Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009586.1 Kokia drynarioides strain JFW-HI SEQ_124300, 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: 123302
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:13765 original size:18 final size:19
Alignment explanation
Indices: 13737--13774 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
13727 ATCTTTTTGC
*
13737 TTTTCAAAATTAAATTTTA
1 TTTTCAAAATTAAAATTTA
13756 TTTT-AAAATTAAAATTTA
1 TTTTCAAAATTAAAATTTA
13774 T
1 T
13775 ATTATTATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTCAAAATTAAAATTTA
Found at i:13770 original size:19 final size:20
Alignment explanation
Indices: 13737--13777 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
13727 ATCTTTTTGC
13737 TTTTCAAAATTAAATTT-TA
1 TTTTCAAAATTAAATTTATA
13756 TTTT-AAAATTAAAATTTATA
1 TTTTCAAAATT-AAATTTATA
13776 TT
1 TT
13778 ATTATAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 10 0.50
20 4 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTAAATTTATA
Found at i:14125 original size:26 final size:26
Alignment explanation
Indices: 14076--14126 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
14066 ATAATTTTCA
* *
14076 ATCAAAAAAAGAAAAAGTAGTCCAAT
1 ATCAAAAAAAGAAAAAGCAATCCAAT
14102 ATCAACAAAAA-AAAAAGCAATCCAA
1 ATCAA-AAAAAGAAAAAGCAATCCAA
14127 AAGCAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.65, C:0.16, G:0.08, T:0.12
Consensus pattern (26 bp):
ATCAAAAAAAGAAAAAGCAATCCAAT
Found at i:14587 original size:3 final size:3
Alignment explanation
Indices: 14579--14604 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
14569 TTACGATAAT
14579 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
14605 GGGGTTGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:14885 original size:15 final size:14
Alignment explanation
Indices: 14849--14888 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
14839 TTGTATATTG
14849 AATTTAAATTTTAT
1 AATTTAAATTTTAT
*
14863 ATACTTAAATTTTAAT
1 A-ATTTAAATTTT-AT
14879 AATTTAAATT
1 AATTTAAATT
14889 ATGAATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 1 0.05
15 18 0.82
16 3 0.14
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTAAATTTTAT
Found at i:19783 original size:36 final size:36
Alignment explanation
Indices: 19713--19833 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
19703 TGGCCTTATG
* **
19713 CTCTAATCGAGACATAAGCACTTCCTTATTATTACA
1 CTCTAATCGAGACATAAGCAATTCCTTAGCATTACA
** *
19749 CTCTAATCGAGACATAAGCAATTATTTAGCATTACG
1 CTCTAATCGAGACATAAGCAATTCCTTAGCATTACA
* * *
19785 CTCTAA-CTGAGACGTAAG-AACTTCCATAGCAATACA
1 CTCTAATC-GAGACATAAGCAA-TTCCTTAGCATTACA
*
19821 CTCTAACCGAGAC
1 CTCTAATCGAGAC
19834 GTATGCAAAC
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
35 3 0.04
36 66 0.94
37 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (36 bp):
CTCTAATCGAGACATAAGCAATTCCTTAGCATTACA
Found at i:35264 original size:18 final size:18
Alignment explanation
Indices: 35227--35266 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
35217 GAGGAGAGAG
*
35227 ATTAATTATTTTATATAA
1 ATTAATTATTTTATAAAA
35245 ATTAATTTATTTTA-AAAA
1 ATTAA-TTATTTTATAAAA
35263 ATTA
1 ATTA
35267 TATATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAATTATTTTATAAAA
Found at i:39788 original size:16 final size:16
Alignment explanation
Indices: 39767--39906 Score: 73
Period size: 16 Copynumber: 7.8 Consensus size: 16
39757 ATCTAAAATT
39767 CAGGCTATGTGCCTAG
1 CAGGCTATGTGCCTAG
* *
39783 CAGGCTTTGTGCCGGTGTATT
1 CAGGCTATGTGCC----TA-G
39804 CAGGCTATGTGCCTAG
1 CAGGCTATGTGCCTAG
* *
39820 CAGGCTTTGTGCCGGTGTATT
1 CAGGCTATGTGCC----TA-G
39841 CAGGCTATGTGCCTAG
1 CAGGCTATGTGCCTAG
* * *
39857 CAAGCTTTGTGCCAGTGTATT
1 CAGGCTATGTGCC----TA-G
39878 CAGGCTATGTGCCTAG
1 CAGGCTATGTGCCTAG
*
39894 CAGGCTTTGTGCC
1 CAGGCTATGTGCC
39907 GGTGTATTCG
Statistics
Matches: 94, Mismatches: 15, Indels: 30
0.68 0.11 0.22
Matches are distributed among these distances:
16 47 0.50
17 6 0.06
20 6 0.06
21 35 0.37
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (16 bp):
CAGGCTATGTGCCTAG
Found at i:39809 original size:21 final size:20
Alignment explanation
Indices: 39783--39920 Score: 84
Period size: 21 Copynumber: 7.3 Consensus size: 20
39773 ATGTGCCTAG
39783 CAGGCTTTGTGCCGGTGTATT
1 CAGGCTTTGTGCC-GTGTATT
* *
39804 CAGGCTATGTGCC---TA-G
1 CAGGCTTTGTGCCGTGTATT
39820 CAGGCTTTGTGCCGGTGTATT
1 CAGGCTTTGTGCC-GTGTATT
* *
39841 CAGGCTATGTGCC---TA-G
1 CAGGCTTTGTGCCGTGTATT
*
39857 CAAGCTTTGTGCCAGTGTATT
1 CAGGCTTTGTGCC-GTGTATT
* *
39878 CAGGCTATGTGCC---TA-G
1 CAGGCTTTGTGCCGTGTATT
39894 CAGGCTTTGTGCCGGTGTATT
1 CAGGCTTTGTGCC-GTGTATT
*
39915 CGGGCT
1 CAGGCT
39921 ATATGCCTAG
Statistics
Matches: 87, Mismatches: 15, Indels: 30
0.66 0.11 0.23
Matches are distributed among these distances:
16 35 0.40
17 6 0.07
20 6 0.07
21 40 0.46
ACGTcount: A:0.14, C:0.22, G:0.32, T:0.33
Consensus pattern (20 bp):
CAGGCTTTGTGCCGTGTATT
Found at i:39814 original size:37 final size:37
Alignment explanation
Indices: 39764--39943 Score: 317
Period size: 37 Copynumber: 4.9 Consensus size: 37
39754 TATATCTAAA
39764 ATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
1 ATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
39801 ATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
1 ATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
* *
39838 ATTCAGGCTATGTGCCTAGCAAGCTTTGTGCCAGTGT
1 ATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
39875 ATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
1 ATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
* *
39912 ATTCGGGCTATATGCCTAGCA-GCTTTGTGCCG
1 ATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCG
39944 ATGATCCAAG
Statistics
Matches: 137, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 11 0.08
37 126 0.92
ACGTcount: A:0.15, C:0.22, G:0.31, T:0.32
Consensus pattern (37 bp):
ATTCAGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
Found at i:41430 original size:53 final size:53
Alignment explanation
Indices: 41367--41556 Score: 281
Period size: 53 Copynumber: 3.6 Consensus size: 53
41357 AATGCAAAAA
41367 GGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGGATTAAG
1 GGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGGATTAAG
* * * **
41420 GGTCCGATGACTCTGTATCATCGTAAGTTATATGAATCCTAACACGGATTAAG
1 GGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGGATTAAG
* * * *
41473 GGTCCGATGACTCTATGTCATTATGAGTTATATGAATCCTATTACAGATTAAA
1 GGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGGATTAAG
* *
41526 GGTCCGATGACTTTGTGTCATCGTGAGTTAT
1 GGTCCGATGACTCTGTGTCATCATGAGTTAT
41557 CAAATGTGAA
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 119 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (53 bp):
GGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATTACGGATTAAG
Found at i:54323 original size:53 final size:53
Alignment explanation
Indices: 54238--54478 Score: 311
Period size: 53 Copynumber: 4.5 Consensus size: 53
54228 ATGCAAAAAA
* * * ** *
54238 TCCGATGACTTTGTGTCATCGTGAGTTTTATGAATCCTATTACAGATTAAGGG
1 TCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTAACACAGATTAAAGG
* * * * *
54291 TCTGATGACTCTGTGTCATCGTGAGTTATATGAAACCTAACACGGATTAAGGG
1 TCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTAACACAGATTAAAGG
* *
54344 TCCGATGACTCTATGTCATCATGAGTTATATGAATCCTAACACAGAATAAAGG
1 TCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTAACACAGATTAAAGG
* ** *
54397 TCCGATGACTCTATGTCATCATGAGTTATATGAATCCTATTACGGATTAAAGG
1 TCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTAACACAGATTAAAGG
* *
54450 TTCGATGACTCTGTGTTATCATGAGTTAT
1 TCCGATGACTCTGTGTCATCATGAGTTAT
54479 CAAATGTGAA
Statistics
Matches: 167, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 167 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (53 bp):
TCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTAACACAGATTAAAGG
Found at i:55196 original size:21 final size:21
Alignment explanation
Indices: 55170--55224 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
55160 TACAAGTAAT
* *
55170 ACTTGTTTCAGTAGAAGAGTC
1 ACTTGTATCAGTAGAACAGTC
* *
55191 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCAGTAGAACAGTC
55212 ACTTGTATCAGTA
1 ACTTGTATCAGTA
55225 AAAGTTTGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (21 bp):
ACTTGTATCAGTAGAACAGTC
Found at i:59547 original size:20 final size:19
Alignment explanation
Indices: 59492--59557 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
59482 CAATTTAGTG
* *
59492 TCGATACTGATTTAAAATTA
1 TCGATACT-TTTTAAAAATA
* *
59512 TCAATACGTTTATAAAAATA
1 TCGATAC-TTTTTAAAAATA
59532 TCGATACTCTTTT-AAAATA
1 TCGATACT-TTTTAAAAATA
*
59551 TTGATAC
1 TCGATAC
59558 CACGGGCTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 13 0.35
20 23 0.62
21 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (19 bp):
TCGATACTTTTTAAAAATA
Found at i:62266 original size:11 final size:11
Alignment explanation
Indices: 62228--62266 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
62218 TTAAATAGCA
62228 TAAAATAAAAG
1 TAAAATAAAAG
62239 ATAAAATAAACAG
1 -TAAAATAAA-AG
62252 -AAAATAAAAG
1 TAAAATAAAAG
62262 TAAAA
1 TAAAA
62267 AGTTAAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 12 0.48
12 9 0.36
13 2 0.08
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (11 bp):
TAAAATAAAAG
Found at i:64062 original size:22 final size:23
Alignment explanation
Indices: 64029--64071 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
64019 ATTCACATGT
64029 TTTCTTACTCATAATTCTTTTTG
1 TTTCTTACTCATAATTCTTTTTG
**
64052 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATAATTCTTTT
64072 CTTTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTCTTACTCATAATTCTTTTTG
Found at i:67609 original size:12 final size:13
Alignment explanation
Indices: 67566--67610 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
67556 GGTTTTTAAT
67566 AGCATAAAATAAA
1 AGCATAAAATAAA
67579 AG-ATAAAAT-AA
1 AGCATAAAATAAA
*
67590 A-CAGAAAATAAA
1 AGCATAAAATAAA
67602 AGCA-AAAAT
1 AGCATAAAAT
67611 TTGAGATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 9 0.32
12 15 0.54
13 4 0.14
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.13
Consensus pattern (13 bp):
AGCATAAAATAAA
Found at i:73300 original size:23 final size:23
Alignment explanation
Indices: 73272--73670 Score: 525
Period size: 23 Copynumber: 17.3 Consensus size: 23
73262 ATTATATCTA
*
73272 TGCTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
73295 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
73318 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
73341 TGATTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
73364 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
73387 TGCTCAAATATTAATATCATTTG
1 TGCTTAAATATTAATGTGATTTG
*
73410 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
73433 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * * *
73456 TTCTCAAATATTAATGTGGTTTA
1 TGCTTAAATATTAATGTGATTTG
*
73479 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
73502 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
73525 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
73548 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
73571 TGCTCAAATATTAATG-CAGTTTG
1 TGCTTAAATATTAATGTGA-TTTG
*
73594 -GCCTTAAATATTAATATGATTTG
1 TG-CTTAAATATTAATGTGATTTG
*
73617 TG-TTGAAATATTAATGTGATTTA
1 TGCTT-AAATATTAATGTGATTTG
*
73640 TGCTTAAATATTAATGTCATTTG
1 TGCTTAAATATTAATGTGATTTG
73663 TGCTTAAA
1 TGCTTAAA
73671 GAATTAAGAT
Statistics
Matches: 330, Mismatches: 40, Indels: 12
0.86 0.10 0.03
Matches are distributed among these distances:
22 4 0.01
23 322 0.98
24 4 0.01
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:74400 original size:20 final size:21
Alignment explanation
Indices: 74355--74405 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
74345 AGAACTTCGA
**
74355 GTATCGATACCTGCTAAAAGG
1 GTATCGATACCTAATAAAAGG
74376 GTATCGATACCTAATAAAA-G
1 GTATCGATACCTAATAAAAGG
*
74396 GTATCAATAC
1 GTATCGATAC
74406 TTTTTGTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (21 bp):
GTATCGATACCTAATAAAAGG
Found at i:81358 original size:25 final size:25
Alignment explanation
Indices: 81322--81457 Score: 139
Period size: 25 Copynumber: 5.4 Consensus size: 25
81312 ACCAAATATT
* * * *
81322 AGGCTTTTTGCTTATGTTACCTTTC
1 AGGCTTTGTGCTGATGTTATCTATC
* *
81347 AGGCTTTGTGCTGGTGTTATCTATT
1 AGGCTTTGTGCTGATGTTATCTATC
* * * *
81372 AGGCTTTTTGATGGTTTTATCTATC
1 AGGCTTTGTGCTGATGTTATCTATC
*
81397 AGGCTTTGTG-TCAGTGTTATCTATC
1 AGGCTTTGTGCTGA-TGTTATCTATC
*
81422 AGGCTTTGTGCCGATGTTATCTATC
1 AGGCTTTGTGCTGATGTTATCTATC
*
81447 AAGCTTTGTGC
1 AGGCTTTGTGC
81458 CGGTGTTACC
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
24 1 0.01
25 90 0.98
26 1 0.01
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46
Consensus pattern (25 bp):
AGGCTTTGTGCTGATGTTATCTATC
Found at i:81399 original size:50 final size:50
Alignment explanation
Indices: 81318--81478 Score: 182
Period size: 50 Copynumber: 3.2 Consensus size: 50
81308 TGTTACCAAA
* * *
81318 TATTAGGCTTTTTGCTTATGTTACCTTTCAGGCTTTGTGCTGGTGTTATC
1 TATTAGGCTTTTTGCTGATGTTATCTATCAGGCTTTGTGCTGGTGTTATC
* * * *
81368 TATTAGGCTTTTTGATGGTTTTATCTATCAGGCTTTGTG-TCAGTGTTATC
1 TATTAGGCTTTTTGCTGATGTTATCTATCAGGCTTTGTGCT-GGTGTTATC
* * * * * *
81418 TATCAGGCTTTGTGCCGATGTTATCTATCAAGCTTTGTGCCGGTGTTACC
1 TATTAGGCTTTTTGCTGATGTTATCTATCAGGCTTTGTGCTGGTGTTATC
81468 TATTAGG-TTTT
1 TATTAGGCTTTT
81479 GAGACAATGA
Statistics
Matches: 90, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
49 4 0.04
50 86 0.96
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (50 bp):
TATTAGGCTTTTTGCTGATGTTATCTATCAGGCTTTGTGCTGGTGTTATC
Found at i:81458 original size:25 final size:25
Alignment explanation
Indices: 81335--81479 Score: 130
Period size: 25 Copynumber: 5.8 Consensus size: 25
81325 CTTTTTGCTT
* * *
81335 ATGTTACCTTTCAGGCTTTGTGCTG
1 ATGTTATCTATCAGGCTTTGTGCCG
* * * **
81360 GTGTTATCTATTAGGCTTTTTGATG
1 ATGTTATCTATCAGGCTTTGTGCCG
* * *
81385 GTTTTATCTATCAGGCTTTGTGTC-
1 ATGTTATCTATCAGGCTTTGTGCCG
81409 AGTGTTATCTATCAGGCTTTGTGCCG
1 A-TGTTATCTATCAGGCTTTGTGCCG
*
81435 ATGTTATCTATCAAGCTTTGTGCCG
1 ATGTTATCTATCAGGCTTTGTGCCG
* * * *
81460 GTGTTACCTATTAGGTTTTG
1 ATGTTATCTATCAGGCTTTG
81480 AGACAATGAT
Statistics
Matches: 98, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
25 97 0.99
26 1 0.01
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46
Consensus pattern (25 bp):
ATGTTATCTATCAGGCTTTGTGCCG
Found at i:90807 original size:15 final size:17
Alignment explanation
Indices: 90787--90826 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
90777 AATTTTTTTA
90787 TTTAATCACTT-AAT-T
1 TTTAATCACTTAAATAT
90802 TTTAAT-A-TTAAATAT
1 TTTAATCACTTAAATAT
90817 TTTAATCACT
1 TTTAATCACT
90827 CTAACTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.10
14 4 0.19
15 13 0.62
16 1 0.05
17 1 0.05
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAATCACTTAAATAT
Found at i:91436 original size:15 final size:15
Alignment explanation
Indices: 91416--91445 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
91406 TAAATTTAAA
*
91416 TTTAATTTTTTATAT
1 TTTAATTTTTAATAT
91431 TTTAATTTTTAATAT
1 TTTAATTTTTAATAT
91446 AATTTAGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTAATAT
Found at i:92413 original size:25 final size:26
Alignment explanation
Indices: 92378--92426 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
92368 TTCTATTATT
92378 ATTTATATTTAATTG-TTTATTTTGAC
1 ATTTATATTT-ATTGATTTATTTTGAC
*
92404 ATTTA-ATTTATTGATTTTTTTTG
1 ATTTATATTTATTGATTTATTTTG
92427 TTTATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 12 0.57
26 5 0.24
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.65
Consensus pattern (26 bp):
ATTTATATTTATTGATTTATTTTGAC
Found at i:92580 original size:24 final size:25
Alignment explanation
Indices: 92552--92604 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
92542 CTTGTTATTA
*
92552 TTTATTTTCATGT-CATTTATTGTT
1 TTTATTTTAATGTACATTTATTGTT
*
92576 TTTA-TTTAATTTACATTTATTGTT
1 TTTATTTTAATGTACATTTATTGTT
*
92600 ATTAT
1 TTTAT
92605 CTTATTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTATTTTAATGTACATTTATTGTT
Found at i:92581 original size:102 final size:101
Alignment explanation
Indices: 92373--92563 Score: 244
Period size: 106 Copynumber: 1.8 Consensus size: 101
92363 TTCTTTTCTA
92373 TTATTATTTATATTTAATTGTTTATTTTGACATTTAATTTATTGATTTTTTTTGTTTATTTATTT
1 TTATTATTTATATTTAATTGTTTATTTTGACATTTAATTTATTGATTTTTTTTGTTTATTTATTT
92438 ATTTGTCATTTATTTTCATGCTTAATCTCAATTATTT
66 ATTTGTCATTTATTTTCATGC-TAATCTCAATTATTT
* ** *
92475 TTATTGTTTATATTTGTTTGTTTATTTT-AGCATTTAATTTTTATTTTTATTTTTTTTGTTTATT
1 TTATTATTTATATTTAATTGTTTATTTTGA-CATTTAA--TTTA--TTGATTTTTTTTGTTTATT
*
92539 TATCTTGTTAT-T-ATTTATTTTCATG
61 TAT-TTATT-TGTCATTTATTTTCATG
92564 TCATTTATTG
Statistics
Matches: 77, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
101 1 0.01
102 32 0.42
104 4 0.05
106 34 0.44
107 5 0.06
108 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.68
Consensus pattern (101 bp):
TTATTATTTATATTTAATTGTTTATTTTGACATTTAATTTATTGATTTTTTTTGTTTATTTATTT
ATTTGTCATTTATTTTCATGCTAATCTCAATTATTT
Found at i:92625 original size:16 final size:14
Alignment explanation
Indices: 92514--92627 Score: 61
Period size: 15 Copynumber: 8.5 Consensus size: 14
92504 GCATTTAATT
92514 TTTATTT-TTATT-
1 TTTATTTGTTATTA
92526 TTT-TTTG-T-TTA
1 TTTATTTGTTATTA
92537 TTTATCTTGTTATTA
1 TTTAT-TTGTTATTA
*
92552 TTTATTT-TCATGTCA
1 TTTATTTGTTAT-T-A
*
92567 TTTA-TTGTTTTTA
1 TTTATTTGTTATTA
* *
92580 TTTA-AT-TTA-CA
1 TTTATTTGTTATTA
92591 TTTA-TTGTTATTA
1 TTTATTTGTTATTA
92604 TCTTATTTGTTTATTTA
1 T-TTATTTG-TTA-TTA
92621 TTTATTT
1 TTTATTT
92628 ATCATTAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
10 2 0.03
11 13 0.16
12 9 0.11
13 14 0.18
14 10 0.13
15 18 0.23
16 9 0.11
17 4 0.05
ACGTcount: A:0.19, C:0.04, G:0.05, T:0.71
Consensus pattern (14 bp):
TTTATTTGTTATTA
Found at i:101668 original size:49 final size:49
Alignment explanation
Indices: 101598--102555 Score: 787
Period size: 49 Copynumber: 19.5 Consensus size: 49
101588 CATAGAGTTT
* * * * *
101598 GAAGAAGGATGGGTTGAAGCCGCAATGGCGGACCTAACATCC-TAAAATT
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACA-CCTTAAAATC
* * * *
101647 GAAGAGGGGA-AGGTTGAAGCCGCAACGGCAGAGCTTACACCTTAAAA-C
1 GAAGA-GGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * ** * *
101695 TGAAGAGGGATAGGTTGAAGTCGTAACGACAAAGCTAACACCTTAAAACC
1 -GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * ** * * * *
101745 AAAGAGGGAAAGATTAAAGTTGTAACGACGGATCTTAGACCTTAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * ** **
101794 GAAAAGTGATAGGTTGAAGCCATAACGACGGACCTAACACCCAAAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACA-CCTTAAAATC
* * * * * * * *
101844 AAAGAGGGAAAGATTGAAGTCGCAACGAAGGATCTTACACCTTAAAATT
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * *
101893 GAAGAGGGATAGGTTGAAGTCACAACGACAGACATAACACCTTAAAATT
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * ** * *
101942 GAAGAGGGATAGATTGAAGCTGCAACGGTGGATCTAACACCTTAAAACC
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * * * ** *
101991 AAAAAGGAAAAGGTTAAAGCCGTAACGGTGGACCTTACACCTTAAAA-C
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* ** *
102039 TGAATAGGGATAGGTTGAAG-CGCAACGATAGACCTAACACCTAAAAATC
1 -GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* ** * * * *
102088 GAAGAGGGAAAGACTGAAGTCGCAACGGCGGATCTTACACCTTAAAA-C
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * *
102136 TGAAGAAGGATAGGTTAAAGCCGCAACGGCAGACCTAACACCTAAAAATC
1 -GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* ** * * * * * *
102186 GAAGAGGGAAAGACTGAAGTCGCAACGGCGAATCTTACACCTTAAAATT
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
*
102235 GAAGAGGGATAGGTTGAAGCCACAACGACGGACCTAACACCTTAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* *
102284 GAAGAGGGATAGGTTGAAGCCGTAACGATGGACCTAACACCTTAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * *
102333 GAAGAGGGATAGATTGAAGCTGCAACGACAGATCTAACACCTTAAAATT
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * * *
102382 GAAGAGGGATAAGTTGAAGCCGTAATGGCAGACCTAACACCCTAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * * * * * *
102431 GAAGAGGGAAAGATTGAAGTCGCAACGATGAATCTTACACCTTAAAACC
1 GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
* * * *
102480 AAAGAGGGATAGGTTGAAGGCG-AGACGACGAACCTAACACCTTAAAACC
1 GAAGAGGGATAGGTTGAAGCCGCA-ACGACGGACCTAACACCTTAAAATC
* *
102529 AAAGAGGGAATAGATTGAAGCCGCAAC
1 GAAGAGGG-ATAGGTTGAAGCCGCAAC
102556 AGCGAATCTT
Statistics
Matches: 720, Mismatches: 175, Indels: 27
0.78 0.19 0.03
Matches are distributed among these distances:
48 46 0.06
49 618 0.86
50 55 0.08
51 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (49 bp):
GAAGAGGGATAGGTTGAAGCCGCAACGACGGACCTAACACCTTAAAATC
Found at i:103482 original size:25 final size:26
Alignment explanation
Indices: 103435--103483 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
103425 TTTTATTATT
103435 ATTTATATTTAGTTGTTTATTTTGAC
1 ATTTATATTTAGTTGTTTATTTTGAC
*
103461 ATTTA-ATTTA-TTGATTTCTTTTG
1 ATTTATATTTAGTTG-TTTATTTTG
103484 TTTATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.22, C:0.04, G:0.10, T:0.63
Consensus pattern (26 bp):
ATTTATATTTAGTTGTTTATTTTGAC
Found at i:103637 original size:29 final size:27
Alignment explanation
Indices: 103598--103672 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 27
103588 TTTATTTATC
*
103598 TTGTTA-TTATTTATTTTCATGCCGTTTA
1 TTGTTATTTATTTATTTTCAT--CATTTA
* *
103626 TTGTTTTTTATTTAATTT-A-CATTTA
1 TTGTTATTTATTTATTTTCATCATTTA
103651 TTGTTATTTATTTATTTATCAT
1 TTGTTATTTATTTATTT-TCAT
103673 TAAATTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
25 20 0.53
26 1 0.03
27 1 0.03
28 6 0.16
29 10 0.26
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (27 bp):
TTGTTATTTATTTATTTTCATCATTTA
Found at i:103650 original size:25 final size:25
Alignment explanation
Indices: 103622--103673 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
103612 TTTCATGCCG
*
103622 TTTATTGTTTTTTATTTAATTTA-CA
1 TTTATTGTTATTTATTT-ATTTATCA
103647 TTTATTGTTATTTATTTATTTATCA
1 TTTATTGTTATTTATTTATTTATCA
103672 TT
1 TT
103674 AAATTTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTATTGTTATTTATTTATTTATCA
Found at i:103992 original size:23 final size:24
Alignment explanation
Indices: 103963--104018 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
103953 TATTTAAAAC
* *
103963 TTTAATTATATCTTTATTGTGTT-A
1 TTTAATTATAT-TTGATTGTCTTCA
103987 -TTAATTATATTTGATTGTCTTCA
1 TTTAATTATATTTGATTGTCTTCA
104010 TTTAATTAT
1 TTTAATTAT
104019 TTATATTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.32
23 11 0.39
24 8 0.29
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (24 bp):
TTTAATTATATTTGATTGTCTTCA
Found at i:108708 original size:3 final size:3
Alignment explanation
Indices: 108700--108757 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
108690 TCTCCATTTC
108700 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
108748 TCT TCT TCT T
1 TCT TCT TCT T
108758 AAATTGGGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:110874 original size:15 final size:15
Alignment explanation
Indices: 110856--110896 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
110846 CAGCTCACAC
*
110856 ATAAACAATTCGCAT
1 ATAAACAATTCGCAG
* *
110871 ATAAAGAGTTCGCAG
1 ATAAACAATTCGCAG
110886 ATAAACAATTC
1 ATAAACAATTC
110897 AATCTAGTGG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.24
Consensus pattern (15 bp):
ATAAACAATTCGCAG
Found at i:112106 original size:38 final size:38
Alignment explanation
Indices: 112054--112353 Score: 189
Period size: 38 Copynumber: 8.0 Consensus size: 38
112044 CTTTGTGTCG
*
112054 GTGATATCGAGCTTTATGCCTAGCAAGCCTTCGTGCCA
1 GTGATATCGGGCTTTATGCCTAGCAAGCCTTCGTGCCA
* * * *
112092 GTGGTATCGGGCTTTATGCCTAGTAGGCGTTCGTGCCA
1 GTGATATCGGGCTTTATGCCTAGCAAGCCTTCGTGCCA
* * * * * * * ***
112130 ATGTTACCAGGCTATGTGCCTAGC-AGCCTTCATGTTG
1 GTGATATCGGGCTTTATGCCTAGCAAGCCTTCGTGCCA
* * **
112167 GTGATATCGGGCTTTATGCCTAGC-AGGCTTTGTGATA
1 GTGATATCGGGCTTTATGCCTAGCAAGCCTTCGTGCCA
* * ***
112204 GTGATATCGGGCTTTATGCCTA-AAAGGCCTTTGTGTTG
1 GTGATATCGGGCTTTATGCCTAGCAA-GCCTTCGTGCCA
* * * * * *
112242 GAGTTATTGGGCTATGTGCCTAGC-AGACTTCGTGCC-
1 GTGATATCGGGCTTTATGCCTAGCAAGCCTTCGTGCCA
* * * **
112278 GATGATATCGAGCTTTATACCTAGCAAGCCTTTGTTTC-
1 G-TGATATCGGGCTTTATGCCTAGCAAGCCTTCGTGCCA
* * *
112316 GATGATATCGAGTTTTATGCCTAGCAAGCCTTTGTGCC
1 G-TGATATCGGGCTTTATGCCTAGCAAGCCTTCGTGCC
112354 GATGTGATCG
Statistics
Matches: 199, Mismatches: 58, Indels: 10
0.75 0.22 0.04
Matches are distributed among these distances:
36 1 0.01
37 79 0.40
38 119 0.60
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (38 bp):
GTGATATCGGGCTTTATGCCTAGCAAGCCTTCGTGCCA
Found at i:112264 original size:112 final size:113
Alignment explanation
Indices: 112052--112358 Score: 307
Period size: 112 Copynumber: 2.7 Consensus size: 113
112042 GGCTTTGTGT
* ** * **
112052 CGGTGATATCGAGCTTTATGCCTAGCAAGCCTTCGTGCCAGTGGTATCGGGCTTTATGCCTAGTA
1 CGGTGATATCGAGCTTTATGCCTAGCAAGCCTTTGTGATAGTGATATCGGGCTTTATGCCTAAAA
* * * *
112117 GGCGTTCGTGCCAATGTTACCAGGCTATGTGCCTAGCAGCCTTCATGT
66 GGCCTTTGTGCCAATGTTACCAGGCTATGTGCCTAGCAGACTTCATGC
* * *
112165 TGGTGATATCGGGCTTTATGCCTAGC-AGGCTTTGTGATAGTGATATCGGGCTTTATGCCTAAAA
1 CGGTGATATCGAGCTTTATGCCTAGCAAGCCTTTGTGATAGTGATATCGGGCTTTATGCCTAAAA
*** *** *
112229 GGCCTTTGTGTTGGA-GTTATTGGGCTATGTGCCTAGCAGACTTCGTGC
66 GGCCTTTGTG-CCAATGTTACCAGGCTATGTGCCTAGCAGACTTCATGC
* * * * * * *
112277 CGATGATATCGAGCTTTATACCTAGCAAGCCTTTGT-TTCGATGATATCGAGTTTTATGCCTAGC
1 CGGTGATATCGAGCTTTATGCCTAGCAAGCCTTTGTGATAG-TGATATCGGGCTTTATGCCTA-A
*
112341 AA-GCCTTTGTGCCGATGT
64 AAGGCCTTTGTGCCAATGT
112359 GATCGGCATT
Statistics
Matches: 157, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
112 92 0.59
113 63 0.40
114 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (113 bp):
CGGTGATATCGAGCTTTATGCCTAGCAAGCCTTTGTGATAGTGATATCGGGCTTTATGCCTAAAA
GGCCTTTGTGCCAATGTTACCAGGCTATGTGCCTAGCAGACTTCATGC
Found at i:112308 original size:150 final size:150
Alignment explanation
Indices: 111954--112351 Score: 353
Period size: 150 Copynumber: 2.7 Consensus size: 150
111944 TGTTATCACA
* * * * * *
111954 CTATGTGCCTACCAGGCTTCGTGCCGGTGATATCGAGATTTATGCCT-GTAGGCCCTCATGTTGG
1 CTATGTGCCTAGCAGGCTTCGTGCCGATGATATCGAGCTTTATGCCTAGCAAGCCTTCATGTTGG
* * * ** * *
112018 TGTTATC-ATGCTATGTGCCTATTAGGCTTTGTGTCGGTGATATCGAGCTTTATGCCTAGCAAGC
66 TGATATCGA-GCTTTATGCCTAGCAGGCTTTGTGTCAGTGATATCGAGCTTTATGCCTAGAAAGC
*
112082 CTTCGTGCCAGTGGTATCGGG
130 CTTCGTGCCAGAGGTATCGGG
* * * * * * * *
112103 CTTTATGCCTAGTAGGCGTTCGTGCCAATGTTA-CCAGGCTATGTGCCTAGC-AGCCTTCATGTT
1 CTATGTGCCTAGCAGGC-TTCGTGCCGATGATATCGA-GCTTTATGCCTAGCAAGCCTTCATGTT
* *
112166 GGTGATATCGGGCTTTATGCCTAGCAGGCTTTGTGAT-AGTGATATCGGGCTTTATGCCTA-AAA
64 GGTGATATCGAGCTTTATGCCTAGCAGGCTTTGTG-TCAGTGATATCGAGCTTTATGCCTAGAAA
* *** * *
112229 GGCCTTTGTGTTGGAGTTATTGGG
128 -GCCTTCGTGCCAGAGGTATCGGG
* *
112253 CTATGTGCCTAGCAGACTTCGTGCCGATGATATCGAGCTTTATACCTAGCAAGCCTT--TGTTTC
1 CTATGTGCCTAGCAGGCTTCGTGCCGATGATATCGAGCTTTATGCCTAGCAAGCCTTCATG-TT-
* * *
112316 GATGATATCGAGTTTTATGCCTAGCAAGCCTTTGTG
64 GGTGATATCGAGCTTTATGCCTAGC-AGGCTTTGTG
112352 CCGATGTGAT
Statistics
Matches: 194, Mismatches: 44, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
148 2 0.01
149 43 0.22
150 138 0.71
151 11 0.06
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (150 bp):
CTATGTGCCTAGCAGGCTTCGTGCCGATGATATCGAGCTTTATGCCTAGCAAGCCTTCATGTTGG
TGATATCGAGCTTTATGCCTAGCAGGCTTTGTGTCAGTGATATCGAGCTTTATGCCTAGAAAGCC
TTCGTGCCAGAGGTATCGGG
Found at i:112312 original size:75 final size:75
Alignment explanation
Indices: 111954--112309 Score: 281
Period size: 75 Copynumber: 4.8 Consensus size: 75
111944 TGTTATCACA
* * * * * * *
111954 CTATGTGCCTACCAGGCTTCGTGCCGGTGATATCGAGATTTATGCCT-GTAGGCCCTCATGTTGG
1 CTATGTGCCTAGCAGGCTTCGTGCCGATGATATCGAGCTTTATGCCTAGCAAGCCTTCGTGTTGG
**
112018 TGTTATCATG
66 TGTTATCGGG
** * * * ***
112028 CTATGTGCCTATTAGGCTTTGTGTCGGTGATATCGAGCTTTATGCCTAGCAAGCCTTCGTGCCAG
1 CTATGTGCCTAGCAGGCTTCGTGCCGATGATATCGAGCTTTATGCCTAGCAAGCCTTCGTGTTGG
*
112093 TGGTATCGGG
66 TGTTATCGGG
* * * * * * * * *
112103 CTTTATGCCTAGTAGGCGTTCGTGCCAATGTTA-CCAGGCTATGTGCCTAGC-AGCCTTCATGTT
1 CTATGTGCCTAGCAGGC-TTCGTGCCGATGATATCGA-GCTTTATGCCTAGCAAGCCTTCGTGTT
*
112166 GGTGATATCGGG
64 GGTGTTATCGGG
* * * ** * * *
112178 CTTTATGCCTAGCAGGCTTTGTG-ATAGTGATATCGGGCTTTATGCCTA-AAAGGCCTTTGTGTT
1 CTATGTGCCTAGCAGGCTTCGTGCCGA-TGATATCGAGCTTTATGCCTAGCAA-GCCTTCGTGTT
* *
112241 GGAGTTATTGGG
64 GGTGTTATCGGG
* *
112253 CTATGTGCCTAGCAGACTTCGTGCCGATGATATCGAGCTTTATACCTAGCAAGCCTT
1 CTATGTGCCTAGCAGGCTTCGTGCCGATGATATCGAGCTTTATGCCTAGCAAGCCTT
112310 TGTTTCGATG
Statistics
Matches: 218, Mismatches: 55, Indels: 17
0.75 0.19 0.06
Matches are distributed among these distances:
73 1 0.00
74 62 0.28
75 130 0.60
76 25 0.11
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (75 bp):
CTATGTGCCTAGCAGGCTTCGTGCCGATGATATCGAGCTTTATGCCTAGCAAGCCTTCGTGTTGG
TGTTATCGGG
Found at i:114089 original size:13 final size:13
Alignment explanation
Indices: 114071--114098 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
114061 TACTAGTGTT
114071 TACTCTATACATC
1 TACTCTATACATC
114084 TACTCTATACATC
1 TACTCTATACATC
114097 TA
1 TA
114099 GGAAGTACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (13 bp):
TACTCTATACATC
Found at i:115834 original size:20 final size:18
Alignment explanation
Indices: 115811--115887 Score: 69
Period size: 20 Copynumber: 4.4 Consensus size: 18
115801 CCACGTCAGT
115811 AAATTATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
115831 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
115851 AAATTA--TTAAAAT-T-
1 AAATTATTTTAAAATATA
115865 -AA-T-TTTTAAAATATA
1 AAATTATTTTAAAATATA
115880 AAATTATT
1 AAATTATT
115888 AAAATCATCA
Statistics
Matches: 48, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
12 1 0.02
13 9 0.19
14 1 0.02
15 1 0.02
16 9 0.19
17 1 0.02
18 2 0.04
20 14 0.29
21 2 0.04
22 8 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:115846 original size:13 final size:13
Alignment explanation
Indices: 115823--115876 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
115813 ATTATTTTAA
*
115823 AATTATTAAAATT
1 AATTTTTAAAATT
*
115836 ATTTTTTAAAATAT
1 AATTTTTAAAAT-T
*
115850 AAAATTATTAAAATT
1 --AATTTTTAAAATT
115865 AATTTTTAAAAT
1 AATTTTTAAAAT
115877 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 21 0.64
14 1 0.03
15 1 0.03
16 10 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTTTTAAAATT
Found at i:115862 original size:29 final size:29
Alignment explanation
Indices: 115820--115892 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
115810 TAAATTATTT
*
115820 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTAATTTTTAAAATA
115849 TAAAATTATTAAAATTAATTTTTAAAATA
1 TAAAATTATTAAAATTAATTTTTAAAATA
115878 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
115893 CATCATCATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAAATTATTAAAATTAATTTTTAAAATA
Found at i:119092 original size:22 final size:22
Alignment explanation
Indices: 119067--119123 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
119057 ACGCTTATTG
119067 TTTAGTACTGTGTATGCTTCTA
1 TTTAGTACTGTGTATGCTTCTA
* *
119089 TTTAGTACTGTGTGTGCTTCTG
1 TTTAGTACTGTGTATGCTTCTA
* *
119111 TTCAGCACTGTGT
1 TTTAGTACTGTGT
119124 GTGCCTACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.47
Consensus pattern (22 bp):
TTTAGTACTGTGTATGCTTCTA
Found at i:119168 original size:25 final size:24
Alignment explanation
Indices: 119132--119210 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 24
119122 GTGTGCCTAC
*
119132 TGTTTCCTAGCACTTATGTGCTTT
1 TGTTTCCCAGCACTTATGTGCTTT
*
119156 TGTTTCTCCAGCACTTATGTACTTCT
1 TGTTTC-CCAGCACTTATGTGCTT-T
* *
119182 AT-TTTCCCCATCACTTATGCGCTTT
1 -TGTTT-CCCAGCACTTATGTGCTTT
119207 TGTT
1 TGTT
119211 AATTACTTCG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
24 7 0.16
25 18 0.40
26 18 0.40
27 2 0.04
ACGTcount: A:0.14, C:0.25, G:0.13, T:0.48
Consensus pattern (24 bp):
TGTTTCCCAGCACTTATGTGCTTT
Found at i:119196 original size:26 final size:25
Alignment explanation
Indices: 119132--119210 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 25
119122 GTGTGCCTAC
* *
119132 TGTTT-CCTAGCACTTATGTGCTTT
1 TGTTTCCCCAGCACTTATGTACTTT
*
119156 TGTTTCTCCAGCACTTATGTACTTCT
1 TGTTTCCCCAGCACTTATGTACTT-T
* **
119182 AT-TTTCCCCATCACTTATGCGCTTT
1 -TGTTTCCCCAGCACTTATGTACTTT
119207 TGTT
1 TGTT
119211 AATTACTTCG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
24 6 0.14
25 18 0.41
26 19 0.43
27 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.13, T:0.48
Consensus pattern (25 bp):
TGTTTCCCCAGCACTTATGTACTTT
Found at i:120120 original size:75 final size:75
Alignment explanation
Indices: 120033--120438 Score: 330
Period size: 75 Copynumber: 5.4 Consensus size: 75
120023 TTAACAGATT
* * * * * *
120033 TTCGTGCTGGTGTTATCGGGCTATGTGCCTAGTAGG-CTTCATGCCGGTGATATCGAGCTTTATG
1 TTCGTGCCGGTGATATCGGGCTTTATGCCTAGCAGGCCTTCATGCCGGTGATATCGAGCTATATG
120097 CCTAGCAGGCC
66 CCTAGCAGG-C
* * * * * * * * * * * * *
120108 TTCATTCCGGTGTTATCGAGCTATGTGCTTAGCAGG-TTTCGTACCAGTGATATCGGGCTTTATG
1 TTCGTGCCGGTGATATCGGGCTTTATGCCTAGCAGGCCTTCATGCCGGTGATATCGAGCTATATG
*
120172 CCTAGTAGGCC
66 CCTAGCAGG-C
* * ** * * ** * *
120183 TTCGTGCCAGTGATATCGAGCTTTATGCCTAGCAGGCCTTTGTGTCGGTGTTATTAAGCTATGTT
1 TTCGTGCCGGTGATATCGGGCTTTATGCCTAGCAGGCCTTCATGCCGGTGATATCGAGCTATATG
*
120248 CCTAGTAGGC
66 CCTAGCAGGC
* * * *
120258 TTCGTGCCGGTGATATCAGGCTTTATGCCTAGCAGGCCTTCATGCCGGTGTTATCGGGCTATGTG
1 TTCGTGCCGGTGATATCGGGCTTTATGCCTAGCAGGCCTTCATGCCGGTGATATCGAGCTATATG
*
120323 CTTAGCAGGC
66 CCTAGCAGGC
* * * ** * * * * *
120333 TTCGTACCGATGATATCGGGCTTTATGCCTAGCAAGCCTTCATATCGATGTTATCGGGCTATTTT
1 TTCGTGCCGGTGATATCGGGCTTTATGCCTAGCAGGCCTTCATGCCGGTGATATCGAGCTATATG
*
120398 CCTAGCATGC
66 CCTAGCAGGC
** *
120408 TTCGTGCCAATGATATTGGGCTTTATGCCTA
1 TTCGTGCCGGTGATATCGGGCTTTATGCCTA
120439 CCGGTGTTAT
Statistics
Matches: 273, Mismatches: 57, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
75 248 0.91
76 25 0.09
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (75 bp):
TTCGTGCCGGTGATATCGGGCTTTATGCCTAGCAGGCCTTCATGCCGGTGATATCGAGCTATATG
CCTAGCAGGC
Found at i:120218 original size:113 final size:113
Alignment explanation
Indices: 120046--120332 Score: 362
Period size: 113 Copynumber: 2.5 Consensus size: 113
120036 GTGCTGGTGT
* *
120046 TATCGGGCTATGTGCCTAGTAGG-CTTCATGCCGGTGATATCGAGCTTTATGCCTAGCAGGCCTT
1 TATCGGGCTTTATGCCTAGTAGGCCTTCATGCCGGTGATATCGAGCTTTATGCCTAGCAGGCCTT
* * *
120110 CAT-TCCGGTGTTATCGAGCTATGTGCTTAGCAGGTTTCGTACCAGTGA
66 CATGT-CGGTGTTATCAAGCTATGTGCCTAGCAGGCTTCGTACCAGTGA
* *
120158 TATCGGGCTTTATGCCTAGTAGGCCTTCGTGCCAGTGATATCGAGCTTTATGCCTAGCAGGCCTT
1 TATCGGGCTTTATGCCTAGTAGGCCTTCATGCCGGTGATATCGAGCTTTATGCCTAGCAGGCCTT
** * * * * *
120223 TGTGTCGGTGTTATTAAGCTATGTTCCTAGTAGGCTTCGTGCCGGTGA
66 CATGTCGGTGTTATCAAGCTATGTGCCTAGCAGGCTTCGTACCAGTGA
* * * * * * *
120271 TATCAGGCTTTATGCCTAGCAGGCCTTCATGCCGGTGTTATCGGGCTATGTGCTTAGCAGGC
1 TATCGGGCTTTATGCCTAGTAGGCCTTCATGCCGGTGATATCGAGCTTTATGCCTAGCAGGC
120333 TTCGTACCGA
Statistics
Matches: 150, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
112 21 0.14
113 128 0.85
114 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (113 bp):
TATCGGGCTTTATGCCTAGTAGGCCTTCATGCCGGTGATATCGAGCTTTATGCCTAGCAGGCCTT
CATGTCGGTGTTATCAAGCTATGTGCCTAGCAGGCTTCGTACCAGTGA
Found at i:120391 original size:38 final size:38
Alignment explanation
Indices: 120043--120438 Score: 160
Period size: 38 Copynumber: 10.6 Consensus size: 38
120033 TTCGTGCTGG
* * * * * *
120043 TGTTATCGGGCTATGTGCCTAG-TAGGCTTCATGCCGG
1 TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
* * * * *
120080 TGATATCGAGCTTTATGCCTAGCAGGCCTTCATTCCGG
1 TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
* * * * ** *
120118 TGTTATCGAGCTATGTGCTTAGC-AGGTTTCGTACC-A
1 TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
* * * * *
120154 GTGATATCGGGCTTTATGCCTAGTAGGCCTTCGTGCC-A
1 -TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
* * * ** ** *
120192 GTGATATCGAGCTTTATGCCTAGCAGGCCTTTGTGTCGG
1 -TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
*** * * * * * * * *
120231 TGTTATTAAGCTATGTTCCTAG-TAGGCTTCGTGCCGG
1 TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
* * * * *
120268 TGATATCAGGCTTTATGCCTAGCAGGCCTTCATGCCGG
1 TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
* * * * *
120306 TGTTATCGGGCTATGTGCTTAGC-AGGCTTCGTACCGA
1 TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
* *
120343 TGATATCGGGCTTTATGCCTAGCAAGCCTTCATATCGA
1 TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
* * * * *
120381 TGTTATCGGGCTATT-TTCCTAGCATG-CTTCGTGCCAA
1 TGTTATCGGGCT-TTATGCCTAGCAAGCCTTCATACCGA
* *
120418 TGATATTGGGCTTTATGCCTA
1 TGTTATCGGGCTTTATGCCTA
120439 CCGGTGTTAT
Statistics
Matches: 270, Mismatches: 81, Indels: 16
0.74 0.22 0.04
Matches are distributed among these distances:
36 2 0.01
37 118 0.44
38 148 0.55
39 2 0.01
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (38 bp):
TGTTATCGGGCTTTATGCCTAGCAAGCCTTCATACCGA
Found at i:121690 original size:10 final size:10
Alignment explanation
Indices: 121675--121705 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
121665 TCTTACAATA
121675 ACACATTTAT
1 ACACATTTAT
121685 ACACATTTAT
1 ACACATTTAT
121695 ACACATTTAT
1 ACACATTTAT
121705 A
1 A
121706 GTTCACATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (10 bp):
ACACATTTAT
Done.