Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 112 of 444
Found at i:28325448 original size:12 final size:12
Alignment explanation
Indices: 28325428--28325463 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
28325418 TGGGATATGC
*
28325428 AATGTATGAATG
1 AATGCATGAATG
28325440 AATGCATGAATG
1 AATGCATGAATG
28325452 AATGCATGAATG
1 AATGCATGAATG
28325464 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:28327452 original size:10 final size:11
Alignment explanation
Indices: 28327413--28327452 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
28327403 TGGTATTTAA
28327413 ATATATA-TAT
1 ATATATAGTAT
28327423 ATATATA-TAT
1 ATATATAGTAT
28327433 ATATAT-GTAT
1 ATATATAGTAT
28327443 ATA-ATAGTAT
1 ATATATAGTAT
28327453 TTAAGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.07
10 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (11 bp):
ATATATAGTAT
Found at i:28327464 original size:2 final size:2
Alignment explanation
Indices: 28327413--28327445 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28327403 TGGTATTTAA
*
28327413 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28327446 ATAGTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28327703 original size:12 final size:12
Alignment explanation
Indices: 28327666--28327708 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
28327656 ATGTATATAT
28327666 AAAGAAAGAAAAA
1 AAAGAAAG-AAAA
* *
28327679 AAACAACACAAAA
1 AAAGAA-AGAAAA
28327692 AAAGAAAGAAAA
1 AAAGAAAGAAAA
28327704 AAAGA
1 AAAGA
28327709 TTCGAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 10 0.40
13 14 0.56
14 1 0.04
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:28328006 original size:18 final size:18
Alignment explanation
Indices: 28327978--28328059 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
28327968 GGCTAGGTTT
28327978 TTTTATCTTTTTTGTTAGG
1 TTTT-TCTTTTTTGTTAGG
* **
28327997 TTTTTCTTTTTTCTT-CT
1 TTTTTCTTTTTTGTTAGG
*
28328014 TTTTTTTTTTTTGGTTAGG
1 TTTTTCTTTTTT-GTTAGG
** *
28328033 -TTTT-TTTTGGGGTAGG
1 TTTTTCTTTTTTGTTAGG
28328049 TTTTTCTTTTT
1 TTTTTCTTTTT
28328060 CTTTTTTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
16 5 0.10
17 19 0.40
18 20 0.42
19 4 0.08
ACGTcount: A:0.05, C:0.06, G:0.16, T:0.73
Consensus pattern (18 bp):
TTTTTCTTTTTTGTTAGG
Found at i:28328036 original size:16 final size:16
Alignment explanation
Indices: 28328017--28328100 Score: 61
Period size: 16 Copynumber: 5.5 Consensus size: 16
28328007 TTCTTCTTTT
28328017 TTTTTTTTTGGTTAGG
1 TTTTTTTTTGGTTAGG
* *
28328033 TTTTTTTTGGGGTAGG
1 TTTTTTTTTGGTTAGG
* *
28328049 TTTTTCTTT--TT--C
1 TTTTTTTTTGGTTAGG
* * *
28328061 TTTTTTTTT-CTTTGT
1 TTTTTTTTTGGTTAGG
28328076 TTTTTTTTTGGGTTAGG
1 TTTTTTTTT-GGTTAGG
28328093 TTTTTTTT
1 TTTTTTTT
28328101 GGGGGGCTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
12 8 0.15
13 2 0.04
14 1 0.02
15 9 0.17
16 21 0.40
17 11 0.21
ACGTcount: A:0.04, C:0.04, G:0.19, T:0.74
Consensus pattern (16 bp):
TTTTTTTTTGGTTAGG
Found at i:28328065 original size:44 final size:45
Alignment explanation
Indices: 28328004--28328097 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 45
28327994 AGGTTTTTCT
* *
28328004 TTTTTCTTCTTTTTTTTTTTTTGGTTAG-GTTTTTTTTGGGGTAGG
1 TTTTTCTTCTTTCTTTTTTTTT-CTTAGTGTTTTTTTTGGGGTAGG
* * *
28328049 TTTTTCTT-TTTCTTTTTTTTTCTTTGTTTTTTTTTTGGGTTAGG
1 TTTTTCTTCTTTCTTTTTTTTTCTTAGTGTTTTTTTTGGGGTAGG
28328093 TTTTT
1 TTTTT
28328098 TTTGGGGGGC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 3 0.07
44 32 0.74
45 8 0.19
ACGTcount: A:0.03, C:0.05, G:0.17, T:0.74
Consensus pattern (45 bp):
TTTTTCTTCTTTCTTTTTTTTTCTTAGTGTTTTTTTTGGGGTAGG
Found at i:28328640 original size:29 final size:29
Alignment explanation
Indices: 28328600--28328702 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
28328590 GTTGAGAGAT
*
28328600 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
28328629 TGGCACTAAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
* **
28328658 TGGCACTAAGTGTGCGAG-TTTAAAGTATA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TGCA
28328687 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28328703 CGGCTGATTA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 5 0.07
29 64 0.93
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATGCA
Found at i:28332299 original size:16 final size:15
Alignment explanation
Indices: 28332278--28332325 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
28332268 GATGTGAATA
28332278 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
28332294 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
28332309 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
28332325 A
1 A
28332326 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:28332308 original size:8 final size:8
Alignment explanation
Indices: 28332274--28332325 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
28332264 CAATGATGTG
*
28332274 AATAATAA
1 AATATTAA
28332282 AATATATAA
1 AATAT-TAA
28332291 AATA-TAA
1 AATATTAA
28332298 AATATTAA
1 AATATTAA
*
28332306 AATATCAA
1 AATATTAA
*
28332314 AATATTAG
1 AATATTAA
28332322 AATA
1 AATA
28332326 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:28332325 original size:24 final size:24
Alignment explanation
Indices: 28332273--28332329 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
28332263 ACAATGATGT
*
28332273 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
28332297 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
28332321 GAATAATAA
1 GAATAATAA
28332330 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:28332543 original size:22 final size:24
Alignment explanation
Indices: 28332480--28332544 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
28332470 CGTGATAATA
*
28332480 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
28332505 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
28332528 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
28332545 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:28333272 original size:30 final size:30
Alignment explanation
Indices: 28333235--28333323 Score: 144
Period size: 30 Copynumber: 3.0 Consensus size: 30
28333225 TGGAGCAAGT
* *
28333235 GTGGCTAGTGGATTTGGTGGTGGAAAATGTA
1 GTGGCTAGTGGAGTTGGTGGTGGAAAA-GGA
28333266 -TGGCTAGTGGAGTTGGTGGTGGAAAAGGA
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
28333295 GTGGCTAGTGGAGTTGGTGGTGGAAAAGG
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAGG
28333324 CTAAGATTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
29 2 0.04
30 53 0.96
ACGTcount: A:0.22, C:0.03, G:0.47, T:0.27
Consensus pattern (30 bp):
GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
Found at i:28339888 original size:14 final size:14
Alignment explanation
Indices: 28339865--28339894 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28339855 TTGAAATTAT
28339865 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
28339879 GTTGATTTGGATTG
1 GTTGAATTGGATTG
28339893 GT
1 GT
28339895 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:28340839 original size:2 final size:2
Alignment explanation
Indices: 28340832--28340865 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28340822 ACCAGAACAG
28340832 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
28340866 GTGGCGAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28351564 original size:24 final size:24
Alignment explanation
Indices: 28351536--28351598 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
28351526 TTTCTAGAAG
* *
28351536 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
28351560 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
* *
28351584 ATTTGGCATTGATTA
1 ATTTAGCATTTATTA
28351599 CAATTAGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:28352863 original size:22 final size:22
Alignment explanation
Indices: 28352824--28352868 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28352814 TTAGACAAAG
* *
28352824 AAAAATGTAAGTATCAAATTGA
1 AAAAATGTAAGTACCAAACTGA
* *
28352846 AAAAATTTAAGTGCCAAACTGA
1 AAAAATGTAAGTACCAAACTGA
28352868 A
1 A
28352869 CATTTAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.24
Consensus pattern (22 bp):
AAAAATGTAAGTACCAAACTGA
Found at i:28354587 original size:21 final size:22
Alignment explanation
Indices: 28354558--28354599 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
28354548 TGTTGAATCT
*
28354558 AATTAATTTTTTTAT-TTAAAA
1 AATTAATTTTTATATATTAAAA
*
28354579 AATTTATTTTTATATATTAAA
1 AATTAATTTTTATATATTAAA
28354600 TCAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTAATTTTTATATATTAAAA
Found at i:28357023 original size:19 final size:21
Alignment explanation
Indices: 28356999--28357038 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28356989 ATTATATAAA
28356999 AAATTTA-AAT-AATAAATAT
1 AAATTTATAATAAATAAATAT
*
28357018 AAATTTATATTAAATAAATAT
1 AAATTTATAATAAATAAATAT
28357039 CATTTTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTTATAATAAATAAATAT
Found at i:28365820 original size:2 final size:2
Alignment explanation
Indices: 28365813--28365851 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
28365803 ACACATACTC
*
28365813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28365852 ACCAACCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:28366192 original size:21 final size:20
Alignment explanation
Indices: 28366168--28366218 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
28366158 ATTCATAACA
*
28366168 TATTCAATTCTCATCACTTGC
1 TATTCAAATCTCAT-ACTTGC
28366189 TATTTCAAATCTCATACTTGC
1 TA-TTCAAATCTCATACTTGC
*
28366210 TATACAAAT
1 TATTCAAAT
28366219 AGCTTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 6 0.22
21 10 0.37
22 11 0.41
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (20 bp):
TATTCAAATCTCATACTTGC
Found at i:28366195 original size:22 final size:21
Alignment explanation
Indices: 28366170--28366212 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
28366160 TCATAACATA
*
28366170 TTCAATTCTCATCACTTGCTAT
1 TTCAAATCTCAT-ACTTGCTAT
28366192 TTCAAATCTCATACTTGCTAT
1 TTCAAATCTCATACTTGCTAT
28366213 ACAAATAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCAAATCTCATACTTGCTAT
Found at i:28366703 original size:2 final size:2
Alignment explanation
Indices: 28366696--28366727 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28366686 AATTCATTCA
28366696 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
28366728 CTACTAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28367495 original size:5 final size:5
Alignment explanation
Indices: 28367496--28367534 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
28367486 TTTATATTAT
28367496 TATAA TATAA TATAA TATAA TATAA TAT-A TATATA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATA
28367535 TTTACTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.12
5 23 0.72
6 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:28371155 original size:28 final size:28
Alignment explanation
Indices: 28371086--28371186 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28371076 GACAAGATTG
* * * *
28371086 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
28371116 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28371144 GCACTAAGTGTGCGAG-CTGATTGTATATA
1 GCACTAAGTGTGCGAGTTTGA-T-TATATA
28371173 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28371187 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 23 0.36
29 20 0.31
30 18 0.28
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28371180 original size:29 final size:28
Alignment explanation
Indices: 28371115--28371186 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
28371105 AAAATTGTAC
*
28371115 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
28371143 AGCACTAAGTGTGCGAG-CTGATTGTATAT
1 AGCACTAAGTGTGCGAGTCTGA-T-TATAT
28371172 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28371187 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 3 0.07
28 18 0.44
29 20 0.49
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:28378799 original size:28 final size:28
Alignment explanation
Indices: 28378730--28378830 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28378720 GACAAGATTG
* * * *
28378730 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
28378760 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28378788 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
28378817 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28378831 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28378824 original size:29 final size:28
Alignment explanation
Indices: 28378759--28378830 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
28378749 AAAATTGTAC
*
28378759 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
28378787 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
28378816 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28378831 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:28382728 original size:30 final size:30
Alignment explanation
Indices: 28382692--28382822 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
28382682 GACAAGATTG
* * * * *
28382692 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
28382722 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
28382750 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
28382780 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
28382809 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28382823 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:28382783 original size:58 final size:58
Alignment explanation
Indices: 28382692--28382822 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
28382682 GACAAGATTG
* * * * * *
28382692 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
28382750 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
28382809 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28382823 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:28390699 original size:28 final size:29
Alignment explanation
Indices: 28390630--28390703 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
28390620 GACAAGATTG
* *
28390630 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-AAATTATACA
* *
28390660 GCACTAAGTGTGCGAGTTT-GATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTATACA
28390688 GCACTAAGTGTGCGAG
1 GCACTAAGTGTGCGAG
28390704 CTGAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 22 0.55
30 18 0.45
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTTAAATTATACA
Found at i:28390714 original size:28 final size:28
Alignment explanation
Indices: 28390659--28390723 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
28390649 AAAATTGTAC
* **
28390659 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGAAAATAT
28390687 AGCACTAAGTGTGCGAG-CTGAAAAATAT
1 AGCACTAAGTGTGCGAGTCTG-AAAATAT
*
28390715 A-TACTAAGT
1 AGCACTAAGT
28390724 AAGTGTGCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGAAAATAT
Found at i:28392999 original size:15 final size:15
Alignment explanation
Indices: 28392979--28393009 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28392969 GTTCTTTTGA
28392979 TATGTTTGAATGTGG
1 TATGTTTGAATGTGG
*
28392994 TATGTTTGGATGTGG
1 TATGTTTGAATGTGG
28393009 T
1 T
28393010 TGACATATGG
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:0.16, C:0.00, G:0.35, T:0.48
Consensus pattern (15 bp):
TATGTTTGAATGTGG
Found at i:28403145 original size:46 final size:46
Alignment explanation
Indices: 28403095--28403270 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
28403085 TGGTTGAGCA
28403095 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
28403141 TCCGAACTCGTTGAGTTGAGTCCGAGTT---TGA-GAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
*
28403186 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28403234 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28403271 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 8, Indels: 22
0.79 0.06 0.16
Matches are distributed among these distances:
42 3 0.03
43 7 0.06
45 1 0.01
46 62 0.56
47 28 0.25
48 1 0.01
50 6 0.05
51 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28403206 original size:93 final size:93
Alignment explanation
Indices: 28403092--28403261 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 93
28403082 GGATGGTTGA
* *
28403092 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28403157 TGAGTCCGAGTTTGAGAGATGTAACTAG
66 TGAGTCCGAGTTTGAGAGATGTAACTAG
*
28403185 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28403250 TGAGTCCGAGTT
66 TGAGTCCGAGTT
28403262 CGCTTATGGG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTTGAGAGATGTAACTAG
Found at i:28410679 original size:46 final size:46
Alignment explanation
Indices: 28410629--28410802 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
28410619 GGTTGAGCAT
28410629 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* *
28410675 CGAACTCGTTGAGTTGAGTCCGAGTT---TGA-GAGATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G--TC
* *
28410722 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* *
28410768 CGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28410803 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
42 3 0.03
43 7 0.06
45 1 0.01
46 60 0.55
47 28 0.26
48 1 0.01
50 6 0.06
51 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
Found at i:28410739 original size:93 final size:92
Alignment explanation
Indices: 28410625--28410793 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 92
28410615 GGATGGTTGA
* *
28410625 GCATCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 GCATCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
28410690 GAGTCCGAGTTTGAGAGATGTAACTAG
66 GAGTCCGAGTTTGAGAGATGTAACTAG
*
28410717 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCAT-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28410782 TGAGTCCGAGTT
65 TGAGTCCGAGTT
28410794 CGCTTATGGG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 4 0.05
93 69 0.95
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (92 bp):
GCATCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTTGAGAGATGTAACTAG
Found at i:28414278 original size:31 final size:31
Alignment explanation
Indices: 28414240--28414334 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
28414230 CCTTTTCATA
* *
28414240 TTTCATATTTCATAATACTGGGTCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
28414271 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
28414302 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
28414333 TT
1 TT
28414335 ACTGTAAACG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:28414577 original size:24 final size:24
Alignment explanation
Indices: 28414526--28414644 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
28414516 GCTTTATCAT
*
28414526 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
28414551 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
28414575 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
28414598 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
28414622 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
28414645 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.26
24 52 0.60
25 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:28414605 original size:47 final size:48
Alignment explanation
Indices: 28414526--28414644 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
28414516 GCTTTATCAT
*
28414526 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
28414575 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
28414622 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
28414645 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 44 0.68
48 9 0.14
49 12 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Found at i:28414720 original size:20 final size:20
Alignment explanation
Indices: 28414695--28414754 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
28414685 TATGATTACC
28414695 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
28414715 TCATGTGCATATCATACATT
1 TCATGTGCATATCATACATA
28414735 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
28414755 CCATATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:28414725 original size:11 final size:11
Alignment explanation
Indices: 28414695--28414749 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
28414685 TATGATTACC
28414695 TCATGTGCATA
1 TCATGTGCATA
*
28414706 TCA--TACATA
1 TCATGTGCATA
28414715 TCATGTGCATA
1 TCATGTGCATA
* *
28414726 TCA--TACATT
1 TCATGTGCATA
28414735 TCATGTGCATA
1 TCATGTGCATA
28414746 TCAT
1 TCAT
28414750 ACATACCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:28414829 original size:25 final size:25
Alignment explanation
Indices: 28414797--28414844 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28414787 ATACATAAAC
* * *
28414797 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
28414822 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
28414845 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:28420692 original size:22 final size:22
Alignment explanation
Indices: 28420665--28420723 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 22
28420655 GTGTCGAAGG
* *
28420665 CACACGGGAGTGTCCCTGTGTC
1 CACACGGGCGTGTCCCTATGTC
28420687 CACACGGGCGTATGTCCCTATGTC
1 CACACGGGCG--TGTCCCTATGTC
28420711 CACACGGGCGTGT
1 CACACGGGCGTGT
28420724 GACCCTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 12 0.36
24 21 0.64
ACGTcount: A:0.15, C:0.32, G:0.31, T:0.22
Consensus pattern (22 bp):
CACACGGGCGTGTCCCTATGTC
Found at i:28420710 original size:24 final size:24
Alignment explanation
Indices: 28420675--28420721 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
28420665 CACACGGGAG
*
28420675 TGTCCCTGTGTCCACACGGGCGTA
1 TGTCCCTATGTCCACACGGGCGTA
28420699 TGTCCCTATGTCCACACGGGCGT
1 TGTCCCTATGTCCACACGGGCGT
28420722 GTGACCCTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.26
Consensus pattern (24 bp):
TGTCCCTATGTCCACACGGGCGTA
Found at i:28433584 original size:287 final size:287
Alignment explanation
Indices: 28433020--28433545 Score: 790
Period size: 287 Copynumber: 1.8 Consensus size: 287
28433010 ATTACTTATA
* * * ** *
28433020 TCTGGAGCTACAGAACTCCAAATTAAGATTAGCCAATTCTCCTTGAAACTAGACTCACATATCTT
1 TCTGAAGCTACAGAACTCAAAATTAAGATTAGCAAATTCTCCTCCAAACTAGACCCACATATCTT
** *
28433085 CTTACCATAAAATTTTTAGAATTTTTGGTCTAGCCAATAAGTACAGTTTATTCTTTAAAGTCTCC
66 CTTACCATAAAATTTTTAGAATTTTTACTCTAGCCAATAAGTACAATTTATTCTTTAAAGTCTCC
* *
28433150 CTGTTTTGCTGTTTGACAGCTTCAACCTTTCTTCACTAAAATTTATTTATCTCTTAGTACGAGAT
131 CTGTTTTACTGTTTGACAACTTCAACCTTTCTTCACTAAAATTTATTTATCTCTTAGTACGAGAT
* *
28433215 TCAAATAATGTTCCTATCTATTTCTCTTGATAATACACTCATTAAGGGCTGAGCCATATGAATTC
196 TCAAATAATGTTCCTATCTATTTCTCTTGAAAATACACTCATTAAGGGCTGAGCAATATGAATTC
28433280 TAACCTAATATTATTTTTTTTAAAATT
261 TAACCTAATATTATTTTTTTTAAAATT
* *
28433307 TCTGAAGCTACGGAACTCAAAATTAAGATCTA-CAAATTTTCC-CCAAAGCTAGACCCACATATC
1 TCTGAAGCTACAGAACTCAAAATTAAGAT-TAGCAAATTCTCCTCCAAA-CTAGACCCACATATC
* *
28433370 TTCTTA-CATAAAATTTTTAGAATTTTTACTCTAGCCAGTAAGTACAATTTATTCTTTAAATTCT
64 TTCTTACCATAAAATTTTTAGAATTTTTACTCTAGCCAATAAGTACAATTTATTCTTTAAAGTCT
* *
28433434 CCCCTGTTTTACTGTTTGATAACTTCGACCTTTCTTCACTAAAATTTATTTATCTCTTAGTACGA
129 -CCCTGTTTTACTGTTTGACAACTTCAACCTTTCTTCACTAAAATTTATTTATCTCTTAGTACGA
* * *
28433499 GATTCAGATAATGTT-CTCGTCTATTTCTCTTGAAAATATACTCATTA
193 GATTCAAATAATGTTCCT-ATCTATTTCTCTTGAAAATACACTCATTA
28433546 CAGGCTTATT
Statistics
Matches: 214, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
286 58 0.27
287 154 0.72
288 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (287 bp):
TCTGAAGCTACAGAACTCAAAATTAAGATTAGCAAATTCTCCTCCAAACTAGACCCACATATCTT
CTTACCATAAAATTTTTAGAATTTTTACTCTAGCCAATAAGTACAATTTATTCTTTAAAGTCTCC
CTGTTTTACTGTTTGACAACTTCAACCTTTCTTCACTAAAATTTATTTATCTCTTAGTACGAGAT
TCAAATAATGTTCCTATCTATTTCTCTTGAAAATACACTCATTAAGGGCTGAGCAATATGAATTC
TAACCTAATATTATTTTTTTTAAAATT
Found at i:28434208 original size:48 final size:48
Alignment explanation
Indices: 28434137--28434324 Score: 179
Period size: 48 Copynumber: 3.9 Consensus size: 48
28434127 TAAAGTACCA
* *
28434137 ATGCCATATCCTC-GACATGGTCTTACA-TGAATCCACATATCATCGCCG
1 ATGCCATGTCC-CAGACATGGTCTTACACTG-ATCCACATATCATCACCG
* * **
28434185 ATGCCATGTCCTAGACATGGTCTTACACTG-GCACACATATCATCACTA
1 ATGCCATGTCCCAGACATGGTCTTACACTGATC-CACATATCATCACCG
* * * *
28434233 ATGCCATG-CCCAGATATGGTCTTACACCGGGA-ACATATATCATCACCG
1 ATGCCATGTCCCAGACATGGTCTTACA-C-TGATCCACATATCATCACCG
* * *
28434281 ATGCCATGTCCCAAACATGGTCTTACACTGGTACACATATCATC
1 ATGCCATGTCCCAGACATGGTCTTACACTGATCCACATATCATC
28434325 TCCAATGTAA
Statistics
Matches: 114, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
47 18 0.16
48 77 0.68
49 19 0.17
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGATCCACATATCATCACCG
Found at i:28437155 original size:20 final size:20
Alignment explanation
Indices: 28437132--28437169 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28437122 CACATCCAAA
*
28437132 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
28437152 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
28437170 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:28445111 original size:20 final size:20
Alignment explanation
Indices: 28445088--28445125 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28445078 CACATCCAAA
*
28445088 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
28445108 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
28445126 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:28447969 original size:38 final size:38
Alignment explanation
Indices: 28447901--28447973 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
28447891 ACCAGTTTGG
*
28447901 CACCCAGTGCCTCATCGGATAGTTCAAAGTAAAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCAAAGTAAAGTTGA
* * *
28447939 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAAAGT
1 CACCCAGTGCCTCATCGG-ATAGTCCAAAGTAAAGT
28447974 GGTACCTAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 27 0.90
39 3 0.10
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGATAGTCCAAAGTAAAGTTGA
Found at i:28448684 original size:17 final size:18
Alignment explanation
Indices: 28448650--28448685 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28448640 TGAATTTCTA
28448650 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
28448668 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
28448685 T
1 T
28448686 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:28449216 original size:24 final size:25
Alignment explanation
Indices: 28449184--28449251 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 25
28449174 TGTTTTATTT
*
28449184 ATTTTATTAATT-TAATATAT-TATA
1 ATTTAATTAATTATAA-ATATCTATA
*
28449208 ATTTAATT-ATTATAAATATCTATC
1 ATTTAATTAATTATAAATATCTATA
* *
28449232 ATATAATTAATAATATAATA
1 ATTTAATTAATTATA-AATA
28449252 CAAATGTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 7 0.19
24 20 0.56
25 5 0.14
26 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTAATTAATTATAAATATCTATA
Found at i:28449220 original size:14 final size:15
Alignment explanation
Indices: 28449191--28449222 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28449181 TTTATTTTAT
28449191 TAATTTAATATATTA
1 TAATTTAATATATTA
28449206 TAATTTAAT-TATTA
1 TAATTTAATATATTA
28449220 TAA
1 TAA
28449223 ATATCTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTTAATATATTA
Found at i:28449364 original size:19 final size:19
Alignment explanation
Indices: 28449340--28449392 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
28449330 TAAAAATATT
*
28449340 ATAAATAATTATTTAATTA
1 ATAAATAATTATTTAAATA
*
28449359 ATAAAT-ATTATTAAAAATA
1 ATAAATAATTATT-TAAATA
28449378 ATAAA-AATCTATTTA
1 ATAAATAAT-TATTTA
28449393 CTTTGATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 6 0.21
19 18 0.64
20 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAATAATTATTTAAATA
Found at i:28452983 original size:42 final size:43
Alignment explanation
Indices: 28452906--28453007 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 43
28452896 TCTCGAACAT
* * **
28452906 GGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGATAG
1 GGTCTTACACGTAAATCAATATCGATGCCGATGTCCCAGATAG
*
28452949 GGTCTTACACG-AAATCAGATA-CGATGCCGATGTCCCAGATAT
1 GGTCTTACACGTAAATCA-ATATCGATGCCGATGTCCCAGATAG
*
28452991 GGTCTTATACGTAAATC
1 GGTCTTACACGTAAATC
28453008 TCAATCGAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
42 33 0.65
43 18 0.35
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAATATCGATGCCGATGTCCCAGATAG
Found at i:28464551 original size:48 final size:48
Alignment explanation
Indices: 28464480--28464666 Score: 186
Period size: 48 Copynumber: 3.9 Consensus size: 48
28464470 TAAAGTACCA
* *
28464480 ATGCCATGTCCTCA-ACATGGTCTTACA-T-GAATCCACATATCATTGTCG
1 ATGCCATGTCC-CAGACATGGTCTTACACTGGCA--CACATATCATTGACG
* * * *
28464528 ATGCCATGTCCTAGACATGGTCTTACATTGGCACACATATCA-TCACTA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATTGAC-G
* * *
28464576 ATGCCATG-CCCAGACATGGTCTTACACCGGGCACATATATCATTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACA-CTGGCACACATATCATTGACG
* * *
28464624 ATGCCATGTCCCAAACATGGTCTTACACTGGTACACATGTCAT
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAT
28464667 CACCAAAACA
Statistics
Matches: 115, Mismatches: 17, Indels: 14
0.79 0.12 0.10
Matches are distributed among these distances:
47 20 0.17
48 73 0.63
49 20 0.17
50 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATTGACG
Found at i:28468060 original size:40 final size:40
Alignment explanation
Indices: 28468015--28468221 Score: 222
Period size: 40 Copynumber: 5.2 Consensus size: 40
28468005 CGGAATATAA
* *
28468015 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATAAC-TCGCACAAATGCCTTCGGGCCTTAGC
* *
28468055 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
* *
28468095 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
** * * * *
28468135 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
** * * *
28468175 CCGGATATAATTTC-CAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATAACTC-GCACAAATGCCTTCGGGCCTTAGC
28468214 CCGGATAT
1 CCGGATAT
28468222 CATTCAATTT
Statistics
Matches: 146, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
39 14 0.10
40 132 0.90
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
Found at i:28469069 original size:17 final size:19
Alignment explanation
Indices: 28469046--28469091 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
28469036 AAGAAGCATG
28469046 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
28469064 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
28469082 AATCATGCTC
1 AATCATGCTC
28469092 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:28476111 original size:40 final size:40
Alignment explanation
Indices: 28476066--28476272 Score: 222
Period size: 40 Copynumber: 5.2 Consensus size: 40
28476056 CGGAATATAA
* *
28476066 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATAAC-TCGCACAAATGCCTTCGGGCCTTAGC
* *
28476106 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
* *
28476146 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
** * * * *
28476186 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
** * * *
28476226 CCGGATATAATTTC-CAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATAACTC-GCACAAATGCCTTCGGGCCTTAGC
28476265 CCGGATAT
1 CCGGATAT
28476273 CATTCAATTT
Statistics
Matches: 146, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
39 14 0.10
40 132 0.90
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAATAACTCGCACAAATGCCTTCGGGCCTTAGC
Found at i:28477121 original size:17 final size:19
Alignment explanation
Indices: 28477098--28477143 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
28477088 AAGAAGCATG
28477098 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
28477116 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
28477134 AATCATGCTC
1 AATCATGCTC
28477144 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:28481027 original size:26 final size:26
Alignment explanation
Indices: 28480998--28481048 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
28480988 AGTATCAGAT
28480998 CGAACTGCTCAATCACAATATCGCAC
1 CGAACTGCTCAATCACAATATCGCAC
* * *
28481024 CGAAGTGCTCAATCATATTATCGCA
1 CGAACTGCTCAATCACAATATCGCA
28481049 TCAAAATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (26 bp):
CGAACTGCTCAATCACAATATCGCAC
Found at i:28484157 original size:18 final size:19
Alignment explanation
Indices: 28484136--28484181 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
28484126 ATATTAAATG
**
28484136 TAAAATGTGATTTTTTA-A
1 TAAAATGTGATTTTAAAGA
*
28484154 TAAAAT-TTATTTTAAAGA
1 TAAAATGTGATTTTAAAGA
28484172 TAAAATGTGA
1 TAAAATGTGA
28484182 AATTAATACC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (19 bp):
TAAAATGTGATTTTAAAGA
Found at i:28504500 original size:31 final size:31
Alignment explanation
Indices: 28504465--28504528 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
28504455 GAATATGAAA
28504465 TGATAGTATGGCGTGAAATTGAATTATTCAT
1 TGATAGTATGGCGTGAAATTGAATTATTCAT
28504496 TGATAGTATGGCGTGAAATTGAATTATTCAT
1 TGATAGTATGGCGTGAAATTGAATTATTCAT
28504527 TG
1 TG
28504529 GAAAATGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.39
Consensus pattern (31 bp):
TGATAGTATGGCGTGAAATTGAATTATTCAT
Found at i:28504710 original size:49 final size:49
Alignment explanation
Indices: 28504657--28505028 Score: 563
Period size: 49 Copynumber: 7.7 Consensus size: 49
28504647 GATTCTACGC
* * *
28504657 GATGAATGTGAATGTGTATAAATATGAGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGT
*
28504706 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGT
*
28504755 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGT
*
28504804 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGT
*
28504853 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGT
* *
28504902 GATGAATGTGAAAATGTAT--ATATGTGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGT
* * * * * * *
28504949 GATGAATGTGAAAGTGTACATATATGTGATAGGGCCGAGTGGCCAACGT
1 GATGAATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGT
*
28504998 GATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 GATGAATGTGAAAGTGTATACATATGTGATAAG
28505029 TCCCGAAGGG
Statistics
Matches: 304, Mismatches: 17, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
47 53 0.17
48 1 0.00
49 250 0.82
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.28
Consensus pattern (49 bp):
GATGAATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGT
Found at i:28507189 original size:40 final size:40
Alignment explanation
Indices: 28507129--28507438 Score: 548
Period size: 40 Copynumber: 7.8 Consensus size: 40
28507119 GAATTGAGAT
*
28507129 TGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
28507169 TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
*
28507209 TGATGTATCCGGACTAAGCTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
*
28507249 TGATGTATCCGGACTAAGCTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
28507289 TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
*
28507329 TGATGTATCCGGACTAAGTTCTGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
*
28507369 TGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCTAG
1 TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
* * *
28507409 TGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 TGATGTATCCGGACTAAGTTCCGAAGAGCA
28507439 ATCATGCTGG
Statistics
Matches: 262, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 262 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAG
Found at i:28511006 original size:31 final size:31
Alignment explanation
Indices: 28510971--28511034 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
28510961 GAATATGAAA
28510971 TGATAGTATGGCGTGAAATTGAATTATTCAT
1 TGATAGTATGGCGTGAAATTGAATTATTCAT
28511002 TGATAGTATGGCGTGAAATTGAATTATTCAT
1 TGATAGTATGGCGTGAAATTGAATTATTCAT
28511033 TG
1 TG
28511035 GAAAATGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.39
Consensus pattern (31 bp):
TGATAGTATGGCGTGAAATTGAATTATTCAT
Found at i:28511216 original size:49 final size:49
Alignment explanation
Indices: 28511163--28511681 Score: 803
Period size: 49 Copynumber: 10.7 Consensus size: 49
28511153 GATTCTACGC
* * * *
28511163 GATGAATGTGAATGTGTATAAATATGAGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
* *
28511212 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
*
28511261 GATGAATGTGAAAGCATATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
*
28511310 GATGAATGTGAAAGCATATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
*
28511359 GATGAATGTGAAAGCCTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
28511408 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
* *
28511457 GATGAATGTGAAAGCATATACATATGTGATAAGGCGTAATGGCCGATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
28511506 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
** *
28511555 GATGAATGTGAAAATGTAT--ATATGTGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
* ** * * * *
28511602 GATGAATGTGAAAGTGTATATTTATGTGATAGGGCCGAGTGGCCAATGT
1 GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
* *
28511651 GATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 GATGAATGTGAAAGCGTATACATATGTGATAAG
28511682 TCCCGAAGGG
Statistics
Matches: 445, Mismatches: 23, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
47 54 0.12
49 391 0.88
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (49 bp):
GATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGATGT
Found at i:28517322 original size:13 final size:13
Alignment explanation
Indices: 28517304--28517330 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28517294 GAAGTAATCG
28517304 CACACGGGCGTGT
1 CACACGGGCGTGT
28517317 CACACGGGCGTGT
1 CACACGGGCGTGT
28517330 C
1 C
28517331 CCTGCCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:28532607 original size:42 final size:41
Alignment explanation
Indices: 28532504--28532611 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
28532494 TACCATACCA
* *
28532504 ATGCCATATCCCAGATATGGTCTTACATGGGATTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAGATTCATATCG
* * * **
28532545 ATGCCAATAGCTCAGCTATGGTCTTACACGA-AGTCTTGTATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAGA-T-TCATATCG
28532588 ATGCCATATCCCAGATATGGTCTT
1 ATGCCATATCCCAGATATGGTCTT
28532612 TCATGTAATC
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
41 6 0.11
42 37 0.69
43 11 0.20
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACACGAGATTCATATCG
Found at i:28537424 original size:42 final size:42
Alignment explanation
Indices: 28537322--28537426 Score: 106
Period size: 43 Copynumber: 2.5 Consensus size: 42
28537312 TACAATTCCA
* * * *
28537322 ATGTCCTAGACGTGGTCTTACATGTAATCAAATATCGATGCC
1 ATGTCCAAGACATGGTCTTACACGAAATCAAATATCGATGCC
* *
28537364 ACTGTCCAAAACCA-GGTCTTACACGAAATCAAATAT-GATGCTG
1 A-TGTCCAAGA-CATGGTCTTACACGAAATCAAATATCGATGC-C
*
28537407 ATGTCCCAGACATGGTCTTA
1 ATGTCCAAGACATGGTCTTA
28537427 TACGTAATTC
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
41 2 0.04
42 20 0.39
43 28 0.55
44 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (42 bp):
ATGTCCAAGACATGGTCTTACACGAAATCAAATATCGATGCC
Found at i:28538592 original size:13 final size:13
Alignment explanation
Indices: 28538574--28538598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28538564 ACAAACGATT
28538574 AAATTTTCATACG
1 AAATTTTCATACG
28538587 AAATTTTCATAC
1 AAATTTTCATAC
28538599 ATACTATTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
AAATTTTCATACG
Found at i:28539694 original size:41 final size:40
Alignment explanation
Indices: 28539649--28539758 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
28539639 ATGACAAATT
*
28539649 GGCTATATATGGCACTTAGTGTGTGAGATCAAGATAGTTTC
1 GGCTATATATGGCACTTAGTGTGTGAGATCAA-ATAGCTTC
** *
28539690 GGCTATATATGGCACTTAGTGTGTGATTTGAAATAGCTTC
1 GGCTATATATGGCACTTAGTGTGTGAGATCAAATAGCTTC
* * * *
28539730 GGCTATGTACGACACTTGGTGTGTGAGAT
1 GGCTATATATGGCACTTAGTGTGTGAGAT
28539759 ATCGAGTATT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
40 30 0.51
41 29 0.49
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.35
Consensus pattern (40 bp):
GGCTATATATGGCACTTAGTGTGTGAGATCAAATAGCTTC
Found at i:28543926 original size:42 final size:43
Alignment explanation
Indices: 28543879--28543964 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
28543869 ATGAAAAAAG
28543879 TTAGTTTGATA-TTTTTATTTGTTAATTTAGATATAATTCAAC
1 TTAGTTTGATATTTTTTATTTGTTAATTTAGATATAATTCAAC
28543921 TTAGTTTGATATTTTTTATTTGTTAATTTAGATATAATTCAAC
1 TTAGTTTGATATTTTTTATTTGTTAATTTAGATATAATTCAAC
28543964 T
1 T
28543965 CTTATTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 11 0.26
43 32 0.74
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (43 bp):
TTAGTTTGATATTTTTTATTTGTTAATTTAGATATAATTCAAC
Found at i:28544589 original size:15 final size:16
Alignment explanation
Indices: 28544569--28544602 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28544559 ACTATAGTGG
*
28544569 AATGAC-TCGTGACTA
1 AATGACTTCATGACTA
28544584 AATGACTTCATGACTA
1 AATGACTTCATGACTA
28544600 AAT
1 AAT
28544603 AAGTGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (16 bp):
AATGACTTCATGACTA
Found at i:28548324 original size:27 final size:26
Alignment explanation
Indices: 28548287--28548365 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 26
28548277 AGCATGGCTG
* *
28548287 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
28548313 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
28548341 CCAGAACAGATATATGTGGCAGAGC
1 CCAGAACAGATA-ATGTGGCAGAGC
28548366 AGAATACAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 5 0.11
27 25 0.54
28 16 0.35
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28548574 original size:27 final size:26
Alignment explanation
Indices: 28548539--28548648 Score: 123
Period size: 27 Copynumber: 4.2 Consensus size: 26
28548529 AGCATGGCTG
* * *
28548539 CCAGAACAGATAATGTGACACAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
28548565 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
28548593 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
28548620 CCAGATCAGAT-TTGTGGCATAGCCA
1 CCAGAACAGATAATGTGGCAGAGCCA
28548645 CCAG
1 CCAG
28548649 GATGCTTCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
25 16 0.22
26 5 0.07
27 37 0.51
28 15 0.21
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28550089 original size:24 final size:24
Alignment explanation
Indices: 28550073--28550132 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
28550063 CCCATGTCTG
28550073 CTCCTAAATCCTATCCCTTATCAA
1 CTCCTAAATCCTATCCCTTATCAA
28550097 CTCCTAAATCCTATCCCTTATCAA
1 CTCCTAAATCCTATCCCTTATCAA
28550121 CTCCTAAATCCT
1 CTCCTAAATCCT
28550133 CTCCTAACAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.28, C:0.38, G:0.00, T:0.33
Consensus pattern (24 bp):
CTCCTAAATCCTATCCCTTATCAA
Found at i:28552562 original size:46 final size:45
Alignment explanation
Indices: 28552490--28552892 Score: 157
Period size: 47 Copynumber: 8.7 Consensus size: 45
28552480 TGATATGTGC
28552490 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGGA
** * * *
28552535 GCCAGTGTAAGACCATGTCTACGACATGGCATC-A--GCATTGAGACAGGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCACATT---A-TGGA
* * *
28552583 GCTAGTCTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATG-GA
* * *
28552629 GCTAGTGTAAGACCATGTTTGGGACATGGCATCG---GCATTGA-GACGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCACATT-ATG--GA
* * * * * *
28552675 GTGCTAGTGTAAGATATGTCTGGGACATGCATCGGCCTCGGA-CAT-AA
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCGACCAC--ATTATGGA
* * * * * * *
28552722 GTCAATGTAAGACATGTCTGGGACATGCATCGGCTATGA-GAT-GT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCA-CATTATGGA
* * * * * * *
28552766 GTCAATGTAAGACCATGTTTGGGACATGGCGTCGGAACA-AATATGTGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATC-GACCACATTATG-GA
* * * *
28552814 GCTAGTATAAGACATGTCTGGGACATGCATCAACCACA-TAGTGAAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTA-TG-GA
* *
28552860 GCTAGTGTCAGACCATGTCTGGGACATGGCATC
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
28552893 AGCTTGATAT
Statistics
Matches: 274, Mismatches: 51, Indels: 63
0.71 0.13 0.16
Matches are distributed among these distances:
44 19 0.07
45 67 0.24
46 63 0.23
47 73 0.27
48 45 0.16
49 6 0.02
51 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGGA
Found at i:28552608 original size:47 final size:47
Alignment explanation
Indices: 28552538--28552844 Score: 182
Period size: 47 Copynumber: 6.6 Consensus size: 47
28552528 TTATGGAGCC
** *
28552538 AGTGTAAGACCATGTCTACGACATGGCATCAGCATTGAGACAGGTGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGACAGGTGCT
* *
28552586 AGTCTAAGA-CATGTCTGGGACATGCATCGGCCACATT-ATG--A-GAGCT
1 AGTGTAAGACCATGTCTGGGACATGCATCGG---CATTGA-GACAGGTGCT
*
28552632 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGAC-GAGTGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGACAG-GTGCT
* * * *
28552680 AGTGTAAGA-TATGTCTGGGACATGCATCGGCCTCG-GACATAAGT-C-
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCATTGAGAC--AGGTGCT
* *
28552725 AATGTAAGA-CATGTCTGGGACATGCATCGGC-TATGAG--ATGTG-T
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCAT-TGAGACAGGTGCT
* * * ** * *
28552768 CAATGTAAGACCATGTTTGGGACATGGCGTCGG-A-ACAAATATGTGTGCT
1 -AGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGACA-G-GTGCT
*
28552817 AGTATAAGA-CATGTCTGGGACATGCATC
1 AGTGTAAGACCATGTCTGGGACATGCATC
28552845 AACCACATAG
Statistics
Matches: 205, Mismatches: 27, Indels: 56
0.71 0.09 0.19
Matches are distributed among these distances:
42 3 0.01
44 11 0.05
45 51 0.25
46 42 0.20
47 53 0.26
48 39 0.19
49 6 0.03
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCATTGAGACAGGTGCT
Found at i:28552671 original size:94 final size:93
Alignment explanation
Indices: 28552497--28552711 Score: 333
Period size: 94 Copynumber: 2.3 Consensus size: 93
28552487 TGCGCCAGTG
*
28552497 TAAGACATGTCTGGGACATGCATCGACCACATTATGGAGCCAGTGTAAGACCATGTCTACGACAT
1 TAAGACATGTCTGGGACATGCATCGGCCACATTATGGAGCCAGTGTAAGACCATGTCTACGACAT
28552562 GGCATCAGCATTGAGAC-AGGTGCTAGTC
66 GGCATCAGCATTGAGACGA-GTGCTAGTC
* * **
28552590 TAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCTAGTGTAAGACCATGTTTGGGACA
1 TAAGACATGTCTGGGACATGCATCGGCCACATTATG-GAGCCAGTGTAAGACCATGTCTACGACA
* *
28552655 TGGCATCGGCATTGAGACGAGTGCTAGTG
65 TGGCATCAGCATTGAGACGAGTGCTAGTC
*
28552684 TAAGATATGTCTGGGACATGCATCGGCC
1 TAAGACATGTCTGGGACATGCATCGGCC
28552712 TCGGACATAA
Statistics
Matches: 112, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
93 35 0.31
94 76 0.68
95 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (93 bp):
TAAGACATGTCTGGGACATGCATCGGCCACATTATGGAGCCAGTGTAAGACCATGTCTACGACAT
GGCATCAGCATTGAGACGAGTGCTAGTC
Found at i:28552816 original size:137 final size:136
Alignment explanation
Indices: 28552590--28552844 Score: 334
Period size: 137 Copynumber: 1.8 Consensus size: 136
28552580 GGTGCTAGTC
*
28552590 TAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCTAGTGTAAGACCATGTTTGGGACA
1 TAAGACATGTCTGGGACATGCATCGG-C-CA-TATGAGAGCTAATGTAAGACCATGTTTGGGACA
* *** * *
28552655 TGGCATCGGCATTGAGACGAGTGCTAGTGTAAGATATGTCTGGGACATGCATCGGCCTCGGACAT
63 TGGCATCGGAACAAAGACGAGTGCTAGTATAAGACATGTCTGGGACATGCATCGGCCTCGGACAT
28552720 AAGTCAATG
128 AAGTCAATG
*
28552729 TAAGACATGTCTGGGACATGCATCGG-C-TATGAGATGTGTCAATGTAAGACCATGTTTGGGACA
1 TAAGACATGTCTGGGACATGCATCGGCCATATGAGA-G-CT-AATGTAAGACCATGTTTGGGACA
* * * *
28552792 TGGCGTCGGAACAAATATGTGTGCTAGTATAAGACATGTCTGGGACATGCATC
63 TGGCATCGGAACAAAGACGAGTGCTAGTATAAGACATGTCTGGGACATGCATC
28552845 AACCACATAG
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
134 7 0.07
135 1 0.01
136 2 0.02
137 65 0.64
139 26 0.26
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (136 bp):
TAAGACATGTCTGGGACATGCATCGGCCATATGAGAGCTAATGTAAGACCATGTTTGGGACATGG
CATCGGAACAAAGACGAGTGCTAGTATAAGACATGTCTGGGACATGCATCGGCCTCGGACATAAG
TCAATG
Found at i:28558257 original size:19 final size:19
Alignment explanation
Indices: 28558233--28558278 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
28558223 CGGGTATGGG
28558233 ACACGGGCATGTCCTTAGC
1 ACACGGGCATGTCCTTAGC
28558252 ACACGGGCATGTCCTTAGC
1 ACACGGGCATGTCCTTAGC
28558271 ACACGGGC
1 ACACGGGC
28558279 GTGTGCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (19 bp):
ACACGGGCATGTCCTTAGC
Found at i:28558837 original size:16 final size:18
Alignment explanation
Indices: 28558811--28558844 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28558801 TTAAAATTAG
28558811 ATTGAGAAAATT-ATTTA
1 ATTGAGAAAATTAATTTA
28558828 ATTG-GAAAATTAATTTA
1 ATTGAGAAAATTAATTTA
28558845 TCTAAGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
ATTGAGAAAATTAATTTA
Found at i:28580908 original size:93 final size:93
Alignment explanation
Indices: 28580795--28580966 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28580785 CGCCCATAAG
* *
28580795 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28580860 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
28580888 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28580953 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28580967 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28580963 original size:46 final size:46
Alignment explanation
Indices: 28580788--28580963 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
28580778 TGTAACCCGC
* * *
28580788 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28580834 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28580884 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28580927 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28580964 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28582463 original size:40 final size:40
Alignment explanation
Indices: 28582408--28582489 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
28582398 TAATAGCATT
28582408 AAATCAGCCGGAAAACAAATGTCTCGAAATATGAACGGAC
1 AAATCAGCCGGAAAACAAATGTCTCGAAATATGAACGGAC
28582448 AAATCAGCCGGAAAACAAATGTCTCGAAATATGAACGGAC
1 AAATCAGCCGGAAAACAAATGTCTCGAAATATGAACGGAC
28582488 AA
1 AA
28582490 TTCTTGCAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (40 bp):
AAATCAGCCGGAAAACAAATGTCTCGAAATATGAACGGAC
Found at i:28587610 original size:28 final size:28
Alignment explanation
Indices: 28587564--28587632 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
28587554 TTTAAAACCC
*
28587564 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
28587591 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
28587619 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
28587633 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:28589285 original size:20 final size:20
Alignment explanation
Indices: 28589262--28589299 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28589252 CACATCCAAA
*
28589262 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
28589282 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
28589300 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:28590717 original size:21 final size:21
Alignment explanation
Indices: 28590642--28590707 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 21
28590632 GTCTTGAATT
28590642 TGTTAGATATTGAATTTATTA
1 TGTTAGATATTGAATTTATTA
* *
28590663 TGTTTTAAGCTTGTTGAATTTATTA
1 TG--TT-AG-ATATTGAATTTATTA
28590688 TGTTAGATATTGAATTTATT
1 TGTTAGATATTGAATTTATT
28590708 TGGTTGGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 14 0.38
22 2 0.05
23 4 0.11
24 2 0.05
25 15 0.41
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.55
Consensus pattern (21 bp):
TGTTAGATATTGAATTTATTA
Found at i:28592118 original size:14 final size:14
Alignment explanation
Indices: 28592099--28592136 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
28592089 CCAAAAAAGT
28592099 AAATCATTTTCCAG
1 AAATCATTTTCCAG
28592113 AAATCATTTTCCAG
1 AAATCATTTTCCAG
28592127 AAATCATTTT
1 AAATCATTTT
28592137 TCGAAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:28594150 original size:10 final size:10
Alignment explanation
Indices: 28594135--28594194 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
28594125 AAATTTTAGG
28594135 ATTTAT-TTT
1 ATTTATCTTT
28594144 CATTTATCTTT
1 -ATTTATCTTT
28594155 ATTTATCTTT
1 ATTTATCTTT
*
28594165 AATTATCTTT
1 ATTTATCTTT
28594175 ATTTAT-TTGT
1 ATTTATCTT-T
28594185 ATTTATCTTT
1 ATTTATCTTT
28594195 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:28595118 original size:11 final size:12
Alignment explanation
Indices: 28595104--28595136 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
28595094 CCTACTTCCC
28595104 TTTTACTATTA-
1 TTTTACTATTAT
28595115 TTTTACTATTAT
1 TTTTACTATTAT
28595127 TTTTACTATT
1 TTTTACTATT
28595137 TTGCAGGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTACTATTAT
Found at i:28595759 original size:42 final size:42
Alignment explanation
Indices: 28595695--28595780 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
28595685 TATGGTTTGC
*
28595695 CTTAGTACGAAACCTCAGGGGGTAACTGAGAATCAAATTAAA
1 CTTAGTACGAAACCTCAAGGGGTAACTGAGAATCAAATTAAA
* *
28595737 CTTAGTATGAAACCTCAAGGGGTAACTGAGGATCAAATTAAA
1 CTTAGTACGAAACCTCAAGGGGTAACTGAGAATCAAATTAAA
28595779 CT
1 CT
28595781 GTGTGCTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (42 bp):
CTTAGTACGAAACCTCAAGGGGTAACTGAGAATCAAATTAAA
Found at i:28600615 original size:5 final size:5
Alignment explanation
Indices: 28600601--28600678 Score: 92
Period size: 5 Copynumber: 16.0 Consensus size: 5
28600591 GCAACCCAAT
28600601 TTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* *
28600651 TCTTA --TTA TTTTA TTATT- TATTA TTTTA
1 TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA
28600679 GATATTAATA
Statistics
Matches: 64, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
3 3 0.05
4 6 0.09
5 48 0.75
6 7 0.11
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:28600685 original size:27 final size:27
Alignment explanation
Indices: 28600607--28600678 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
28600597 CAATTTTTAT
28600607 TTTTATTTTATTTTATTTTAT--T-TTA
1 TTTTATTTTA-TTTATTTTATCATATTA
*
28600632 TTTTATTTTATTTATTTTATCTTATTA
1 TTTTATTTTATTTATTTTATCATATTA
28600659 TTTTATTATT-TATTATTTTA
1 TTTTATT-TTAT-TTATTTTA
28600679 GATATTAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.24
25 10 0.24
26 1 0.02
27 11 0.26
28 10 0.24
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTATTTTATTTATTTTATCATATTA
Found at i:28602336 original size:10 final size:9
Alignment explanation
Indices: 28602321--28602376 Score: 58
Period size: 10 Copynumber: 5.7 Consensus size: 9
28602311 AAATTTTAGG
28602321 ATTTATTTT
1 ATTTATTTT
28602330 CATTTATCTTT
1 -ATTTAT-TTT
28602341 ATTTATTTTT
1 ATTTA-TTTT
*
28602351 AATTATCTTT
1 ATTTAT-TTT
28602361 ATTTATTTGT
1 ATTTATTT-T
28602371 ATTTAT
1 ATTTAT
28602377 CTTTTAGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 3 0.08
10 33 0.82
11 4 0.10
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (9 bp):
ATTTATTTT
Found at i:28602344 original size:20 final size:19
Alignment explanation
Indices: 28602321--28602380 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 19
28602311 AAATTTTAGG
28602321 ATTTATTTTCATTTATCTTT
1 ATTTATTTT-ATTTATCTTT
*
28602341 ATTTATTTTTAATTATCTTT
1 ATTTA-TTTTATTTATCTTT
28602361 ATTTATTTGTATTTATCTTT
1 ATTTATTT-TATTTATCTTT
28602381 TAGAATTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.08
20 29 0.81
21 4 0.11
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTATTTTATTTATCTTT
Found at i:28602365 original size:30 final size:31
Alignment explanation
Indices: 28602323--28602382 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
28602313 ATTTTAGGAT
28602323 TTATTTTCATTTATCTT-TATTTAT-TTTTAA
1 TTATTTTCATTTAT-TTGTATTTATCTTTTAA
28602353 TTATCTTT-ATTTATTTGTATTTATCTTTTA
1 TTAT-TTTCATTTATTTGTATTTATCTTTTA
28602383 GAATTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 2 0.07
30 17 0.63
31 8 0.30
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.70
Consensus pattern (31 bp):
TTATTTTCATTTATTTGTATTTATCTTTTAA
Found at i:28603309 original size:12 final size:12
Alignment explanation
Indices: 28603292--28603324 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
28603282 CTACTTCCCA
28603292 TTTACTATTATT
1 TTTACTATTATT
28603304 TTTACTATTATT
1 TTTACTATTATT
28603316 TTTACTATT
1 TTTACTATT
28603325 TTACAGGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTACTATTATT
Found at i:28607718 original size:19 final size:19
Alignment explanation
Indices: 28607683--28607720 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
28607673 CTCATACATC
28607683 ATAACATAACTAGAAACTA
1 ATAACATAACTAGAAACTA
*
28607702 ATAACTATAATTA-AAACTA
1 ATAAC-ATAACTAGAAACTA
28607721 CTATTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (19 bp):
ATAACATAACTAGAAACTA
Found at i:28611067 original size:12 final size:12
Alignment explanation
Indices: 28611050--28611084 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
28611040 AAAGTAACTT
28611050 TAATAATAATGA
1 TAATAATAATGA
*
28611062 TAATAATAAAGA
1 TAATAATAATGA
28611074 TAATAA-AATGA
1 TAATAATAATGA
28611085 AAACATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (12 bp):
TAATAATAATGA
Found at i:28611094 original size:25 final size:24
Alignment explanation
Indices: 28611064--28611110 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
28611054 AATAATGATA
28611064 ATAATAAAGATAATA-AAATGAAAAC
1 ATAATAAAGA-AATAGAAA-GAAAAC
28611089 ATAATAAAGAAATAGAAAGAAA
1 ATAATAAAGAAATAGAAAGAAA
28611111 GTGGACAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.17
Consensus pattern (24 bp):
ATAATAAAGAAATAGAAAGAAAAC
Found at i:28611358 original size:29 final size:29
Alignment explanation
Indices: 28611319--28611374 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
28611309 TTGTTTAAGA
28611319 TTTTAGATGTTGACATTGTTGAATAGTTT
1 TTTTAGATGTTGACATTGTTGAATAGTTT
*
28611348 TTTTAGATGTTGAGATTGTTGAATAGT
1 TTTTAGATGTTGACATTGTTGAATAGT
28611375 ATAAGTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.50
Consensus pattern (29 bp):
TTTTAGATGTTGACATTGTTGAATAGTTT
Found at i:28611930 original size:25 final size:25
Alignment explanation
Indices: 28611882--28611930 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28611872 CATAATTGAA
* *
28611882 ATGAAATAGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
28611907 ATGAAAT-GTATTGATTATGAATAT
1 ATGAAATAG-ATTGATTATGAATAT
28611931 GTGTGTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:28613308 original size:30 final size:30
Alignment explanation
Indices: 28613235--28613308 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
28613225 ACAGCTTGGC
* *
28613235 CACATGGGTGTGTCTCACATACAGGCAACA
1 CACATGGGTGTGTGTCACACACAGGCAACA
* *
28613265 CACATGGGCGTGTGTCACACACGGGCAACA
1 CACATGGGTGTGTGTCACACACAGGCAACA
*
28613295 CACATGGATGTGTG
1 CACATGGGTGTGTG
28613309 ACCCAAGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.19
Consensus pattern (30 bp):
CACATGGGTGTGTGTCACACACAGGCAACA
Found at i:28613835 original size:93 final size:91
Alignment explanation
Indices: 28613678--28613862 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 91
28613668 TCTGACATTT
* *
28613678 AAGAAGGGATAAATAGTGATAAGAATAGATAGTGGAAGATTAAGTTTAGCAATGTATAAATAGTG
1 AAGAAGGGATAAATAGTGATAAGAATAGACAGTGGAAGACTAAGTTTAGCAATGTATAAATAGTG
*
28613743 ATAAGAGTGTAGACAATGGAAGGCCA
66 ATAAGAGTGTAGACAATGGAAGACCA
*
28613769 AAGAAGGGATAAATAGTGATAAGAATGTAGACAGTGGAAGACTCAGTTTAGCAATGTATAAATAG
1 AAGAAGGGATAAATAGTGATAAGAA--TAGACAGTGGAAGACTAAGTTTAGCAATGTATAAATAG
28613834 TGATAAGAGTGTAGACAATGGAAGACCA
64 TGATAAGAGTGTAGACAATGGAAGACCA
28613862 A
1 A
28613863 GTTTAGCATT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
91 25 0.28
93 63 0.72
ACGTcount: A:0.45, C:0.06, G:0.27, T:0.22
Consensus pattern (91 bp):
AAGAAGGGATAAATAGTGATAAGAATAGACAGTGGAAGACTAAGTTTAGCAATGTATAAATAGTG
ATAAGAGTGTAGACAATGGAAGACCA
Found at i:28613839 original size:49 final size:48
Alignment explanation
Indices: 28613686--28613870 Score: 202
Period size: 49 Copynumber: 3.9 Consensus size: 48
28613676 TTAAGAAGGG
* * **
28613686 ATAAATAGTGATAAGAA--TAGATAGTGGAAGATTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAATGTAGACAATGGAAGA-CCAGTTTAGCAATGT
* * * * *
28613733 ATAAATAGTGATAAGAGTGTAGACAATGGAAGGCCA---AAG-AAGGG
1 ATAAATAGTGATAAGAATGTAGACAATGGAAGACCAGTTTAGCAATGT
*
28613777 ATAAATAGTGATAAGAATGTAGACAGTGGAAGACTCAGTTTAGCAATGT
1 ATAAATAGTGATAAGAATGTAGACAATGGAAGAC-CAGTTTAGCAATGT
*
28613826 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAGTTTAGCA
1 ATAAATAGTGATAAGAATGTAGACAATGGAAGACC-AGTTTAGCA
28613871 TTACATAGCA
Statistics
Matches: 113, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
44 34 0.30
45 4 0.04
47 16 0.14
48 4 0.04
49 55 0.49
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (48 bp):
ATAAATAGTGATAAGAATGTAGACAATGGAAGACCAGTTTAGCAATGT
Found at i:28620020 original size:29 final size:29
Alignment explanation
Indices: 28619978--28620044 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
28619968 GGTGGAGAAC
* * *
28619978 TTGTTCATTGAGAGTTCATGATGAAAAAT
1 TTGTTCGTTAAGAGTTCATGACGAAAAAT
* *
28620007 TTGTTCGTTAAGAGTTCGTGACGAAGAAT
1 TTGTTCGTTAAGAGTTCATGACGAAAAAT
28620036 TTGTTCGTT
1 TTGTTCGTT
28620045 GAGAATTTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (29 bp):
TTGTTCGTTAAGAGTTCATGACGAAAAAT
Found at i:28620521 original size:30 final size:30
Alignment explanation
Indices: 28620487--28620617 Score: 149
Period size: 30 Copynumber: 4.4 Consensus size: 30
28620477 TCTTAGCATC
* *
28620487 TTCCACCACCAACTCCACTAGCCACTCCTT
1 TTCCACCACCAACTCCACTAGCCACACATT
28620517 TTCCACCACCAACTCCACTAGCCACACATT
1 TTCCACCACCAACTCCACTAGCCACACATT
*
28620547 TTCCACCACCAAATCCACTAGCCACAC-TT
1 TTCCACCACCAACTCCACTAGCCACACATT
* ** * *
28620576 GCTCCATTACCTACTCCACTAACCACAC-TT
1 -TTCCACCACCAACTCCACTAGCCACACATT
*
28620606 GCTCCACCACCA
1 -TTCCACCACCA
28620618 CTTGTACCTA
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 2 0.02
30 86 0.98
ACGTcount: A:0.27, C:0.47, G:0.04, T:0.21
Consensus pattern (30 bp):
TTCCACCACCAACTCCACTAGCCACACATT
Found at i:28621191 original size:27 final size:25
Alignment explanation
Indices: 28621110--28621231 Score: 74
Period size: 25 Copynumber: 5.0 Consensus size: 25
28621100 ATTATATTTC
* *
28621110 TTAATATTATATTATATATAT-TCT
1 TTAATACTATATTATATATATATAT
* **
28621134 TT--TAATATATTAGGTATAT-T-T
1 TTAATACTATATTATATATATATAT
* *
28621155 TAAATTCTATATTACGTATATATATAT
1 TTAATACTATATTA--TATATATATAT
* * * *
28621182 TTTATACTATTTTATTTATATATCT
1 TTAATACTATATTATATATATATAT
* *
28621207 TTAATATTATATTATTTATATATAT
1 TTAATACTATATTATATATATATAT
28621232 AAATTTTTTT
Statistics
Matches: 74, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
21 2 0.03
22 15 0.20
23 8 0.11
24 2 0.03
25 35 0.47
26 1 0.01
27 11 0.15
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATACTATATTATATATATATAT
Found at i:28621201 original size:25 final size:25
Alignment explanation
Indices: 28621173--28621231 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
28621163 ATATTACGTA
* *
28621173 TATATATATTTTATACTATTTTATT
1 TATATATATTTAATACTATATTATT
* *
28621198 TATATATCTTTAATATTATATTATT
1 TATATATATTTAATACTATATTATT
28621223 TATATATAT
1 TATATATAT
28621232 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATATATTTAATACTATATTATT
Found at i:28621283 original size:22 final size:24
Alignment explanation
Indices: 28621255--28621313 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
28621245 ACATGTTATC
28621255 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
28621277 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
28621302 TTATGTACATAT
1 TTATGTATATAT
28621314 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:28621303 original size:25 final size:25
Alignment explanation
Indices: 28621271--28621319 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28621261 ATATATCTTA
**
28621271 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
28621296 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
28621320 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:28621496 original size:16 final size:15
Alignment explanation
Indices: 28621472--28621519 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
28621462 TAATTATTAC
*
28621472 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
28621488 TATTTTAATATTTTA
1 TATTTTAATATTTTA
28621503 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
28621519 T
1 T
28621520 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:28621507 original size:7 final size:8
Alignment explanation
Indices: 28621472--28621523 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
28621462 TAATTATTAC
*
28621472 TATTCTAA
1 TATTTTAA
*
28621480 TATTTTGA
1 TATTTTAA
28621488 TATTTTAA
1 TATTTTAA
28621496 TATTTT-A
1 TATTTTAA
28621503 TATTTTATA
1 TATTTTA-A
*
28621512 TATTTTAT
1 TATTTTAA
28621520 TATT
1 TATT
28621524 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:28625079 original size:12 final size:12
Alignment explanation
Indices: 28625062--28625097 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
28625052 AACATTTTGA
28625062 CATTCATACATT
1 CATTCATACATT
**
28625074 CATTCATGTATT
1 CATTCATACATT
28625086 CATTCATACATT
1 CATTCATACATT
28625098 GCATATCCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (12 bp):
CATTCATACATT
Found at i:28633502 original size:87 final size:88
Alignment explanation
Indices: 28633356--28633773 Score: 716
Period size: 89 Copynumber: 4.8 Consensus size: 88
28633346 TGTTCCAAAG
* *
28633356 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATTTCAATTTATGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
28633421 TTCAATTT-TGCTCTTCAAAAAA
66 TTCAATTTCTGCTCTTCAAAAAA
28633443 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
*
28633508 TTCAATTTCTG-TTTTC-AAAAA
66 TTCAATTTCTGCTCTTCAAAAAA
* *
28633529 ATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGGCGCGCTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTG-T
28633594 TTTCAATTTCTGCTCTTCAAAAAA
65 TTTCAATTTCTGCTCTTCAAAAAA
* *
28633618 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATTTCAATTTATGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
*
28633683 TTTAATTTCTGCTCTTCAAAAAAA
66 TTCAATTTCTGCTCTTC-AAAAAA
*
28633707 ATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
28633772 TT
66 TT
28633774 GAGGCACGCT
Statistics
Matches: 312, Mismatches: 14, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
86 66 0.21
87 88 0.28
88 24 0.08
89 134 0.43
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (88 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
TTCAATTTCTGCTCTTCAAAAAA
Found at i:28633511 original size:13 final size:13
Alignment explanation
Indices: 28633493--28633525 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
28633483 CGCTGAGGTA
28633493 TTTTCAATTTCTG
1 TTTTCAATTTCTG
28633506 TTTTCAATTTCTG
1 TTTTCAATTTCTG
28633519 TTTTCAA
1 TTTTCAA
28633526 AAAATCAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.61
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:28633598 original size:14 final size:14
Alignment explanation
Indices: 28633579--28633605 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28633569 CGCTGAGGTA
28633579 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
28633593 TTTTCAATTTCTG
1 TTTTCAATTTCTG
28633606 CTCTTCAAAA
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:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:28633660 original size:175 final size:176
Alignment explanation
Indices: 28633356--28633773 Score: 716
Period size: 175 Copynumber: 2.4 Consensus size: 176
28633346 TGTTCCAAAG
* *
28633356 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATTTCAATTTATG-T
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
28633420 TTTCAATTTTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
66 TTTCAATTTTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
* * *
28633485 CTGAGGTATTTTCAATTTCTGTTTTCAATTTCTG-TTTTC-AAAAA
131 CTGAGGTAATTTCAATTTATGTTTTCAATTTCTGCTCTTCAAAAAA
* *
28633529 ATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGGCGCGCTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
28633594 TTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
66 TTTCAATTT-TGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
*
28633659 GCTGAGGTAATTTCAATTTATGTTTTTAATTTCTGCTCTTCAAAAAAA
130 GCTGAGGTAATTTCAATTTATGTTTTCAATTTCTGCTCTTC-AAAAAA
*
28633707 ATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
28633772 TT
66 TT
28633774 GAGGCACGCT
Statistics
Matches: 229, Mismatches: 11, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
173 59 0.26
174 10 0.04
175 87 0.38
176 4 0.02
178 69 0.30
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (176 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTT
TTTCAATTTTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
CTGAGGTAATTTCAATTTATGTTTTCAATTTCTGCTCTTCAAAAAA
Done.