Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold164
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: 2248410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 15 of 15
Found at i:2203521 original size:8 final size:8
Alignment explanation
Indices: 2203508--2203535 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2203498 AACATTGGTA
2203508 TTAAAATT
1 TTAAAATT
2203516 TTAAAATT
1 TTAAAATT
2203524 TTAAAATT
1 TTAAAATT
2203532 TTAA
1 TTAA
2203536 CATGTGAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTAAAATT
Found at i:2207925 original size:36 final size:36
Alignment explanation
Indices: 2207846--2207925 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
2207836 TTATTATTTA
* **
2207846 ATAATAAAA-ATAAAATATTTTATTTAAATTTTATT
1 ATAATAAAATATAAAATATTTTATATAAATAATATT
2207881 ATAA-AAAATATATAAATATTTTA-ATAATATAATA-T
1 ATAATAAAATATA-AAATATTTTATATAA-ATAATATT
2207916 ATAATAAAAT
1 ATAATAAAAT
2207926 TAATATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 4 0.11
35 15 0.39
36 19 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (36 bp):
ATAATAAAATATAAAATATTTTATATAAATAATATT
Found at i:2212935 original size:21 final size:20
Alignment explanation
Indices: 2212911--2212952 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
2212901 ATATTTCATT
2212911 TAAAT-TTAATTATAAATAATA
1 TAAATATTAA-TATAAA-AATA
2212932 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
2212952 T
1 T
2212953 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATATTAATATAAAAATA
Found at i:2213453 original size:3 final size:3
Alignment explanation
Indices: 2213445--2213479 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2213435 AACTTTACAT
2213445 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2213480 GTTTTCCCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2214090 original size:2 final size:2
Alignment explanation
Indices: 2214083--2214155 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
2214073 AAAATAAAAT
2214083 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2214124 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2214156 AAAACACCAC
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2220302 original size:20 final size:19
Alignment explanation
Indices: 2220270--2220344 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
2220260 AAAAAGACAT
*
2220270 AATGTATCAATACATTGAA
1 AATGTATCGATACATTGAA
* *
2220289 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
2220310 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
2220330 AATGTATCGATACAT
1 AATGTATCGATACAT
2220345 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:2220315 original size:40 final size:39
Alignment explanation
Indices: 2220267--2220344 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
2220257 GGTAAAAAGA
*
2220267 CATAATGTATCAATACATTGAAGAATATATCGATACATT
1 CATAATGTATCAATACATTGAAAAATATATCGATACATT
* * *
2220306 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCAATACATTGAAAAATATATCGATACAT
2220345 CTGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (39 bp):
CATAATGTATCAATACATTGAAAAATATATCGATACATT
Found at i:2221042 original size:28 final size:28
Alignment explanation
Indices: 2220951--2222161 Score: 1416
Period size: 28 Copynumber: 42.5 Consensus size: 28
2220941 CACCGACACA
* * *
2220951 TGTGGGCTTTGAAAAGAGTTACTACTGGCT
1 TGTGGGCTTTGAAAAG-G-TGCCACTGACT
* *
2220981 TGTGAGCTTTGAAAAGAGTGTCACTGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
*
2221010 TGTGGGCTTTGAAAATGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
2221038 TGTGGGCTTTG-AAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
2221066 TGTGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* *
2221094 TATGGGCTTTGAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* * *
2221122 TGTGGGC-TTGAAAAAGTGTTCATTGACT
1 TGTGGGCTTTGAAAAGGTG-CCACTGACT
*
2221150 TGTGGGCTTTGAAAAGGTGCCACTGACA
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
2221178 TGTGGGCTTTGAAAAGTGTGTCACTAACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
*
2221207 TGTGGGCTTTGAAAAGGTGTCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
2221235 TGTGGGCTTTG-AAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGG-TGCCACTGACT
* *
2221263 TGTGGGCTTTAAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
2221291 TGTGGGC-TTGAAAAAGGTGCCACTGACT
1 TGTGGGCTTTG-AAAAGGTGCCACTGACT
*
2221319 CGTGGGCTTTGAAAAGGTGCCACTGACTT
1 TGTGGGCTTTGAAAAGGTGCCACTGAC-T
*
2221348 GTGTGGGCTTT-AAAAGGGTACCACTGACT
1 -TGTGGGCTTTGAAAA-GGTGCCACTGACT
2221377 TGCGTGGGCTTTG-AAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAAGG-TGCCACTGACT
2221407 TGTGGGCTTTG-AAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
*
2221435 CGTGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
2221463 CGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
2221490 CGTGGGCTTTG-AAAGAGTGCCACAGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
*
2221518 CGTGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
2221546 TGCGTGGGCTTT-AAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAA-GGTGCCACTGACT
2221576 TGCGTGGGCTTTG-AAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAAGG-TGCCACTGACT
*
2221606 TGTAGGCTTTG-AAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
* *
2221634 CGTGGGCTTTGAAAAAGGTGCCACTAACT
1 TGTGGGCTTTG-AAAAGGTGCCACTGACT
** * *
2221663 CATGGGCTTTGAAAAGGTGCCCCTAACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
2221691 TGCGTGGGCTTTCAAAGGGTGCCACTGACTT
1 T--GTGGGCTTTGAAAAGGTGCCACTGAC-T
** *
2221722 GTGTGGGCTTTGAAAATATGCCACTGAAT
1 -TGTGGGCTTTGAAAAGGTGCCACTGACT
2221751 TGTGGGCTTT-AAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
* *
2221779 CGTGGGCTTTGAAAATGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
* *
2221807 CGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
2221834 TGCGTGGGCTTT-AAAAGGGTGCCACTGTCT
1 T--GTGGGCTTTGAAAA-GGTGCCACTGACT
* * *
2221864 TGCGTGGGCTTTGAAATGATGCAACTGACT
1 T--GTGGGCTTTGAAAAGGTGCCACTGACT
* *
2221894 TGTGGGCTCTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
*
2221922 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
2221950 TGTGGGCTTTG-AAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
*
2221978 TGTGGGC-TTGAAAAGTTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
2222005 TGTGGGCTTTG-AAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
*
2222033 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACTGACT
2222061 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAG-GTGCCACTGACT
* *
2222090 TGTGGGGTTTGAAGAGGGTGCCACTGACT
1 TGTGGGCTTTGAA-AAGGTGCCACTGACT
* *
2222119 CGTGGGCTTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAAGGTGCCACTGACT
*
2222148 CGTGGGCTTTGAAA
1 TGTGGGCTTTGAAA
2222162 GGGATGAACA
Statistics
Matches: 1044, Mismatches: 89, Indels: 98
0.85 0.07 0.08
Matches are distributed among these distances:
27 101 0.10
28 544 0.52
29 198 0.19
30 196 0.19
31 4 0.00
32 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:2221521 original size:199 final size:196
Alignment explanation
Indices: 2220951--2222164 Score: 1410
Period size: 199 Copynumber: 6.1 Consensus size: 196
2220941 CACCGACACA
* * * * * * *
2220951 TGTGGGCTTTGAAAAGAGTTACTACTGGCTTGTGAGCTTTGAAAAGAGTGTCACTGACTTGTGGG
1 TGTGGGCTTT-AAAAG-GGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGG
* *
2221016 CTTTGAAA-ATGTGCCACTGACTTGTGGGCTTTG-AAAGGTTGCCACTAACTTGTGGGCTTTGAA
63 CTTTGAAAGA-GTGCCACTGACTCGTGGGCTTTGAAAAGG-TGCCACTAACTCGTGGGCTTTGAA
* * * * * *
2221079 AGGATGCCACTGACTTATGGGCTTTGAAAAAGTGCCACTGACTTGTGGGC-TTGAAAAAGTGTTC
126 AGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTG-CC
*
2221143 ATTGACT
190 ACTGACT
* * *
2221150 TGTGGGCTTTGAAAA-GGTGCCACTGACATGTGGGCTTTGAAAAGTG-TGTCACTAACTTGTGGG
1 TGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAG-GATGCCACTGACTTGTGGG
* * * *
2221213 CTTTGAAA-AGGTGTCACTGACTTGTGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCTTTAAA
63 CTTTGAAAGA-GTGCCACTGACTCGTGGGCTTTGAAAAGG-TGCCACTAACTCGTGGGCTTTGAA
** *
2221276 AAAGTGCCACTGACTTGTGGGC-TTGAAAAAGGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCC
126 AGGGTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACTCGTGGGCTTTGAAAAGGTGCC
2221340 ACTGACTT
190 ACTGAC-T
*
2221348 GTGTGGGCTTTAAAAGGGTACCACTGACTTGCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGG
1 -TGTGGGCTTTAAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGATGCCACTGACTTGTGGG
*
2221413 CTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTCGTGGGC-TTGAAAG
63 CTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAACTCGTGGGCTTTGAAAG
* *
2221477 GGTGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACAGACTCGTGGGCTTTGAAAAGGTGCCACT
128 GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACT
2221542 GACT
193 GACT
*
2221546 TGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCCACTGACTTGTAG
1 T--GTGGGCTTTAAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGGATGCCACTGACTTGTGG
*
2221611 GCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAAGGTGCCACTAACTCATGGGCTTTGAA
62 GCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTG-AAAAGGTGCCACTAACTCGTGGGCTTTGAA
* * * * * * **
2221676 AAGGTGCCCCTAACTTGCGTGGGCTTTCAAAGGGTGCCACTGACTTGTGTGGGCTTTGAAAATAT
126 AGGGTGCCACTGACTT--GTGGGCTTTGAAAGAGTGCCACTGAC-T-CGTGGGCTTTGAAAAGGT
*
2221741 GCCACTGAAT
187 GCCACTGACT
* * * *
2221751 TGTGGGCTTTAAAAGAGTGCCACTGACTCGTGGGCTTTGAAAATG-TGCCACTGACTCGTGGGC-
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCT
* **
2221814 TTGAAAGGGTGCCACTGACTTGCGTGGGCTTT-AAAAGGGTGCCACTGTCTTGCGTGGGCTTTGA
65 TTGAAAGAGTGCCACTGAC-T-CGTGGGCTTTGAAAA-GGTGCCACTAAC-T-CGTGGGCTTTGA
* * * * * * *
2221878 AATGATGCAACTGACTTGTGGGCTCTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCC
125 AAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCC
2221943 ACTGACT
190 ACTGACT
* * * *
2221950 TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC-TTGAAAAGTTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
* * * * *
2222014 TGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG
66 TGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAACTCGTGGGCTTTG-AAAGGG
* * *
2222079 TGCCACTGACTTGTGGGGTTTGAAGAGGGTGCCACTGACTCGTGGGCTTTGAAAAAAGTGCCACT
130 TGCCACTGACTTGTGGGCTTTGAA-AGAGTGCCACTGACTCGTGGGCTTTG-AAAAGGTGCCACT
2222144 GACT
193 GACT
* *
2222148 CGTGGGCTTTGAAAGGG
1 TGTGGGCTTTAAAAGGG
2222165 ATGAACATTC
Statistics
Matches: 893, Mismatches: 89, Indels: 67
0.85 0.08 0.06
Matches are distributed among these distances:
195 10 0.01
196 33 0.04
197 185 0.21
198 73 0.08
199 269 0.30
200 116 0.13
201 94 0.11
202 15 0.02
203 72 0.08
204 1 0.00
205 25 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (196 bp):
TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
TGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAACTCGTGGGCTTTGAAAGGGT
GCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGAC
T
Found at i:2223404 original size:1 final size:1
Alignment explanation
Indices: 2223400--2223457 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
2223390 TTTTTCTTGG
* * * * * *
2223400 TTTTTTTTGTTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTTGTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2223458 GGGTGTAAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.90
Consensus pattern (1 bp):
T
Found at i:2223411 original size:9 final size:9
Alignment explanation
Indices: 2223389--2223458 Score: 69
Period size: 9 Copynumber: 8.0 Consensus size: 9
2223379 TTTTTTGCTA
2223389 TTTTTTCTTGG
1 TTTTTT-TT-G
2223400 TTTTTTTTG
1 TTTTTTTTG
2223409 TTTTTTTTTG
1 -TTTTTTTTG
2223419 TTTTTTTTG
1 TTTTTTTTG
2223428 ----TTTTG
1 TTTTTTTTG
2223433 TTTTTTTTG
1 TTTTTTTTG
*
2223442 -TTTTTTTA
1 TTTTTTTTG
2223450 TTTTTTTTG
1 TTTTTTTTG
2223459 GGTGTAAAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
5 5 0.10
8 7 0.14
9 22 0.43
10 11 0.22
11 6 0.12
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:2223412 original size:19 final size:19
Alignment explanation
Indices: 2223390--2223431 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2223380 TTTTTGCTAT
2223390 TTTTTCTTGGTTTTTTTTG
1 TTTTTCTTGGTTTTTTTTG
* *
2223409 TTTTTTTTTGTTTTTTTTG
1 TTTTTCTTGGTTTTTTTTG
2223428 TTTT
1 TTTT
2223432 GTTTTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (19 bp):
TTTTTCTTGGTTTTTTTTG
Found at i:2223415 original size:33 final size:33
Alignment explanation
Indices: 2223378--2223448 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
2223368 GACCTTTTTC
2223378 TTTTTTTGCTATTTTTT-CTTGGTTTTTTTTGTT
1 TTTTTTTG-TATTTTTTGCTTGGTTTTTTTTGTT
* * *
2223411 TTTTTTTGTTTTTTTTGTTTTGTTTTTTTTGTT
1 TTTTTTTGTATTTTTTGCTTGGTTTTTTTTGTT
2223444 TTTTT
1 TTTTT
2223449 ATTTTTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (33 bp):
TTTTTTTGTATTTTTTGCTTGGTTTTTTTTGTT
Found at i:2223417 original size:14 final size:14
Alignment explanation
Indices: 2223389--2223455 Score: 73
Period size: 14 Copynumber: 4.7 Consensus size: 14
2223379 TTTTTTGCTA
* *
2223389 TTTTTTCTTGGTTT
1 TTTTTTTTTTGTTT
2223403 TTTTTGTTTTT-TTT
1 TTTTT-TTTTTGTTT
*
2223417 TGTTTTTTTTGTTT
1 TTTTTTTTTTGTTT
*
2223431 TGTTTTTTTTGTTT
1 TTTTTTTTTTGTTT
2223445 TTTTATTTTTT
1 TTTT-TTTTTT
2223456 TTGGGTGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
13 5 0.11
14 32 0.70
15 9 0.20
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:2223454 original size:23 final size:23
Alignment explanation
Indices: 2223372--2223454 Score: 87
Period size: 23 Copynumber: 3.5 Consensus size: 23
2223362 CATCTAGACC
* * *
2223372 TTTTTCTTTTTTTGCTATTTTTTC
1 TTTTT-TTTTTTTGTTTTTTTTTG
**
2223396 TTGGTTTTTTTTGTTTTTTTTTG
1 TTTTTTTTTTTTGTTTTTTTTTG
2223419 TTTTTTTTGTTTTG-TTTTTTTTG
1 TTTTTTTT-TTTTGTTTTTTTTTG
2223442 TTTTTTTATTTTT
1 TTTTTTT-TTTTT
2223455 TTTGGGTGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
23 41 0.82
24 9 0.18
ACGTcount: A:0.02, C:0.04, G:0.10, T:0.84
Consensus pattern (23 bp):
TTTTTTTTTTTTGTTTTTTTTTG
Found at i:2227356 original size:32 final size:32
Alignment explanation
Indices: 2227315--2227540 Score: 416
Period size: 32 Copynumber: 7.0 Consensus size: 32
2227305 AGTAGCTTAT
2227315 ATTGTATCGATACAAGACTTATGTATCGATAC
1 ATTGTATCGATACAAGACTTATGTATCGATAC
2227347 ATTGTATCGATACAAGACTTATGTATCGATAC
1 ATTGTATCGATACAAGACTTATGTATCGATAC
2227379 ATTGTATCGATACAAGACTTATGTATCGATAC
1 ATTGTATCGATACAAGACTTATGTATCGATAC
2227411 ATTGTATCGATACAAGACTTATGTATCGATAC
1 ATTGTATCGATACAAGACTTATGTATCGATAC
*
2227443 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAGACTTATGTATCGATAC
*
2227475 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAGACTTATGTATCGATAC
*
2227507 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAGAC-TTATGTATCGATAC
2227540 A
1 A
2227541 AATCGTTGAA
Statistics
Matches: 192, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
32 177 0.92
33 15 0.08
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAAGACTTATGTATCGATAC
Found at i:2243468 original size:15 final size:15
Alignment explanation
Indices: 2243448--2243477 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2243438 CACTTTTGTG
2243448 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
*
2243463 AAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAC
2243478 TTGTGGAATC
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:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:2243586 original size:1 final size:1
Alignment explanation
Indices: 2243582--2243615 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
2243572 AAACCAACCA
* *
2243582 GGGGGGGTGGGGGGGGGGGGGGGGGGGTGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2243616 AGTTTGGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.94, T:0.06
Consensus pattern (1 bp):
G
Found at i:2243681 original size:17 final size:17
Alignment explanation
Indices: 2243655--2243698 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2243645 TTGTGGTATA
2243655 TTTTTTTG-TTATTTTT
1 TTTTTTTGTTTATTTTT
2243671 TTTTATTTGTTTATTTTT
1 TTTT-TTTGTTTATTTTT
2243689 GTATTTTTTG
1 -T-TTTTTTG
2243699 GTTTTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 8 0.33
19 5 0.21
20 3 0.12
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTTTTGTTTATTTTT
Found at i:2243806 original size:22 final size:22
Alignment explanation
Indices: 2243756--2243806 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
2243746 GTTTTTGTTT
*
2243756 GTTTA-TTT-TATTCTTGTTTG
1 GTTTATTTTGTATTCTTGGTTG
*
2243776 GTTTTTTTTGTATT-TTGGTTG
1 GTTTATTTTGTATTCTTGGTTG
2243797 GTTGTATTTT
1 GTT-TATTTT
2243807 TTTTTTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 4 0.16
21 12 0.48
22 9 0.36
ACGTcount: A:0.08, C:0.02, G:0.20, T:0.71
Consensus pattern (22 bp):
GTTTATTTTGTATTCTTGGTTG
Found at i:2243860 original size:7 final size:6
Alignment explanation
Indices: 2243845--2243909 Score: 51
Period size: 7 Copynumber: 9.8 Consensus size: 6
2243835 TGTTGTCTTT
2243845 TTTTTG TTTTTGG TTTTT- TTGTTTG TTTTTGG TTTGTTG TTTTCTG TTTTGTGG
1 TTTTTG TTTTT-G TTTTTG TT-TTTG TTTTT-G TTT-TTG TTTT-TG TTTT-T-G
*
2243899 TTATTG TTTTT
1 TTTTTG TTTTT
2243910 TTGTTTATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
5 2 0.04
6 17 0.35
7 24 0.49
8 6 0.12
ACGTcount: A:0.02, C:0.02, G:0.22, T:0.75
Consensus pattern (6 bp):
TTTTTG
Found at i:2243879 original size:11 final size:11
Alignment explanation
Indices: 2243847--2243882 Score: 51
Period size: 9 Copynumber: 3.5 Consensus size: 11
2243837 TTGTCTTTTT
2243847 TTTGTTTTTGG
1 TTTGTTTTTGG
2243858 -TT-TTTTT-G
1 TTTGTTTTTGG
2243866 TTTGTTTTTGG
1 TTTGTTTTTGG
2243877 TTTGTT
1 TTTGTT
2243883 GTTTTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.05
9 7 0.32
10 7 0.32
11 7 0.32
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (11 bp):
TTTGTTTTTGG
Found at i:2243895 original size:15 final size:14
Alignment explanation
Indices: 2243835--2243915 Score: 58
Period size: 14 Copynumber: 5.6 Consensus size: 14
2243825 GTTAGATTTC
2243835 TGTTGTCTTTT-TTT
1 TGTTGT-TTTTGTTT
*
2243849 TGTT-TTTGGTTTTTT
1 TGTTGTTT--TTGTTT
*
2243864 TGTTTGTTTTTGGTT
1 TG-TTGTTTTTGTTT
2243879 TGTTGTTTTCTGTTT
1 TGTTGTTTT-TGTTT
* *
2243894 TGTGGTTATTGTTT
1 TGTTGTTTTTGTTT
*
2243908 TTTTGTTT
1 TGTTGTTT
2243916 ATTGATGTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.04
13 1 0.02
14 23 0.43
15 22 0.42
16 2 0.04
17 3 0.06
ACGTcount: A:0.01, C:0.02, G:0.21, T:0.75
Consensus pattern (14 bp):
TGTTGTTTTTGTTT
Found at i:2243919 original size:15 final size:14
Alignment explanation
Indices: 2243843--2243915 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 14
2243833 TCTGTTGTCT
2243843 TTTTTTTGTTTTTGG
1 TTTTTTTGTTTTT-G
*
2243858 TTTTTTTGTTTGTTT
1 TTTTTTTGTTT-TTG
2243873 TTGGTTTGTTGTTTTCTG
1 TT--TTT-TTGTTTT-TG
* * *
2243891 TTTTGTGGTTATTG
1 TTTTTTTGTTTTTG
2243905 TTTTTTTGTTT
1 TTTTTTTGTTT
2243916 ATTGATGTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
14 10 0.22
15 18 0.40
16 4 0.09
17 4 0.09
18 9 0.20
ACGTcount: A:0.01, C:0.01, G:0.21, T:0.77
Consensus pattern (14 bp):
TTTTTTTGTTTTTG
Found at i:2244098 original size:20 final size:18
Alignment explanation
Indices: 2244032--2244120 Score: 74
Period size: 20 Copynumber: 4.7 Consensus size: 18
2244022 CCCCACCCCA
*
2244032 CCACCCGAAGCCCAACAAAC
1 CCACCC-AAACCCAAC-AAC
*
2244052 CAACCCAAACCCAACCCAAC
1 CCACCCAAACCCAA--CAAC
*
2244072 CCCCCCAAACCCAACAAGC
1 CCACCCAAACCCAACAA-C
2244091 GCCACCCAACACCC-A-AAC
1 -CCACCCAA-ACCCAACAAC
2244109 CCACCCAAACCC
1 CCACCCAAACCC
2244121 CAACCACACC
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
16 4 0.07
17 8 0.14
18 4 0.07
19 10 0.17
20 28 0.47
21 5 0.08
ACGTcount: A:0.39, C:0.56, G:0.04, T:0.00
Consensus pattern (18 bp):
CCACCCAAACCCAACAAC
Found at i:2244114 original size:17 final size:16
Alignment explanation
Indices: 2244060--2244131 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 16
2244050 ACCAACCCAA
2244060 ACCC-AACCC-AACCC
1 ACCCAAACCCAAACCC
*
2244074 CCCCAAACCCAACAAGCGCC
1 ACCCAAACCC-A-AA-C-CC
2244094 ACCCAACACCCAAACCC
1 ACCCAA-ACCCAAACCC
*
2244111 ACCCAAACCCCAACCAC
1 ACCCAAACCCAAACC-C
2244128 ACCC
1 ACCC
2244132 CCCACCCCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
14 3 0.06
15 5 0.11
16 8 0.17
17 13 0.28
18 3 0.06
19 3 0.06
20 8 0.17
21 4 0.09
ACGTcount: A:0.38, C:0.60, G:0.03, T:0.00
Consensus pattern (16 bp):
ACCCAAACCCAAACCC
Found at i:2244115 original size:10 final size:10
Alignment explanation
Indices: 2244047--2244120 Score: 59
Period size: 10 Copynumber: 7.7 Consensus size: 10
2244037 CGAAGCCCAA
*
2244047 CAAACCAACC
1 CAAACCCACC
2244057 CAAACCCAACC
1 CAAACCC-ACC
*
2244068 C-AACCCCCC
1 CAAACCCACC
*
2244077 CAAACCCA-A
1 CAAACCCACC
*
2244086 CAAGCGCCACC
1 CAAAC-CCACC
2244097 C-AA--CACC
1 CAAACCCACC
2244104 CAAACCCACC
1 CAAACCCACC
2244114 CAAACCC
1 CAAACCC
2244121 CAACCACACC
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 7 0.14
10 31 0.62
11 5 0.10
ACGTcount: A:0.41, C:0.57, G:0.03, T:0.00
Consensus pattern (10 bp):
CAAACCCACC
Found at i:2244173 original size:15 final size:16
Alignment explanation
Indices: 2244129--2244175 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
2244119 CCCAACCACA
2244129 CCCCCCACCCCAACGCCC
1 CCCCCCA-CCC-ACGCCC
2244147 CCCCCCAAACCCAC-CCC
1 CCCCCC--ACCCACGCCC
2244164 CCCCCCACCCAC
1 CCCCCCACCCAC
2244176 AACCGCCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.22
17 9 0.33
18 8 0.30
19 3 0.11
20 1 0.04
ACGTcount: A:0.19, C:0.79, G:0.02, T:0.00
Consensus pattern (16 bp):
CCCCCCACCCACGCCC
Found at i:2244299 original size:20 final size:20
Alignment explanation
Indices: 2244276--2244349 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
2244266 CCACCCACCA
2244276 ACCACCCACCCCAACCCAAC
1 ACCACCCACCCCAACCCAAC
2244296 ACCACCC-CCCCACACCCAGAGC
1 ACCACCCACCCCA-ACCCA-A-C
* * *
2244318 ACC-CCAACCCCCACCCACC
1 ACCACCCACCCCAACCCAAC
*
2244337 ACGCCCCCACCCC
1 AC-CACCCACCCC
2244350 CACACACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
19 8 0.18
20 13 0.30
21 15 0.34
22 8 0.18
ACGTcount: A:0.27, C:0.69, G:0.04, T:0.00
Consensus pattern (20 bp):
ACCACCCACCCCAACCCAAC
Found at i:2244392 original size:31 final size:31
Alignment explanation
Indices: 2244333--2244417 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
2244323 AACCCCCACC
* *
2244333 CACCACGCCCCCACCCCCACACACAACACAA
1 CACCACACCCCCACCCCCCCACACAACACAA
* **
2244364 CACCACACCCCCACACCCCCCCCA-AACACCC
1 CACCACACCCCCAC-CCCCCCACACAACACAA
2244395 CGACC-CACCCCCA-CCCCCCACAC
1 C-ACCACACCCCCACCCCCCCACAC
2244418 CCACACACAC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 8 0.18
31 27 0.60
32 10 0.22
ACGTcount: A:0.29, C:0.68, G:0.02, T:0.00
Consensus pattern (31 bp):
CACCACACCCCCACCCCCCCACACAACACAA
Found at i:2244401 original size:25 final size:24
Alignment explanation
Indices: 2244373--2244477 Score: 70
Period size: 25 Copynumber: 4.2 Consensus size: 24
2244363 ACACCACACC
2244373 CCCACACCCCCCCCAAACACCCCGA
1 CCCACACCCCCCCCAAACACCCC-A
**
2244398 CCCAC-CCCCACCCCCCACA-CCCA
1 CCCACACCCC-CCCCAAACACCCCA
* * * *
2244421 CACACACCCCCCACACACACCACAA
1 CCCACACCCCCCCCAAACACC-CCA
* *
2244446 CCACCACCAACCCCCCCAAACACACCA
1 -C-CCA-CACCCCCCCCAAACACCCCA
2244473 CCCAC
1 CCCAC
2244478 CCTAACGCCC
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
23 12 0.20
24 13 0.21
25 17 0.28
26 2 0.03
27 4 0.07
28 13 0.21
ACGTcount: A:0.31, C:0.68, G:0.01, T:0.00
Consensus pattern (24 bp):
CCCACACCCCCCCCAAACACCCCA
Found at i:2244419 original size:19 final size:19
Alignment explanation
Indices: 2244366--2244441 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
2244356 CAACACAACA
2244366 CCACACCCCCACACCC-CCC
1 CCAC-CCCCCACACCCACCC
* *
2244385 CCAAACACCCC-GACCCACCC
1 CC--ACCCCCCACACCCACCC
*
2244405 CCACCCCCCACACCCACAC
1 CCACCCCCCACACCCACCC
* *
2244424 ACACCCCCCACACACACC
1 CCACCCCCCACACCCACC
2244442 ACAACCACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.13
19 28 0.62
20 9 0.20
21 2 0.04
ACGTcount: A:0.28, C:0.71, G:0.01, T:0.00
Consensus pattern (19 bp):
CCACCCCCCACACCCACCC
Found at i:2244459 original size:48 final size:46
Alignment explanation
Indices: 2244366--2244461 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 46
2244356 CAACACAACA
* * * *
2244366 CCACACCCCCACACCCCCCCCAAACACCCCGACCCACCCCCACCCC
1 CCACACCCCCACACCCCCCACAAACACCACGAACCACCCCAACCCC
*
2244412 CCACACCCACACACACCCCCCACACACACCAC-AACCACCACCAACCCC
1 CCACACCC-C-CACACCCCCCACAAACACCACGAACCACC-CCAACCCC
2244460 CC
1 CC
2244462 CAAACACACC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
46 8 0.19
47 7 0.17
48 27 0.64
ACGTcount: A:0.29, C:0.70, G:0.01, T:0.00
Consensus pattern (46 bp):
CCACACCCCCACACCCCCCACAAACACCACGAACCACCCCAACCCC
Found at i:2244653 original size:14 final size:14
Alignment explanation
Indices: 2244636--2244663 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2244626 CCAGAAACCT
2244636 CACCCCCCCCCCCC
1 CACCCCCCCCCCCC
2244650 CACCCCCCCCCCCC
1 CACCCCCCCCCCCC
2244664 ACCACCCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.93, G:0.00, T:0.00
Consensus pattern (14 bp):
CACCCCCCCCCCCC
Found at i:2244657 original size:13 final size:13
Alignment explanation
Indices: 2244639--2244666 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2244629 GAAACCTCAC
2244639 CCCCCCCCCCCCA
1 CCCCCCCCCCCCA
2244652 CCCCCCCCCCCCA
1 CCCCCCCCCCCCA
2244665 CC
1 CC
2244667 ACCCACCAGC
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:0.07, C:0.93, G:0.00, T:0.00
Consensus pattern (13 bp):
CCCCCCCCCCCCA
Found at i:2244724 original size:18 final size:19
Alignment explanation
Indices: 2244696--2244743 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2244686 ACCAACCCCG
2244696 CCAAAGACCCCCCC-CACC-
1 CCAAA-ACCCCCCCACACCA
2244714 CCAAAACCCCCCCACACCA
1 CCAAAACCCCCCCACACCA
*
2244733 CCCAAACCCCC
1 CCAAAACCCCC
2244744 GCGACCCACC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.30
18 9 0.33
19 10 0.37
ACGTcount: A:0.31, C:0.67, G:0.02, T:0.00
Consensus pattern (19 bp):
CCAAAACCCCCCCACACCA
Found at i:2244757 original size:15 final size:16
Alignment explanation
Indices: 2244745--2244785 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2244735 CAAACCCCCG
2244745 CGACCCACCCCCCACC
1 CGACCCACCCCCCACC
*
2244761 CGCCCCA-CCCCCACC
1 CGACCCACCCCCCACC
2244776 C--CCCACCCCC
1 CGACCCACCCCC
2244786 AACCACACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 9 0.39
16 6 0.26
ACGTcount: A:0.15, C:0.80, G:0.05, T:0.00
Consensus pattern (16 bp):
CGACCCACCCCCCACC
Found at i:2244785 original size:28 final size:28
Alignment explanation
Indices: 2244748--2244804 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
2244738 ACCCCCGCGA
* * *
2244748 CCCACCCCCCACCCGCCCCACCCCCACCC
1 CCCACCCCCCAACCACACCACCCCC-CCC
2244777 CCCA-CCCCCAACCACACCACCCCCCCC
1 CCCACCCCCCAACCACACCACCCCCCCC
2244804 C
1 C
2244805 AACACCACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.16
28 17 0.68
29 4 0.16
ACGTcount: A:0.18, C:0.81, G:0.02, T:0.00
Consensus pattern (28 bp):
CCCACCCCCCAACCACACCACCCCCCCC
Found at i:2244794 original size:19 final size:19
Alignment explanation
Indices: 2244772--2244826 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
2244762 GCCCCACCCC
2244772 CACCCCCCACCCCCAACCA
1 CACCCCCCACCCCCAACCA
2244791 CACCACCCC-CCCCCAA-CA
1 CACC-CCCCACCCCCAACCA
* *
2244809 C-CACCACACCCCCAACCA
1 CACCCCCCACCCCCAACCA
2244827 ACTAGTCAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 3 0.10
17 8 0.26
18 5 0.16
19 11 0.35
20 4 0.13
ACGTcount: A:0.29, C:0.71, G:0.00, T:0.00
Consensus pattern (19 bp):
CACCCCCCACCCCCAACCA
Found at i:2244796 original size:22 final size:22
Alignment explanation
Indices: 2244749--2244801 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
2244739 CCCCCGCGAC
*
2244749 CCACCCCCCACCCGCCCCACCC
1 CCACCCCCCACCCGCCCCACCA
2244771 CCACCCCCCACCC-CCAACCA-CA
1 CCACCCCCCACCCGCC--CCACCA
2244793 CCACCCCCC
1 CCACCCCCC
2244802 CCCAACACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 23 0.82
23 3 0.11
ACGTcount: A:0.19, C:0.79, G:0.02, T:0.00
Consensus pattern (22 bp):
CCACCCCCCACCCGCCCCACCA
Found at i:2244809 original size:16 final size:17
Alignment explanation
Indices: 2244790--2244824 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2244780 ACCCCCAACC
*
2244790 ACACCACC-CCCCCCCA
1 ACACCACCACACCCCCA
2244806 ACACCACCACACCCCCA
1 ACACCACCACACCCCCA
2244823 AC
1 AC
2244825 CAACTAGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (17 bp):
ACACCACCACACCCCCA
Found at i:2244827 original size:21 final size:19
Alignment explanation
Indices: 2244778--2244828 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
2244768 CCCCCACCCC
2244778 CCACCCCCAACC-ACACCA
1 CCACCCCCAACCAACACCA
2244796 CC-CCCCC--CCAACACCA
1 CCACCCCCAACCAACACCA
2244812 CCACACCCCCAACCAAC
1 -C-CACCCCCAACCAAC
2244829 TAGTCAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.07
16 6 0.22
17 6 0.22
18 3 0.11
19 5 0.19
21 5 0.19
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (19 bp):
CCACCCCCAACCAACACCA
Found at i:2246238 original size:5 final size:5
Alignment explanation
Indices: 2246230--2246271 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
2246220 ACAAAATAAA
2246230 AAAAG AAAA- AAAAG AAAA- AAAAG AAAAGAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAA-AG AAAAG AAAAG AA
2246272 CCTACTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 8 0.24
5 17 0.52
6 6 0.18
7 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2246239 original size:9 final size:9
Alignment explanation
Indices: 2246207--2246256 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
2246197 TCTTTTTTCA
*
2246207 AAAAAAAAC
1 AAAAAAAAG
2246216 AAAAACAAA-
1 AAAAA-AAAG
2246225 ATAAAAAAAG
1 A-AAAAAAAG
2246235 AAAAAAAAG
1 AAAAAAAAG
2246244 AAAAAAAAG
1 AAAAAAAAG
2246253 AAAA
1 AAAA
2246257 GAGAAAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 30 0.79
10 8 0.21
ACGTcount: A:0.88, C:0.04, G:0.06, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:2247496 original size:60 final size:61
Alignment explanation
Indices: 2247240--2247961 Score: 856
Period size: 61 Copynumber: 12.0 Consensus size: 61
2247230 ACCTTTTAAT
* * * *
2247240 CTTTCAGTCCTCAAAAAGTAGGACGTCTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * ** * *
2247301 CTTTTAGTCCTCAAAGAGTAGGA--CATTTTTTTTGTTAAAG-CCATACAAGTTGGTGGAAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTT-TTAAAGCCCACACAAGTTGGTGGCAC
* *
2247360 CTTTTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * *
2247421 CTTTCAGTCCCCAAAGAGGATGACGCCTTTTCCTTTTAAAGCCTAC-CAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * *
2247481 CTTTCAGTCCTCAAAGAGCAAGACACCTTTT-CTTTTAAAAGCCTACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCAC
* * *
2247542 CTTTCAGTCCT-AAAGAGTAGGACACC-TTTCCTTTTAAAGCCCACGCAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* *
2247601 CTTTCAATCCTCAAAGAGCAGGACGCCTTTTCC-TTTAAAGCCCACATAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * *
2247661 CTTTCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGTCCACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * **
2247722 CTTTCAGTCCTTAAAGAGCAGGACG-C----CCTTTTAAAGCCCATACAAGTTGGTGATAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
*
2247778 CTTTCAGTCCTCAAAGAGTAGGACGCC----CCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * *
2247835 CTTTCAGTCCTCAAAGAGCAGGGCACC-TTTCCTTTTAAAG-CC-CATAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * *
2247893 C-TTCTAGTCCCCAAAGTGCAGGAGTCTCCCTCTTTTCCATTTAAAGCCCACACAAGTTGGGTGG
1 CTTTC-AGTCCTCAAAGAGCAGGA----CGC-CTTTTCCTTTTAAAGCCCACACAAGTT-GGTGG
2247957 CAC
59 CAC
2247960 CT
1 CT
2247962 ATCTACTTCA
Statistics
Matches: 578, Mismatches: 58, Indels: 43
0.85 0.09 0.06
Matches are distributed among these distances:
56 49 0.08
57 55 0.10
58 31 0.05
59 87 0.15
60 159 0.28
61 164 0.28
62 2 0.00
63 1 0.00
64 12 0.02
65 2 0.00
66 7 0.01
67 9 0.02
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (61 bp):
CTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
Found at i:2247574 original size:180 final size:178
Alignment explanation
Indices: 2247240--2247895 Score: 875
Period size: 180 Copynumber: 3.7 Consensus size: 178
2247230 ACCTTTTAAT
* * *
2247240 CTTTCAGTCCTCAAAAAGTAGGACGTCTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACCTTT
1 CTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* * * ** * * *
2247305 TAGTCCTCAAAGAGTAGGACA-TTTTTTTTGTTAAAGCCATACAAGTTGGTGGAACCTTTTAGTC
66 CAGTCCTCAAAGAGCAGGACACCTTTCCTT-TTAAAGCCACACAAGTTGGTGGCACCTTTCAGTC
2247369 CTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
130 CT-AAAGAGTAGGAC-CC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * * *
2247421 CTTTCAGTCCCCAAAGAGGATGACGCCTTTTCCTTTTAAAGCCTAC-CAAGTTGGTGGCACCTTT
1 CTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* *
2247485 CAGTCCTCAAAGAGCAAGACACCTTTTCTTTTAAAAGCCTACACAAGTTGGTGGCACCTTTCAGT
66 CAGTCCTCAAAGAGCAGGACACCTTTCCTTTT-AAAGCC-ACACAAGTTGGTGGCACCTTTCAGT
*
2247550 CCTAAAGAGTAGGACACCTTTCCTTTTAAAGCCCACGCAAGTTGGTGGCAC
129 CCTAAAGAGTAGGAC-CCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* * *
2247601 CTTTCAATCCTCAAAGAGCAGGACGCCTTTTCC-TTTAAAGCCCACATAAGTTGGTGGCACCTTT
1 CTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
**
2247665 CAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGTCCACACAAGTTGGTGGCACCTTTCAGT
66 CAGTCCTCAAAGAGCAGGACACCTT-TCCTTTTAAAG-CCACACAAGTTGGTGGCACCTTTCAGT
* * * **
2247730 CCTTAAAGAGCAGGACGC---CCTTTTAAAGCCCATACAAGTTGGTGATAC
129 CC-TAAAGAGTAGGACCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
2247778 CTTTCAGTCCTCAAAGAGTAGGACGCC----CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 CTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
* *
2247839 CAGTCCTCAAAGAGCAGGGCACCTTTCCTTTTAAAGCC-CATAAGTTGGTGGCACCTT
66 CAGTCCTCAAAGAGCAGGACACCTTTCCTTTTAAAGCCACACAAGTTGGTGGCACCTT
2247896 CTAGTCCCCA
Statistics
Matches: 427, Mismatches: 40, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
171 18 0.04
172 2 0.00
173 13 0.03
174 52 0.12
177 51 0.12
179 11 0.03
180 170 0.40
181 85 0.20
182 25 0.06
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (178 bp):
CTTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT
CAGTCCTCAAAGAGCAGGACACCTTTCCTTTTAAAGCCACACAAGTTGGTGGCACCTTTCAGTCC
TAAAGAGTAGGACCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
Done.