGATGACAGAT-AGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCGGAGCTAAGT
*
21524 GTAGTCAAACTCGAAGGTC
65 GTAATCAAACTCGAAGGTC
* * * ** * * *
21543 TTTTGTTGGA-AAATAGCCCTTCTTGCCTTGAGTTATATTGCAAATGATGTGCCTTGAAGCTGAG
1 -TTTGAT-GACAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCGGAGCTAAG
*
21607 TGTAGTCAAACTCGAAGGTC
64 TGTAATCAAACTCGAAGGTC
* * * * * * *
21627 TTTGCTGACAGATAGCCCTTATAGCCTTGAGCTATGCTGTAAATGATGCGCCTTGGAGCTGAGTG
1 TTTGATGACAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCGGAGCTAAGTG
*
21692 TAATCGAACTCGAAGGTC
66 TAATCAAACTCGAAGGTC
*
21710 TTTGTTGACAGATA
1 TTTGATGACAGATA
21724 CTCCTACTTT
Statistics
Matches: 222, Mismatches: 36, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
82 4 0.02
83 113 0.51
84 66 0.30
85 38 0.17
86 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (83 bp):
TTTGATGACAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCGGAGCTAAGTG
TAATCAAACTCGAAGGTC
Found at i:22137 original size:168 final size:169
Alignment explanation
Indices: 21929--22277 Score: 565
Period size: 168 Copynumber: 2.1 Consensus size: 169
21919 TATCCTCCGC
* * *
21929 CGTGAAGTTGAAATTGGTTCTGGAACTGGGAATTTGTTTGTTGACAACCAGCCATCCCTTCGTTG
1 CGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTG
* *
21994 TGAAGTTGAACTTATGTTGTCTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAA
66 TGAAGTTGAACTTATGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTAAA
22059 ATTGGGAAATTATTTATTGACAAACAGCGGTCCCTTCAT
131 ATTGGGAAATTATTTATTGACAAACAGCGGTCCCTTCAT
* *
22098 -GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTG
1 CGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTG
* *
22162 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAA
66 TGAAGTTGAACTTATGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTAAA
* * * * *
22227 ATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGT
131 ATTGGGAAATTATTTATTGACAAACAGCGGTCCCTTCAT
22266 CGTGAAGTTGAA
1 CGTGAAGTTGAA
22278 CTTGCGTTGT
Statistics
Matches: 165, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
168 154 0.93
169 11 0.07
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (169 bp):
CGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACAACCAGCCATCCCTTCGTTG
TGAAGTTGAACTTATGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTAAA
ATTGGGAAATTATTTATTGACAAACAGCGGTCCCTTCAT
Found at i:22141 original size:62 final size:63
Alignment explanation
Indices: 22030--22171 Score: 223
Period size: 62 Copynumber: 2.3 Consensus size: 63
22020 TCCAATATCA
* *
22030 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAAACAGCGGTCCC
1 TTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAAACAGCCGTCCC
* * *
22093 TTC-ATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCC
1 TTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAAACAGCCGTCCC
*
22155 TTCGTTGTGAAGTTGAA
1 TTCGATGTGAAGTTGAA
22172 CTTGTGTTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
62 57 0.79
63 15 0.21
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (63 bp):
TTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAAACAGCCGTCCC
Found at i:22287 original size:106 final size:106
Alignment explanation
Indices: 22097--22612 Score: 870
Period size: 106 Copynumber: 4.9 Consensus size: 106
22087 GGTCCCTTCA
* *
22097 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTG
1 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
22162 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
66 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
* *
22203 TGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
* * *
22268 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGA
66 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
* * *
22309 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAACCGTCCCTTCGTTG
1 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
*
22374 TGAAGTTGAACTTGTGTTTTCTCGAGTCCAATATCCTTCGC
66 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
* *
22415 TGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCG
1 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
* *
22480 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGC
66 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
* *
22521 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAACGGTCCCTTCGTCG
1 TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
*
22586 TGAAGTTGAACTTGTTTTGTCTCGAGT
66 TGAAGTTGAACTTGTGTTGTCTCGAGT
22613 GGCACGATAT
Statistics
Matches: 379, Mismatches: 31, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 379 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGC
Found at i:24223 original size:22 final size:20
Alignment explanation
Indices: 24198--24262 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
24188 TGCATGTGCT
24198 TTTTTGTCCCTTTTTCTTTTTC
1 TTTTTGT-CCTTTTT-TTTTTC
*
24220 TTTTTGTTCTTTTTTTTTT-
1 TTTTTGTCCTTTTTTTTTTC
* * *
24239 GTTTTGTTCTTTTTTGTTTC
1 TTTTTGTCCTTTTTTTTTTC
24259 TTTT
1 TTTT
24263 CTTTTTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 17 0.45
20 8 0.21
21 6 0.16
22 7 0.18
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (20 bp):
TTTTTGTCCTTTTTTTTTTC
Found at i:24229 original size:15 final size:14
Alignment explanation
Indices: 24214--24275 Score: 72
Period size: 15 Copynumber: 4.2 Consensus size: 14
24204 TCCCTTTTTC
24214 TTTTTCTTTTTGTT
1 TTTTTCTTTTTGTT
24228 CTTTTT-TTTTTGTT
1 -TTTTTCTTTTTGTT
*
24242 TTGTTCTTTTTTGTT
1 TTTTTC-TTTTTGTT
24257 TCTTTTCTTTTTTGTT
1 T-TTTTC-TTTTTGTT
24273 TTT
1 TTT
24276 ACCCTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.10
14 8 0.19
15 16 0.38
16 14 0.33
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTGTT
Found at i:24233 original size:16 final size:16
Alignment explanation
Indices: 24220--24275 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
24210 TTTCTTTTTC
*
24220 TTTTTGTTCTT-TT-T
1 TTTTTGTTTTTGTTCT
24234 TTTTTG-TTTTGTTCT
1 TTTTTGTTTTTGTTCT
24249 TTTTTGTTTCTT-TTCT
1 TTTTTGTTT-TTGTTCT
24265 TTTTTGTTTTT
1 TTTTTGTTTTT
24276 ACCCTTTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
13 3 0.08
14 8 0.22
15 9 0.24
16 15 0.41
17 2 0.05
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTTTGTTTTTGTTCT
Found at i:24243 original size:19 final size:19
Alignment explanation
Indices: 24207--24275 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
24197 TTTTTTGTCC
24207 CTTTTTCTTTTTCTTTTTGTT
1 CTTTTT-TTTTTC-TTTTGTT
*
24228 CTTTTTTTTTTGTTTTGTT
1 CTTTTTTTTTTCTTTTGTT
* *
24247 CTTTTTTGTTTCTTTTCTT
1 CTTTTTTTTTTCTTTTGTT
24266 -TTTTGTTTTT
1 CTTTT-TTTTT
24276 ACCCTTTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 27 0.64
20 5 0.12
21 6 0.14
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (19 bp):
CTTTTTTTTTTCTTTTGTT
Found at i:24284 original size:31 final size:30
Alignment explanation
Indices: 24219--24287 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
24209 TTTTCTTTTT
*
24219 CTTTTTG-TTCTTTTTTTTTTGTTTTGTTC
1 CTTTTTGTTTCTTTTTTTTTTGTTTTGTCC
*
24248 TTTTTTGTTTCTTTTCTTTTTTGTTTT-TACC
1 CTTTTTGTTTCTTTT-TTTTTTGTTTTGT-CC
24279 CTTTTTGTT
1 CTTTTTGTT
24288 CTGATTGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.18
30 8 0.24
31 20 0.59
ACGTcount: A:0.01, C:0.12, G:0.09, T:0.78
Consensus pattern (30 bp):
CTTTTTGTTTCTTTTTTTTTTGTTTTGTCC
Found at i:28400 original size:32 final size:32
Alignment explanation
Indices: 28359--28422 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
28349 AATTACCTTA
*
28359 GCCTGACTCACTTACCTGTGTCCCCAGCGGAG
1 GCCTGACTCACTTACATGTGTCCCCAGCGGAG
28391 GCCTGACTCACTTACATGTGTCCCCAGCGGAG
1 GCCTGACTCACTTACATGTGTCCCCAGCGGAG
28423 TCGCCAAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.17, C:0.36, G:0.25, T:0.22
Consensus pattern (32 bp):
GCCTGACTCACTTACATGTGTCCCCAGCGGAG
Found at i:29828 original size:65 final size:65
Alignment explanation
Indices: 29668--29828 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
29658 TTGTTTAAGG
* * * **
29668 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
29731 A
65 A
* *
29732 TGCATCGATTCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
29796 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
29829 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.71
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:30430 original size:17 final size:19
Alignment explanation
Indices: 30408--30443 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
30398 GATTTAAATG
30408 AATACATGT-ATAT-ATAT
1 AATACATGTGATATGATAT
30425 AATACATGTGATATGATAT
1 AATACATGTGATATGATAT
30444 GAGATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (19 bp):
AATACATGTGATATGATAT
Found at i:30671 original size:31 final size:31
Alignment explanation
Indices: 30577--30684 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
30567 AGTCGAGGGT
* *
30577 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
30608 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
30639 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
30670 TTT-CCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
30685 ATGACCTCTG
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
30 11 0.17
31 50 0.78
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:30691 original size:30 final size:31
Alignment explanation
Indices: 30599--30705 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
30589 TTTCGAGACA
* * * * *
30599 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGTTTACCGAGGTTCTTTAGG-ACC
* *
30630 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
*
30661 TATGGACAGTTT-CCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
* *
30691 TCTGGATAG-TTACCG
1 TATGGACAGTTTACCG
30706 GGGTCTGTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.03
30 25 0.39
31 34 0.53
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTTAGGACC
Found at i:32594 original size:11 final size:11
Alignment explanation
Indices: 32578--32612 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
32568 ATACAAGTAT
32578 AAGAAATGATA
1 AAGAAATGATA
32589 AAGAAATGATA
1 AAGAAATGATA
32600 AAGAAATGA-A
1 AAGAAATGATA
32610 AAG
1 AAG
32613 GATTGGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (11 bp):
AAGAAATGATA
Found at i:34047 original size:65 final size:65
Alignment explanation
Indices: 33887--34047 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
33877 TTGTTTAAGG
* * * **
33887 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
33950 A
65 A
*
33951 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
34015 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
34048 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:34645 original size:14 final size:16
Alignment explanation
Indices: 34624--34659 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
34614 AATGATTTAC
34624 ATGA-ATACATGT-AT
1 ATGATATACATGTGAT
34638 AT-ATATACATGTGAT
1 ATGATATACATGTGAT
34653 ATGATAT
1 ATGATAT
34660 GAGATATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.05
14 10 0.53
15 4 0.21
16 4 0.21
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.39
Consensus pattern (16 bp):
ATGATATACATGTGAT
Found at i:34887 original size:31 final size:31
Alignment explanation
Indices: 34793--34900 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
34783 AGTCGAGGGT
* *
34793 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** * *
34824 TATACCTATGTTCTAAGGAACTTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
34855 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
34886 TTT-CCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
34901 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 11 0.17
31 49 0.78
32 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:34907 original size:30 final size:31
Alignment explanation
Indices: 34815--34921 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
34805 TTTCGAGACA
* * * * *
34815 TATGGACAGTATACCTATGTTC-TAAGGAACT
1 TATGGACAGTTTACCGAGGTTCTTTAGG-ACC
* *
34846 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
*
34877 TATGGACAGTTT-CCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
* *
34907 TCTGGATAG-TTACCG
1 TATGGACAGTTTACCG
34922 GGGTCTGTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.03
30 25 0.39
31 34 0.53
32 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTTAGGACC
Found at i:35746 original size:13 final size:13
Alignment explanation
Indices: 35730--35782 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 13
35720 CATAATGAAA
*
35730 ATAAATAAATAGT
1 ATAAATAAATAAT
35743 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
35757 A-AAATAAA-AAT
1 ATAAATAAATAAT
35768 AT--ATAAA-AAT
1 ATAAATAAATAAT
35778 ATAAA
1 ATAAA
35783 AATGTATGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 10 0.29
11 4 0.11
12 4 0.11
13 10 0.29
14 7 0.20
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:36001 original size:2 final size:2
Alignment explanation
Indices: 35996--36022 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35986 AATAATAATA
35996 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 A
36023 ATAGGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36109 original size:29 final size:28
Alignment explanation
Indices: 36054--36123 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
36044 ACGCAAAGAA
*
36054 AAATGAAAAAA-AATTATAATAAATAAAT
1 AAAT-AAAAAATAATTATAATAAATAAAC
36082 AAATAAAAAATAATTA-AATATATATAAAC
1 AAATAAAAAATAATTATAATA-A-ATAAAC
* *
36111 ATATAAATAATAA
1 AAATAAAAAATAA
36124 GGGTTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 10 0.28
28 10 0.28
29 16 0.44
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (28 bp):
AAATAAAAAATAATTATAATAAATAAAC
Found at i:36557 original size:37 final size:37
Alignment explanation
Indices: 36508--36600 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
36498 ATGCTTGTGG
* * *
36508 ATCCTATCTTTAGGAGTTTAAATAATAATAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTCT
* * ** * *
36545 ATCTTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTCT
36582 ATCCTATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
36601 GAATCCTAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTCT
Found at i:39531 original size:42 final size:42
Alignment explanation
Indices: 39443--39531 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
39433 ACTCGTTAAA
* * **
39443 CTCGTTGCTCATTAAGTTCGATGCTTGTTGCTCGTTGTTTGC
1 CTCGTTGCTCATTAAGGTCGATGCTCGTTGCTCGTTCATTGC
* *
39485 CTCGTTGCTCGTTAAGGTCGATGCTCGTTGCTTGTCTCATTG-
1 CTCGTTGCTCATTAAGGTCGATGCTCGTTGCTCGT-TCATTGC
39527 CTCGT
1 CTCGT
39532 CTCATTGCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
42 36 0.90
43 4 0.10
ACGTcount: A:0.09, C:0.24, G:0.25, T:0.43
Consensus pattern (42 bp):
CTCGTTGCTCATTAAGGTCGATGCTCGTTGCTCGTTCATTGC
Found at i:39533 original size:12 final size:12
Alignment explanation
Indices: 39512--39543 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39502 TCGATGCTCG
*
39512 TTGCTTGTCTCA
1 TTGCTCGTCTCA
39524 TTGCTCGTCTCA
1 TTGCTCGTCTCA
39536 TTGCTCGT
1 TTGCTCGT
39544 TAAGCTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.28, G:0.19, T:0.47
Consensus pattern (12 bp):
TTGCTCGTCTCA
Found at i:39969 original size:23 final size:23
Alignment explanation
Indices: 39939--39988 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
39929 TACTCGTTAA
39939 GCTCGTTGCTTATTAAG-TTCGAT
1 GCTCGTTGCTTATTAAGCTT-GAT
*
39962 GCTCGTTGCTTGTTAAGCTTGAT
1 GCTCGTTGCTTATTAAGCTTGAT
39985 GCTC
1 GCTC
39989 ATTGTTCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (23 bp):
GCTCGTTGCTTATTAAGCTTGAT
Found at i:40008 original size:35 final size:34
Alignment explanation
Indices: 39966--40086 Score: 154
Period size: 35 Copynumber: 3.5 Consensus size: 34
39956 TTCGATGCTC
* *
39966 GTTGCTTGTTAAGCTTGATGCTCATTGTTCTCCCT
1 GTTGCTTGTTAAGCTCGATGCTCGTTGTT-TCCCT
*
40001 GTTGCTTGTTAAGCTCGATGCTCGTTGTTTGCCCC
1 GTTGCTTGTTAAGCTCGATGCTCGTTGTTT-CCCT
*
40036 GTTGCTTGTTAAGCTCGGTGCTCGTTGCTTT-CCT
1 GTTGCTTGTTAAGCTCGATGCTCGTTG-TTTCCCT
*
40070 CGTTGCTCGTTAAGCTC
1 -GTTGCTTGTTAAGCTC
40087 ACTGAAATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
34 3 0.04
35 71 0.92
36 3 0.04
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (34 bp):
GTTGCTTGTTAAGCTCGATGCTCGTTGTTTCCCT
Found at i:40414 original size:17 final size:17
Alignment explanation
Indices: 40380--40414 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40370 TAGTAAATTA
*
40380 ATAATTTTTTGAATGAT
1 ATAATTTTTTGAAAGAT
*
40397 ATAATTTTTTTAAAGAT
1 ATAATTTTTTGAAAGAT
40414 A
1 A
40415 ACTGCTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (17 bp):
ATAATTTTTTGAAAGAT
Found at i:41469 original size:15 final size:15
Alignment explanation
Indices: 41449--41479 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41439 ATTCATATAT
*
41449 TCGGGTCAGGTTGGG
1 TCGGGTCAGGTCGGG
41464 TCGGGTCAGGTCGGG
1 TCGGGTCAGGTCGGG
41479 T
1 T
41480 GAAACTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.16, G:0.52, T:0.26
Consensus pattern (15 bp):
TCGGGTCAGGTCGGG
Found at i:44575 original size:14 final size:14
Alignment explanation
Indices: 44550--44595 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
44540 CCACTAACTG
*
44550 CTTACAACATAACA
1 CTTACTACATAACA
44564 CTTGA-TACATAACA
1 CTT-ACTACATAACA
44578 CTTACTACATAACA
1 CTTACTACATAACA
44592 CTTA
1 CTTA
44596 AACCAGAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.28
Consensus pattern (14 bp):
CTTACTACATAACA
Found at i:44605 original size:28 final size:28
Alignment explanation
Indices: 44550--44606 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
44540 CCACTAACTG
* *
44550 CTTACAACATAACACTTGATACATAACA
1 CTTACAACATAACACTTGAAACAGAACA
*
44578 CTTACTACATAACACTT-AAACCAGAACA
1 CTTACAACATAACACTTGAAA-CAGAACA
44606 C
1 C
44607 CCTTCAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.46, C:0.28, G:0.04, T:0.23
Consensus pattern (28 bp):
CTTACAACATAACACTTGAAACAGAACA
Found at i:48381 original size:20 final size:20
Alignment explanation
Indices: 48356--48446 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
48346 TAAATTAAAT
*
48356 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
48376 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
48396 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
48408 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
48428 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
48447 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:48471 original size:53 final size:52
Alignment explanation
Indices: 48355--48504 Score: 275
Period size: 53 Copynumber: 2.9 Consensus size: 52
48345 CTAAATTAAA
*
48355 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
48407 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
48460 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
48505 GTTGCTAATT
Statistics
Matches: 96, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 10 0.10
52 35 0.36
53 51 0.53
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:48486 original size:20 final size:20
Alignment explanation
Indices: 48461--48500 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
48451 TCTATTAGTT
*
48461 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
48481 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
48501 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:53095 original size:20 final size:20
Alignment explanation
Indices: 53070--53160 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
53060 TAAATTAAAT
*
53070 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
53090 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
53110 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
53122 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
53142 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
53161 TTTATTCTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:53147 original size:52 final size:53
Alignment explanation
Indices: 53069--53195 Score: 229
Period size: 54 Copynumber: 2.4 Consensus size: 53
53059 CTAAATTAAA
*
53069 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
53121 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTTATTCTATTAGT
53175 TATTAGATAGGATCATTTTTA
1 TATTAGATAGGATCATTTTTA
53196 TTCTGTTGCT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 35 0.49
54 37 0.51
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (53 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
Found at i:57549 original size:18 final size:17
Alignment explanation
Indices: 57527--57561 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
57517 ACACTCAGTG
57527 GAAAAAGTTACTTTGCT
1 GAAAAAGTTACTTTGCT
57544 GAAAAAGTTACTTTGCT
1 GAAAAAGTTACTTTGCT
57561 G
1 G
57562 CAAACATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (17 bp):
GAAAAAGTTACTTTGCT
Found at i:62850 original size:15 final size:15
Alignment explanation
Indices: 62830--62862 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
62820 AGATATATGT
*
62830 ATTAATGATTAAGAG
1 ATTAATGATCAAGAG
62845 ATTAATGATCAAGAG
1 ATTAATGATCAAGAG
62860 ATT
1 ATT
62863 TTGAATAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.33
Consensus pattern (15 bp):
ATTAATGATCAAGAG
Found at i:63314 original size:42 final size:42
Alignment explanation
Indices: 63254--63347 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
63244 TGGAGAAGTC
* * * *
63254 CATTTTTCATCTTAATTTTCCAATGCATGTAAATGATTGTCA
1 CATTTATCATCTTAATTTTCCAATACATGTAAACGATTATCA
* *
63296 CATTTATCATCTTCATTTTCCAATACATGTGAACGATTATCA
1 CATTTATCATCTTAATTTTCCAATACATGTAAACGATTATCA
63338 C-TTTATCATC
1 CATTTATCATC
63348 ATCTTTATGC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 9 0.20
42 37 0.80
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (42 bp):
CATTTATCATCTTAATTTTCCAATACATGTAAACGATTATCA
Found at i:65874 original size:17 final size:16
Alignment explanation
Indices: 65852--65885 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
65842 TAAAAACAGT
65852 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
65869 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
65885 A
1 A
65886 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:66401 original size:23 final size:23
Alignment explanation
Indices: 66358--66403 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
66348 ATAAAAAACC
*
66358 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
66381 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
66404 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:69700 original size:19 final size:20
Alignment explanation
Indices: 69678--69721 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
69668 GAGAAAAGGT
69678 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
69697 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
69717 AAAAG
1 AAAAG
69722 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Done.