Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008558.1 Hibiscus syriacus cultivar Beakdansim tig00111463_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2950132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 14
Found at i:3190 original size:13 final size:13
Alignment explanation
Indices: 3174--3221 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
3164 CTTTTTGAAC
3174 TTCTCTTTTTCTT
1 TTCTCTTTTTCTT
3187 TTCT-TTTCTTCTT
1 TTCTCTTT-TTCTT
*
3200 TTCTTCTTCTTCTT
1 TTC-TCTTTTTCTT
*
3214 TTGTCTTT
1 TTCTCTTT
3222 CTTTCTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 3 0.10
13 16 0.55
14 8 0.28
15 2 0.07
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (13 bp):
TTCTCTTTTTCTT
Found at i:3204 original size:24 final size:24
Alignment explanation
Indices: 3177--3231 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
3167 TTTGAACTTC
*
3177 TCTTTTTCTT-TTCTTTTC-TTCTTT
1 TCTTTTTCTTCTT-TTGTCTTTC-TT
*
3201 TCTTCTTCTTCTTTTGTCTTTCTT
1 TCTTTTTCTTCTTTTGTCTTTCTT
3225 TCTTTTT
1 TCTTTTT
3232 GTACTCCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (24 bp):
TCTTTTTCTTCTTTTGTCTTTCTT
Found at i:3227 original size:21 final size:20
Alignment explanation
Indices: 3179--3230 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
3169 TGAACTTCTC
*
3179 TTTTTCTTTTCTTTTCTTCT
1 TTTTTCTTTTCTTTTCGTCT
3199 TTTCTTCTTCTTCTTTT-GTCT
1 TTT-TTCTT-TTCTTTTCGTCT
3220 TTCTTTCTTTT
1 TT-TTTCTTTT
3231 TGTACTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.18
21 15 0.54
22 8 0.29
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTCTTTTCTTTTCGTCT
Found at i:8611 original size:14 final size:14
Alignment explanation
Indices: 8594--8628 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
8584 TTTATTTCTT
8594 TTCTTTTCT-TTTTC
1 TTCTTTT-TGTTTTC
8608 TTCTTTTTGTTTTC
1 TTCTTTTTGTTTTC
8622 TTCTTTT
1 TTCTTTT
8629 GGAGTGCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 1 0.05
14 19 0.95
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (14 bp):
TTCTTTTTGTTTTC
Found at i:11476 original size:23 final size:23
Alignment explanation
Indices: 11450--11494 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
11440 CGAAGAGATG
*
11450 TTCATCAAAATCAGAA-TGACCAC
1 TTCAGCAAAATCA-AAGTGACCAC
*
11473 TTCAGCAACATCAAAGTGACCA
1 TTCAGCAAAATCAAAGTGACCA
11495 TTCTTCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (23 bp):
TTCAGCAAAATCAAAGTGACCAC
Found at i:27900 original size:23 final size:25
Alignment explanation
Indices: 27874--27925 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
27864 GGATAATTCA
*
27874 ATGGTTAA-GGAATGGTGAT-GAAT
1 ATGGTTAATGGAATGGTGATAGAAG
*
27897 ATGG-TAATGGGATGGTGATAGAAG
1 ATGGTTAATGGAATGGTGATAGAAG
27921 ATGGT
1 ATGGT
27926 GATGTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 3 0.12
23 14 0.58
24 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.29
Consensus pattern (25 bp):
ATGGTTAATGGAATGGTGATAGAAG
Found at i:28340 original size:19 final size:20
Alignment explanation
Indices: 28302--28344 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
28292 GAAACCACTT
*
28302 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
28322 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
28341 TGAA
1 TGAA
28345 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:30944 original size:32 final size:32
Alignment explanation
Indices: 30883--30944 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
30873 GCAAAATTAA
*
30883 AAGAAAGAAATGATGAAAATGGAATATGGAGG
1 AAGAAAGAAATGATGAAAAAGGAATATGGAGG
30915 AAGAAAGGAAATGAT-AAGAAAGGAA-ATGGA
1 AAGAAA-GAAATGATGAA-AAAGGAATATGGA
30945 TAGAAATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.13
Consensus pattern (32 bp):
AAGAAAGAAATGATGAAAAAGGAATATGGAGG
Found at i:37105 original size:22 final size:20
Alignment explanation
Indices: 37080--37119 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
37070 ATGTTTGTTT
37080 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
37102 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
37120 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:41373 original size:22 final size:20
Alignment explanation
Indices: 41348--41387 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41338 ATGTTTGTTT
41348 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
41370 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
41388 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:41621 original size:15 final size:15
Alignment explanation
Indices: 41598--41633 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41588 ACTAATATTC
* *
41598 TTATCATAATATATA
1 TTATAATAACATATA
41613 TTATAATAACATATA
1 TTATAATAACATATA
41628 TTATAA
1 TTATAA
41634 AGCTAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATAATAACATATA
Found at i:44611 original size:86 final size:85
Alignment explanation
Indices: 44503--44673 Score: 290
Period size: 86 Copynumber: 2.0 Consensus size: 85
44493 GAGTTATTAC
44503 TTCTTCATTTGACGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAAAAATT-GG
1 TTCTTCATTTGACGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTC--AAAAAAATTCGG
44567 CATCGAATCTGAAACATTAAAG
64 CATCGAATCTGAAACATTAAAG
* *
44589 TTCTTCCTTTGATGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAAATTCGGCA
1 TTCTTCATTTGACGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAAATTCGGCA
*
44654 TCGAGTCTGAAACATTAAAG
66 TCGAATCTGAAACATTAAAG
44674 GGAGTAACAT
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
84 9 0.11
85 23 0.28
86 49 0.60
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (85 bp):
TTCTTCATTTGACGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAAATTCGGCA
TCGAATCTGAAACATTAAAG
Found at i:50275 original size:33 final size:33
Alignment explanation
Indices: 50233--50301 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
50223 GTTGATGAAT
*
50233 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
50266 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
50299 GAA
1 GAA
50302 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:50306 original size:13 final size:12
Alignment explanation
Indices: 50287--50383 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
50277 TTATTGGCGT
50287 GATATGGTGATG
1 GATATGGTGATG
50299 GAATATGGTGAT-
1 G-ATATGGTGATG
*
50311 GATATAGGCG-T-
1 GATAT-GGTGATG
50322 GATAATGGTGATG
1 GAT-ATGGTGATG
50335 GACTATGGTGAT-
1 GA-TATGGTGATG
*
50347 GATATAGGCG-T-
1 GATAT-GGTGATG
*
50358 GATAATGGAGATG
1 GAT-ATGGTGATG
50371 GATTATGGTGATG
1 GA-TATGGTGATG
50384 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:50342 original size:36 final size:36
Alignment explanation
Indices: 50272--50384 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
50262 AATGGAAGGA
* *
50272 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
50307 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
50343 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
50379 TGATGA
1 TGATGA
50385 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:54328 original size:35 final size:36
Alignment explanation
Indices: 54253--54328 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
54243 ATACTATTTT
* * *
54253 CATCACCATAATCCATCTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCACCATTATCACGCCAATAA
*
54289 CATCACCATATTCCATCACCA-TATCACGCCAATAA
1 CATCACCATAATCCATCACCATTATCACGCCAATAA
54324 CATCA
1 CATCA
54329 TCCTTCCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 17 0.47
36 19 0.53
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (36 bp):
CATCACCATAATCCATCACCATTATCACGCCAATAA
Found at i:54343 original size:33 final size:33
Alignment explanation
Indices: 54299--54367 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
54289 CATCACCATA
*
54299 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
54332 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
54365 TTC
1 TTC
54368 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:58693 original size:35 final size:36
Alignment explanation
Indices: 58618--58693 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
58608 ATACTATTTT
* * *
58618 CATCACCATAATCCATCTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCACCATTATCACGCCAATAA
*
58654 CATCACCATATTCCATCACCA-TATCACGCCAATAA
1 CATCACCATAATCCATCACCATTATCACGCCAATAA
58689 CATCA
1 CATCA
58694 TCCTTCCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 17 0.47
36 19 0.53
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (36 bp):
CATCACCATAATCCATCACCATTATCACGCCAATAA
Found at i:58708 original size:33 final size:33
Alignment explanation
Indices: 58664--58732 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
58654 CATCACCATA
*
58664 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
58697 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
58730 TTC
1 TTC
58733 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:60214 original size:2 final size:2
Alignment explanation
Indices: 60207--60248 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
60197 AGTTATTTTC
60207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60248 A
1 A
60249 GTTATTATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61356 original size:2 final size:2
Alignment explanation
Indices: 61344--61415 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
61334 TGGTAGCAGA
61344 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61416 ATGGTGATAG
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72696 original size:45 final size:45
Alignment explanation
Indices: 72646--72749 Score: 181
Period size: 45 Copynumber: 2.3 Consensus size: 45
72636 TTATGGACGA
*
72646 GCATTCACTTTCATAACAGCATGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
72691 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
* *
72736 ACATTAACATTCAT
1 GCATTCACATTCAT
72750 GTCAGCATAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (45 bp):
GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
Found at i:72729 original size:22 final size:22
Alignment explanation
Indices: 72659--72729 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
72649 TTCACTTTCA
72659 TAACAGCATGTTATCATTTTGT
1 TAACAGCATGTTATCATTTTGT
* * * ** **
72681 TAAC-TCACGTGCATTCACATTCA
1 TAACAGCATGT-TA-TCATTTTGT
72704 TAACAGCATGTTATCATTTTGT
1 TAACAGCATGTTATCATTTTGT
72726 TAAC
1 TAAC
72730 TCACGTACAT
Statistics
Matches: 32, Mismatches: 14, Indels: 6
0.62 0.27 0.12
Matches are distributed among these distances:
21 4 0.12
22 14 0.44
23 10 0.31
24 4 0.12
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (22 bp):
TAACAGCATGTTATCATTTTGT
Found at i:72770 original size:45 final size:45
Alignment explanation
Indices: 72655--72768 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 45
72645 AGCATTCACT
** * * *
72655 TTCATAACAGCATGTTATCATTTTGTTAACTCACGTGCATTCACA
1 TTCATAACAGCATCATAGCATTTTGTTAACTCACGTACATTAACA
** *
72700 TTCATAACAGCATGTTATCATTTTGTTAACTCACGTACATTAACA
1 TTCATAACAGCATCATAGCATTTTGTTAACTCACGTACATTAACA
**
72745 TTCATGTCAGCATACATAGCATTT
1 TTCATAACAGCAT-CATAGCATTT
72769 GTGTGGTTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
45 54 0.89
46 7 0.11
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (45 bp):
TTCATAACAGCATCATAGCATTTTGTTAACTCACGTACATTAACA
Found at i:73322 original size:35 final size:35
Alignment explanation
Indices: 73238--73339 Score: 152
Period size: 34 Copynumber: 2.9 Consensus size: 35
73228 ATGGTAAGGG
*
73238 AATGGTGATGATATAGGCGTGAAATGGTGATAGAA
1 AATGGTGATGATATAGGCGTGAAATGGTGATGGAA
* * *
73273 GAT-GTGATGATATAGGCATGCAATGGTGATGGAA
1 AATGGTGATGATATAGGCGTGAAATGGTGATGGAA
73307 AATGGTGATGATATAGGCGTGAAAATGGTGATG
1 AATGGTGATGATATAGGCGTG-AAATGGTGATG
73340 AACAGATAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
34 30 0.52
35 18 0.31
36 10 0.17
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.26
Consensus pattern (35 bp):
AATGGTGATGATATAGGCGTGAAATGGTGATGGAA
Found at i:73720 original size:19 final size:20
Alignment explanation
Indices: 73682--73724 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
73672 GAAACCCCTT
*
73682 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
73702 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
73721 TGAA
1 TGAA
73725 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:77168 original size:35 final size:35
Alignment explanation
Indices: 77123--77238 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
77113 TGGTAAGGGA
*
77123 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
** *
77158 ATGGTGATGATATAGGAATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
*
77193 AAGGTGATGATATAGGCGTGAAAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATGGAAG
77229 ATGGTGATGA
1 ATGGTGATGA
77239 ACATATAGTA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 48 0.68
36 23 0.32
ACGTcount: A:0.34, C:0.03, G:0.38, T:0.25
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
Found at i:87964 original size:24 final size:21
Alignment explanation
Indices: 87930--87972 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
87920 TCCACAAGAT
*
87930 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
87952 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
87973 ATAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:95117 original size:14 final size:13
Alignment explanation
Indices: 95060--95117 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
95050 AAATTTTGGC
* *
95060 TTTTTTTGGCTCT
1 TTTTTTTGCCTTT
95073 TTTTTTTG--TTT
1 TTTTTTTGCCTTT
*
95084 TTTTTTTGCCGTT
1 TTTTTTTGCCTTT
95097 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
95110 TTTGTTTT
1 TTT-TTTT
95118 TTTTTGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.26
13 25 0.64
14 4 0.10
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:95130 original size:13 final size:13
Alignment explanation
Indices: 95072--95133 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
95062 TTTTTGGCTC
95072 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
**
95085 TTTTTTGCCGTTTT
1 TTTTTT-TTGTTTT
95099 TTTTTGCCTTT-TTTGT
1 TTTTT---TTTGTTT-T
95115 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
95128 TTTTTT
1 TTTTTT
95134 GAAAAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
13 16 0.41
14 13 0.33
15 3 0.08
16 6 0.15
17 1 0.03
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTTTTGTTTT
Found at i:95134 original size:11 final size:10
Alignment explanation
Indices: 95072--95132 Score: 61
Period size: 10 Copynumber: 5.8 Consensus size: 10
95062 TTTTTGGCTC
95072 TTTTTTTTGTT
1 TTTTTTTTG-T
95083 TTTTTTTTGCCGT
1 TTTTTTTT---GT
95096 TTTTTTTTG-
1 TTTTTTTTGT
**
95105 CCTTTTTTGT
1 TTTTTTTTGT
95115 TTTTTTTTGT
1 TTTTTTTTGT
95125 TTTTTTTT
1 TTTTTTTT
95133 TGAAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
9 7 0.17
10 17 0.40
11 8 0.19
13 9 0.21
14 1 0.02
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.84
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:95980 original size:22 final size:22
Alignment explanation
Indices: 95952--95994 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
95942 CCCAACCTTA
95952 ATCCTAATAAAATAA-TAATCTG
1 ATCCTAA-AAAATAATTAATCTG
*
95974 ATCCTAAAAGATAATTAATCT
1 ATCCTAAAAAATAATTAATCT
95995 CCTATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.33
Consensus pattern (22 bp):
ATCCTAAAAAATAATTAATCTG
Found at i:96790 original size:15 final size:15
Alignment explanation
Indices: 96770--96802 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
96760 GGACTCCAAT
*
96770 GCTAGCTTTAGGTCA
1 GCTAGCTTTAAGTCA
96785 GCTAGCTTTAAGTCA
1 GCTAGCTTTAAGTCA
96800 GCT
1 GCT
96803 CCCATCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (15 bp):
GCTAGCTTTAAGTCA
Found at i:105089 original size:24 final size:21
Alignment explanation
Indices: 105055--105097 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
105045 TGCACAAGAT
*
105055 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
105077 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
105098 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:108297 original size:19 final size:19
Alignment explanation
Indices: 108269--108310 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
108259 AGCATATATC
*
108269 TTCATTAAAATCATGTATT
1 TTCATCAAAATCATGTATT
108288 TTCATCAAAATCATGTATT
1 TTCATCAAAATCATGTATT
108307 TTCA
1 TTCA
108311 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (19 bp):
TTCATCAAAATCATGTATT
Found at i:112157 original size:45 final size:45
Alignment explanation
Indices: 112107--112210 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
112097 TTATGGACGA
* *
112107 GCATTCACTTTCATAACAGCATGTTATCATTTTGTTAACTCAAGT
1 GCATTCACATTCATAACAACATGTTATCATTTTGTTAACTCAAGT
* *
112152 GCATTCACATTCATAACAACCTGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAACATGTTATCATTTTGTTAACTCAAGT
*
112197 ACATTCACATTCAT
1 GCATTCACATTCAT
112211 GTCAGCATAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (45 bp):
GCATTCACATTCATAACAACATGTTATCATTTTGTTAACTCAAGT
Found at i:115178 original size:11 final size:12
Alignment explanation
Indices: 115140--115178 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
115130 AAAAAAACAC
115140 AAAAAAAAGGCA
1 AAAAAAAAGGCA
115152 AAAAAAAAGGCA
1 AAAAAAAAGGCA
*
115164 AAAAAAAAGCCA
1 AAAAAAAAGGCA
115176 AAA
1 AAA
115179 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGGCA
Found at i:115178 original size:23 final size:23
Alignment explanation
Indices: 115130--115178 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
115120 TCAAAAAAAT
*
115130 AAAAAAACACAAAAAAAAGGCAA
1 AAAAAAACACAAAAAAAAAGCAA
** *
115153 AAAAAAAGGCAAAAAAAAAGCCA
1 AAAAAAACACAAAAAAAAAGCAA
115176 AAA
1 AAA
115179 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (23 bp):
AAAAAAACACAAAAAAAAAGCAA
Found at i:123293 original size:45 final size:45
Alignment explanation
Indices: 123235--123338 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 45
123225 TTATGGACGA
* *
123235 GCATTCACTTTCATAACATCATGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
123280 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
* *
123325 ACATTAACATTCAT
1 GCATTCACATTCAT
123339 GTCAGCATAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (45 bp):
GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
Found at i:123878 original size:34 final size:35
Alignment explanation
Indices: 123832--123946 Score: 155
Period size: 34 Copynumber: 3.3 Consensus size: 35
123822 TGGTAAGGGA
123832 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
* * *
123867 AT-GTGATGATATAGGCAT-ACAATGGTGATGGAAA
1 ATGGTGATGATATAGGCGTGA-AATGGTGATAGAAG
123901 ATGGTGATGATATAGGCGTGAAAATGGTGATCA-AAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGAT-AGAAG
123937 ATGGTGATGA
1 ATGGTGATGA
123947 ACAGATAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
33 1 0.01
34 29 0.42
35 17 0.25
36 21 0.30
37 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.26
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
Found at i:124327 original size:19 final size:20
Alignment explanation
Indices: 124289--124331 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
124279 GAAACCCCTT
*
124289 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
124309 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
124328 TGAA
1 TGAA
124332 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:127795 original size:35 final size:35
Alignment explanation
Indices: 127750--127865 Score: 169
Period size: 35 Copynumber: 3.3 Consensus size: 35
127740 TGGTAAGGGA
*
127750 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
** *
127785 ATGGTGATGATATAGGAATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* *
127820 AAGGTGATGATATAGGCGTGAAAATGGTTATGGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATGGAAG
127856 ATGGTGATGA
1 ATGGTGATGA
127866 ACATATAGTA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
35 48 0.69
36 22 0.31
ACGTcount: A:0.34, C:0.03, G:0.37, T:0.26
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
Found at i:134546 original size:45 final size:45
Alignment explanation
Indices: 134496--134599 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
134486 TTATGAACGA
* *
134496 GCATTCACTTTCATAACAGCATGTTATCATTTTGTTAACTCAAGT
1 GCATTCACATTCATAACAACATGTTATCATTTTGTTAACTCAAGT
* * *
134541 GCATTCACATTCATAACAACCTGTTGTCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAACATGTTATCATTTTGTTAACTCAAGT
*
134586 ACATTCACATTCAT
1 GCATTCACATTCAT
134600 GTCAGCATAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (45 bp):
GCATTCACATTCATAACAACATGTTATCATTTTGTTAACTCAAGT
Found at i:137921 original size:25 final size:22
Alignment explanation
Indices: 137887--137944 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 22
137877 GTATGCTTGA
137887 ATAATCATATGTTATTATTCACTTGC
1 ATAAT-ATATGTTATT-TTCA--TGC
*
137913 ATACTATATG--ATTTTCATGC
1 ATAATATATGTTATTTTCATGC
137933 ATAATATATGTT
1 ATAATATATGTT
137945 TCCACATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 12 0.43
22 4 0.14
23 3 0.11
25 5 0.18
26 4 0.14
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.47
Consensus pattern (22 bp):
ATAATATATGTTATTTTCATGC
Found at i:138003 original size:30 final size:31
Alignment explanation
Indices: 137967--138026 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
137957 CTTATTTTTA
137967 TATTATGTTTACATAT-ACTTTAGAT-TCATT
1 TATTATGTTTACATATCA-TTTAGATATCATT
*
137997 TATTATGTTTCCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
138027 GGCAGTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.52
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:138964 original size:17 final size:18
Alignment explanation
Indices: 138928--138965 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
138918 ATCTTTATTT
138928 AAATCATGTATTTGCATAAA
1 AAATCATGTATTT--ATAAA
138948 AAATCATGTATTT-TAAA
1 AAATCATGTATTTATAAA
138965 A
1 A
138966 GGGGTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (18 bp):
AAATCATGTATTTATAAA
Found at i:139390 original size:5 final size:5
Alignment explanation
Indices: 139380--139438 Score: 82
Period size: 5 Copynumber: 11.4 Consensus size: 5
139370 TCTCATCCTT
* *
139380 ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTATC TTTATC ATTTA
1 ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATTTC ATT-TC ATT-TC ATTTC
139432 ATTTC AT
1 ATTTC AT
139439 CTTCTTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 40 0.82
6 9 0.18
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTC
Found at i:139454 original size:27 final size:27
Alignment explanation
Indices: 139380--139457 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
139370 TCTCATCCTT
*
139380 ATTTCATTTCATT-TCATT--TCATTTC
1 ATTTCATTTCATTAT-ATTAATCATTTA
* *
139405 ATTTCATTTCATTATCTTTATCATTTA
1 ATTTCATTTCATTATATTAATCATTTA
*
139432 ATTTCATCTTC-TTTTATTAATCATTT
1 ATTTCAT-TTCATTATATTAATCATTT
139458 TCCTTTCTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 15 0.34
26 1 0.02
27 25 0.57
28 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTCATTTCATTATATTAATCATTTA
Found at i:142392 original size:12 final size:13
Alignment explanation
Indices: 142375--142403 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
142365 TTATGTATTG
142375 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
142387 GAAATAAAGAAAT
1 GAAATAAAGAAAT
142400 GAAA
1 GAAA
142404 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:150529 original size:30 final size:30
Alignment explanation
Indices: 150495--150551 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
150485 GATGTAGGAG
* *
150495 TCTTTTTCT-TTTCTTTTTGTTTTTATTATT
1 TCTTTTTCTCTTT-TTGTTGCTTTTATTATT
150525 TCTTTTTCTCTTTTTGTTGCTTTTATT
1 TCTTTTTCTCTTTTTGTTGCTTTTATT
150552 GCAACACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.77
Consensus pattern (30 bp):
TCTTTTTCTCTTTTTGTTGCTTTTATTATT
Found at i:152359 original size:14 final size:14
Alignment explanation
Indices: 152340--152367 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
152330 ATAATATAAA
152340 ATCTCTTACCATTT
1 ATCTCTTACCATTT
152354 ATCTCTTACCATTT
1 ATCTCTTACCATTT
152368 TACCCAAAAT
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:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (14 bp):
ATCTCTTACCATTT
Found at i:152434 original size:47 final size:44
Alignment explanation
Indices: 152371--152459 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
152361 ACCATTTTAC
*
152371 CCAAAATACTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTT
1 CCAAAATACTTACCA-TT--ATTCCATAAGCTCATAAGCTTATTTTT
* * *
152418 CCAATATACTTGCCATTATTCCGTAAGCTCATAAGCTTATTT
1 CCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTT
152460 GCATGGTTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 23 0.61
46 2 0.05
47 13 0.34
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.38
Consensus pattern (44 bp):
CCAAAATACTTACCATTATTCCATAAGCTCATAAGCTTATTTTT
Found at i:152608 original size:40 final size:40
Alignment explanation
Indices: 152564--152683 Score: 190
Period size: 40 Copynumber: 3.0 Consensus size: 40
152554 ACCGTAGTTC
*
152564 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
* *
152604 TACACATAAGGTCGTGCTCACCATATACA-CTAAGTGTA-
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
152642 TACACATAAGGTCATGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
152682 TA
1 TA
152684 TAAACCTGCA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
38 27 0.37
39 16 0.22
40 30 0.41
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:157703 original size:44 final size:44
Alignment explanation
Indices: 157653--157741 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
157643 CCAGATCCAT
157653 AGGAATTATTCTTGAACATTTACAACATTTTCCATCTCAAATGA
1 AGGAATTATTCTTGAACATTTACAACATTTTCCATCTCAAATGA
157697 AGGAATTATTCTTGAACATTTACAACATTTTCCATCTCAAATGA
1 AGGAATTATTCTTGAACATTTACAACATTTTCCATCTCAAATGA
157741 A
1 A
157742 AATTTCATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (44 bp):
AGGAATTATTCTTGAACATTTACAACATTTTCCATCTCAAATGA
Found at i:159426 original size:44 final size:47
Alignment explanation
Indices: 159305--159431 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 47
159295 TATAAACTCT
*
159305 CTTACCATTT-A-TCTCATAAGCTCGTAAACTTATTTTACCCAAAATA
1 CTTACCATTTAATTC-CATAAGCTCGTAAGCTTATTTTACCCAAAATA
* *
159351 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTT-TCCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCCAAAATA
* * *
159398 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
159432 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
44 23 0.32
46 12 0.17
47 13 0.18
48 22 0.31
49 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (47 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCCAAAATA
Found at i:159580 original size:40 final size:40
Alignment explanation
Indices: 159536--159656 Score: 217
Period size: 39 Copynumber: 3.0 Consensus size: 40
159526 ACCGCAGTGC
* *
159536 TACACATAAGGTCGTGCCCACCATATACACCGAACTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
159576 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTA-
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
159615 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
159655 TA
1 TA
159657 TAAACCTGCA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
39 39 0.50
40 39 0.50
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:190853 original size:18 final size:19
Alignment explanation
Indices: 190830--190869 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
190820 TGTAGGAGTC
*
190830 TTTTCTTC-CTCTTTTTGT
1 TTTTCTTCTCTCTTTTTCT
*
190848 TTTTCTTCTTTCTTTTTCT
1 TTTTCTTCTCTCTTTTTCT
190867 TTT
1 TTT
190870 GTTACTTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTCTTCTCTCTTTTTCT
Found at i:193279 original size:29 final size:31
Alignment explanation
Indices: 193230--193288 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
193220 CTTAGCTTTA
*
193230 TATTATGTTTACATATGATTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
193260 TATTATG-TTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
193289 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:195824 original size:14 final size:14
Alignment explanation
Indices: 195805--195831 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
195795 TGTTCATAAC
195805 CATCTTTCCATCAT
1 CATCTTTCCATCAT
195819 CATCTTTCCATCA
1 CATCTTTCCATCA
195832 ACATTCACGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (14 bp):
CATCTTTCCATCAT
Found at i:195998 original size:15 final size:15
Alignment explanation
Indices: 195978--196011 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
195968 TCTTTGCTAA
195978 CAATTCTATCCATTT
1 CAATTCTATCCATTT
*
195993 CAATTCTTTCCATTT
1 CAATTCTATCCATTT
196008 -AATT
1 CAATT
196012 TTAATTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (15 bp):
CAATTCTATCCATTT
Found at i:196305 original size:22 final size:23
Alignment explanation
Indices: 196275--196319 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
196265 AATTCGGTGC
196275 AAAAGAAATAAAAGAAAAAGAAG
1 AAAAGAAATAAAAGAAAAAGAAG
*
196298 AAAA-AAATCAAAGAAAAAGAAG
1 AAAAGAAATAAAAGAAAAAGAAG
196320 TGAAGAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (23 bp):
AAAAGAAATAAAAGAAAAAGAAG
Found at i:199390 original size:18 final size:19
Alignment explanation
Indices: 199356--199401 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
199346 GGCCAAGAGT
*
199356 ATGTATCTTCACT-AAAATC
1 ATGTAT-TTCACTAAAAATA
199375 ATGTATTTCA-TAAAAAATA
1 ATGTATTTCACT-AAAAATA
199394 ATGTATTT
1 ATGTATTT
199402 TCAAAGGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 4 0.17
19 19 0.79
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (19 bp):
ATGTATTTCACTAAAAATA
Found at i:199759 original size:14 final size:14
Alignment explanation
Indices: 199740--199776 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
199730 TACTATTGTT
199740 CATCACCATATCTC
1 CATCACCATATCTC
* *
199754 CATCACCATCTTTC
1 CATCACCATATCTC
199768 CATCACCAT
1 CATCACCAT
199777 TCACGCCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.27, C:0.43, G:0.00, T:0.30
Consensus pattern (14 bp):
CATCACCATATCTC
Found at i:199966 original size:21 final size:21
Alignment explanation
Indices: 199918--199967 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
199908 TCTTTGCTAA
199918 CAATTATCCATTTCAATTCTTT
1 CAATT-TCCATTTCAATTCTTT
*
199940 CCATTTCCATTTC-ATTCATTT
1 CAATTTCCATTTCAATTC-TTT
*
199961 TAATTTC
1 CAATTTC
199968 TTAATTATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 16 0.67
22 4 0.17
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (21 bp):
CAATTTCCATTTCAATTCTTT
Found at i:205158 original size:17 final size:18
Alignment explanation
Indices: 205132--205167 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
205122 TATCTTCACT
*
205132 AAAATCATGTA-TTTCAA
1 AAAATAATGTATTTTCAA
205149 AAAATAATGTATTTTCAA
1 AAAATAATGTATTTTCAA
205167 A
1 A
205168 GGGGTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (18 bp):
AAAATAATGTATTTTCAA
Found at i:205515 original size:14 final size:14
Alignment explanation
Indices: 205496--205532 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
205486 ACTATTTGTT
205496 CATCACCATATCTC
1 CATCACCATATCTC
* *
205510 CATCACCATCTTTC
1 CATCACCATATCTC
205524 CATCACCAT
1 CATCACCAT
205533 TCACGCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.27, C:0.43, G:0.00, T:0.30
Consensus pattern (14 bp):
CATCACCATATCTC
Found at i:208203 original size:20 final size:21
Alignment explanation
Indices: 208180--208218 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
208170 TGAACGTCCA
*
208180 ATACCTTCTATC-TAGCTTAT
1 ATACATTCTATCTTAGCTTAT
*
208200 ATACATTTTATCTTAGCTT
1 ATACATTCTATCTTAGCTT
208219 CTAGACGATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (21 bp):
ATACATTCTATCTTAGCTTAT
Found at i:208931 original size:18 final size:19
Alignment explanation
Indices: 208908--208956 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
208898 CGGCCAAGAG
* *
208908 CATGTATCTTCAT-TAAAT
1 CATGTATTTTCATCAAAAT
208926 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
208945 CATGTATTTTCA
1 CATGTATTTTCA
208957 AAGGGATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:209310 original size:13 final size:14
Alignment explanation
Indices: 209281--209313 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
209271 TACTATTTGT
209281 CATCACCATCTTTC
1 CATCACCATCTTTC
209295 CATCACCATC-TTC
1 CATCACCATCTTTC
209308 CATCAC
1 CATCAC
209314 ATTCACGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.30
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:212165 original size:22 final size:23
Alignment explanation
Indices: 212127--212173 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 23
212117 CTCTCATAGT
212127 TAGCTACCAAGACACTCACCTAGC
1 TAGCTACCAAGA-ACTCACCTAGC
212151 TAGCTACCAAG-ACTCACCTAGC
1 TAGCTACCAAGAACTCACCTAGC
212173 T
1 T
212174 TACCATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 12 0.52
24 11 0.48
ACGTcount: A:0.32, C:0.36, G:0.13, T:0.19
Consensus pattern (23 bp):
TAGCTACCAAGAACTCACCTAGC
Found at i:212434 original size:18 final size:19
Alignment explanation
Indices: 212411--212459 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
212401 CGGCCAAGAG
* *
212411 CATGTATCTTCAT-TAAAT
1 CATGTATTTTCATCAAAAT
212429 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
212448 CATGTATTTTCA
1 CATGTATTTTCA
212460 AAGGGATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:212823 original size:13 final size:14
Alignment explanation
Indices: 212794--212829 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
212784 ACTATTTGTT
*
212794 CATCACAATCTTTC
1 CATCACCATCTTTC
212808 CATCACCATC-TTC
1 CATCACCATCTTTC
212821 CATCACCAT
1 CATCACCAT
212830 TCATGCCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.28, C:0.42, G:0.00, T:0.31
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:212993 original size:15 final size:15
Alignment explanation
Indices: 212973--213003 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
212963 TCTTTGATAA
212973 CAATTCTATCCATTT
1 CAATTCTATCCATTT
*
212988 CAATTCTTTCCATTT
1 CAATTCTATCCATTT
213003 C
1 C
213004 CATTTACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (15 bp):
CAATTCTATCCATTT
Found at i:213299 original size:14 final size:14
Alignment explanation
Indices: 213276--213317 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
213266 TTAGGAGTGC
213276 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAA-A
213291 AAAAG-AAGAAAAA
1 AAAAGAAAGAAAAA
**
213304 AAATCAAAGAAAAA
1 AAAAGAAAGAAAAA
213318 GAAGTGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 15 0.62
15 5 0.21
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAGAAAGAAAAA
Found at i:215464 original size:24 final size:24
Alignment explanation
Indices: 215434--215492 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
215424 TCAGCTATAG
*
215434 CTCACCTAGTTAGCTACCAAGACA
1 CTCACCTAGCTAGCTACCAAGACA
*
215458 CTTACCTAGCTAGCTACCAAGACA
1 CTCACCTAGCTAGCTACCAAGACA
215482 CTCACCTAGCT
1 CTCACCTAGCT
215493 TACCACTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.31, C:0.36, G:0.12, T:0.22
Consensus pattern (24 bp):
CTCACCTAGCTAGCTACCAAGACA
Found at i:215627 original size:17 final size:17
Alignment explanation
Indices: 215605--215646 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
215595 AATAGGCTGC
215605 CATGTGCATCATTCAAG
1 CATGTGCATCATTCAAG
215622 CATGTGCATCATTCAAG
1 CATGTGCATCATTCAAG
215639 CATGTGCA
1 CATGTGCA
215647 CTCCATGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (17 bp):
CATGTGCATCATTCAAG
Found at i:215835 original size:18 final size:19
Alignment explanation
Indices: 215797--215845 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
215787 CGGCCAAGAG
*
215797 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
*
215816 CATGTATTTTCA-TCAAAT
1 CATGTATTTTCATTAAAAT
215834 CATGTATTTTCA
1 CATGTATTTTCA
215846 AAGGGATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:216209 original size:13 final size:14
Alignment explanation
Indices: 216180--216211 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
216170 ACTATTTGTT
216180 CATCACCATCTTTC
1 CATCACCATCTTTC
216194 CATCACCATC-TTC
1 CATCACCATCTTTC
216207 CATCA
1 CATCA
216212 TCTTTCACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.25, C:0.44, G:0.00, T:0.31
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:218859 original size:16 final size:16
Alignment explanation
Indices: 218823--218856 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
218813 TCACGTGAGA
218823 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
218839 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
218856 T
1 T
218857 ATTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:225130 original size:19 final size:21
Alignment explanation
Indices: 225093--225135 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
225083 TAACTTTTTC
225093 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
225113 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
225133 TTT
1 TTT
225136 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:225141 original size:19 final size:20
Alignment explanation
Indices: 225092--225141 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
225082 TTAACTTTTT
*
225092 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
225112 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
225131 CTTTTACCTTT
1 CTTTTACCTTT
225142 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:229059 original size:33 final size:33
Alignment explanation
Indices: 228980--229082 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
228970 ATACAATCTG
* *
228980 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
229016 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * *
229049 TCCATTACCAT-TCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
229081 TC
1 TC
229083 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
32 13 0.22
33 18 0.30
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:229066 original size:35 final size:34
Alignment explanation
Indices: 228980--229082 Score: 99
Period size: 35 Copynumber: 3.1 Consensus size: 34
228970 ATACAATCTG
* *
228980 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCATTATCACGCCAATAACATCATCC---T
229016 TCCATCACCA-TATCACGCCAATAACATCATCCT
1 TCCATCACCATTATCACGCCAATAACATCATCCT
* *
229049 TCCATTACCATTCATCA--CCATTAA-ATCATCCT
1 TCCATCACCATT-ATCACGCCAATAACATCATCCT
229081 TC
1 TC
229083 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
32 10 0.17
33 16 0.27
34 1 0.02
35 21 0.35
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.30
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCATCCT
Found at i:233072 original size:33 final size:33
Alignment explanation
Indices: 232993--233096 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
232983 ATACAATCTG
* *
232993 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
233029 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
233062 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
233095 TC
1 TC
233097 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:236760 original size:17 final size:16
Alignment explanation
Indices: 236729--236762 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
236719 CACGTGAGGA
236729 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
236745 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
236762 T
1 T
236763 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:239731 original size:15 final size:15
Alignment explanation
Indices: 239711--239741 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
239701 TCTTTGATAA
239711 CAATTCTATCCATTT
1 CAATTCTATCCATTT
*
239726 CAATTCTTTCCATTT
1 CAATTCTATCCATTT
239741 C
1 C
239742 CTTTTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (15 bp):
CAATTCTATCCATTT
Found at i:240031 original size:11 final size:11
Alignment explanation
Indices: 240015--240053 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
240005 AGTGCAAAAG
240015 AAAGAAAAGAA
1 AAAGAAAAGAA
240026 AAAGAAGAA-AA
1 AAAGAA-AAGAA
*
240037 AAATAAAAGAA
1 AAAGAAAAGAA
240048 AAAGAA
1 AAAGAA
240054 GTGAAGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 2 0.08
11 20 0.83
12 2 0.08
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:240044 original size:22 final size:23
Alignment explanation
Indices: 240010--240063 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
240000 TTTGGAGTGC
240010 AAAAGAAAGAAAAGAAAAAGAAG
1 AAAAGAAAGAAAAGAAAAAGAAG
*
240033 AAAA-AAATAAAAGAAAAAGAAG
1 AAAAGAAAGAAAAGAAAAAGAAG
**
240055 TGAAGAAAG
1 AAAAGAAAG
240064 TTGCAAAGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (23 bp):
AAAAGAAAGAAAAGAAAAAGAAG
Found at i:242825 original size:24 final size:24
Alignment explanation
Indices: 242798--242856 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
242788 CAAGCTATAG
*
242798 CTCACCTAGTTAGCTACCAAGACA
1 CTCACCTAGCTAGCTACCAAGACA
242822 CTCACCTAGCTAGCTACCAAGACA
1 CTCACCTAGCTAGCTACCAAGACA
*
242846 CTTACCTAGCT
1 CTCACCTAGCT
242857 TACCGTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.36, G:0.12, T:0.22
Consensus pattern (24 bp):
CTCACCTAGCTAGCTACCAAGACA
Found at i:243190 original size:19 final size:19
Alignment explanation
Indices: 243147--243196 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
243137 CGGCCAAGAG
* * *
243147 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATCAAAAC
243166 CATGTATTTTCATCAAAAC
1 CATGTATTTTCATCAAAAC
*
243185 CGTGTATTTTCA
1 CATGTATTTTCA
243197 AAGGGATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAC
Found at i:243566 original size:13 final size:14
Alignment explanation
Indices: 243535--243572 Score: 69
Period size: 13 Copynumber: 2.8 Consensus size: 14
243525 ATACTATTTG
243535 TCCATCACCATCTT
1 TCCATCACCATCTT
243549 TCCATCACCATC-T
1 TCCATCACCATCTT
243562 TCCATCACCAT
1 TCCATCACCAT
243573 TCACGCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.32
Consensus pattern (14 bp):
TCCATCACCATCTT
Found at i:243936 original size:7 final size:6
Alignment explanation
Indices: 243917--243957 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
243907 GTGCTGCAAC
* *
243917 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG CAAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
243958 GACTCCTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:244036 original size:23 final size:23
Alignment explanation
Indices: 243984--244027 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
243974 TTGGAGTGCA
**
243984 AAAGAAAGAAAAGAAAAAGAATC
1 AAAGAAATTAAAGAAAAAGAATC
244007 AAAGAAATTAAAGAAAAAGAA
1 AAAGAAATTAAAGAAAAAGAA
244028 GTGAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.07
Consensus pattern (23 bp):
AAAGAAATTAAAGAAAAAGAATC
Found at i:247189 original size:19 final size:20
Alignment explanation
Indices: 247165--247215 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
247155 CGGCCAAGAG
* *
247165 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
247184 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
247204 CATGTATTTTCA
1 CATGTATTTTCA
247216 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:247447 original size:122 final size:122
Alignment explanation
Indices: 247288--247528 Score: 437
Period size: 122 Copynumber: 2.0 Consensus size: 122
247278 TAAATAGGCT
247288 AGGCTATTTACATTGCAAGACAACCCTTTGATAATATAAAAATCCTTGTGAGATTATTCTCTCTT
1 AGGCTATTTACATTGCAAGACAACCCTTTGATAATATAAAAATCCTTGTGAGATTATTCTCTCTT
247353 CAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAAGTTTATGGCGTTA
66 CAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAAGTTTATGGCGTTA
* * * *
247410 AGGCTATTTACATTGTAAGATAACCTTTTGATAATATAAAAATCCTTGTGATATTATTCTCTCTT
1 AGGCTATTTACATTGCAAGACAACCCTTTGATAATATAAAAATCCTTGTGAGATTATTCTCTCTT
*
247475 CAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAAGTTTGTGGCG
66 CAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAAGTTTATGGCG
247529 GCAATCCCTT
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 114 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (122 bp):
AGGCTATTTACATTGCAAGACAACCCTTTGATAATATAAAAATCCTTGTGAGATTATTCTCTCTT
CAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAAGTTTATGGCGTTA
Found at i:247708 original size:13 final size:14
Alignment explanation
Indices: 247679--247714 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
247669 ACTATTTGTT
*
247679 CATCATCATCTTTC
1 CATCACCATCTTTC
247693 CATCACCATC-TTC
1 CATCACCATCTTTC
247706 CATCACCAT
1 CATCACCAT
247715 TCACGCCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.25, C:0.42, G:0.00, T:0.33
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:247879 original size:15 final size:15
Alignment explanation
Indices: 247859--247889 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
247849 TCTTTGATAA
247859 CAATTCTATCCATTT
1 CAATTCTATCCATTT
*
247874 CAATTCTTTCCATTT
1 CAATTCTATCCATTT
247889 C
1 C
247890 TATTTCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (15 bp):
CAATTCTATCCATTT
Found at i:248128 original size:18 final size:18
Alignment explanation
Indices: 248101--248158 Score: 100
Period size: 18 Copynumber: 3.2 Consensus size: 18
248091 GTGCTGCAAC
248101 AAAAAGCAAAAGAAAGAAG
1 AAAAA-CAAAAGAAAGAAG
248120 AAAAACAAAAGAAAGAAG
1 AAAAACAAAAGAAAGAAG
248138 AAAAACAAAAGAAA-AAG
1 AAAAACAAAAGAAAGAAG
248155 AAAA
1 AAAA
248159 GACTCCTACA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.18
18 27 0.69
19 5 0.13
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAGAAAGAAG
Found at i:248147 original size:24 final size:24
Alignment explanation
Indices: 248101--248158 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
248091 GTGCTGCAAC
* *
248101 AAAAAGCAAAAGAAAGAAGAAAA-
1 AAAAAGAAAAAGAAAGAACAAAAG
248124 ACAAAAGAAAGAAGAAA-AACAAAAG
1 A-AAAAGAAA-AAGAAAGAACAAAAG
248149 AAAAAGAAAA
1 AAAAAGAAAA
248159 GACTCCTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 2 0.07
24 21 0.70
25 7 0.23
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAGAACAAAAG
Found at i:248153 original size:6 final size:6
Alignment explanation
Indices: 248101--248158 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
248091 GTGCTGCAAC
* * *
248101 AAAAAG CAAAAG AAAGAAG AAAAA- CAAAAG AAAGAAG AAAAA- CAAAAG
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG
248149 AAAAAG AAAA
1 AAAAAG AAAA
248159 GACTCCTACA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 8 0.19
6 22 0.52
7 12 0.29
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:257592 original size:18 final size:19
Alignment explanation
Indices: 257554--257592 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
257544 AAGGAAAAAG
*
257554 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
257573 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
257591 AA
1 AA
257593 AAAAGCAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:258820 original size:24 final size:21
Alignment explanation
Indices: 258786--258828 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
258776 TGTACAAGAT
*
258786 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
258808 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
258829 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:263352 original size:122 final size:122
Alignment explanation
Indices: 263135--263379 Score: 454
Period size: 122 Copynumber: 2.0 Consensus size: 122
263125 TAAATAGGCT
* *
263135 AGGCTATTTACATTGTAAGACAACCCTTTGATAATATAAAAATCCTTGTGAGATTATTCTCTCTT
1 AGGCTATTTACATTGTAAGACAACCCTTTGATAATATAAAAATCCTTGTAAGACTATTCTCTCTT
263200 CAAGTTCTTTTTAGAACTATATCAATTAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
66 CAAGTTCTTTTTAGAACTATATCAATTAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
*
263257 AGGCTATTTACATTGTAAGATAACCCTTTGATAATATAAAAATCCTTGTAAGACTATTCTCTCTT
1 AGGCTATTTACATTGTAAGACAACCCTTTGATAATATAAAAATCCTTGTAAGACTATTCTCTCTT
*
263322 CAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
66 CAAGTTCTTTTTAGAACTATATCAATTAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
263379 A
1 A
263380 TCCCTTCCTT
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (122 bp):
AGGCTATTTACATTGTAAGACAACCCTTTGATAATATAAAAATCCTTGTAAGACTATTCTCTCTT
CAAGTTCTTTTTAGAACTATATCAATTAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
Found at i:263556 original size:13 final size:14
Alignment explanation
Indices: 263526--263561 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
263516 ACTATTTGTT
*
263526 CATCACCATCTTTC
1 CATCACCATCTATC
263540 CATCACCATC-ATC
1 CATCACCATCTATC
263553 CATCACCAT
1 CATCACCAT
263562 TCACACCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.28, C:0.44, G:0.00, T:0.28
Consensus pattern (14 bp):
CATCACCATCTATC
Found at i:267387 original size:13 final size:14
Alignment explanation
Indices: 267358--267393 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
267348 ACTATTTGTT
267358 CATCACCATCTTTC
1 CATCACCATCTTTC
267372 CATCACCATC-TTC
1 CATCACCATCTTTC
267385 CATCACCAT
1 CATCACCAT
267394 TCACGCCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.25, C:0.44, G:0.00, T:0.31
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:267876 original size:15 final size:15
Alignment explanation
Indices: 267856--267892 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
267846 TTTGGAGCGC
*
267856 AAAAGAAAGAAAAGA
1 AAAAGAAAAAAAAGA
*
267871 AAAAGAAAAAAAATA
1 AAAAGAAAAAAAAGA
267886 AAAAGAA
1 AAAAGAA
267893 GTGAAGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAAAAGA
Found at i:270987 original size:19 final size:19
Alignment explanation
Indices: 270963--271012 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
270953 CGGCCAAGAG
* *
270963 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATGAAAAT
270982 CATGTATTTTCATGAAAAT
1 CATGTATTTTCATGAAAAT
271001 CATGTATTTTCA
1 CATGTATTTTCA
271013 AATGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATGAAAAT
Found at i:271237 original size:121 final size:122
Alignment explanation
Indices: 271085--271328 Score: 445
Period size: 122 Copynumber: 2.0 Consensus size: 122
271075 TAAATAGGCT
271085 AGGCTATTTACATTGTAAGACAACCCTTTGATAATAT-AAAATCCTTGTGAGATTATTCTCTCTT
1 AGGCTATTTACATTGTAAGACAACCCTTTGATAATATAAAAATCCTTGTGAGATTATTCTCTCTT
* *
271149 CAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
66 CAAGTTCTTTTGAGAACTATATCGATAAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
271206 AGGCTATTTACATTGTAAGACAACCCTTTGATAATATAAAAATCCTTGTGAGATTATTCTCTCTT
1 AGGCTATTTACATTGTAAGACAACCCTTTGATAATATAAAAATCCTTGTGAGATTATTCTCTCTT
* *
271271 CAAGTTCTTTTGAGAACTATTTTGATAAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
66 CAAGTTCTTTTGAGAACTATATCGATAAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
271328 A
1 A
271329 ACCCTTCATT
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
121 37 0.31
122 81 0.69
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (122 bp):
AGGCTATTTACATTGTAAGACAACCCTTTGATAATATAAAAATCCTTGTGAGATTATTCTCTCTT
CAAGTTCTTTTGAGAACTATATCGATAAAGCAAGCTTTTCTAAAGTTTGTGGCGTCA
Found at i:271504 original size:13 final size:14
Alignment explanation
Indices: 271475--271510 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
271465 ACTATTTGTT
*
271475 CATCACCATATTTC
1 CATCACCATACTTC
271489 CATCACCAT-CTTC
1 CATCACCATACTTC
271502 CATCACCAT
1 CATCACCAT
271511 TCACGTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.28, C:0.42, G:0.00, T:0.31
Consensus pattern (14 bp):
CATCACCATACTTC
Found at i:271686 original size:15 final size:15
Alignment explanation
Indices: 271666--271696 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
271656 TCTTTGATAA
271666 CAATTCTATCCATTT
1 CAATTCTATCCATTT
*
271681 CAATTCTTTCCATTT
1 CAATTCTATCCATTT
271696 C
1 C
271697 CATTTCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (15 bp):
CAATTCTATCCATTT
Found at i:272002 original size:14 final size:14
Alignment explanation
Indices: 271979--272020 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
271969 TTTCAAGTGC
271979 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAA-A
271994 AAAAG-AAGAAAAA
1 AAAAGAAAGAAAAA
**
272007 AAATCAAAGAAAAA
1 AAAAGAAAGAAAAA
272021 GAACTGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 15 0.62
15 5 0.21
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAGAAAGAAAAA
Found at i:275159 original size:19 final size:20
Alignment explanation
Indices: 275135--275180 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
275125 TGGCCAAGAG
*
275135 CATGTATCTTAAT-TAAAAT
1 CATGTATCTTAATCAAAAAT
* *
275154 CATGTATTTTCATCAAAAAT
1 CATGTATCTTAATCAAAAAT
275174 CATGTAT
1 CATGTAT
275181 TTTCAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (20 bp):
CATGTATCTTAATCAAAAAT
Found at i:275995 original size:20 final size:19
Alignment explanation
Indices: 275960--275999 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
275950 GTGCTGCAAC
275960 AAAAAGCAAAAGAAAGAAG
1 AAAAAGCAAAAGAAAGAAG
*
275979 AAAAA-CAAAAGCAA-AAG
1 AAAAAGCAAAAGAAAGAAG
275996 AAAA
1 AAAA
276000 GACTCCTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAGCAAAAGAAAGAAG
Found at i:279602 original size:13 final size:14
Alignment explanation
Indices: 279575--279610 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
279565 ACTATTTTTT
279575 CATCACCATCTTTC
1 CATCACCATCTTTC
279589 CATCACCATC-TTC
1 CATCACCATCTTTC
279602 CATCACCAT
1 CATCACCAT
279611 TCACGCCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.25, C:0.44, G:0.00, T:0.31
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:279786 original size:15 final size:15
Alignment explanation
Indices: 279766--279796 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
279756 TCTTTGATAA
279766 CAATTCTATCCATTT
1 CAATTCTATCCATTT
*
279781 CAATTCTTTCCATTT
1 CAATTCTATCCATTT
279796 C
1 C
279797 CATTTCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (15 bp):
CAATTCTATCCATTT
Found at i:280337 original size:19 final size:16
Alignment explanation
Indices: 280313--280356 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 16
280303 TATATTTGCT
280313 TAACCATTCTATCATACC
1 TAACCATTCTAT-AT-CC
280331 ATAACCATTTCTATATCC
1 -TAACCA-TTCTATATCC
280349 TAACCATT
1 TAACCATT
280357 TCATTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 6 0.25
18 2 0.08
19 8 0.33
20 6 0.25
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (16 bp):
TAACCATTCTATATCC
Found at i:280354 original size:17 final size:20
Alignment explanation
Indices: 280313--280358 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 20
280303 TATATTTGCT
280313 TAACCA-TTCTATCATACCA
1 TAACCATTTCTATCATACCA
280332 TAACCATTTCTAT-AT-CC-
1 TAACCATTTCTATCATACCA
280349 TAACCATTTC
1 TAACCATTTC
280359 ATTTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.38
18 2 0.08
19 8 0.31
20 6 0.23
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (20 bp):
TAACCATTTCTATCATACCA
Found at i:282043 original size:13 final size:14
Alignment explanation
Indices: 282011--282045 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
282001 ACTATTTGTT
282011 CATCACCATCTTTA
1 CATCACCATCTTTA
*
282025 CATCACCATC-TTC
1 CATCACCATCTTTA
282038 CATCACCA
1 CATCACCA
282046 GTCACGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (14 bp):
CATCACCATCTTTA
Found at i:282222 original size:15 final size:15
Alignment explanation
Indices: 282202--282232 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
282192 TCTTTGATAA
282202 CAATTCTATCCATTT
1 CAATTCTATCCATTT
*
282217 CAATTCTTTCCATTT
1 CAATTCTATCCATTT
282232 C
1 C
282233 CATTTCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.48
Consensus pattern (15 bp):
CAATTCTATCCATTT
Found at i:282479 original size:20 final size:19
Alignment explanation
Indices: 282444--282483 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
282434 GTGCTGGAAC
282444 AAAAAGCAAAAGAAAGAAG
1 AAAAAGCAAAAGAAAGAAG
*
282463 AAAAA-CAAAAGCAA-AAG
1 AAAAAGCAAAAGAAAGAAG
282480 AAAA
1 AAAA
282484 GACTCCTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAGCAAAAGAAAGAAG
Done.