Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011572.1 Kokia drynarioides strain JFW-HI SEQ_126561, 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: 159573
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3678 original size:20 final size:19
Alignment explanation
Indices: 3641--3680 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3631 TTCAGAAGGC
3641 TTTTAAAATTAAAATTTTT
1 TTTTAAAATTAAAATTTTT
*
3660 TTTTATAAATT-TAATTTTT
1 TTTTA-AAATTAAAATTTTT
3679 TT
1 TT
3681 GGAACTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAAAATTAAAATTTTT
Found at i:8064 original size:7 final size:7
Alignment explanation
Indices: 8052--8077 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8042 CCCTACGTTT
8052 TCTCTTC
1 TCTCTTC
8059 TCTCTTC
1 TCTCTTC
8066 TCTCTTC
1 TCTCTTC
8073 TCTCT
1 TCTCT
8078 AATTCTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TCTCTTC
Found at i:8100 original size:17 final size:17
Alignment explanation
Indices: 8052--8101 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
8042 CCCTACGTTT
8052 TCTCTTCTCT-CTTCTC
1 TCTCTTCTCTACTTCTC
*
8068 TCT-TCTCTCTAATTCTC
1 TCTCT-TCTCTACTTCTC
*
8085 TCTCTTTTCTACTTCTC
1 TCTCTTCTCTACTTCTC
8102 GGAGACTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.04
16 8 0.29
17 18 0.64
18 1 0.04
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (17 bp):
TCTCTTCTCTACTTCTC
Found at i:11874 original size:7 final size:7
Alignment explanation
Indices: 11862--11887 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11852 TCTCCCTACG
11862 TCTCTTC
1 TCTCTTC
11869 TCTCTTC
1 TCTCTTC
11876 TCTCTTC
1 TCTCTTC
11883 TCTCT
1 TCTCT
11888 AATTCCCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (7 bp):
TCTCTTC
Found at i:20870 original size:16 final size:16
Alignment explanation
Indices: 20849--20879 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20839 ATATAAATAC
20849 TATATATATAAAGAAA
1 TATATATATAAAGAAA
*
20865 TATATATCTAAAGAA
1 TATATATATAAAGAA
20880 TTAGTTGATG
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:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (16 bp):
TATATATATAAAGAAA
Found at i:26189 original size:34 final size:34
Alignment explanation
Indices: 26146--26214 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
26136 AGTTCCTATG
26146 GCAACTTTAGAATTTTTTGATTATGCCTTGAGTT
1 GCAACTTTAGAATTTTTTGATTATGCCTTGAGTT
26180 GCAACTTTAGAATTTTTTGATTATGCCTTGAGTT
1 GCAACTTTAGAATTTTTTGATTATGCCTTGAGTT
26214 G
1 G
26215 GTAGACTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (34 bp):
GCAACTTTAGAATTTTTTGATTATGCCTTGAGTT
Found at i:28757 original size:104 final size:104
Alignment explanation
Indices: 28568--28762 Score: 270
Period size: 104 Copynumber: 1.9 Consensus size: 104
28558 GGTCCGATAG
* * * *
28568 CTAAGTGTCATTGTGAGTATACGAATCCTTTACAGATTAAACGGTCTGATGAATCTATGTCATCG
1 CTAAGTGTCATGGTGAGTATAAGAATCCTTTACAGATTAAACGGTCCGACGAATCTATGTCATCG
*
28633 TGAGTATATAAATCCTTTACGGATTAAACGGTTCGATGA
66 TGAGTATACAAATCCTTTACGGATTAAACGGTTCGATGA
* *
28672 CTAAGTGTCATGGTGAGTATATAG-ATCCTTTACGGATTAAGA-GGTCCGACGAATCTGTGTCAT
1 CTAAGTGTCATGGTGAGTATA-AGAATCCTTTACAGATTAA-ACGGTCCGACGAATCTATGTCAT
*
28735 CGTGAGTATACGAATCAC-TTACGGATTA
64 CGTGAGTATACAAATC-CTTTACGGATTA
28763 TAAGGTCCGG
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
104 77 0.96
105 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (104 bp):
CTAAGTGTCATGGTGAGTATAAGAATCCTTTACAGATTAAACGGTCCGACGAATCTATGTCATCG
TGAGTATACAAATCCTTTACGGATTAAACGGTTCGATGA
Found at i:28769 original size:52 final size:52
Alignment explanation
Indices: 28572--28771 Score: 219
Period size: 52 Copynumber: 3.8 Consensus size: 52
28562 CGATAGCTAA
* * *
28572 GTGTCATTGTGAGTATACGAATCCTTTACAGATTAAACGGTCTGATGAATCT
1 GTGTCATCGTGAGTATACGAATCCTTTACGGATTAAACGGTCCGATGAATCT
* ** * * **
28624 ATGTCATCGTGAGTATATAAATCCTTTACGGATTAAACGGTTCGATGACTAA
1 GTGTCATCGTGAGTATACGAATCCTTTACGGATTAAACGGTCCGATGAATCT
* * *
28676 GTGTCATGGTGAGTATA-TAGATCCTTTACGGATTAAGA-GGTCCGACGAATCT
1 GTGTCATCGTGAGTATACGA-ATCCTTTACGGATTAA-ACGGTCCGATGAATCT
28728 GTGTCATCGTGAGTATACGAATCAC-TTACGGATTATAA-GGTCCG
1 GTGTCATCGTGAGTATACGAATC-CTTTACGGATTA-AACGGTCCG
28772 GTGGCTATGG
Statistics
Matches: 123, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
51 1 0.01
52 118 0.96
53 4 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (52 bp):
GTGTCATCGTGAGTATACGAATCCTTTACGGATTAAACGGTCCGATGAATCT
Found at i:28792 original size:104 final size:104
Alignment explanation
Indices: 28558--28797 Score: 249
Period size: 104 Copynumber: 2.3 Consensus size: 104
28548 ATAAAGAAGA
** * * *
28558 GGTCCGAT-AGCTAAGTGTCATTGTGAGTATA-CGAATCCTTTACAGATTAAACGGTCTGATGAA
1 GGTCCGATGA-CTAAGTGTCACCGTGAGTATATAG-ATCCTTTACAGATTAAACGGTCCGACGAA
*
28621 TCTATGTCATCGTGAGTATATAAATCCTTTACGGATTAAAC
64 TCTATGTCATCGTGAGTATACAAATCCTTTACGGATTAAAC
* ** *
28662 GGTTCGATGACTAAGTGTCATGGTGAGTATATAGATCCTTTACGGATTAAGA-GGTCCGACGAAT
1 GGTCCGATGACTAAGTGTCACCGTGAGTATATAGATCCTTTACAGATTAA-ACGGTCCGACGAAT
* *
28726 CTGTGTCATCGTGAGTATACGAATCAC-TTACGGATTATAA-
65 CTATGTCATCGTGAGTATACAAATC-CTTTACGGATTA-AAC
* * *
28766 GGTCCGGTGGCTATG-GATCACCGTGAGTATAT
1 GGTCCGATGACTAAGTG-TCACCGTGAGTATAT
28798 GAATGAAGTG
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
103 1 0.01
104 108 0.94
105 6 0.05
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (104 bp):
GGTCCGATGACTAAGTGTCACCGTGAGTATATAGATCCTTTACAGATTAAACGGTCCGACGAATC
TATGTCATCGTGAGTATACAAATCCTTTACGGATTAAAC
Found at i:35908 original size:52 final size:52
Alignment explanation
Indices: 35798--35997 Score: 179
Period size: 52 Copynumber: 3.8 Consensus size: 52
35788 GAAAAAGTCC
* * * * * **
35798 GATGACTAAGTGTTATCATGAGTATATGAATCCTTTACGAATTGAACGGTTT
1 GATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATTAAACGGTCA
* *
35850 GATGACTCTA-TGTCATCTTGAGTATATAAATCCTTTACGGATTAAACGGTCA
1 GATGACT-AAGTGTCATCGTGAGTATATAAATCCTTTACGGATTAAACGGTCA
* * * * *
35902 GGTGACTAAGTGTTATCGTGAGTATATAGATCCTTTATGGATTAAGA-GGTCC
1 GATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATTAA-ACGGTCA
** * ** * *
35954 GATGACTTTGTATCATCGTGAGTATACGAATCCCTTACAGATTA
1 GATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATTA
35998 TAAGCCCAGT
Statistics
Matches: 119, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
51 1 0.01
52 116 0.97
53 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (52 bp):
GATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATTAAACGGTCA
Found at i:35986 original size:104 final size:104
Alignment explanation
Indices: 35800--35997 Score: 238
Period size: 104 Copynumber: 1.9 Consensus size: 104
35790 AAAAGTCCGA
* ** *
35800 TGACTAAGTGTTATCATGAGTATATGAATCCTTTACGAATTGAACGGTTTGATGACTCTATGTCA
1 TGACTAAGTGTTATCATGAGTATATGAATCCTTTACGAATTGAAAGGTCCGATGACTCTATATCA
* * * *
35865 TCTTGAGTATATAAATCCTTTACGGATTAAACGGTCAGG
66 TCGTGAGTATACAAATCCCTTACAGATTAAACGGTCAGG
* * * * *
35904 TGACTAAGTGTTATCGTGAGTATAT-AGATCCTTTATGGATT-AAGAGGTCCGATGACTTTGTAT
1 TGACTAAGTGTTATCATGAGTATATGA-ATCCTTTACGAATTGAA-AGGTCCGATGACTCTATAT
*
35967 CATCGTGAGTATACGAATCCCTTACAGATTA
64 CATCGTGAGTATACAAATCCCTTACAGATTA
35998 TAAGCCCAGT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
103 3 0.04
104 75 0.96
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (104 bp):
TGACTAAGTGTTATCATGAGTATATGAATCCTTTACGAATTGAAAGGTCCGATGACTCTATATCA
TCGTGAGTATACAAATCCCTTACAGATTAAACGGTCAGG
Found at i:37824 original size:60 final size:62
Alignment explanation
Indices: 37721--37894 Score: 207
Period size: 60 Copynumber: 2.9 Consensus size: 62
37711 CATTGTGAGT
* * *
37721 AAATGAATTCCTATACGGAACAAAGGGGTCTGATGACTATATGTCATTGTGAGTATTAAATG
1 AAATGAGTTCCAATACGGAACAAAGGGGTCTGATGACTATATGTCATCGTGAGTATTAAATG
37783 AAATGAGTTCCAATACGGAAC-AA-GGGTCCT-ATGACTATATGTCATCGTGAGTATTAAATG
1 AAATGAGTTCCAATACGGAACAAAGGGGT-CTGATGACTATATGTCATCGTGAGTATTAAATG
* * * * * *
37843 AAATGAGTTTCAAT-GGAGAAC-AA-GAGTTTGATGACTTTGTGTCATCGTGAGT
1 AAATGAGTTCCAATACG-GAACAAAGGGGTCTGATGACTATATGTCATCGTGAGT
37895 CACAAATGCG
Statistics
Matches: 100, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
59 2 0.02
60 75 0.75
61 4 0.04
62 19 0.19
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (62 bp):
AAATGAGTTCCAATACGGAACAAAGGGGTCTGATGACTATATGTCATCGTGAGTATTAAATG
Found at i:43077 original size:51 final size:51
Alignment explanation
Indices: 42943--43078 Score: 202
Period size: 51 Copynumber: 2.7 Consensus size: 51
42933 CGAAAGAGTC
* * *
42943 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACTGATTAAAGGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATTCATGACTGATTAAAGGTT
*
42994 TGATGACTAAGTGTCATCGTGAGTAAATGAATTCATGAC-GAATTAAAGGTT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATTCATGACTG-ATTAAAGGTT
* *
43045 CGATGACTAAGTGTGATCGTGAGGAAATGAATTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATTC
43079 CTATATGGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 1 0.01
51 76 0.99
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATTCATGACTGATTAAAGGTT
Found at i:43237 original size:60 final size:60
Alignment explanation
Indices: 43068--43242 Score: 224
Period size: 60 Copynumber: 2.9 Consensus size: 60
43058 TGATCGTGAG
* * * ** *
43068 GAAATGAATTCCTATATGGAACAAAGGGGTCCGATGACTATATGTCATTATGAATATTAAAT
1 GAAATGAGTTCCAATACGGAAC-AA-GGGTCCGATGACTATATGTCATCGTGAGTATTAAAT
*
43130 GAAATGAGTTCCAATACGGAACAAGGGTCCAATGACTATATGTCATCGTGAGTATTAAAT
1 GAAATGAGTTCCAATACGGAACAAGGGTCCGATGACTATATGTCATCGTGAGTATTAAAT
* * * * *
43190 GAAATGAGTTTCAATGCGGAACAATGGTCCGATGACTTTGTGTCATCGTGAGT
1 GAAATGAGTTCCAATACGGAACAAGGGTCCGATGACTATATGTCATCGTGAGT
43243 CACAAATGCT
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 79 0.79
61 2 0.02
62 19 0.19
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (60 bp):
GAAATGAGTTCCAATACGGAACAAGGGTCCGATGACTATATGTCATCGTGAGTATTAAAT
Found at i:48502 original size:52 final size:52
Alignment explanation
Indices: 48429--48672 Score: 276
Period size: 52 Copynumber: 4.7 Consensus size: 52
48419 TAAATGAAGA
* *
48429 GGTCCAATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAT
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAT
* * *
48481 GGTCCGATGACTCTGTGTCATCATGAGTATATAAATCCTTTACGGATTAAAT
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAT
* * * *
48533 AGTCCGATGACTAAGTGTCATCGTGAGTATATGGATCCTTTACGGATTAAAA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAT
* * * * * *
48585 GGTTCGATGACTTTATGTTATCGTAAGTATACGAATCAC-TTACGGATTATAA-
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATC-CTTTACGGATTA-AAT
* * * * *
48637 GGTCCGGTGGCTATGGGTCACCGTGAATATATGAAT
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
48673 GAAGTGAAAT
Statistics
Matches: 158, Mismatches: 32, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
52 155 0.98
53 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAAT
Found at i:56263 original size:23 final size:24
Alignment explanation
Indices: 56218--56265 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
56208 TTTTTTCTCA
*
56218 CACTCTCTTTTATTTTTGGAATTT
1 CACTCTCTTTTATTTTTGCAATTT
56242 CACTCTCATTTT-TTTTT-CAATTT
1 CACTCTC-TTTTATTTTTGCAATTT
56265 C
1 C
56266 TTTATCTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 12 0.55
25 4 0.18
ACGTcount: A:0.17, C:0.21, G:0.04, T:0.58
Consensus pattern (24 bp):
CACTCTCTTTTATTTTTGCAATTT
Found at i:57241 original size:23 final size:22
Alignment explanation
Indices: 57212--57262 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
57202 AAGAAATTGA
57212 TTTTTTATACTCAATTTTTTTCT
1 TTTTTTA-ACTCAATTTTTTTCT
* **
57235 TTTTTTAATTTGATTTTTTTCT
1 TTTTTTAACTCAATTTTTTTCT
57257 TTTTTT
1 TTTTTT
57263 TTTTTTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTTTAACTCAATTTTTTTCT
Found at i:57275 original size:30 final size:28
Alignment explanation
Indices: 57226--57326 Score: 78
Period size: 30 Copynumber: 3.4 Consensus size: 28
57216 TTATACTCAA
*
57226 TTTTTTTCTTTTTT-TAATTTGATTTTTTTC
1 TTTTTTT-TTTTTTCAAATTTGA--TTTTTC
* * *
57256 TTTTTTTTTTTTTCAAATTTCAAATTTTA
1 TTTTTTTTTTTTTCAAATTT-GATTTTTC
**
57285 TTTGATTTTTTTTCAATATTTTGATTTTTC
1 TTTTTTTTTTTTTCAA-A-TTTGATTTTTC
*
57315 TTTTCTTTTTTT
1 TTTTTTTTTTTT
57327 CACTTTTTCG
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
29 24 0.43
30 28 0.50
31 4 0.07
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (28 bp):
TTTTTTTTTTTTTCAAATTTGATTTTTC
Found at i:57283 original size:29 final size:30
Alignment explanation
Indices: 57251--57326 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 30
57241 AATTTGATTT
*
57251 TTTTCTTTTTTTTTTTTTCAA-ATTTCAAA
1 TTTTCTTTTATTTTTTTTCAATATTTCAAA
* * ** *
57280 TTTTATTTGATTTTTTTTCAATATTTTGAT
1 TTTTCTTTTATTTTTTTTCAATATTTCAAA
*
57310 TTTTCTTTTCTTTTTTT
1 TTTTCTTTTATTTTTTT
57327 CACTTTTTCG
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74
Consensus pattern (30 bp):
TTTTCTTTTATTTTTTTTCAATATTTCAAA
Found at i:57972 original size:80 final size:80
Alignment explanation
Indices: 57862--58011 Score: 255
Period size: 80 Copynumber: 1.9 Consensus size: 80
57852 ACTAATTTCA
* * * * *
57862 TTTTAACTCTTGTAGGGAAGCTAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGTTGAAAAG
1 TTTTAACTCTTGTAGGAAAACCAATAAGTCATGTCTCTTCATTAGGATCTGATGTAGCTGAAAAG
57927 GCATGGCAATTTCGT
66 GCATGGCAATTTCGT
57942 TTTTAACTCTTGTAGGAAAACCAATAAGTCATGTCTCTTCATTAGGATCTGATGTAGCTGAAAAG
1 TTTTAACTCTTGTAGGAAAACCAATAAGTCATGTCTCTTCATTAGGATCTGATGTAGCTGAAAAG
58007 GCATG
66 GCATG
58012 ACATTTCTCC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (80 bp):
TTTTAACTCTTGTAGGAAAACCAATAAGTCATGTCTCTTCATTAGGATCTGATGTAGCTGAAAAG
GCATGGCAATTTCGT
Found at i:58562 original size:48 final size:48
Alignment explanation
Indices: 58461--58590 Score: 183
Period size: 48 Copynumber: 2.8 Consensus size: 48
58451 CAAGGCATTT
* * * *
58461 AACAAAGATGCTTTTAACAAAC-AAACAGTTAATAATGCATATTACTA
1 AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAGATTACTA
* * *
58508 AACAAAGATGCATTTAACAAACAAAACACTTTATGATGTAGATTATTA
1 AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAGATTACTA
58556 AACAAAGATGCATTTAACAAA-AAAACACTTAATGA
1 AACAAAGATGCATTTAACAAACAAAACACTTAATGA
58591 AGCATAAATA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
47 34 0.46
48 40 0.54
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (48 bp):
AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAGATTACTA
Found at i:61390 original size:191 final size:195
Alignment explanation
Indices: 61003--61395 Score: 500
Period size: 192 Copynumber: 2.0 Consensus size: 195
60993 TTTAATACTT
*
61003 GTGTGAGCAGCATCGTGAGTTGAGAAATGAGAAAAGAATCTAAGAATGGATTACAGGCCCTACAA
1 GTGTGAGCAGCATCGTGAGTGGAGAAATGAGAAAAGAATCTAAGAATGGATTACAGGCCCTACAA
* *
61068 TGGCTGAGATTTATGCATAAGTGCATATTCTCGACAGCTCGTGTGAGCAACATCATTAGGGAACA
66 TGGCTGAGATTTATGCATAAATGCATATTCTCGACAGCTCGTGTGAGAAACATCATTAGGGAACA
* * * *
61133 GTTATATGCACAGATACCGTATCGATGGCTAAGGTGCCGCATATGTTACGAGTCCTCGATAACTC
131 GTTATAAGCACAGATACCATATCGATGGCTAAGGTACCGCATATGTTACGAGTCCTCGACAACTC
* * *
61198 GTGTGAGCAGCATCGTGAGTCGGA-AAAT-AG-TATGAATCCT-A-AATGGATTATAGGCCCTA-
1 GTGTGAGCAGCATCGTGAGT-GGAGAAATGAGAAAAGAAT-CTAAGAATGGATTACAGGCCCTAC
* * *
61257 AGATGGCTGAGATTTATGC-TAAAATGCATCTTCTTGACAGCTCGTGTGA-AAAGCATCGTTAGG
64 A-ATGGCTGAGATTTATGCAT-AAATGCATATTCTCGACAGCTCGTGTGAGAAA-CATCATTAGG
* * ** *
61320 GGATAGTT-TACAG-ACAGATACCATATCGATGGCTGCGGTACCGCATATGTTGCGAGTCCTCGA
126 GAACAGTTATA-AGCACAGATACCATATCGATGGCTAAGGTACCGCATATGTTACGAGTCCTCGA
61383 CAACTC
190 CAACTC
61389 GTGTGAG
1 GTGTGAG
61396 TAGTATTTAG
Statistics
Matches: 174, Mismatches: 18, Indels: 16
0.84 0.09 0.08
Matches are distributed among these distances:
191 63 0.36
192 75 0.43
193 6 0.03
194 4 0.02
195 24 0.14
196 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (195 bp):
GTGTGAGCAGCATCGTGAGTGGAGAAATGAGAAAAGAATCTAAGAATGGATTACAGGCCCTACAA
TGGCTGAGATTTATGCATAAATGCATATTCTCGACAGCTCGTGTGAGAAACATCATTAGGGAACA
GTTATAAGCACAGATACCATATCGATGGCTAAGGTACCGCATATGTTACGAGTCCTCGACAACTC
Found at i:85237 original size:12 final size:12
Alignment explanation
Indices: 85220--85244 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
85210 CACCAGCCCA
85220 ACAAGAAGTTGG
1 ACAAGAAGTTGG
85232 ACAAGAAGTTGG
1 ACAAGAAGTTGG
85244 A
1 A
85245 GAAGGGAGTC
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:0.44, C:0.08, G:0.32, T:0.16
Consensus pattern (12 bp):
ACAAGAAGTTGG
Found at i:85601 original size:56 final size:56
Alignment explanation
Indices: 85534--85639 Score: 203
Period size: 56 Copynumber: 1.9 Consensus size: 56
85524 GTAAGAGTAG
85534 GATTAGAAATTATTTTTGTATATATGCTTTAATTCTTTTTGTAGGAACCCTAGATT
1 GATTAGAAATTATTTTTGTATATATGCTTTAATTCTTTTTGTAGGAACCCTAGATT
*
85590 GATTAGGAATTATTTTTGTATATATGCTTTAATTCTTTTTGTAGGAACCC
1 GATTAGAAATTATTTTTGTATATATGCTTTAATTCTTTTTGTAGGAACCC
85640 CAAATTATGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.48
Consensus pattern (56 bp):
GATTAGAAATTATTTTTGTATATATGCTTTAATTCTTTTTGTAGGAACCCTAGATT
Found at i:85828 original size:38 final size:38
Alignment explanation
Indices: 85777--85854 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
85767 TTAAGGATAA
85777 TGTGTTTTCTAAAATGTGGGGGGTAACATAGGAATTTT
1 TGTGTTTTCTAAAATGTGGGGGGTAACATAGGAATTTT
85815 TGTGTTTTCTAAAATGTGGGGGGTAACATAGGAATTTT
1 TGTGTTTTCTAAAATGTGGGGGGTAACATAGGAATTTT
85853 TG
1 TG
85855 ACATATAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.26, C:0.05, G:0.29, T:0.40
Consensus pattern (38 bp):
TGTGTTTTCTAAAATGTGGGGGGTAACATAGGAATTTT
Found at i:89746 original size:24 final size:21
Alignment explanation
Indices: 89713--89769 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
89703 CAAGTATTCA
*
89713 AACTACCGATACTACTATGAATAG
1 AACTATCGATACTACTAT---TAG
*
89737 AACTATCGATACTTCTATTAG
1 AACTATCGATACTACTATTAG
*
89758 TACTATCGATAC
1 AACTATCGATAC
89770 AATGCAAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.47
24 16 0.53
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (21 bp):
AACTATCGATACTACTATTAG
Found at i:90489 original size:78 final size:79
Alignment explanation
Indices: 90321--90490 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 79
90311 TTCTCATTTA
* * * * * *
90321 ATAACTTACGATGCCATAAAGAATCCGCAACAAATGCAGAATCTCAGTCATTGGACCTTTAATCT
1 ATAACTCACGATGCCATAAAGAATCCACAACAAATGCAGAATCTCAATCATCGAACCTTTAATCC
90386 GTAATAGAATTCAT
66 GTAATAGAATTCAT
* *
90400 ATATCTCACGATGCCATAGAA-AATCCACAACAAATGCAGGATCTCAATC-TCGAACCTTTAATC
1 ATAACTCACGATGCCATA-AAGAATCCACAACAAATGCAGAATCTCAATCATCGAACCTTTAATC
*
90463 CGTAATAGGATTCAT
65 CGTAATAGAATTCAT
90478 ATAACTCACGATG
1 ATAACTCACGATG
90491 ACACAGAGTC
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
78 37 0.46
79 41 0.51
80 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (79 bp):
ATAACTCACGATGCCATAAAGAATCCACAACAAATGCAGAATCTCAATCATCGAACCTTTAATCC
GTAATAGAATTCAT
Found at i:90607 original size:53 final size:54
Alignment explanation
Indices: 90449--90672 Score: 353
Period size: 54 Copynumber: 4.2 Consensus size: 54
90439 GATCTCAATC
90449 TCGAACCTTTAATCCGTAATAGGA-TTCATATAACTCACGATGACACAGAGTCA
1 TCGAACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGAGTCA
* * *
90502 TTGGACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACATAGAGTCA
1 TCGAACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGAGTCA
* ** * *
90556 TCAAACCTTTAATCTATAATAGGA-TTCATATAACTCATGATGACATAGAGTCA
1 TCGAACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGAGTCA
*
90609 TCGAACCTTTAATCCGTAATAAGATTTCATATAACTCACGATGACACAGAGTCA
1 TCGAACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGAGTCA
90663 TCGAACCTTT
1 TCGAACCTTT
90673 TTGCATTTAC
Statistics
Matches: 154, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
53 70 0.45
54 84 0.55
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (54 bp):
TCGAACCTTTAATCCGTAATAGGATTTCATATAACTCACGATGACACAGAGTCA
Found at i:90638 original size:107 final size:107
Alignment explanation
Indices: 90452--90672 Score: 361
Period size: 107 Copynumber: 2.1 Consensus size: 107
90442 CTCAATCTCG
* * *
90452 AACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGAGTCATTGGACCTTTAATCC
1 AACCTTTAATCCATAATAGGATTCATATAACTCACGATGACACAGAGTCATCGAACCTTTAATCC
* *
90517 GTAATAGGATTTCATATAACTCACGATGACATAGAGTCATCA
66 GTAATAAGATTTCATATAACTCACGATGACACAGAGTCATCA
* * *
90559 AACCTTTAATCTATAATAGGATTCATATAACTCATGATGACATAGAGTCATCGAACCTTTAATCC
1 AACCTTTAATCCATAATAGGATTCATATAACTCACGATGACACAGAGTCATCGAACCTTTAATCC
*
90624 GTAATAAGATTTCATATAACTCACGATGACACAGAGTCATCG
66 GTAATAAGATTTCATATAACTCACGATGACACAGAGTCATCA
90666 AACCTTT
1 AACCTTT
90673 TTGCATTTAC
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (107 bp):
AACCTTTAATCCATAATAGGATTCATATAACTCACGATGACACAGAGTCATCGAACCTTTAATCC
GTAATAAGATTTCATATAACTCACGATGACACAGAGTCATCA
Found at i:92942 original size:17 final size:17
Alignment explanation
Indices: 92922--92954 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
92912 TTTAAGGACT
92922 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
92939 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
92955 TAAGTGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:93227 original size:50 final size:50
Alignment explanation
Indices: 93148--93303 Score: 156
Period size: 50 Copynumber: 3.1 Consensus size: 50
93138 TGACATCCAT
*
93148 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAG
1 TAACTCTCATG-TTAGTTAAATTTGCATCATAAATAATGACATGCATTAAG
* * ** *
93199 TAACT-TACATGTTAGTTAAATATGCATCATAAGTCCT-ATCATGCATTATG
1 TAACTCT-CATGTTAGTTAAATTTGCATCATAAATAATGA-CATGCATTAAG
* * *
93249 TAACTCTCATGTTAGTTAAAGTTTGCATCTTTAAATCAA-GTCATGCATTTAG
1 TAACTCTCATGTTAGTTAAA-TTTGCATC-ATAAAT-AATGACATGCATTAAG
93301 TAA
1 TAA
93304 TTCGTTAGTT
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
49 1 0.01
50 50 0.60
51 17 0.20
52 16 0.19
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (50 bp):
TAACTCTCATGTTAGTTAAATTTGCATCATAAATAATGACATGCATTAAG
Found at i:108495 original size:17 final size:18
Alignment explanation
Indices: 108462--108500 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
108452 TTATAAATAT
108462 AAATAAATAAACAAAA-C
1 AAATAAATAAACAAAACC
108479 AAATAAATAAA-ATAAACC
1 AAATAAATAAACA-AAACC
108497 AAAT
1 AAAT
108501 TTGTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (18 bp):
AAATAAATAAACAAAACC
Found at i:110895 original size:20 final size:19
Alignment explanation
Indices: 110853--110895 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
110843 GTATTTTTAT
*
110853 ATGTTGATTTGATAAATAT
1 ATGTTGATTTGATAAATAC
* *
110872 ATGTTGATATTGTTGAATAC
1 ATGTTGAT-TTGATAAATAC
110892 ATGT
1 ATGT
110896 CTATAGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (19 bp):
ATGTTGATTTGATAAATAC
Found at i:122079 original size:13 final size:13
Alignment explanation
Indices: 122061--122085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
122051 TGTTATTAAT
122061 AAATAAATAAAAC
1 AAATAAATAAAAC
122074 AAATAAATAAAA
1 AAATAAATAAAA
122086 TAAACCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAATAAAAC
Found at i:123511 original size:17 final size:17
Alignment explanation
Indices: 123483--123534 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
123473 TTTGTTTTAT
123483 TCATTATTTATTTGTTAC
1 TCATT-TTTATTTGTTAC
123501 TCATTTTTATTAT-TTAC
1 TCATTTTTATT-TGTTAC
*
123518 TATATTTTTTATTTGTT
1 T-CA-TTTTTATTTGTT
123535 GCATTTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 11 0.38
18 8 0.28
19 10 0.34
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (17 bp):
TCATTTTTATTTGTTAC
Found at i:127506 original size:37 final size:37
Alignment explanation
Indices: 127465--127538 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
127455 CCTAAGTGGG
*
127465 TAGGCTATTATAAGCGATGTGGACCTAACAGATCGCT
1 TAGGCTATTATAAGCGACGTGGACCTAACAGATCGCT
127502 TAGGCTATTATAAGCGACGTGGACCTAACAGATCGCT
1 TAGGCTATTATAAGCGACGTGGACCTAACAGATCGCT
127539 CACTATCTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (37 bp):
TAGGCTATTATAAGCGACGTGGACCTAACAGATCGCT
Found at i:135728 original size:50 final size:50
Alignment explanation
Indices: 135659--135814 Score: 163
Period size: 50 Copynumber: 3.1 Consensus size: 50
135649 TTACATCCAT
*
135659 TAACTCTCATGATTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAG
1 TAACTCACATG-TTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAG
* * * ** *
135710 TAACTTACATGTTAGTTAAATATGCATCATAAATCCT-ATCATGCATTATG
1 TAACTCACATGTTAGTTAAGTTTGCATCATAAATAATGA-CATGCATTAAG
* * *
135760 TAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATCAA-GTCATGCATTTAG
1 TAACTCACATGTTAGTT-AAGTTTGCATCA-TAAAT-AATGACATGCATTAAG
135812 TAA
1 TAA
135815 TCCATTAGTT
Statistics
Matches: 84, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
49 1 0.01
50 47 0.56
51 19 0.23
52 17 0.20
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAG
Found at i:141377 original size:13 final size:13
Alignment explanation
Indices: 141361--141385 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
141351 ACAGCTAATC
141361 AAATAAAATAAAA
1 AAATAAAATAAAA
141374 AAATAAAATAAA
1 AAATAAAATAAA
141386 TTTAAGTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:143168 original size:26 final size:26
Alignment explanation
Indices: 143116--143189 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
143106 ATTCGTATCA
* * * *
143116 AGCTCTTACTAGCCCAGATAAAGTTT
1 AGCTCTTACAAGCCCAGACAGATTTT
* *
143142 AGCTCATT-CGAGCCTAGACAGATTTT
1 AGCTC-TTACAAGCCCAGACAGATTTT
143168 AGCTCTTACAAGCCCAGACAGA
1 AGCTCTTACAAGCCCAGACAGA
143190 GTATGCTCTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.05
26 35 0.90
27 2 0.05
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (26 bp):
AGCTCTTACAAGCCCAGACAGATTTT
Found at i:143207 original size:26 final size:27
Alignment explanation
Indices: 143116--143207 Score: 68
Period size: 26 Copynumber: 3.6 Consensus size: 27
143106 ATTCGTATCA
* * * *
143116 AGCTCTTAC-TAGCCCAGATAAAGTTT
1 AGCTCTTACAGAGCCCAGACAGAGTAT
* * *
143142 AGCTCATT-C-GAGCCTAGACAGATTTT
1 AGCTC-TTACAGAGCCCAGACAGAGTAT
143168 AGCTCTTACA-AGCCCAGACAGAGTAT
1 AGCTCTTACAGAGCCCAGACAGAGTAT
*
143194 -GCTCTTATAGAGCC
1 AGCTCTTACAGAGCC
143208 AAAATTTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
25 10 0.19
26 41 0.77
27 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (27 bp):
AGCTCTTACAGAGCCCAGACAGAGTAT
Found at i:144099 original size:3 final size:3
Alignment explanation
Indices: 144091--144115 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
144081 AAATTTACAT
144091 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
144116 GCTAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:150430 original size:50 final size:49
Alignment explanation
Indices: 150364--150556 Score: 194
Period size: 50 Copynumber: 3.8 Consensus size: 49
150354 ACTTGTTTTA
* * *
150364 ATGATGCAAACTTTAACTAACATGGGAGTTAGATAATGCATGAT-ATAATTT
1 ATGATGCATAC-TTAACTAACATGGAAGTTACATAATGCATG-TCAT-ATTT
* * * * * *
150415 ATTATGCATATTTAACTAACATGTAAGTAACTTTATGCATGTCATTATTT
1 ATGATGCATACTTAACTAACATGGAAGTTACATAATGCATGTCA-TATTT
*
150465 ATGATGCAAACTTAACTAATCAT-GAGAGTTACATAATGCATGTCAGTATTT
1 ATGATGCATACTTAACTAA-CATGGA-AGTTACATAATGCATGTCA-TATTT
*
150516 CTGATGCATACTTAACTAACAT-GAACGTTACATAATGCATG
1 ATGATGCATACTTAACTAACATGGAA-GTTACATAATGCATG
150557 ACCTTATTAA
Statistics
Matches: 118, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.02
50 66 0.56
51 50 0.42
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (49 bp):
ATGATGCATACTTAACTAACATGGAAGTTACATAATGCATGTCATATTT
Found at i:150554 original size:101 final size:101
Alignment explanation
Indices: 150364--150556 Score: 250
Period size: 101 Copynumber: 1.9 Consensus size: 101
150354 ACTTGTTTTA
* * * *
150364 ATGATGCAAACTTTAACTAACATGGGAGTTAGATAATGCATGATATAATTTATTATGCATATTTA
1 ATGATGCAAACTTTAACTAACATGAGAGTTACATAATGCATGATATAATTTATGATGCATACTTA
* *
150429 ACTAACATGTAAGTAACTTTATGCATGTCATTATTT
66 ACTAACATGTAAGTAACATAATGCATGTCATTATTT
*
150465 ATGATGCAAAC-TTAACTAATCATGAGAGTTACATAATGCATG-TCAGT-ATTTCTGATGCATAC
1 ATGATGCAAACTTTAACTAA-CATGAGAGTTACATAATGCATGAT-A-TAATTTATGATGCATAC
*
150527 TTAACTAACATG-AACGTTACATAATGCATG
63 TTAACTAACATGTAA-GTAACATAATGCATG
150557 ACCTTATTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
100 11 0.14
101 68 0.85
102 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (101 bp):
ATGATGCAAACTTTAACTAACATGAGAGTTACATAATGCATGATATAATTTATGATGCATACTTA
ACTAACATGTAAGTAACATAATGCATGTCATTATTT
Found at i:152255 original size:17 final size:17
Alignment explanation
Indices: 152236--152289 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
152226 CACTTTCTCT
152236 TTTTTCAACTTCTTTT-
1 TTTTTCAACTTCTTTTC
152252 TTTTCTCAA--T-TTTTC
1 TTTT-TCAACTTCTTTTC
*
152267 TTCTTCAACTTCTTTTC
1 TTTTTCAACTTCTTTTC
152284 TTTTTC
1 TTTTTC
152290 TTTCAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 4 0.13
16 5 0.16
17 14 0.45
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTCAACTTCTTTTC
Found at i:152350 original size:15 final size:18
Alignment explanation
Indices: 152329--152369 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 18
152319 TCAACTTTTT
152329 TTTTCTTTTT-TCTCA-A
1 TTTTCTTTTTGTCTCATA
152345 -TTTCTTTTTGTCTCATA
1 TTTTCTTTTTGTCTCATA
152362 TTTTCTTT
1 TTTTCTTT
152370 ACAAGATGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.41
16 5 0.23
17 1 0.05
18 7 0.32
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTCTTTTTGTCTCATA
Found at i:154341 original size:51 final size:49
Alignment explanation
Indices: 154261--154453 Score: 228
Period size: 51 Copynumber: 3.8 Consensus size: 49
154251 ACGTGTTTTA
* **
154261 ATGATGCAAACTTTAAC-AACATGTGAGTTACATAATGCATGAT-ATAATTT
1 ATGATGCATA-TTTAACTAACATGAAAGTTACATAATGCATG-TCAT-ATTT
* *
154311 ATTATGCATATTTAACTAACATGTAAAGTTACTTAATGCATGTCATTATTT
1 ATGATGCATATTTAACTAACATG-AAAGTTACATAATGCATGTCA-TATTT
* * *
154362 ATGATGCAAACTTAACTAATCATGAGAGTTACATAATGCATGTCAGTATTT
1 ATGATGCATATTTAACTAA-CATGAAAGTTACATAATGCATGTCA-TATTT
*
154413 CTGATGCATATTTAACTAACATGAAAGTTACATAATGCATG
1 ATGATGCATATTTAACTAACATGAAAGTTACATAATGCATG
154454 ACTTTATTAA
Statistics
Matches: 123, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
49 6 0.05
50 36 0.29
51 76 0.62
52 5 0.04
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (49 bp):
ATGATGCATATTTAACTAACATGAAAGTTACATAATGCATGTCATATTT
Found at i:154391 original size:102 final size:100
Alignment explanation
Indices: 154261--154453 Score: 284
Period size: 102 Copynumber: 1.9 Consensus size: 100
154251 ACGTGTTTTA
* *
154261 ATGATGCAAACTTTAACAACATGTGAGTTACATAATGCATGAT-A-TAATTTATTATGCATATTT
1 ATGATGCAAACTTTAACAACATGAGAGTTACATAATGCATG-TCAGT-ATTTATGATGCATATTT
*
154324 AACTAACATGTAAAGTTACTTAATGCATGTCATTATTT
64 AACTAACATG-AAAGTTACATAATGCATGTCATTATTT
*
154362 ATGATGCAAAC-TTAACTAATCATGAGAGTTACATAATGCATGTCAGTATTTCTGATGCATATTT
1 ATGATGCAAACTTTAAC-AA-CATGAGAGTTACATAATGCATGTCAGTATTTATGATGCATATTT
154426 AACTAACATGAAAGTTACATAATGCATG
64 AACTAACATGAAAGTTACATAATGCATG
154454 ACTTTATTAA
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
100 5 0.06
101 31 0.37
102 47 0.56
103 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (100 bp):
ATGATGCAAACTTTAACAACATGAGAGTTACATAATGCATGTCAGTATTTATGATGCATATTTAA
CTAACATGAAAGTTACATAATGCATGTCATTATTT
Found at i:154627 original size:17 final size:17
Alignment explanation
Indices: 154605--154640 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
154595 ACAAATACAT
154605 AATTAAATTAAAA-TTAA
1 AATTAAA-TAAAACTTAA
154622 AATTAAATAAAACTTAA
1 AATTAAATAAAACTTAA
154639 AA
1 AA
154641 ATATAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAATAAAACTTAA
Found at i:157903 original size:216 final size:216
Alignment explanation
Indices: 157505--158735 Score: 1344
Period size: 216 Copynumber: 5.7 Consensus size: 216
157495 TCTTGTATCA
* ** * * *
157505 TTTGGTCTCTGAATTAAAATTTTATTTATGTGAGAATTGTTTCTCTCTTGGTCCTTGACCTAAAT
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCTAAAT
* * * * *
157570 TCTTAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTTTTCAATACGAT
66 TCTGAACTTGTCAAACTTTTATAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAT
* * *
157635 CCATTCCTTTGAGCAATTTTTCGAACATTCCATGCTCAGGTAATCGCATCATTTGGTCTAAATAG
131 CCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCAGGAAATCACATCATTTGGTCTAAATAG
157700 TTTGTCATTTTGTAAACAACT
196 TTTGTCATTTTGTAAACAACT
* *
157721 TTTGGACTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCTAAAA
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCTAAAT
* * * * * * *
157786 TCCGAACTTGTCAAACTCTTATGAGTTTTTTTATTACTTCGATTCCTTAAAGTATTCAATACGAT
66 TCTGAACTTGTCAAACTTTTATAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAT
* * * * * * ** ***
157851 CCATTCATTCGAGCAATTCTCCGAACATGCCAAGATCAAAAAATCACATCATTTAACCTAAATAG
131 CCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCAGGAAATCACATCATTTGGTCTAAATAG
*
157916 TTTGTCATTTTGTAAACAAAT
196 TTTGTCATTTTGTAAACAACT
* ** * * * *
157937 TTTGGTCTTTAAATTAAAATTTTATTTATGTGAGTACTGTTTCTCTCTTGGTTATTGG-CTAAAC
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCTAAA-
* * * * * * **
158001 TTCTTAACTTGTTAAACTTTTACAAGTTCTTTTACAACTTCGGAT-CTTCTAAGTATTCAAGATT
65 TTCTGAACTTGTCAAACTTTTATAAGTTCTTTTATAACTTCGGTTCCTT-AAAGTATTCAAGACG
** * *
158065 ATCCATTCCTTTAAGCAACTTTTAGAACATTCCATGCTCAGGAAATCGA-ATCATTTGGTCTAAA
129 ATCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCAGGAAATC-ACATCATTTGGTCTAAA
* *
158129 TAGTTTTTCATTGTGTAAACAACT
193 TAGTTTGTCATTTTGTAAACAACT
** * * ** * *
158153 ACTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTTTTGCTTCTCCGCCGAACT
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCTAAAT
* * * * * *
158218 TCCGAACTTGTCAAACTTTTATGAGTTCTTTTATATCTTTGGTTCCTTAAAATATTCAAGATGGA
66 TCTGAACTTGTCAAACTTTTATAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGA-CGA
* * * * * *
158283 -CCATTCCTTCGAGCAATTTTTTGAACATTCCATGATC-GAAAAATCACACCATTCGGCCTAAAT
130 TCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCAG-GAAATCACATCATTTGGTCTAAAT
*
158346 AGTTTGTCATTTTGTAAATAACT
194 AGTTTGTCATTTTGTAAACAACT
* * * * *
158369 TTTGGTCTTTAAATTAAAAACTTATTTACGTGAGTATTGTTTCCCTCTTGGTTATTGGTC-AAAC
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCTAAA-
* *
158433 TTCTGAACTTGTCAAACTTTTATAAGTTCTTTTTTAACTTCGGTTCCTT-AAGTATTCAAGACTA
65 TTCTGAACTTGTCAAACTTTTATAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGA
* * *
158497 TCCATTCCTTCAAACAATTTTTTGAACATTCCATGCTCAGGAAATCACATCATTTGGTCTAAATA
130 TCCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCAGGAAATCACATCATTTGGTCTAAATA
* * *
158562 GTTTGCCATATTGTAATCAACT
195 GTTTGTCATTTTGTAAACAACT
* * *
158584 TTTGGTCTTTGAGTTAAAAACTTTTTTACGTGAGAATTGTTTCTCTCTTGG-TCTTTGTCCT-AA
1 TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTC-TTGGCCTAAA
* ** * * *
158647 --CT--TC-T-T-AAACTTTTACGAGTTCTTTTACAACTTCGGTT-ATTCTAAGTATTCAAGACG
65 TTCTGAACTTGTCAAACTTTTATAAGTTCTTTTATAACTTCGGTTCCTT-AAAGTATTCAAGACG
** * *
158704 ATCCATTCCTTTTAGCAACTTTTCGAGCATTC
129 ATCCATTCCTTCGAGCAATTTTTCGAACATTC
158736 TATGTGATAT
Statistics
Matches: 833, Mismatches: 167, Indels: 38
0.80 0.16 0.04
Matches are distributed among these distances:
206 2 0.00
207 28 0.03
208 40 0.05
209 1 0.00
210 1 0.00
212 2 0.00
214 2 0.00
215 148 0.18
216 601 0.72
217 8 0.01
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.42
Consensus pattern (216 bp):
TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCTAAAT
TCTGAACTTGTCAAACTTTTATAAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGAT
CCATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCAGGAAATCACATCATTTGGTCTAAATAG
TTTGTCATTTTGTAAACAACT
Found at i:158327 original size:432 final size:430
Alignment explanation
Indices: 157505--158633 Score: 1530
Period size: 432 Copynumber: 2.6 Consensus size: 430
157495 TCTTGTATCA
* * * ** *
157505 TTTGGTCTCTGAATTAAAATTTTATTTATGTGAGAATTGTTTCTCTCTTGGTCCTTGACCTAAA-
1 TTTGGTCTTTAAATTAAAATTTTATTTATGTGAGTATTGTTTCTCTCTTGGTTATTG-GCTAAAC
* * * * *
157569 TTCTTAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTTAAAGTTTTCAATACGA
65 TTCTTAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTT-CTTTAAGTATTCAAGACTA
* * * *
157634 TCCATTCCTTTGAGCAATTTTTCGAACATTCCATGCTCAGGTAATCGCATCATTTGGTCTAAATA
129 TCCATTCCTTTAAGCAATTTTTAGAACATTCCATGCTCAGGAAATCGAATCATTTGGTCTAAATA
*
157699 GTTTGTCATTTTGTAAACAACTTTTGGACTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
194 GTTTGTCA-TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
* ** * *
157764 TCTCTTGGTTCTTGGCCTAAAATCCGAACTTGTCAAACTCTTATGAGTTTTTTTATTACTTCGAT
258 TCTCTTGCTTCTCCGCCGAAAATCCGAACTTGTCAAACTCTTATGAGTTCTTTTATTACTTCGAT
* *
157829 TCCTTAAAGTATTCAATACGATCCATTCATTCGAGCAATTCTCCGAACATGCCAAGATCAAAAAA
323 TCCTTAAAATATTCAAGACGATCCATTCATTCGAGCAATTCTCCGAACATGCCAAGATCAAAAAA
* *
157894 TCACATCATTTAACCTAAATAGTTTGTCATTTTGTAAACAAAT
388 TCACACCATTCAACCTAAATAGTTTGTCATTTTGTAAACAAAT
*
157937 TTTGGTCTTTAAATTAAAATTTTATTTATGTGAGTACTGTTTCTCTCTTGGTTATTGGCTAAACT
1 TTTGGTCTTTAAATTAAAATTTTATTTATGTGAGTATTGTTTCTCTCTTGGTTATTGGCTAAACT
* * * *
158002 TCTTAACTTGTTAAACTTTTACAAGTTCTTTTACAACTTCGGATCTTCTAAGTATTCAAGATTAT
66 TCTTAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCTT-TAAGTATTCAAGACTAT
*
158067 CCATTCCTTTAAGCAACTTTTAGAACATTCCATGCTCAGGAAATCGAATCATTTGGTCTAAATAG
130 CCATTCCTTTAAGCAATTTTTAGAACATTCCATGCTCAGGAAATCGAATCATTTGGTCTAAATAG
* **
158132 TTTTTCATTGTGTAAACAACTACTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCT
195 TTTGTCATT-TGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCT
* ** * * *
158197 CTTTTGCTTCTCCGCCGAACTTCCGAACTTGTCAAACTTTTATGAGTTCTTTTA-TATCTTTGGT
259 CTCTTGCTTCTCCGCCGAAAATCCGAACTTGTCAAACTCTTATGAGTTCTTTTATTA-CTTCGAT
* * * ** * * *
158261 TCCTTAAAATATTCAAGATGGA-CCATTCCTTCGAGCAATTTTTTGAACATTCCATGATCGAAAA
323 TCCTTAAAATATTCAAGA-CGATCCATTCATTCGAGCAATTCTCCGAACATGCCAAGATCAAAAA
** * *
158325 ATCACACCATTCGGCCTAAATAGTTTGTCATTTTGTAAATAACT
387 ATCACACCATTCAACCTAAATAGTTTGTCATTTTGTAAACAAAT
** * *
158369 TTTGGTCTTTAAATTAAAAACTTATTTACGTGAGTATTGTTTCCCTCTTGGTTATTGG-TCAAAC
1 TTTGGTCTTTAAATTAAAATTTTATTTATGTGAGTATTGTTTCTCTCTTGGTTATTGGCT-AAAC
* * * *
158433 TTCTGAACTTGTCAAACTTTTATAAGTTCTTTTTTAACTTCGGTTCCTTAAGTATTCAAGACTAT
65 TTCTTAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCTTTAAGTATTCAAGACTAT
* * *
158498 CCATTCCTTCAAACAATTTTTTGAACATTCCATGCTCAGGAAATC-ACATCATTTGGTCTAAATA
130 CCATTCCTTTAAGCAATTTTTAGAACATTCCATGCTCAGGAAATCGA-ATCATTTGGTCTAAATA
* * * *
158562 GTTTGCCATATTGTAATCAACTTTTGGTCTTTGAGTTAAAAACTTTTTTACGTGAGAATTGTTTC
194 GTTTGTCAT-TTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC
158627 TCTCTTG
258 TCTCTTG
158634 GTCTTTGTCC
Statistics
Matches: 612, Mismatches: 77, Indels: 17
0.87 0.11 0.02
Matches are distributed among these distances:
430 1 0.00
431 149 0.24
432 460 0.75
433 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.42
Consensus pattern (430 bp):
TTTGGTCTTTAAATTAAAATTTTATTTATGTGAGTATTGTTTCTCTCTTGGTTATTGGCTAAACT
TCTTAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCTTTAAGTATTCAAGACTATC
CATTCCTTTAAGCAATTTTTAGAACATTCCATGCTCAGGAAATCGAATCATTTGGTCTAAATAGT
TTGTCATTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
CTTGCTTCTCCGCCGAAAATCCGAACTTGTCAAACTCTTATGAGTTCTTTTATTACTTCGATTCC
TTAAAATATTCAAGACGATCCATTCATTCGAGCAATTCTCCGAACATGCCAAGATCAAAAAATCA
CACCATTCAACCTAAATAGTTTGTCATTTTGTAAACAAAT
Done.