Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003963.1 Hibiscus syriacus cultivar Beakdansim tig00008588_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: 164510
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2571 original size:12 final size:12
Alignment explanation
Indices: 2552--2583 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2542 ACATATCATT
2552 TCATTATTCTTA
1 TCATTATTCTTA
*
2564 TTATTATTCTTA
1 TCATTATTCTTA
2576 TCATTATT
1 TCATTATT
2584 AACCAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (12 bp):
TCATTATTCTTA
Found at i:2891 original size:21 final size:21
Alignment explanation
Indices: 2844--2920 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
2834 CATATACATA
* *
2844 TTCCAATGGACCAAATA-AGTG
1 TTCCAAAGGACCACATATA-TG
* *
2865 TACCAAAGTACCACATATATG
1 TTCCAAAGGACCACATATATG
**
2886 TTCCAAAGGATTACATATATG
1 TTCCAAAGGACCACATATATG
* *
2907 TCCCGAAGGACCAC
1 TTCCAAAGGACCAC
2921 GTAGAACCCT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (21 bp):
TTCCAAAGGACCACATATATG
Found at i:11856 original size:20 final size:20
Alignment explanation
Indices: 11819--11857 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11809 GACAGCTCGA
*
11819 TTTACCGATCTGCAGGAGAG
1 TTTACAGATCTGCAGGAGAG
11839 TTTACAGAT-TGCATGGAGA
1 TTTACAGATCTGCA-GGAGA
11858 TGGCAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (20 bp):
TTTACAGATCTGCAGGAGAG
Found at i:12227 original size:2 final size:2
Alignment explanation
Indices: 12220--12246 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12210 TCAATCTACA
12220 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 A
12247 AAATTTACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14808 original size:138 final size:138
Alignment explanation
Indices: 14558--14811 Score: 334
Period size: 138 Copynumber: 1.8 Consensus size: 138
14548 CTAAAGTGCC
* * *
14558 GAAATGGAAATTCACAAACATATTATGAATTCCATGGATGTACTCATAGTGACAAAAGTACATAT
1 GAAATGGAAATTCACAAACATATTATGAATACCATGGATGCACTCATAGTGACAAAAGTACACAT
* **
14623 AGTACTAATATGAAAATGCACCGTTATGCATTAAACAAAATCAATCGATAATTTTTATACATAAT
66 AATACTAATACAAAAATGCACCGTTATGCATTAAACAAAATCAATCGATAATTTTTATACATAAT
14688 TGTATATA
131 TGTATATA
* * * * *
14696 GAAATGGCAATTCATAAAC-TCATTATGAATACCAT-GATTGCACATC-TAGTGTCGAAAGTACG
1 GAAATGGAAATTCACAAACAT-ATTATGAATACCATGGA-TGCAC-TCATAGTGACAAAAGTACA
* * *
14758 CATAATACTAATACAAAAATGCACCGTTATTCATTAATCAAAATCGATCGATAA
63 CATAATACTAATACAAAAATGCACCGTTATGCATTAAACAAAATCAATCGATAA
14812 CTATCATACG
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
137 3 0.03
138 94 0.95
139 2 0.02
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (138 bp):
GAAATGGAAATTCACAAACATATTATGAATACCATGGATGCACTCATAGTGACAAAAGTACACAT
AATACTAATACAAAAATGCACCGTTATGCATTAAACAAAATCAATCGATAATTTTTATACATAAT
TGTATATA
Found at i:15549 original size:11 final size:12
Alignment explanation
Indices: 15527--15552 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15517 CTTACCCATG
15527 TTTTTCATTTTT
1 TTTTTCATTTTT
15539 TTTTTCATTTTT
1 TTTTTCATTTTT
15551 TT
1 TT
15553 CATTTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCATTTTT
Found at i:20195 original size:23 final size:21
Alignment explanation
Indices: 20145--20189 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
20135 GAATCGGATG
20145 CTCACTATTAGCTTCATAGCT
1 CTCACTATTAGCTTCATAGCT
20166 CTCACTATTAGCTTCATAGCT
1 CTCACTATTAGCTTCATAGCT
20187 CTC
1 CTC
20190 TCACTACCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.31, G:0.09, T:0.38
Consensus pattern (21 bp):
CTCACTATTAGCTTCATAGCT
Found at i:20559 original size:3 final size:3
Alignment explanation
Indices: 20547--20584 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
20537 CAAAACACTT
20547 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20585 AAATTTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27201 original size:21 final size:21
Alignment explanation
Indices: 27177--27216 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27167 AAATTGGCCA
*
27177 TTTAATTTTTCAAATTGACTT
1 TTTAACTTTTCAAATTGACTT
*
27198 TTTAACTTTTCGAATTGAC
1 TTTAACTTTTCAAATTGAC
27217 CACTCATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTAACTTTTCAAATTGACTT
Found at i:27346 original size:2 final size:2
Alignment explanation
Indices: 27339--27369 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27329 TTTTTCCTAC
27339 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
27370 ATAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27887 original size:21 final size:22
Alignment explanation
Indices: 27863--27904 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
27853 TCTAATACAT
*
27863 GAATTATGGTACT-TAATTAGG
1 GAATTAGGGTACTATAATTAGG
*
27884 GAATTAGGGTTCTATAATTAG
1 GAATTAGGGTACTATAATTAG
27905 ATTACTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (22 bp):
GAATTAGGGTACTATAATTAGG
Found at i:29675 original size:37 final size:36
Alignment explanation
Indices: 29600--29675 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
29590 TTTTTATATT
*
29600 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
29636 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
29673 TTT
1 TTT
29676 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:35334 original size:27 final size:27
Alignment explanation
Indices: 35304--35357 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
35294 ATCGAGAAAG
35304 TATGATAATGGACCTCGAGACTAACAC
1 TATGATAATGGACCTCGAGACTAACAC
35331 TATGATAATGGACCTCGAGACTAACAC
1 TATGATAATGGACCTCGAGACTAACAC
35358 ACCTCAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (27 bp):
TATGATAATGGACCTCGAGACTAACAC
Found at i:40587 original size:663 final size:664
Alignment explanation
Indices: 39275--40601 Score: 2289
Period size: 663 Copynumber: 2.0 Consensus size: 664
39265 AATTGGAGGT
*
39275 CATTGTTGACAAATTCAAAGAAACAGGCAAATGAACTTCACATAGTTCCTATCGATGGAGGCCTC
1 CATTGTTGACAAATTCAAAGAAACAGGCAAATGAAATTCACATAGTTCCTATCGATGGAGGCCTC
* * * *
39340 TAATGGCATTTCCGTTAGAGAACAGGCTCAGCAAAGGATGAAAGCTAGAGATACAATCATTCGAT
66 CAATGGAATTTCCGTTAGAGAACAAGCTCAGCAAAGGATGAAAGCCAGAGATACAATCATTCGAT
* * * *
39405 ACTTCTGGGAACGAGTATAAAAATCAACTCGTCACTTGCACGATTTAGCTAGAGAATCCGGAGCG
131 ACTTCTGGGAACAAGTACAAAAAGCAACTCGTCACTTGCACGATTTAGCCAGAGAATCCGGAGCG
* *
39470 ATTCGACAGGGTATTCAACCGGTGACAGACGAAGGCAGAAGACTAGTCAACCTGTCAGAAGCTGT
196 ATTCGACAGGGTATTCAACCAGTGACAGACGAAGGAAGAAGACTAGTCAACCTGTCAGAAGCTGT
*
39535 CAGGATGTTTTTGTCTCTTAAGAAATAACACTTTTGTCCCAATAAAGATTATTTATAATAACAAA
261 CAGGATGTTTTTGTCTCTTAAGAAATAACACTATTGTCCCAATAAAGATTATTTATAATAACAAA
*
39600 CATATTTTTCGGATCAATGCTTCAAACATTTCATACATTTTTGCATTTTGCATCTACATTTTATT
326 CATAGTTTTCGGATCAATGCTTCAAACATTTCATACATTTTTGCATTTTGCATCTACATTTTATT
* *
39665 TTTAAGTATTTTCATAAACATGAAATTACTTCATGAAGGATTCGATGAAGTGGTCTTAACCCCAT
391 TTTAAGCATTTTCATAAACATGAAATTACTTCATGAAGGATTCAATGAAGTGGTCTTAACCCCAT
* * * * *
39730 GACACCACCTGAAAGCAAGATTTTAACAATTAAAGAAAAAAACCGAAATCAATACAGTGGGAGTC
456 GACACCACATGAAAGAAAGATTTTAACAATTAAAGAAAAAAACCAAAATCAATACACTGGGAGCC
*
39795 TGATCAGCTGGTTGTAAGACTAAGCCTGTCAGGATGATATGAGAAAATAGTTCCAATATCCTAAG
521 TGATCAGCTGGTTATAAGACTAAGCCTGTCAGGATGATATGAGAAAATAGTTCCAATATCCTAAG
39860 GGCTACGATGTTGAAGTTGTATGCAGTTACCACATAGGAAACTCTAGACATTCCTCTAAGAACTA
586 GGCTACGATGTTGAAGTTGTATGCAGTTACCACATAGGAAACTCTAGACATTCCTCTAAGAACTA
39925 TGGGGCATTGAAGC
651 TGGGGCATTGAAGC
* *
39939 CATTGTTGACGAATTCAAAGAAACAGGCAAATGAAATTCACATAGTTCCTATCGATGGAGGGCTC
1 CATTGTTGACAAATTCAAAGAAACAGGCAAATGAAATTCACATAGTTCCTATCGATGGAGGCCTC
* *
40004 CAATGGAATTTTCGTTAGAGAACAAGCTCAGCAAAGGATGAAATCCAGAGATACAATCATTCGAT
66 CAATGGAATTTCCGTTAGAGAACAAGCTCAGCAAAGGATGAAAGCCAGAGATACAATCATTCGAT
*
40069 ACTTCTGGGAACAAGTACAAAAAGCAACTCGTCACTTGCACGATTTAGCCAGATAATCCGGAGCG
131 ACTTCTGGGAACAAGTACAAAAAGCAACTCGTCACTTGCACGATTTAGCCAGAGAATCCGGAGCG
*
40134 GTTCTG-CAGGGTATTCAACCAGTGACAGACGAAGGAAGAAGACTAGTCAACCTGTCAGAAGCTG
196 ATTC-GACAGGGTATTCAACCAGTGACAGACGAAGGAAGAAGACTAGTCAACCTGTCAGAAGCTG
*
40198 TCAGGATGTTTTTGTCTCTTAAGAAATAACACTATTGTCCCAATAAAGATTATTTATAATAACAG
260 TCAGGATGTTTTTGTCTCTTAAGAAATAACACTATTGTCCCAATAAAGATTATTTATAATAACAA
40263 ACAT-GTTTTCGGATCAATGCTTCAAACATTTCATACATTTTTGCATTTTGCATCTACATTTTAT
325 ACATAGTTTTCGGATCAATGCTTCAAACATTTCATACATTTTTGCATTTTGCATCTACATTTTAT
* * *
40327 TTTTAAGCATTTTTATAAACATGAAATTACTTCATGAAGGATTCAATGAATTGGTCTTAACCGCA
390 TTTTAAGCATTTTCATAAACATGAAATTACTTCATGAAGGATTCAATGAAGTGGTCTTAACCCCA
* *
40392 TGACACCACATGGAAGAAATATTTTAACAATTAAAGAAAAAAACCAAAATCAATACACTGGGAGC
455 TGACACCACATGAAAGAAAGATTTTAACAATTAAAGAAAAAAACCAAAATCAATACACTGGGAGC
* * *
40457 CTGATCAGCTGGTTATAGGACTAAGCCTGTCAGGATGATCTGAGAAAATAGTTCCTATATCCTAA
520 CTGATCAGCTGGTTATAAGACTAAGCCTGTCAGGATGATATGAGAAAATAGTTCCAATATCCTAA
* *
40522 GGGCTACGATGTTGAAGTTGTGTGCAGTTACCACATAGGAAACTCTAGACATTCCTCTGAGAACT
585 GGGCTACGATGTTGAAGTTGTATGCAGTTACCACATAGGAAACTCTAGACATTCCTCTAAGAACT
40587 ATGGGGCATTGAAGC
650 ATGGGGCATTGAAGC
40602 GTAAGGCCCA
Statistics
Matches: 624, Mismatches: 38, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
663 316 0.51
664 307 0.49
665 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (664 bp):
CATTGTTGACAAATTCAAAGAAACAGGCAAATGAAATTCACATAGTTCCTATCGATGGAGGCCTC
CAATGGAATTTCCGTTAGAGAACAAGCTCAGCAAAGGATGAAAGCCAGAGATACAATCATTCGAT
ACTTCTGGGAACAAGTACAAAAAGCAACTCGTCACTTGCACGATTTAGCCAGAGAATCCGGAGCG
ATTCGACAGGGTATTCAACCAGTGACAGACGAAGGAAGAAGACTAGTCAACCTGTCAGAAGCTGT
CAGGATGTTTTTGTCTCTTAAGAAATAACACTATTGTCCCAATAAAGATTATTTATAATAACAAA
CATAGTTTTCGGATCAATGCTTCAAACATTTCATACATTTTTGCATTTTGCATCTACATTTTATT
TTTAAGCATTTTCATAAACATGAAATTACTTCATGAAGGATTCAATGAAGTGGTCTTAACCCCAT
GACACCACATGAAAGAAAGATTTTAACAATTAAAGAAAAAAACCAAAATCAATACACTGGGAGCC
TGATCAGCTGGTTATAAGACTAAGCCTGTCAGGATGATATGAGAAAATAGTTCCAATATCCTAAG
GGCTACGATGTTGAAGTTGTATGCAGTTACCACATAGGAAACTCTAGACATTCCTCTAAGAACTA
TGGGGCATTGAAGC
Found at i:42007 original size:64 final size:64
Alignment explanation
Indices: 41939--42095 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
41929 TTGAAGGTGT
* * *
41939 ATCGATGCATTAGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCTATAATAATA-AAACATCGAATGCATATTA-T
42001 GC
63 GC
* * *
42003 ATCGATGCATAAGTCATGCATCGATGCATCCCTATAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
* * *
42067 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
42096 ACCTTCATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
64 72 0.90
65 8 0.10
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
Found at i:42448 original size:18 final size:18
Alignment explanation
Indices: 42413--42448 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42403 AAAATTGGTA
* *
42413 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
42431 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
42449 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:46336 original size:64 final size:64
Alignment explanation
Indices: 46268--46424 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
46258 TTGAAGGTGT
* * *
46268 ATCGATGCATTAGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCTATAATAATA-AAACATCGAATGCATATTA-T
46330 GC
63 GC
* * *
46332 ATCGATGCATAAGTCATGCATCGATGCATCCCTATAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
* * *
46396 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
46425 ACCTTCATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
64 72 0.90
65 8 0.10
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
Found at i:46780 original size:18 final size:18
Alignment explanation
Indices: 46745--46780 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
46735 AAAATGGGTA
* *
46745 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
46763 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
46781 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:47364 original size:18 final size:18
Alignment explanation
Indices: 47337--47406 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
47327 TTAAGGAGTA
*
47337 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
47355 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
*
47377 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
*
47395 GTCCTACAGGAC
1 GTCCTACGGGAC
47407 GAATACTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 25 0.57
20 4 0.09
22 15 0.34
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.24
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:48309 original size:17 final size:15
Alignment explanation
Indices: 48274--48304 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
48264 ACTCAACAAA
48274 AATATATATATGTAT
1 AATATATATATGTAT
48289 AATATATATATGTAT
1 AATATATATATGTAT
48304 A
1 A
48305 CAATAAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
AATATATATATGTAT
Found at i:48689 original size:189 final size:189
Alignment explanation
Indices: 48311--48679 Score: 603
Period size: 189 Copynumber: 2.0 Consensus size: 189
48301 TATACAATAA
*
48311 AGCTGAGCTATTCCACTAAAGCAATTGGTTATAGAGGAAACTCGAAAGCCCCGGGTTTATGAATA
1 AGCTGAGCTATTCCACTAAAGCAATTGGTTATAGAGGAAACTCGAAAGCCCCGGCTTTATGAATA
* * *
48376 GATTATATTCAAACCATGACATTGATCGGGTACTCGGTAATTCGATGTATGCTCCACTGTGATTG
66 GACTACATTCAAACCATGACATTGATCGGGTACTCGGTAATTCGATGTATGCTCCACTGTGATTA
* * *
48441 TTAAGTCGAAGATTTTGTGACGACATGAATCCTTCAGCTAGCCAAACAAAGAAAATTAT
131 TCAAGTCAAAGACTTTGTGACGACATGAATCCTTCAGCTAGCCAAACAAAGAAAATTAT
* * *
48500 AGCTGAGCTATTCCTCTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGAATA
1 AGCTGAGCTATTCCACTAAAGCAATTGGTTATAGAGGAAACTCGAAAGCCCCGGCTTTATGAATA
* * *
48565 GACTACATTCAAACTATGACATTGATCGGGTACTCGGTAATTCGGTGTATGGTCCACTGTGATTA
66 GACTACATTCAAACCATGACATTGATCGGGTACTCGGTAATTCGATGTATGCTCCACTGTGATTA
* *
48630 TCAAGTCAAATACTTTGTGACGACATGAATCCTTCAGCTAGCCGAACAAA
131 TCAAGTCAAAGACTTTGTGACGACATGAATCCTTCAGCTAGCCAAACAAA
48680 TGCAATTATA
Statistics
Matches: 165, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
189 165 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (189 bp):
AGCTGAGCTATTCCACTAAAGCAATTGGTTATAGAGGAAACTCGAAAGCCCCGGCTTTATGAATA
GACTACATTCAAACCATGACATTGATCGGGTACTCGGTAATTCGATGTATGCTCCACTGTGATTA
TCAAGTCAAAGACTTTGTGACGACATGAATCCTTCAGCTAGCCAAACAAAGAAAATTAT
Found at i:54452 original size:23 final size:23
Alignment explanation
Indices: 54426--54470 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
54416 AAACCATTTC
*
54426 GACCCCTCTTTGTAAACCGTTCT
1 GACCCCTCTTTGCAAACCGTTCT
54449 GACCCCTCTTTGCAAACCGTTC
1 GACCCCTCTTTGCAAACCGTTC
54471 CGGTTGTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.38, G:0.13, T:0.31
Consensus pattern (23 bp):
GACCCCTCTTTGCAAACCGTTCT
Found at i:54745 original size:36 final size:36
Alignment explanation
Indices: 54673--54995 Score: 414
Period size: 36 Copynumber: 8.9 Consensus size: 36
54663 CGATCACCTC
*
54673 TGAGACAGTTTCTCTGGAAACAAAGTTTTGTCTCTCT
1 TGAGACAGTTTCTCTTGAAACAAA-TTTTGTCTCTCT
* *
54710 TGAGACAGTTTCCCTTTAAACAAATTTTGTCTCTCT
1 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
* ** * *
54746 TAAGACAACTTCTCTTGAAACAAATTTCGTCTCCCT
1 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
* *
54782 TAAGACAATTTCTCTTGAAACAAATTTTGTCTCTCT
1 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
54818 TGAGACAGCTTTC-CTTTGAAACAAATTTTGTCTCTCT
1 TGAGACAG-TTTCTC-TTGAAACAAATTTTGTCTCTCT
* * * *
54855 TGAGACAGTTTCCCTTAAAACAAGTTTTGTCTCCCT
1 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
* *
54891 TGAGACAGTTTCTCTTGAAACAAATTTCGTCTCCCT
1 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
* * *
54927 GGAGACAATTTCTCTTGAATCAAATTTTGTCTCTCT
1 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
* * *
54963 TGAGTCTGTTTCTCTTGAAACAACTTTTGTCTC
1 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTC
54996 CCTCGAGATA
Statistics
Matches: 250, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
36 194 0.78
37 56 0.22
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
Found at i:54753 original size:21 final size:20
Alignment explanation
Indices: 54725--54818 Score: 55
Period size: 20 Copynumber: 5.1 Consensus size: 20
54715 CAGTTTCCCT
54725 TTAAACAAATTTTGTCTCTC
1 TTAAACAAATTTTGTCTCTC
*
54745 TTAAGAC-AA--CT-TCTCT-
1 TTAA-ACAAATTTTGTCTCTC
* * *
54761 TGAAACAAATTTCGTCTCCC
1 TTAAACAAATTTTGTCTCTC
54781 TTAAGAC-AA--TT-TCTCT-
1 TTAA-ACAAATTTTGTCTCTC
*
54797 TGAAACAAATTTTGTCTCTC
1 TTAAACAAATTTTGTCTCTC
54817 TT
1 TT
54819 GAGACAGCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 24
0.60 0.12 0.28
Matches are distributed among these distances:
15 4 0.08
16 10 0.19
17 9 0.17
18 4 0.08
19 9 0.17
20 12 0.23
21 4 0.08
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (20 bp):
TTAAACAAATTTTGTCTCTC
Found at i:54819 original size:21 final size:21
Alignment explanation
Indices: 54792--54857 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
54782 TAAGACAATT
54792 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* **
54813 TCTCTTGAGAC--AGCTT-TC
1 TCTCTTGAAACAAATTTTGTC
54831 -CT-TTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
54850 TCTCTTGA
1 TCTCTTGA
54858 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 2 0.06
21 14 0.41
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:54936 original size:145 final size:144
Alignment explanation
Indices: 54673--54995 Score: 495
Period size: 145 Copynumber: 2.2 Consensus size: 144
54663 CGATCACCTC
* *
54673 TGAGACAGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAATTTT
1 TGAGACAGTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTT
* *
54738 GTCTCTCTTAAGACAACTTCTCTTGAAACAAATTTCGTCTCCCTTAAGACAATTTCTCTTGAAAC
65 GTCTCCCTTAAGACAACTTCTCTTGAAACAAATTTCGTCTCCCTGAAGACAATTTCTCTTGAAAC
54803 AAATTTTGTCTCTCT
130 AAATTTTGTCTCTCT
*
54818 TGAGACAGCTTTC-CTTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAGTTT
1 TGAGACAG-TTTCTC-TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTT
* ** * *
54882 TGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCCCTGGAGACAATTTCTCTTGAAT
64 TGTCTCCCTTAAGACAACTTCTCTTGAAACAAATTTCGTCTCCCTGAAGACAATTTCTCTTGAAA
54947 CAAATTTTGTCTCTCT
129 CAAATTTTGTCTCTCT
* * *
54963 TGAGTCTGTTTCTCTTGAAACAACTTTTGTCTC
1 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTC
54996 CCTCGAGATA
Statistics
Matches: 162, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
144 22 0.14
145 127 0.78
146 13 0.08
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (144 bp):
TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTTG
TCTCCCTTAAGACAACTTCTCTTGAAACAAATTTCGTCTCCCTGAAGACAATTTCTCTTGAAACA
AATTTTGTCTCTCT
Found at i:55108 original size:33 final size:34
Alignment explanation
Indices: 55027--55108 Score: 78
Period size: 33 Copynumber: 2.4 Consensus size: 34
55017 AACAACAAAC
* * * *
55027 TTTGAGATGTTTCTCTTGAAACAAATTCAATTTTC
1 TTTGAGATGTTTCTCATGAAACAAA-TCAAATATA
*
55062 TTTGAGACCGTTTCTCATGAAAC-AA-CAAATATA
1 TTTGAGA-TGTTTCTCATGAAACAAATCAAATATA
55095 TTTGAGATTGTTTC
1 TTTGAGA-TGTTTC
55109 CCCTAAAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
33 17 0.44
35 9 0.23
36 13 0.33
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (34 bp):
TTTGAGATGTTTCTCATGAAACAAATCAAATATA
Found at i:57887 original size:12 final size:12
Alignment explanation
Indices: 57866--57905 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
57856 ATTTCATAGA
*
57866 TTTTTATATTTC
1 TTTTTTTATTTC
57878 TTTTTTTATTT-
1 TTTTTTTATTTC
*
57889 TATTTTTATTTC
1 TTTTTTTATTTC
57901 TTTTT
1 TTTTT
57906 AGAAATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTATTTC
Found at i:57902 original size:23 final size:23
Alignment explanation
Indices: 57867--57971 Score: 70
Period size: 25 Copynumber: 4.5 Consensus size: 23
57857 TTTCATAGAT
57867 TTTTATATTTCTTTTTTTATTTTA
1 TTTT-TATTTCTTTTTTTATTTTA
** * *
57891 TTTTTATTTCTTTTTAGAAATTAA
1 TTTTTATTTCTTTTT-TTATTTTA
* *
57915 TATTTTATTTATTTTTTATTTTTTA
1 T-TTTTATTTCTTTTTT-TATTTTA
* * *
57940 TTTTAATAT-TTTATTTATTTT-
1 TTTTTATTTCTTTTTTTATTTTA
*
57961 TATTTATTTCT
1 TTTTTATTTCT
57972 CTTGTGACAT
Statistics
Matches: 60, Mismatches: 17, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
21 6 0.10
22 6 0.10
23 16 0.27
24 15 0.25
25 17 0.28
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTTTATTTCTTTTTTTATTTTA
Found at i:57923 original size:36 final size:32
Alignment explanation
Indices: 57881--57965 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 32
57871 ATATTTCTTT
57881 TTTTATTTTATTTTTATTTCTTTTTAGAAATTAATA
1 TTTTA-TTTATTTTTATTT-TTTTT--AAATTAATA
* **
57917 TTTTATTTATTTTT-TATTTTTTATTTTAATA
1 TTTTATTTATTTTTATTTTTTTTAAATTAATA
57948 TTTTATTTATTTTTATTT
1 TTTTATTTATTTTTATTT
57966 ATTTCTCTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
31 21 0.48
32 2 0.05
33 5 0.11
34 2 0.05
35 9 0.20
36 5 0.11
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (32 bp):
TTTTATTTATTTTTATTTTTTTTAAATTAATA
Found at i:57949 original size:8 final size:8
Alignment explanation
Indices: 57915--57960 Score: 51
Period size: 7 Copynumber: 5.8 Consensus size: 8
57905 TAGAAATTAA
57915 TATTTTATT
1 TATTTTA-T
57924 TATTTT-T
1 TATTTTAT
57931 TATTTT-T
1 TATTTTAT
*
57938 TATTTTAA
1 TATTTTAT
57946 TATTTTATT
1 TATTTTA-T
57955 TATTTT
1 TATTTT
57961 TATTTATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 14 0.42
8 7 0.21
9 12 0.36
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TATTTTAT
Found at i:58065 original size:20 final size:19
Alignment explanation
Indices: 58036--58083 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
58026 AATTATTTCT
58036 TTTTTGTTTAGCAT-TCAATA
1 TTTTT-TTTAGCATCT-AATA
*
58056 TTTTATTTTAGTATCTAATA
1 TTTT-TTTTAGCATCTAATA
58076 TTTTTTTT
1 TTTTTTTT
58084 TTTTACTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 19 0.76
21 2 0.08
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTTTTTAGCATCTAATA
Found at i:58815 original size:2 final size:2
Alignment explanation
Indices: 58808--58835 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58798 ATCTTATGTA
58808 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
58836 TGTAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61419 original size:78 final size:79
Alignment explanation
Indices: 61320--61470 Score: 243
Period size: 78 Copynumber: 1.9 Consensus size: 79
61310 TGTGCTTCTA
* *
61320 ACTCTACCATTAATTGCCTTGGTAACAGC-AGTAGATGAGATTCATTGTATCATCTCAAAGGTCA
1 ACTCTACCATTAATTACCTTGGTAACAGCTA-TAGATGAGATTCATTGTATCATCTCAAAAGTCA
61384 TTTA-ATATAAAACG
65 TTTATATATAAAACG
* *
61398 ACTCTACCATTAATTACCTTGGTAACAGCTATAGATGATATTCATTGTATCATCTCAAAAGTCTT
1 ACTCTACCATTAATTACCTTGGTAACAGCTATAGATGAGATTCATTGTATCATCTCAAAAGTCAT
61463 TTATATAT
66 TTATATAT
61471 TCCATTACCT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
78 62 0.93
79 5 0.07
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (79 bp):
ACTCTACCATTAATTACCTTGGTAACAGCTATAGATGAGATTCATTGTATCATCTCAAAAGTCAT
TTATATATAAAACG
Found at i:66210 original size:46 final size:45
Alignment explanation
Indices: 66122--66217 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 45
66112 GCACTAAGAG
* *
66122 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGA
1 TGCATCAAATGCATTCGATGTTTCAAAATACCCAGAGTGCATCGA
* ** *
66167 TGCATCAAATGCATTTGATGTTTTCATAAA-ACCCTTAGTGCATCGG
1 TGCATCAAATGCATTCGATG-TTTCA-AAATACCCAGAGTGCATCGA
66213 TGCAT
1 TGCAT
66218 GGTATGTGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
45 18 0.42
46 22 0.51
47 3 0.07
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (45 bp):
TGCATCAAATGCATTCGATGTTTCAAAATACCCAGAGTGCATCGA
Found at i:68921 original size:20 final size:20
Alignment explanation
Indices: 68896--68944 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
68886 ACCCTATGGA
68896 TGCATCGATGCATGGCCTTG
1 TGCATCGATGCATGGCCTTG
68916 TGCATCGATGCATGGCCTTG
1 TGCATCGATGCATGGCCTTG
*
68936 TGCAACGAT
1 TGCATCGAT
68945 ACACATTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCATGGCCTTG
Found at i:68997 original size:44 final size:42
Alignment explanation
Indices: 68941--69033 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
68931 CCTTGTGCAA
* * * *
68941 CGATACACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGTAT
1 CGATGCACATTCAAGG-ATACATCGATGCA-CTGTCA-GGTGTAT
*
68985 CGATGCACATTCAAGGATACATCGATGCACTGTTAGGTGTAT
1 CGATGCACATTCAAGGATACATCGATGCACTGTCAGGTGTAT
69027 CGATGCA
1 CGATGCA
69034 TGAAGCACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
42 16 0.37
43 12 0.28
44 15 0.35
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.27
Consensus pattern (42 bp):
CGATGCACATTCAAGGATACATCGATGCACTGTCAGGTGTAT
Found at i:72813 original size:22 final size:21
Alignment explanation
Indices: 72772--72818 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
72762 GAGTTTATTT
*
72772 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
72793 TCATTTTT-ATATTTTAAAA-A
1 TCATTTTTCA-ATTTTAAAACA
72813 -CATTTT
1 TCATTTT
72819 CTCATAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:74784 original size:18 final size:17
Alignment explanation
Indices: 74730--74778 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
74720 TTGGACCCTT
* *
74730 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
74748 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
74766 AGTGCATTCGATG
1 AGTGCA-TCGATG
74779 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:74948 original size:65 final size:64
Alignment explanation
Indices: 74750--74959 Score: 232
Period size: 65 Copynumber: 3.2 Consensus size: 64
74740 TGCACTAAGA
* * ** *
74750 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* *
74814 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
74877 AT-
63 -TG
* *
74879 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
74943 G
64 G
*
74944 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
74960 CTTTGATAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 51 0.41
65 63 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:78729 original size:17 final size:17
Alignment explanation
Indices: 78684--78731 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
78674 AGTATGTTAT
*
78684 TTCATTCAATAAAACTAG
1 TTCATTC-ATTAAACTAG
* * *
78702 TTAACTAATTAAACTAG
1 TTCATTCATTAAACTAG
78719 TTCATTCATTAAA
1 TTCATTCATTAAA
78732 ATTGATTTAA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (17 bp):
TTCATTCATTAAACTAG
Found at i:84739 original size:3 final size:3
Alignment explanation
Indices: 84715--84800 Score: 88
Period size: 3 Copynumber: 29.0 Consensus size: 3
84705 CCATTCTTTG
* **
84715 TTA TTA TT- TT- TTC TTA TT- TTA TTA TTA TTA TTA TTA TTA CCA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* *
84761 TTA TTA TTA TTA TTA TTAA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
84801 ATAAATAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
2 6 0.09
3 61 0.87
4 3 0.04
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:84764 original size:25 final size:25
Alignment explanation
Indices: 84732--84800 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
84722 TTTTTCTTAT
*
84732 TTTATTATTATTATTATTATTACCA
1 TTTATTATTATTATTATTATTAACA
*
84757 TTTATTATTATTATTATTATTAATA
1 TTTATTATTATTATTATTATTAACA
**
84782 AATATTATTATTATTATTA
1 TTTATTATTATTATTATTA
84801 ATAAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTATTATTATTATTATTATTAACA
Found at i:84787 original size:22 final size:22
Alignment explanation
Indices: 84737--84807 Score: 97
Period size: 22 Copynumber: 3.1 Consensus size: 22
84727 CTTATTTTAT
* *
84737 TATTATTATTATTATTACCATTTAT
1 TATTATTATTATTATTA--A-TAAA
84762 TATTATTATTATTATTAATAAA
1 TATTATTATTATTATTAATAAA
84784 TATTATTATTATTATTAATAAA
1 TATTATTATTATTATTAATAAA
84806 TA
1 TA
84808 AAAAAATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
22 26 0.59
23 1 0.02
25 17 0.39
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTATTATTATTATTAATAAA
Found at i:95864 original size:22 final size:23
Alignment explanation
Indices: 95834--95888 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
95824 CAGAGGTAAT
*
95834 CGATACCCCC-TTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
95856 CGATTCCCCCTTTGAAGGGGAAC
1 CGATTCCCCCTTTGAAGGGGAAC
95879 CGATTCCCCC
1 CGATTCCCCC
95889 ATAGGTGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 9 0.29
23 22 0.71
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGGGAAC
Found at i:100071 original size:3 final size:3
Alignment explanation
Indices: 100063--100101 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
100053 AAAGTCAACG
* *
100063 CTT CTT CTT CTT CTG CTT CTT CTT CTT CTG CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
100102 TGCTGGGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.33, G:0.05, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:100082 original size:15 final size:15
Alignment explanation
Indices: 100062--100101 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
100052 AAAAGTCAAC
100062 GCTTCTTCTTCTTCT
1 GCTTCTTCTTCTTCT
100077 GCTTCTTCTTCTTCT
1 GCTTCTTCTTCTTCT
100092 GCTTCTTCTT
1 GCTTCTTCTT
100102 TGCTGGGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (15 bp):
GCTTCTTCTTCTTCT
Found at i:101060 original size:2 final size:2
Alignment explanation
Indices: 101053--101087 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
101043 CCCTTAAATT
101053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
101088 CGAATATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:111027 original size:12 final size:12
Alignment explanation
Indices: 110993--111043 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
110983 AATTTAATTC
*
110993 TTAATTCTT-TT
1 TTAATTCTTAAT
*
111004 TTTATTCTTTAAT
1 TTAATTC-TTAAT
111017 TTAATTCTTAAT
1 TTAATTCTTAAT
111029 TTAATTCTTAAT
1 TTAATTCTTAAT
111041 TTA
1 TTA
111044 GATAGTAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
11 6 0.17
12 22 0.63
13 7 0.20
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (12 bp):
TTAATTCTTAAT
Found at i:123894 original size:27 final size:28
Alignment explanation
Indices: 123842--123895 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
123832 AAAAATCGAC
*
123842 GAGCTTAACGAGCAACGAGTCGAGCAAT
1 GAGCTTAACGAGCAACGAGTCAAGCAAT
123870 GAGCTTAACGAGC-ACGAGTCAAGCAA
1 GAGCTTAACGAGCAACGAGTCAAGCAA
123896 CAAGTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.37, C:0.22, G:0.28, T:0.13
Consensus pattern (28 bp):
GAGCTTAACGAGCAACGAGTCAAGCAAT
Found at i:126442 original size:13 final size:12
Alignment explanation
Indices: 126409--126444 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
126399 TGTATTATTT
*
126409 CTTCCTTTTTTC
1 CTTCTTTTTTTC
126421 CTTCTTTTTTTC
1 CTTCTTTTTTTC
*
126433 CTTCTGTTTTTC
1 CTTCTTTTTTTC
126445 TCTGCCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (12 bp):
CTTCTTTTTTTC
Found at i:127179 original size:3 final size:3
Alignment explanation
Indices: 127171--127208 Score: 58
Period size: 3 Copynumber: 12.0 Consensus size: 3
127161 AAATAGATGT
127171 TAA TAA TAA TAA TAA TAA TAA TAA TAA GTTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA TAA
127209 AATTAGAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 30 0.91
5 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:128348 original size:20 final size:20
Alignment explanation
Indices: 128319--128395 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
128309 ATTCGCGTTG
*
128319 CATTTAGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
128339 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** * *
128360 AAAATCGCGTTACGTTTTTC
1 CATTTCGCGTTGCGATTTTC
128380 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
128396 AGTCTACAGT
Statistics
Matches: 41, Mismatches: 15, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 28 0.68
21 13 0.32
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:128432 original size:41 final size:41
Alignment explanation
Indices: 128387--128472 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
128377 TTCCATTTCG
* * *
128387 CGTTGCGATAGTCTACAGTTGTCGTTGCAATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTATCGTTACAATTTTCCAAATT
*
128428 CGTTGCGATAGTCTACAGTTATCGTTACGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTATCGTTACAATTTTCCAAATT
128469 CGTT
1 CGTT
128473 ACGAAAATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTATCGTTACAATTTTCCAAATT
Found at i:128453 original size:22 final size:21
Alignment explanation
Indices: 128387--128458 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 21
128377 TTCCATTTCG
128387 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
* * * **
128409 CGTTGC-A-ATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTT
128428 CGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATAGTCTACAGTT-T
*
128450 CGTTACGAT
1 CGTTGCGAT
128459 TTTCCAAATT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 7 0.19
20 7 0.19
21 7 0.19
22 15 0.42
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTTT
Found at i:128581 original size:6 final size:6
Alignment explanation
Indices: 128570--128602 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
128560 GATACGTATT
*
128570 ACCACG ACCACG ACCACG ACAACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
128603 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.36, C:0.48, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:129145 original size:6 final size:5
Alignment explanation
Indices: 129097--129141 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
129087 CCGTCTCGTC
129097 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
129142 TGGTAAGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 28 0.72
6 11 0.28
ACGTcount: A:0.00, C:0.20, G:0.56, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:129212 original size:19 final size:19
Alignment explanation
Indices: 129188--129230 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
129178 GAATTTTCGT
129188 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
129207 AACGAATTTGGAAAATCGC
1 AACGAATTTGGAAAATCGC
129226 AACGA
1 AACGA
129231 CAACTGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (19 bp):
AACGAATTTGGAAAATCGC
Found at i:129269 original size:42 final size:41
Alignment explanation
Indices: 129218--129298 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
129208 ACGAATTTGG
129218 AAAATCGCAACGACAACTGT-AGACTATCACAACGCGAAATGA
1 AAAATCGCAACG-CAACTGTCA-ACTATCACAACGCGAAATGA
* * *
129260 AAAATCGCAACGCGATTTTCAACTATCACAACGCGAAAT
1 AAAATCGCAACGCAACTGTCAACTATCACAACGCGAAAT
129299 ATAACGCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 22 0.63
42 13 0.37
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (41 bp):
AAAATCGCAACGCAACTGTCAACTATCACAACGCGAAATGA
Found at i:130036 original size:9 final size:9
Alignment explanation
Indices: 130024--130075 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
130014 TAATATTTTG
130024 TATTTAATT
1 TATTTAATT
*
130033 TATTTAA-G
1 TATTTAATT
130041 TATTTAATT
1 TATTTAATT
130050 TATTTAA--
1 TATTTAATT
*
130057 TATTTTATT
1 TATTTAATT
*
130066 TAATTAATT
1 TATTTAATT
130075 T
1 T
130076 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:130045 original size:17 final size:17
Alignment explanation
Indices: 130023--130072 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
130013 TTAATATTTT
130023 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
130040 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
130057 -TATTTTATTTAATTAA
1 GTATTTAATTTATTTAA
130073 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:132319 original size:13 final size:13
Alignment explanation
Indices: 132295--132345 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
132285 TTTGTATTTA
132295 GTAC-TTTTTATT
1 GTACTTTTTTATT
* *
132307 GTAGTTGTTTATT
1 GTACTTTTTTATT
*
132320 GGACTTTTTTATT
1 GTACTTTTTTATT
*
132333 GTATTTTTTTATT
1 GTACTTTTTTATT
132346 TATCATTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 3 0.10
13 28 0.90
ACGTcount: A:0.16, C:0.04, G:0.14, T:0.67
Consensus pattern (13 bp):
GTACTTTTTTATT
Found at i:135986 original size:15 final size:15
Alignment explanation
Indices: 135966--135995 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
135956 TCTCGACTCC
135966 TCTGCAAATTTGAAG
1 TCTGCAAATTTGAAG
135981 TCTGCAAATTTGAAG
1 TCTGCAAATTTGAAG
135996 CCCCTGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
TCTGCAAATTTGAAG
Found at i:139476 original size:19 final size:19
Alignment explanation
Indices: 139452--139488 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
139442 ATGACCAACA
*
139452 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
139471 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
139489 CACTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:139537 original size:20 final size:20
Alignment explanation
Indices: 139514--139707 Score: 196
Period size: 20 Copynumber: 9.6 Consensus size: 20
139504 GTTTCCAGAT
*
139514 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * * *
139534 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
139554 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* **
139574 TCGCAACACGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
*
139595 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* **
139615 TCGCAACACGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
*
139636 TCGCAACTCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
139656 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
139676 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
139696 TCGCAATGCGAT
1 TCGCAACGCGAT
139708 AATACAAAAT
Statistics
Matches: 142, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.04
20 105 0.74
21 28 0.20
22 4 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:139599 original size:21 final size:21
Alignment explanation
Indices: 139573--139647 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
139563 GATTCTGACT
139573 ATCGCAACACGATAATACATA
1 ATCGCAACACGATAATACATA
**
139594 ATCGCAACGA-GATTCTGAC-T-
1 ATCGCAAC-ACGATAAT-ACATA
139614 ATCGCAACACGATAATACATA
1 ATCGCAACACGATAATACATA
*
139635 ATCGCAACTCGAT
1 ATCGCAACACGAT
139648 TCTGACTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.07
20 13 0.30
21 25 0.57
22 3 0.07
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.21
Consensus pattern (21 bp):
ATCGCAACACGATAATACATA
Found at i:139608 original size:41 final size:41
Alignment explanation
Indices: 139514--139729 Score: 251
Period size: 41 Copynumber: 5.3 Consensus size: 41
139504 GTTTCCAGAT
* ** **
139514 TCGCAACGCGATTTTGACTATCGCAATGCG--AATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAACACGATAATACAT-AA
139554 TCGCAACGCGATTCTGACTATCGCAACACGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACACGATAATACATAA
*
139595 TCGCAACGAGATTCTGACTATCGCAACACGATAATACATAA
1 TCGCAACGCGATTCTGACTATCGCAACACGATAATACATAA
* * **
139636 TCGCAACTCGATTCTGACTATCGCAACGCGATTCTGAC-T-A
1 TCGCAACGCGATTCTGACTATCGCAACACGATAAT-ACATAA
** *
139676 TCGCAACGCGATTCTGACTATCGCAATGCGATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACACGATAATACATAA
* *
139717 TCACAATGCGATT
1 TCGCAACGCGATT
139730 TTCAAAGCGC
Statistics
Matches: 153, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.01
40 59 0.39
41 85 0.56
42 7 0.05
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACACGATAATACATAA
Found at i:139728 original size:61 final size:59
Alignment explanation
Indices: 139553--139729 Score: 178
Period size: 61 Copynumber: 2.9 Consensus size: 59
139543 GAATATGTAA
* *
139553 ATCGCAACGCGATTCTGACTATCGCAACACGATAATACATAATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACTATCGCAA-TCGATAATACA-AATCGCAACGCGATTCTGACT
* ** ** *
139614 ATCGCAACACGATAAT-ACATAATCGCAACTCGATTCTGAC-TATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGAC-T-ATCGCAA-TCGATAAT-ACAAATCGCAACGCGATTCTGACT
* *
139675 ATCGCAACGCGATTCTGACTATCGCAATGCGATAATACAAAATCACAATGCGATT
1 ATCGCAACGCGATTCTGACTATCGCAAT-CGATAATAC-AAATCGCAACGCGATT
139730 TTCAAAGCGC
Statistics
Matches: 93, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
59 3 0.03
60 14 0.15
61 59 0.63
62 15 0.16
63 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (59 bp):
ATCGCAACGCGATTCTGACTATCGCAATCGATAATACAAATCGCAACGCGATTCTGACT
Found at i:139899 original size:22 final size:22
Alignment explanation
Indices: 139874--139924 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
139864 CTACAGTGAC
139874 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
139896 ATCCATCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
139918 ATCCGTC
1 ATCCGTC
139925 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.45, G:0.12, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:140331 original size:14 final size:14
Alignment explanation
Indices: 140309--140340 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
140299 GTGATTTTAG
140309 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
140323 TTTCTCGTTGCGAT
1 TTTCGCGTTGCGAT
140337 TTTC
1 TTTC
140341 ATTTCGCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:140417 original size:20 final size:20
Alignment explanation
Indices: 140321--140418 Score: 81
Period size: 20 Copynumber: 5.0 Consensus size: 20
140311 TCGCGTTGCG
*
140321 ATTTTCTCGTTGCGATTTTC
1 ATTTTCGCGTTGCGATTTTC
**
140341 A-TTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATTTTC
*** **
140360 AAAGTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATTTTC
** *
140380 ATTTTCATGTTGCAATTTTC
1 ATTTTCGCGTTGCGATTTTC
*
140400 ATTTTCGTGTTGCGATTTT
1 ATTTTCGCGTTGCGATTTT
140419 AAGTTTCAGA
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
19 16 0.26
20 46 0.74
ACGTcount: A:0.16, C:0.17, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATTTTC
Found at i:140425 original size:20 final size:20
Alignment explanation
Indices: 140382--140426 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
140372 CGATAGTCAT
* *
140382 TTTCATGTTGCAATTTTCAT
1 TTTCATGTTGCAATTTTAAG
* *
140402 TTTCGTGTTGCGATTTTAAG
1 TTTCATGTTGCAATTTTAAG
140422 TTTCA
1 TTTCA
140427 GAAACTATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (20 bp):
TTTCATGTTGCAATTTTAAG
Found at i:142390 original size:34 final size:34
Alignment explanation
Indices: 142329--142428 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 34
142319 ACGAAACTTA
* * * **
142329 AAAATTGCAACGCAAAAATGATTATCGCAACGGG
1 AAAATCGCAATGCAAAAATAAAAATCGCAACGGG
* *
142363 ATAATCGCAATGCAAAAATAAAAATCGCAACGTG
1 AAAATCGCAATGCAAAAATAAAAATCGCAACGGG
* *
142397 AAAATCGCAATGCGAAAATGAAAATCGCAACG
1 AAAATCGCAATGCAAAAATAAAAATCGCAACG
142429 CGAATTTAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (34 bp):
AAAATCGCAATGCAAAAATAAAAATCGCAACGGG
Found at i:142418 original size:20 final size:20
Alignment explanation
Indices: 142395--142432 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
142385 AATCGCAACG
*
142395 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
142415 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
142433 TTTAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:142517 original size:20 final size:20
Alignment explanation
Indices: 142492--142538 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
142482 GATTATCCCA
142492 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
**
142512 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCG
142532 TTGCGAT
1 TTGCGAT
142539 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:142548 original size:20 final size:20
Alignment explanation
Indices: 142506--142568 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
142496 GATAGTCAAA
** * *
142506 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTAAGT
142526 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
*
142546 TTCGTGTTGCGATTTTAAGT
1 TTCGCGTTGCGATTTTAAGT
142566 TTC
1 TTC
142569 AGAAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTAAGT
Found at i:143101 original size:21 final size:21
Alignment explanation
Indices: 143046--143168 Score: 104
Period size: 21 Copynumber: 5.9 Consensus size: 21
143036 GCCCGACTCA
143046 CCTGTCATCATTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCC
* *
143067 TCT-CCTATCATTCAAGAGGCC
1 CCTGTC-ATCATTCAAGAGGCC
* *
143088 CCTGTCATCCTTCAAGAGTCC
1 CCTGTCATCATTCAAGAGGCC
* * *
143109 CCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCC
* * * *
143130 TCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCATTCAAGAGGCC
** *
143151 CCTCCCACCATTCAAGAG
1 CCTGTCATCATTCAAGAG
143169 CCCGATTCAC
Statistics
Matches: 79, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.01
21 77 0.97
22 1 0.01
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (21 bp):
CCTGTCATCATTCAAGAGGCC
Found at i:143105 original size:42 final size:41
Alignment explanation
Indices: 143046--143168 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 41
143036 GCCCGACTCA
*
143046 CCTGTCATCATTCAAGAGGCCTCTCCTATCATTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCC-CTCCTACCATTCAAGAGGCC
* * *
143088 CCTGTCATCCTTCAAGAGTCCC-CTCTCACCGTTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCCCTC-CT-ACCATTCAAGAGGCC
* * * *
143130 TCTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTGTCATCATTCAAGAGG-CCCTCCTACCATTCAAGAG
143169 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
40 1 0.01
41 3 0.04
42 58 0.87
43 4 0.06
44 1 0.01
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (41 bp):
CCTGTCATCATTCAAGAGGCCCTCCTACCATTCAAGAGGCC
Found at i:144202 original size:185 final size:183
Alignment explanation
Indices: 143887--144274 Score: 625
Period size: 185 Copynumber: 2.1 Consensus size: 183
143877 ATTAAATTTT
* * *
143887 AAATATTAAATATATTATATATAACATATGGGCTCAGTCCAAACTATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
143952 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAAATTATATAAA-TTT
* * *
144017 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTTAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
* *
144072 AAATATTAAATATATTATATATAACATTTGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
* * *
144137 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATCTGAATTTT
66 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
144202 TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* * *
144255 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
144275 AATTAGAAAA
Statistics
Matches: 189, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
182 8 0.04
183 21 0.11
184 42 0.22
185 118 0.62
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:145334 original size:14 final size:14
Alignment explanation
Indices: 145315--145351 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
145305 GCTTGTTTAA
145315 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
145329 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
145343 TTGATTTGT
1 TTGATTTGT
145352 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:145401 original size:35 final size:34
Alignment explanation
Indices: 145351--145458 Score: 113
Period size: 27 Copynumber: 3.3 Consensus size: 34
145341 AGTTGATTTG
145351 TTTAATTGATGTGTAAATAATTCTTATTTGTGCT
1 TTTAATTGATGTGTAAATAATTCTTATTTGTGCT
* * *
145385 TTCTAATTGATTTGT-AA-AAGT-TGA-TT-TG--
1 TT-TAATTGATGTGTAAATAATTCTTATTTGTGCT
145413 TTTAATTGATGTGTAAATAATTCTTATTTGTGCTT
1 TTTAATTGATGTGTAAATAATTCTTATTTGTGC-T
145448 ATTTAATTGAT
1 -TTTAATTGAT
145459 TGAAATGTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
27 11 0.19
28 4 0.07
29 3 0.05
30 4 0.07
31 4 0.07
32 4 0.07
33 3 0.05
34 4 0.07
35 11 0.19
36 10 0.17
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.53
Consensus pattern (34 bp):
TTTAATTGATGTGTAAATAATTCTTATTTGTGCT
Found at i:145426 original size:62 final size:63
Alignment explanation
Indices: 145329--145481 Score: 254
Period size: 62 Copynumber: 2.4 Consensus size: 63
145319 TTTGTAAAAG
145329 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTT-TCTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATCTAA
*
145391 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATCTAA
145454 TTGATTGAAATGTAAAAGTTGATTTGTT
1 TTGATT----TGTAAAAGTTGATTTGTT
145482 GATTTCAATC
Statistics
Matches: 85, Mismatches: 1, Indels: 5
0.93 0.01 0.05
Matches are distributed among these distances:
62 57 0.67
63 10 0.12
67 18 0.21
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (63 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTATCTAA
Found at i:145570 original size:20 final size:20
Alignment explanation
Indices: 145533--145570 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
145523 AGGTAAACTT
*
145533 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACTCAAAA
*
145553 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAACTCAA
145571 TTTGCATTGC
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:0.42, C:0.29, G:0.16, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:145636 original size:20 final size:20
Alignment explanation
Indices: 145609--145739 Score: 157
Period size: 20 Copynumber: 6.8 Consensus size: 20
145599 GCGATTTTCT
*
145609 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* * * *
145629 CATTGCGATAATAAAATTCA
1 CGTTGCGATAGTCAAATTCG
145649 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
145669 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
145689 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
145703 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
145723 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
145740 GAATGTGTAA
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
14 12 0.13
16 1 0.01
18 1 0.01
20 80 0.85
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:145962 original size:140 final size:140
Alignment explanation
Indices: 145710--145992 Score: 530
Period size: 140 Copynumber: 2.0 Consensus size: 140
145700 TTGCGTTGCG
*
145710 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
145775 TAGCAATGTTCAAACTCAAGCTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGCTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
145840 AATACACATA
131 AATACACATA
145850 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
* * *
145915 TAGCAATGTTCAAACTCAAGTTATTAATACATGCCTAACTGAAAATGTTAAACGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGCTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
145980 AATACACATA
131 AATACACATA
145990 ATA
1 ATA
145993 CAACGTTTGC
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
TAGCAATGTTCAAACTCAAGCTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:146073 original size:18 final size:18
Alignment explanation
Indices: 146050--146084 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
146040 AAGCCGGTTG
*
146050 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
146068 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
146085 ACCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:148380 original size:23 final size:24
Alignment explanation
Indices: 148338--148390 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
148328 CTGAAACATC
148338 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
148362 ATCAAAGTCCG-GTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
148385 ATCAAA
1 ATCAAA
148391 TTTAGAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:149251 original size:20 final size:20
Alignment explanation
Indices: 149205--149295 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
149195 TTGAAATTCA
*
149205 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
149225 GCATTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* * **
149245 ACGTTGCGGTTATGT-ATTATC
1 GCGTTGC-GATA-GTCAGAATC
*
149266 GCGTTGCGAAAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
149286 TCGTTGCGAT
1 GCGTTGCGAT
149296 TATATATTAT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.04
20 37 0.69
21 13 0.24
22 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:149267 original size:41 final size:41
Alignment explanation
Indices: 149222--149316 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
149212 GACAGTCAGA
* * *
149222 ATCGCATTGCGATAGTCAGAATCACGTTGCGGTTATGTATT
1 ATCGCGTTGCGATAGTCAGAATCACGTTGCGATTATATATT
* *
149263 ATCGCGTTGCGAAAGTCAGAATCTCGTTGCGATTATATATT
1 ATCGCGTTGCGATAGTCAGAATCACGTTGCGATTATATATT
149304 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
149317 TTACATATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGAATCACGTTGCGATTATATATT
Found at i:149447 original size:19 final size:19
Alignment explanation
Indices: 149423--149459 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
149413 TGCGATACTG
*
149423 GAGATCGCGTTACGATTTA
1 GAGATCGCATTACGATTTA
*
149442 GAGATCGCATTGCGATTT
1 GAGATCGCATTACGATTT
149460 TGTTGGTCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:150369 original size:5 final size:5
Alignment explanation
Indices: 150359--150385 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
150349 TCTAAACATT
150359 TCCCC TCCCC TCCCC TCCCC TCCCC TC
1 TCCCC TCCCC TCCCC TCCCC TCCCC TC
150386 ATGCAACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.78, G:0.00, T:0.22
Consensus pattern (5 bp):
TCCCC
Found at i:153696 original size:19 final size:19
Alignment explanation
Indices: 153669--153707 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
153659 ATTAAATTTT
* *
153669 TAATTTTTTTAATTAAAAA
1 TAATCTTTTTAACTAAAAA
*
153688 TAATCTTTTTTACTAAAAA
1 TAATCTTTTTAACTAAAAA
153707 T
1 T
153708 TTAAAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATCTTTTTAACTAAAAA
Found at i:156980 original size:6 final size:5
Alignment explanation
Indices: 156964--157032 Score: 52
Period size: 5 Copynumber: 13.4 Consensus size: 5
156954 AATCCCCCTT
* *
156964 TTATA TT-TA TTACTA TTAATA TTTATA TTATA TTATT TTAT- TTTTA
1 TTATA TTATA TTA-TA TT-ATA -TTATA TTATA TTATA TTATA TTATA
* *
157010 TTATA TTATTA TTTTA ATATA TT
1 TTATA TTA-TA TTATA TTATA TT
157033 TTTCAACTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
4 7 0.14
5 28 0.55
6 13 0.25
7 3 0.06
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:159354 original size:21 final size:21
Alignment explanation
Indices: 159328--159379 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
159318 ATTGACAATG
159328 GAATTTGATGGTTAGATCGTT
1 GAATTTGATGGTTAGATCGTT
159349 GAATTTGATGGTTAGATCGTT
1 GAATTTGATGGTTAGATCGTT
159370 GAATTTGATG
1 GAATTTGATG
159380 TTACAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.04, G:0.29, T:0.42
Consensus pattern (21 bp):
GAATTTGATGGTTAGATCGTT
Found at i:161629 original size:20 final size:19
Alignment explanation
Indices: 161613--161650 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
161603 ATCTTTTATT
*
161613 TAGTTTAAATAGGTTTTAG
1 TAGTTTAAATAAGTTTTAG
*
161632 TATTTTAAATAAGTTTTAG
1 TAGTTTAAATAAGTTTTAG
161651 GATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (19 bp):
TAGTTTAAATAAGTTTTAG
Found at i:161719 original size:19 final size:19
Alignment explanation
Indices: 161691--161752 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
161681 AGGTATTTAG
*
161691 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
161710 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* *
161729 ATTATATTA-TTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
161749 TTTA
1 TTTA
161753 TTTAAATAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
19 23 0.70
20 10 0.30
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:162383 original size:17 final size:17
Alignment explanation
Indices: 162361--162401 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
162351 TCTTTAATTG
*
162361 TTTATTTAATTATTTTT
1 TTTATTTAATTATTATT
*
162378 TTTATTTAATTCTTATT
1 TTTATTTAATTATTATT
162395 TTTATTT
1 TTTATTT
162402 TAAAATAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTAATTATTATT
Found at i:162466 original size:10 final size:10
Alignment explanation
Indices: 162425--162492 Score: 61
Period size: 13 Copynumber: 6.6 Consensus size: 10
162415 AAAAATCCCC
162425 ATTTTATATTT
1 ATTTTAT-TTT
162436 ATTATTAATATTT
1 ATT-TT-AT-TTT
162449 ATTATTATTTT
1 ATT-TTATTTT
162460 ATTTTATTTT
1 ATTTTATTTT
*
162470 -TCTT-TTTT
1 ATTTTATTTT
162478 A-TTTATTTT
1 ATTTTATTTT
162487 ATTTTA
1 ATTTTA
162493 ATATATCTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
8 6 0.12
9 8 0.16
10 11 0.22
11 9 0.18
12 4 0.08
13 12 0.24
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTATTTT
Found at i:162466 original size:13 final size:13
Alignment explanation
Indices: 162425--162492 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 13
162415 AAAAATCCCC
162425 ATTTTATATTTATT
1 ATTTTAT-TTTATT
*
162439 ATTAATATTTATTATT
1 ATT-TTA-TT-TTATT
162455 ATTTTATTTTATT
1 ATTTTATTTTATT
*
162468 -TTTCTTTTTTATTT
1 ATTT-TATTTTA-TT
162482 ATTTTATTTTA
1 ATTTTATTTTA
162493 ATATATCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 3 0.07
13 11 0.25
14 13 0.30
15 8 0.18
16 9 0.20
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTATTTTATT
Done.