Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 118 of 120
Found at i:36062473 original size:21 final size:21
Alignment explanation
Indices: 36062447--36062495 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
36062437 GTAATGTAAT
*
36062447 ATATATATGATGTCATATATA
1 ATATATATGATGACATATATA
36062468 ATATATATGATGACATATATA
1 ATATATATGATGACATATATA
*
36062489 AAATATA
1 ATATATA
36062496 CAAATAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (21 bp):
ATATATATGATGACATATATA
Found at i:36062840 original size:11 final size:12
Alignment explanation
Indices: 36062819--36062843 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36062809 GTGAAGGGTA
36062819 AGAATTTTTTTT
1 AGAATTTTTTTT
36062831 AGAATTTTTTTT
1 AGAATTTTTTTT
36062843 A
1 A
36062844 AGAAGCTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
AGAATTTTTTTT
Found at i:36065397 original size:8 final size:8
Alignment explanation
Indices: 36065386--36065416 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
36065376 CTTTTACTAA
36065386 TTTAAATT
1 TTTAAATT
36065394 TTTAAATT
1 TTTAAATT
36065402 TTTAAATT
1 TTTAAATT
36065410 TTTAAAT
1 TTTAAAT
36065417 GGCTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTAAATT
Found at i:36065527 original size:21 final size:22
Alignment explanation
Indices: 36065497--36065545 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
36065487 TCACATCAAT
*
36065497 AAATAATTTAAAAATTATAA-AA
1 AAAT-ATTTAAAAATTAAAATAA
*
36065519 AAATATTTAAAATTTAAAATAA
1 AAATATTTAAAAATTAAAATAA
36065541 AAATA
1 AAATA
36065546 AAAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATATTTAAAAATTAAAATAA
Found at i:36065549 original size:19 final size:19
Alignment explanation
Indices: 36065505--36065562 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
36065495 ATAAATAATT
*
36065505 TAAAAATTATAAAAAAATAT
1 TAAAAATT-TAAAAAAATAA
*
36065525 TTAAAATTTAAAATAAA-AA
1 TAAAAATTTAAAA-AAATAA
36065544 TAAAAATTTAAAACAAATA
1 TAAAAATTTAAAA-AAATA
36065563 GCATAAATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAATTTAAAAAAATAA
Found at i:36067904 original size:489 final size:484
Alignment explanation
Indices: 36066821--36067906 Score: 1418
Period size: 489 Copynumber: 2.2 Consensus size: 484
36066811 TTTTCAAAAG
* * *
36066821 AATCAAG-TTCTTACGTTAGATGCTATATGATCACTAATTGAATGAAACTTGACAATAATTAAAC
1 AATCAAGTTTCTTACGTTAGATGCTATGTGATCACTACTTGAAAGAAACTTGACAATAATTAAAC
* * * * * * ** * *
36066885 AATTAATTTCAACCTTTACGTTTAGAACTCACAATTTTCTCAACGATTGTATGTTCCTTGTGATG
66 AATCAATTTCGATCTTTACCTTTAGAACTCAAAATTTTCTCAACCATTACATGTTCCATGTAATG
* * *
36066950 ATTATATTTTAATATTTATAATATAATTTATATATTCAAATTAAATTTTACAAACATCTAACATT
131 ATTATATTTTAATATTTATAACATAATTTATATATTCAAATTAAATTTAACAAACAACTAACATT
* * * * *
36067015 GTTTGCTTAAAAAAATATTTTATATTTATATTTTATATATCAAAATATTAGTTACGAGTTACAAT
196 ATTTGCTT-AAAAAATATTTTAAATTTATATTTTATATATCAAAATATTAATAACGACTTACAAT
*
36067080 AAATTATTTTAATTAAAATATTATAATATTAACAAATTTAAGCATCATTTAAATAAAAATTTTTG
260 AAATTATTTTAATTAAAATATTATAATACTAACAAATTTAAGCATCATTTAAATAAAAATTTTTG
* * * *
36067145 ACAACATCATGTCTAAAATAAAATGTTTTATTTTTCAAAAGTATTTTTTTATCAATAATACTAAA
325 ACAACATCATGTCTAAAATAAAATATTTTATTTTTCAAAAGTATTTTTTAATCAACAATACCAAA
* * *** * **
36067210 CACATAAATCTTAAACTTTTTTTTTAAATAACTATTTTTACAACATTTTTCACTGCACTTTTCAA
390 AACATAAATCTCAAACAACTTTTTAAAATAACTATTTGCACAACATTTTTCACTGCACTTTTCAA
36067275 AAATAAAGATAAACTCGCATTTAATATCTA
455 AAATAAAGATAAACTCGCATTTAATATCTA
* * *
36067305 AATCAAGTGTCTTATGCTAGATGCTATGTGATCACTACTTGAAAGAAACTTGACAATAATTAAAC
1 AATCAAGTTTCTTACGTTAGATGCTATGTGATCACTACTTGAAAGAAACTTGACAATAATTAAAC
* * * *
36067370 AATCAATTTCGATATCTACTTTTAGAACTCAGAAATTTT-TCAACCATTACATG-TGCATGTAAT
66 AATCAATTTCGATCTTTACCTTTAGAACTCA-AAATTTTCTCAACCATTACATGTTCCATGTAAT
* * *
36067433 GATTATATTTTAATATTTATAACATAGTTTATATATTTAAATTAAATTTAACAAATAACTAACAT
130 GATTATATTTTAATATTTATAACATAATTTATATATTCAAATTAAATTTAACAAACAACTAACAT
*
36067498 TATTTGCTT-AAAAATATTTTAAATTTATATTTTATATATTAAAATATTAATAACGACTTACAAT
195 TATTTGCTTAAAAAATATTTTAAATTTATATTTTATATATCAAAATATTAATAACGACTTACAAT
* *****
36067562 AAATTATTTTAATTAAAATATTATAATACTAGCAAATTTAAGCATCATTTAAATGTGTTTTTTTA
260 AAATTATTTTAATTAAAATATTATAATACTAACAAATTTAAGCATCATTTAAA----TAAAAAT-
**
36067627 TTTTGACAACA-CTATGTCTAAAATGGAATATATTT-TTTTTCAAAAGTA-TTTTTAATCAACAA
320 TTTTGACAACATC-ATGTCTAAAATAAAATAT-TTTATTTTTCAAAAGTATTTTTTAATCAACAA
* * *
36067689 TACCAAAAACTTAAATCTCAAACAAAACTTTTTAAAATAACTATTTGCACAACATTTTTTTATTG
383 TACCAAAAACATAAATCTCAAAC--AACTTTTTAAAATAACTATTTGCACAACA-TTTTTCACTG
* * *
36067754 TACTTTTCAAAAGTAACA-ATAAACTCGTATTTAATATCTA
445 CACTTTTCAAAAATAA-AGATAAACTCGCATTTAATATCTA
36067794 AATCAAGTTTCTTACGTTAGATGCTATGTGATCACTACTTGAAAGAAACTTGACAATAATTAAAC
1 AATCAAGTTTCTTACGTTAGATGCTATGTGATCACTACTTGAAAGAAACTTGACAATAATTAAAC
* *
36067859 AATCAATTTTGATCTTTACCTTT-GAAACTGC-TAATTTTCTCAACCATT
66 AATCAATTTCGATCTTTACCTTTAG-AACT-CAAAATTTTCTCAACCATT
36067907 GCAAATCCAC
Statistics
Matches: 520, Mismatches: 66, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
482 101 0.19
484 81 0.16
485 87 0.17
486 40 0.08
487 39 0.08
488 33 0.06
489 137 0.26
490 2 0.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (484 bp):
AATCAAGTTTCTTACGTTAGATGCTATGTGATCACTACTTGAAAGAAACTTGACAATAATTAAAC
AATCAATTTCGATCTTTACCTTTAGAACTCAAAATTTTCTCAACCATTACATGTTCCATGTAATG
ATTATATTTTAATATTTATAACATAATTTATATATTCAAATTAAATTTAACAAACAACTAACATT
ATTTGCTTAAAAAATATTTTAAATTTATATTTTATATATCAAAATATTAATAACGACTTACAATA
AATTATTTTAATTAAAATATTATAATACTAACAAATTTAAGCATCATTTAAATAAAAATTTTTGA
CAACATCATGTCTAAAATAAAATATTTTATTTTTCAAAAGTATTTTTTAATCAACAATACCAAAA
ACATAAATCTCAAACAACTTTTTAAAATAACTATTTGCACAACATTTTTCACTGCACTTTTCAAA
AATAAAGATAAACTCGCATTTAATATCTA
Found at i:36068670 original size:29 final size:29
Alignment explanation
Indices: 36068608--36068670 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
36068598 TTCATTATGA
*
36068608 ATTTAGAATTTTTTAATAATTTTCTTACT
1 ATTTAGAATTTTTTAATAATTTTCTTAAT
* *
36068637 TTTTAGAA-TTTTTATTAAATTTT-TTCAAT
1 ATTTAGAATTTTTTAAT-AATTTTCTT-AAT
36068666 ATTTA
1 ATTTA
36068671 TTGACGTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (29 bp):
ATTTAGAATTTTTTAATAATTTTCTTAAT
Found at i:36070203 original size:53 final size:53
Alignment explanation
Indices: 36070123--36070235 Score: 226
Period size: 53 Copynumber: 2.1 Consensus size: 53
36070113 TATATACACT
36070123 AAATGATGAAAATTTGAAATTTCCGAAATCATTGTAATGTGATAATAATGACA
1 AAATGATGAAAATTTGAAATTTCCGAAATCATTGTAATGTGATAATAATGACA
36070176 AAATGATGAAAATTTGAAATTTCCGAAATCATTGTAATGTGATAATAATGACA
1 AAATGATGAAAATTTGAAATTTCCGAAATCATTGTAATGTGATAATAATGACA
36070229 AAATGAT
1 AAATGAT
36070236 ACGGTGCAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (53 bp):
AAATGATGAAAATTTGAAATTTCCGAAATCATTGTAATGTGATAATAATGACA
Found at i:36076161 original size:31 final size:31
Alignment explanation
Indices: 36076125--36076189 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
36076115 AACAATGCAG
36076125 TGACTTAAATAAAAACTTTT-GAATAATTCAA
1 TGACTTAAATAAAAA-TTTTCGAATAATTCAA
* *
36076156 TGACTTAAATGAAAATTTTCGAATAATTTAA
1 TGACTTAAATAAAAATTTTCGAATAATTCAA
36076187 TGA
1 TGA
36076190 TTATTTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (31 bp):
TGACTTAAATAAAAATTTTCGAATAATTCAA
Found at i:36076671 original size:8 final size:8
Alignment explanation
Indices: 36076658--36076687 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
36076648 ATTAATTATT
36076658 AAAAATTA
1 AAAAATTA
36076666 AAAAATTA
1 AAAAATTA
36076674 AAAAATTA
1 AAAAATTA
36076682 AAAAAT
1 AAAAAT
36076688 AATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAATTA
Found at i:36079766 original size:17 final size:16
Alignment explanation
Indices: 36079743--36079783 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
36079733 ATAGTAAAAA
36079743 TATAATTTTAT-TATT
1 TATAATTTTATATATT
36079758 T-TAATAATTTATATATT
1 TATAAT--TTTATATATT
36079775 TATAATTTT
1 TATAATTTT
36079784 TAAAGGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.18
15 1 0.05
16 8 0.36
17 5 0.23
18 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:36084935 original size:42 final size:42
Alignment explanation
Indices: 36084872--36084953 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
36084862 CTACATTGCG
* *
36084872 TTATTACATTTTTACCTTGTTAATGGCTTATATATACAAGCA
1 TTATTACATTTTTACCATGTTAATAGCTTATATATACAAGCA
* *
36084914 TTATTGCATTTTTACCATGTTAATAGTTTATATATACAAG
1 TTATTACATTTTTACCATGTTAATAGCTTATATATACAAG
36084954 GATAAAATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (42 bp):
TTATTACATTTTTACCATGTTAATAGCTTATATATACAAGCA
Found at i:36085915 original size:5 final size:5
Alignment explanation
Indices: 36085907--36085931 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
36085897 TCCTTTCTTT
36085907 CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA
36085932 ATATTGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:36102096 original size:23 final size:22
Alignment explanation
Indices: 36102053--36102097 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
36102043 AAAATTAAAT
36102053 TATAATTTTTATTATAGTAAAAA
1 TATAATTTTTATTATA-TAAAAA
36102076 TATAATTTTATCATTAT-TAAAA
1 TATAATTTT-T-ATTATATAAAA
36102098 GATTAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 14 0.70
24 1 0.05
25 5 0.25
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TATAATTTTTATTATATAAAAA
Found at i:36102097 original size:22 final size:20
Alignment explanation
Indices: 36102046--36102097 Score: 50
Period size: 23 Copynumber: 2.4 Consensus size: 20
36102036 AGGGGTTAAA
*
36102046 ATTAAATTATAATTTTTATT
1 ATTAAAATATAATTTTTATT
36102066 ATAGTAAAAATATAATTTTATCATT
1 AT--T-AAAATATAATTTT-T-ATT
36102091 ATTAAAA
1 ATTAAAA
36102098 GATTAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
20 2 0.08
22 5 0.19
23 13 0.50
24 1 0.04
25 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTAAAATATAATTTTTATT
Found at i:36112893 original size:17 final size:17
Alignment explanation
Indices: 36112866--36112923 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
36112856 AATTTTATTT
36112866 TTATATAAAAAAATAATA
1 TTAT-TAAAAAAATAATA
36112884 TTATTAAAAAAATTAATA
1 TTATTAAAAAAA-TAATA
* **
36112902 TTATTATATTAATAATA
1 TTATTAAAAAAATAATA
36112919 TTATT
1 TTATT
36112924 TATTTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 18 0.50
18 18 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATTAAAAAAATAATA
Found at i:36112893 original size:18 final size:18
Alignment explanation
Indices: 36112872--36112907 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
36112862 ATTTTTATAT
36112872 AAAAAAATAATATTATTA
1 AAAAAAATAATATTATTA
*
36112890 AAAAAATTAATATTATTA
1 AAAAAAATAATATTATTA
36112908 TATTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAAAATAATATTATTA
Found at i:36113420 original size:15 final size:17
Alignment explanation
Indices: 36113388--36113431 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 17
36113378 TGTATTTTAC
36113388 AATT-TATAAATA-TTT
1 AATTATATAAATATTTT
36113403 AA-TA-ATAAATATTTT
1 AATTATATAAATATTTT
36113418 AATTATATAAATAT
1 AATTATATAAATAT
36113432 GAATATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.32
15 7 0.28
16 2 0.08
17 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTATATAAATATTTT
Found at i:36113427 original size:31 final size:33
Alignment explanation
Indices: 36113351--36113431 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 33
36113341 TTATTAAAAA
36113351 TAATTATA-ATAATATTTCAACAATAAATGTATTT
1 TAATTATATA-AATATTTCAACAATAAA-GTATTT
*
36113385 TACAATT-TATAAATATTT-AATAATAAA-TATTT
1 T--AATTATATAAATATTTCAACAATAAAGTATTT
36113417 TAATTATATAAATAT
1 TAATTATATAAATAT
36113432 GAATATTTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
30 4 0.10
31 9 0.21
32 6 0.14
34 9 0.21
35 9 0.21
36 5 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (33 bp):
TAATTATATAAATATTTCAACAATAAAGTATTT
Found at i:36128404 original size:4 final size:4
Alignment explanation
Indices: 36128395--36128426 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
36128385 CTCCTTTATG
*
36128395 CATA CATA CATA CATA CAAA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
36128427 TATATAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (4 bp):
CATA
Found at i:36133586 original size:23 final size:24
Alignment explanation
Indices: 36133555--36133607 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
36133545 TTAAAAAAGT
*
36133555 TGTTTATAAACAT-TAGATT-AACA
1 TGTTCATAAACATATA-ATTGAACA
36133578 TGTTCATAAACATATAATTGAACA
1 TGTTCATAAACATATAATTGAACA
36133602 TGTTCA
1 TGTTCA
36133608 CAAATAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (24 bp):
TGTTCATAAACATATAATTGAACA
Found at i:36134143 original size:20 final size:21
Alignment explanation
Indices: 36134109--36134147 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
36134099 CCTTGCCCCC
*
36134109 AAAAGAAAATTGAAAAAAATG
1 AAAAGAAAATGGAAAAAAATG
36134130 AAAAG-AAATGGAAAAAAA
1 AAAAGAAAATGGAAAAAAA
36134148 GAAGGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (21 bp):
AAAAGAAAATGGAAAAAAATG
Found at i:36134157 original size:19 final size:19
Alignment explanation
Indices: 36134111--36134157 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
36134101 TTGCCCCCAA
*
36134111 AAGAAAATTGAAAAAAATG
1 AAGAAAATGGAAAAAAATG
*
36134130 AAAAGAAATGGAAAAAAA-G
1 AAGA-AAATGGAAAAAAATG
36134149 AAGGAAAAT
1 AA-GAAAAT
36134158 ACCCTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (19 bp):
AAGAAAATGGAAAAAAATG
Found at i:36154597 original size:31 final size:30
Alignment explanation
Indices: 36154527--36154611 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
36154517 TGTGCAATTG
* *
36154527 TATACATG-AACTTTAATTTGATGCAATTA
1 TATACATGAAACTTTAATTTGATTCAAATA
* * *
36154556 TACACGTGAAACTCTAATTGTGATTCAAATA
1 TATACATGAAACTTTAATT-TGATTCAAATA
* *
36154587 TATACTTGAAATTTTAATTTTGATT
1 TATACATGAAACTTTAA-TTTGATT
36154612 TAATCATACG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
29 6 0.14
30 9 0.20
31 27 0.61
32 2 0.05
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (30 bp):
TATACATGAAACTTTAATTTGATTCAAATA
Found at i:36154792 original size:29 final size:30
Alignment explanation
Indices: 36154738--36154798 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
36154728 ATAATTTACA
* * *
36154738 AAAATTAGACCAAATCAAAATTTCATGTAT
1 AAAATTACACAAAATCAAAAGTTCATGTAT
36154768 AAAATTACACAAAATC-AAAGTTCATGTAT
1 AAAATTACACAAAATCAAAAGTTCATGTAT
36154797 AA
1 AA
36154799 TTTTAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (30 bp):
AAAATTACACAAAATCAAAAGTTCATGTAT
Found at i:36159472 original size:52 final size:54
Alignment explanation
Indices: 36159366--36159472 Score: 130
Period size: 52 Copynumber: 2.0 Consensus size: 54
36159356 ACTACATTAG
* * * *
36159366 TAGTCACCCAACTATATATTTTTTTTTGTCATCCAACTATGAAAAGTTGCAAAA
1 TAGTCACCCAACTATATATCTTTTTTGGTCATCCAACTATAAAAAGTTACAAAA
* *
36159420 TAGTCACCCAACTAT-T-TCTTTTTTGGTCA-CTCAACTGTAAAAAGTTATAAAA
1 TAGTCACCCAACTATATATCTTTTTTGGTCATC-CAACTATAAAAAGTTACAAAA
36159472 T
1 T
36159473 GATCACTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 1 0.02
52 29 0.63
53 1 0.02
54 15 0.33
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (54 bp):
TAGTCACCCAACTATATATCTTTTTTGGTCATCCAACTATAAAAAGTTACAAAA
Found at i:36160287 original size:21 final size:22
Alignment explanation
Indices: 36160263--36160305 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
36160253 AGTTATAGAA
*
36160263 TTCGATTCAATT-GTTTAAAAT
1 TTCGATTAAATTAGTTTAAAAT
*
36160284 TTCGGTTAAATTAAGTTTAAAA
1 TTCGATTAAATT-AGTTTAAAA
36160306 GAGTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (22 bp):
TTCGATTAAATTAGTTTAAAAT
Found at i:36162639 original size:16 final size:16
Alignment explanation
Indices: 36162614--36162644 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36162604 GCTAATGATG
36162614 AACAAGAAAAAAAATT
1 AACAAGAAAAAAAATT
*
36162630 AACAATAAAAAAAAT
1 AACAAGAAAAAAAAT
36162645 CATCAGCACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (16 bp):
AACAAGAAAAAAAATT
Found at i:36168882 original size:18 final size:19
Alignment explanation
Indices: 36168859--36168894 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
36168849 ATAATTGAAT
36168859 AAAAATAAAATAA-AATTA
1 AAAAATAAAATAATAATTA
*
36168877 AAAAATTAAATAATAATT
1 AAAAATAAAATAATAATT
36168895 TTGTAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATAAAATAATAATTA
Found at i:36169733 original size:44 final size:45
Alignment explanation
Indices: 36169649--36169738 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 45
36169639 CCAAATTTAA
* *
36169649 TTTAATTATTTTATTTTTAATTTTGAAGCAATTAAGATTAATTTT
1 TTTAATTATTTTATTTTTAATTTTGAAGAAAATAAGATTAATTTT
*
36169694 TTTAATTATTTTATTTTT-ATTTTGAAGAAAATAATATTAATTTT
1 TTTAATTATTTTATTTTTAATTTTGAAGAAAATAAGATTAATTTT
36169738 T
1 T
36169739 AAGTTTAGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 24 0.57
45 18 0.43
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (45 bp):
TTTAATTATTTTATTTTTAATTTTGAAGAAAATAAGATTAATTTT
Found at i:36172848 original size:3 final size:3
Alignment explanation
Indices: 36172840--36172883 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
36172830 TTTTACACAA
*
36172840 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
36172884 AATTTGTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:36172965 original size:23 final size:22
Alignment explanation
Indices: 36172939--36172983 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
36172929 TTTAAGGTTG
* *
36172939 GTTTTACACTTATAATTTATAGT
1 GTTTCACACTTACAA-TTATAGT
*
36172962 GTTTCACATTTACAATTATAGT
1 GTTTCACACTTACAATTATAGT
36172984 ATATTTGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (22 bp):
GTTTCACACTTACAATTATAGT
Found at i:36183194 original size:7 final size:7
Alignment explanation
Indices: 36183182--36183230 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
36183172 GCTTAAACCA
36183182 AAAAAAT
1 AAAAAAT
36183189 AAAAAAT
1 AAAAAAT
36183196 AAAAAAT
1 AAAAAAT
36183203 AAAAAAAT
1 -AAAAAAT
*
36183211 AAAAAAA
1 AAAAAAT
*
36183218 AATAAAAG
1 AA-AAAAT
36183226 AAAAA
1 AAAAA
36183231 GAAGAAAGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
7 25 0.66
8 13 0.34
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:36183201 original size:15 final size:15
Alignment explanation
Indices: 36183182--36183230 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
36183172 GCTTAAACCA
36183182 AAAAAAT-AAAAAAT
1 AAAAAATAAAAAAAT
36183196 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
*
36183211 AAAAAA-AAATAAAAG
1 AAAAAATAAA-AAAAT
36183226 AAAAA
1 AAAAA
36183231 GAAGAAAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 10 0.31
15 22 0.69
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:36183209 original size:22 final size:23
Alignment explanation
Indices: 36183181--36183230 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
36183171 AGCTTAAACC
* *
36183181 AAAAAAATAAAAAATAA-AAAAT
1 AAAAAAATAAAAAAAAATAAAAG
36183203 AAAAAAATAAAAAAAAATAAAAG
1 AAAAAAATAAAAAAAAATAAAAG
36183226 AAAAA
1 AAAAA
36183231 GAAGAAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (23 bp):
AAAAAAATAAAAAAAAATAAAAG
Found at i:36186689 original size:17 final size:18
Alignment explanation
Indices: 36186667--36186702 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
36186657 CAACCTGAGT
36186667 CAATCATAAATTG-TCAA
1 CAATCATAAATTGCTCAA
*
36186684 CAATCATAACTTGCTCAA
1 CAATCATAAATTGCTCAA
36186702 C
1 C
36186703 TTGAACCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.28
Consensus pattern (18 bp):
CAATCATAAATTGCTCAA
Found at i:36211855 original size:31 final size:31
Alignment explanation
Indices: 36211817--36211881 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
36211807 CTTGGAGGGG
36211817 AAAATGGAAAGCATATTATTAGTTATGGTTC
1 AAAATGGAAAGCATATTATTAGTTATGGTTC
*
36211848 AAAATGGAAAGCATATTATTTGTTATGGTTC
1 AAAATGGAAAGCATATTATTAGTTATGGTTC
36211879 AAA
1 AAA
36211882 TGATGGGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (31 bp):
AAAATGGAAAGCATATTATTAGTTATGGTTC
Found at i:36214353 original size:46 final size:46
Alignment explanation
Indices: 36214278--36214365 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
36214268 TATTGCAATT
*
36214278 AGAGTTTTAGATTTATTTAATTTCTTTATTATACCAGGTTTTATTA
1 AGAGTTTTAGATTTACTTAATTTCTTTATTATACCAGGTTTTATTA
* * **
36214324 AGAGTTTTAGTTTTACTTAGTCTTC-TTATTATATTAGGTTTT
1 AGAGTTTTAGATTTACTTAAT-TTCTTTATTATACCAGGTTTT
36214366 TATTTCCCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
46 33 0.92
47 3 0.08
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.56
Consensus pattern (46 bp):
AGAGTTTTAGATTTACTTAATTTCTTTATTATACCAGGTTTTATTA
Found at i:36220967 original size:2 final size:2
Alignment explanation
Indices: 36220960--36221006 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
36220950 GCTTTATGCT
36220960 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
36221002 TC TC T
1 TC TC T
36221007 TTTGCATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:36229066 original size:24 final size:22
Alignment explanation
Indices: 36229029--36229072 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
36229019 TTTAAGAGTT
*
36229029 TGAGATTAAGATATATATTTTTA
1 TGAGATTAAAATATAT-TTTTTA
36229052 TGAGAGTTAAAATATATTTTT
1 TGAGA-TTAAAATATATTTTT
36229073 CTCATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.48
Consensus pattern (22 bp):
TGAGATTAAAATATATTTTTTA
Found at i:36232140 original size:29 final size:29
Alignment explanation
Indices: 36232073--36232141 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
36232063 ATTTATTTAA
*
36232073 ATATATATAATTAAATCAAAATAAAAATT
1 ATATATATATTTAAATCAAAATAAAAATT
* *
36232102 ATATATATATTTAAA-CTATAATTAAAATT
1 ATATATATATTTAAATC-AAAATAAAAATT
*
36232131 TTATATATATT
1 ATATATATATT
36232142 ATTCTACCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATATATATTTAAATCAAAATAAAAATT
Found at i:36241224 original size:23 final size:23
Alignment explanation
Indices: 36241190--36241238 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
36241180 ATATTTATTT
36241190 TTATATCATAAAAATAAAAT-TAA
1 TTATATCATAAAAA-AAAATATAA
*
36241213 TTATAT-ATTAAATAAAAATATAA
1 TTATATCA-TAAAAAAAAATATAA
36241236 TTA
1 TTA
36241239 AGTTCGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TTATATCATAAAAAAAAATATAA
Found at i:36245152 original size:38 final size:39
Alignment explanation
Indices: 36245095--36245171 Score: 102
Period size: 38 Copynumber: 1.9 Consensus size: 39
36245085 GGTGAGAAAA
*
36245095 TAAAAGTTTGGAGGAAAAATA-AAAAAAATTTGGGGGAG
1 TAAAAGTTTGAAGGAAAAATATAAAAAAATTTGGGGGAG
* *
36245133 TAAAATTTTGAAGGGAAAATATTCAAAAAAATTTGGGGG
1 TAAAAGTTTGAAGGAAAAATA-T-AAAAAAATTTGGGGG
36245172 GGGAAATGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 18 0.55
41 15 0.45
ACGTcount: A:0.48, C:0.01, G:0.26, T:0.25
Consensus pattern (39 bp):
TAAAAGTTTGAAGGAAAAATATAAAAAAATTTGGGGGAG
Found at i:36247040 original size:11 final size:11
Alignment explanation
Indices: 36247021--36247067 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
36247011 AAATAGTAGC
36247021 AAAATTAATAAT
1 AAAA-TAATAAT
36247033 AAAATAATAAT
1 AAAATAATAAT
36247044 AACAA-AATAAT
1 AA-AATAATAAT
36247055 AGAAAT-ATAAT
1 A-AAATAATAAT
36247066 AA
1 AA
36247068 CGAAATGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.03
11 24 0.75
12 7 0.22
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:36247045 original size:14 final size:14
Alignment explanation
Indices: 36247026--36247055 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36247016 GTAGCAAAAT
*
36247026 TAATAATAAAATAA
1 TAATAACAAAATAA
36247040 TAATAACAAAATAA
1 TAATAACAAAATAA
36247054 TA
1 TA
36247056 GAAATATAAT
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:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (14 bp):
TAATAACAAAATAA
Found at i:36247055 original size:22 final size:22
Alignment explanation
Indices: 36247027--36247073 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
36247017 TAGCAAAATT
36247027 AATAATA-AAATAATAATAACAA
1 AATAATAGAAAT-ATAATAACAA
*
36247049 AATAATAGAAATATAATAACGA
1 AATAATAGAAATATAATAACAA
36247071 AAT
1 AAT
36247074 GACAGTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (22 bp):
AATAATAGAAATATAATAACAA
Found at i:36247086 original size:22 final size:21
Alignment explanation
Indices: 36247038--36247086 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
36247028 ATAATAAAAT
*
36247038 AATAATAACAAAATAATAGAA
1 AATAATAACAAAATAACAGAA
* *
36247059 ATATAATAACGAAATGACAGTAA
1 A-ATAATAACAAAATAACAG-AA
36247082 AATAA
1 AATAA
36247087 CACATAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.83
23 3 0.13
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.20
Consensus pattern (21 bp):
AATAATAACAAAATAACAGAA
Found at i:36248110 original size:17 final size:16
Alignment explanation
Indices: 36248090--36248121 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
36248080 TTTAAAAGTG
36248090 TTTTTGAGTAAAAAATA
1 TTTTTGAG-AAAAAATA
36248107 TTTTTGAGAAAAAAT
1 TTTTTGAGAAAAAAT
36248122 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (16 bp):
TTTTTGAGAAAAAATA
Found at i:36248245 original size:18 final size:18
Alignment explanation
Indices: 36248218--36248261 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
36248208 TTTATTTAAT
36248218 AATA-TTTTTATCTCAAA
1 AATATTTTTTATCTCAAA
36248235 AATATTTTTTATCTCAAA
1 AATATTTTTTATCTCAAA
36248253 AATACTTTT
1 AATA-TTTT
36248262 GAGAAGTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATTTTTTATCTCAAA
Found at i:36248530 original size:58 final size:61
Alignment explanation
Indices: 36248410--36248531 Score: 137
Period size: 58 Copynumber: 2.0 Consensus size: 61
36248400 AAAATTAAAA
* * *
36248410 ATAATTTATATTTAATGTATCATTATATTTACAAATAATTTACTAATTATTAAAAAATATTT
1 ATAATATATATTTAATGTATAATTATATTTA-AAATAATTTAATAATTATTAAAAAATATTT
* *
36248472 ATAATATATATTT-ATGTATAATTATA-TT-AAATTATTTAA-ATATTATCTAAACAA-ATTT
1 ATAATATATATTTAATGTATAATTATATTTAAAATAATTTAATA-ATTAT-TAAAAAATATTT
36248530 AT
1 AT
36248532 TTTTAAAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
57 1 0.02
58 20 0.38
59 6 0.11
60 2 0.04
61 12 0.23
62 12 0.23
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (61 bp):
ATAATATATATTTAATGTATAATTATATTTAAAATAATTTAATAATTATTAAAAAATATTT
Found at i:36262238 original size:3 final size:3
Alignment explanation
Indices: 36262230--36262258 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
36262220 TATTTGTGGG
36262230 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
36262259 AGATGGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:36269304 original size:15 final size:15
Alignment explanation
Indices: 36269244--36269305 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
36269234 AGGAGATGAA
* *
36269244 GATGAAGATGAAGAT
1 GATGAGGATGACGAT
* *
36269259 GATGATG-TGGACGAG
1 GATGAGGAT-GACGAT
* *
36269274 GATGAGGACGAGGAT
1 GATGAGGATGACGAT
36269289 GATGAGGATGACGAT
1 GATGAGGATGACGAT
36269304 GA
1 GA
36269306 AGATGACGAC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
14 1 0.03
15 35 0.97
ACGTcount: A:0.35, C:0.05, G:0.42, T:0.18
Consensus pattern (15 bp):
GATGAGGATGACGAT
Found at i:36275857 original size:31 final size:32
Alignment explanation
Indices: 36275807--36275868 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
36275797 ATTCGAGTCA
* * * *
36275807 TTTGAAAATTTTTATTAAACCT-TTCAAAATT
1 TTTGAAAATCTTAACTAAACCTCTTAAAAATT
36275838 TTTGAAAATCTTAACTAAACCTCTTAAAAAT
1 TTTGAAAATCTTAACTAAACCTCTTAAAAAT
36275869 GTTAAAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (32 bp):
TTTGAAAATCTTAACTAAACCTCTTAAAAATT
Found at i:36276022 original size:7 final size:7
Alignment explanation
Indices: 36276005--36276035 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
36275995 GAAATGATTC
36276005 AAATAAAT
1 AAAT-AAT
36276013 AAATAAT
1 AAATAAT
36276020 AAATAAT
1 AAATAAT
36276027 AAATAAT
1 AAATAAT
36276034 AA
1 AA
36276036 TTTGAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:36282525 original size:23 final size:23
Alignment explanation
Indices: 36282498--36282543 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
36282488 ATAACATATA
36282498 TTCAT-TTTATTTTCTTAATATTT
1 TTCATATTTATTTTC-TAATATTT
*
36282521 TTCATATTTGTTTTCTAATATTT
1 TTCATATTTATTTTCTAATATTT
36282544 AGATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (23 bp):
TTCATATTTATTTTCTAATATTT
Found at i:36282749 original size:29 final size:29
Alignment explanation
Indices: 36282669--36282751 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 29
36282659 CTTCAAGTTT
*
36282669 CTATATCTTTTGTAATTTTGAAATTTAATCA
1 CTATAT-TTTT-TAATTTTAAAATTTAATCA
*
36282700 CTCTA-TTTTT-ATTTTCAAAAATTTAATC-
1 CTATATTTTTTAATTTT--AAAATTTAATCA
36282728 CTATATTTTTTAAATTTTAAAATT
1 CTATATTTTTT-AATTTTAAAATT
36282752 CATATCTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 5 0.11
28 5 0.11
29 25 0.57
31 9 0.20
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (29 bp):
CTATATTTTTTAATTTTAAAATTTAATCA
Found at i:36284105 original size:16 final size:17
Alignment explanation
Indices: 36284080--36284112 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
36284070 CTTTCTTTCT
*
36284080 TTATT-TTTTTATTTAA
1 TTATTCTTTTAATTTAA
36284096 TTATTCTTTTAATTTAA
1 TTATTCTTTTAATTTAA
36284113 CGATCAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTCTTTTAATTTAA
Found at i:36289617 original size:24 final size:24
Alignment explanation
Indices: 36289584--36289632 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
36289574 TAATTTGAAT
* *
36289584 AAATTATCCATTTATTATTTTTAAA
1 AAATTATCCACTTA-CATTTTTAAA
36289609 AAATT-TCCACTTACATTTTTAAA
1 AAATTATCCACTTACATTTTTAAA
36289632 A
1 A
36289633 TAAATGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 10 0.45
24 7 0.32
25 5 0.23
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATTATCCACTTACATTTTTAAA
Found at i:36289637 original size:25 final size:26
Alignment explanation
Indices: 36289581--36289637 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 26
36289571 TAGTAATTTG
* *
36289581 AATAAATTATCCATTTATTATTTTTA
1 AATAAATTATCCACTTATCATTTTTA
36289607 AA-AAATT-TCCACTTA-CATTTTTAA
1 AATAAATTATCCACTTATCATTTTT-A
36289631 AATAAAT
1 AATAAAT
36289638 GTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.22
24 10 0.37
25 9 0.33
26 2 0.07
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.46
Consensus pattern (26 bp):
AATAAATTATCCACTTATCATTTTTA
Found at i:36298012 original size:16 final size:16
Alignment explanation
Indices: 36297987--36298019 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
36297977 TTTAATAGCC
*
36297987 ACATCTCAAAAATTTA
1 ACATCCCAAAAATTTA
36298003 ACATCCCAAAAATTTA
1 ACATCCCAAAAATTTA
36298019 A
1 A
36298020 TTGAAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (16 bp):
ACATCCCAAAAATTTA
Found at i:36329336 original size:30 final size:31
Alignment explanation
Indices: 36329302--36329367 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
36329292 TAATGTTTAT
* * *
36329302 ATTTTTATAATTTTTAAAAGATTAAATTA-A
1 ATTTTTATAATTTTAAAAAAATTAAAATATA
36329332 ATTTTTATAATTTTAAAAAAATTAAAATATA
1 ATTTTTATAATTTTAAAAAAATTAAAATATA
36329363 ATTTT
1 ATTTT
36329368 ATTTTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (31 bp):
ATTTTTATAATTTTAAAAAAATTAAAATATA
Found at i:36333880 original size:3 final size:3
Alignment explanation
Indices: 36333872--36333898 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
36333862 TATTAAAAAT
36333872 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
36333899 TCAGTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:36334281 original size:13 final size:13
Alignment explanation
Indices: 36334265--36334291 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
36334255 GGAAATGGCA
36334265 TAACTTAATGAAT
1 TAACTTAATGAAT
36334278 TAACTTAATGAAT
1 TAACTTAATGAAT
36334291 T
1 T
36334292 TAACAGTTAT
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:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TAACTTAATGAAT
Found at i:36340713 original size:14 final size:15
Alignment explanation
Indices: 36340696--36340725 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
36340686 ATTACTATTT
36340696 ATTTTAAAATT-GAA
1 ATTTTAAAATTCGAA
36340710 ATTTTAAAATTCGAA
1 ATTTTAAAATTCGAA
36340725 A
1 A
36340726 CATATAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTTTAAAATTCGAA
Found at i:36342576 original size:2 final size:2
Alignment explanation
Indices: 36342569--36342596 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36342559 TATCTCATAG
36342569 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
36342597 GTATTTATGT
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:36353113 original size:19 final size:20
Alignment explanation
Indices: 36353077--36353114 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
36353067 CCGGTTCGAA
*
36353077 TAAATAAATTATTAAAAATT
1 TAAATAAATTAATAAAAATT
36353097 TAAATAAA-TAATAAAAAT
1 TAAATAAATTAATAAAAAT
36353115 AATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATAAATTAATAAAAATT
Found at i:36356993 original size:16 final size:16
Alignment explanation
Indices: 36356960--36357006 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
36356950 TATTTCTACT
36356960 TTTATA-ATT-TAT-A
1 TTTATATATTATATAA
36356973 TTTATATATTATATAA
1 TTTATATATTATATAA
* *
36356989 TTTATATAATATAAAA
1 TTTATATATTATATAA
36357005 TT
1 TT
36357007 AAATATATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 6 0.21
14 3 0.10
15 3 0.10
16 17 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATATATTATATAA
Found at i:36358096 original size:20 final size:21
Alignment explanation
Indices: 36358062--36358110 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
36358052 AACCTTCAAT
*
36358062 TATTTATTCTAAAAA-TAAAA
1 TATTTATTCTAAAAACCAAAA
36358082 TATTTATT-TAAAAAACCCAAAA
1 TATTTATTCT-AAAAA-CCAAAA
36358104 TATTTAT
1 TATTTAT
36358111 CATGATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 13 0.52
22 11 0.44
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTTATTCTAAAAACCAAAA
Found at i:36359992 original size:25 final size:24
Alignment explanation
Indices: 36359942--36359992 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
36359932 TTTTTTATTA
* * *
36359942 TTTTCCCTTCTTTTTCTTCTCCTT
1 TTTTCCCTTCTTCTTCTCCTCATT
*
36359966 TTTTCTCTCTCTTCTTCTCCTCATT
1 TTTTCCCT-TCTTCTTCTCCTCATT
36359991 TT
1 TT
36359993 CCTTCTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTCCCTTCTTCTTCTCCTCATT
Found at i:36362191 original size:89 final size:89
Alignment explanation
Indices: 36362040--36362414 Score: 732
Period size: 89 Copynumber: 4.2 Consensus size: 89
36362030 TTAATATAAC
36362040 TTTTAGCCCATGAATTTGACAATTAGATCCATTTTGGTACATATATTTTTTTTGTTCATTTTGGT
1 TTTTAGCCCATGAATTTGACAATTAGATCCATTTTGGTACATATATTTTTTTTGTTCATTTTGGT
36362105 ATATGAACTTAACAACTAACTTCA
66 ATATGAACTTAACAACTAACTTCA
36362129 TTTTAGCCCATGAATTTGACAATTAGATCCATTTTGGTACATATATTTTTTTTGTTCATTTTGGT
1 TTTTAGCCCATGAATTTGACAATTAGATCCATTTTGGTACATATATTTTTTTTGTTCATTTTGGT
36362194 ATATGAACTTAACAACTAACTTCA
66 ATATGAACTTAACAACTAACTTCA
36362218 TTTTAGCCCATGAATTTGACAATTAGATCCATTTTGGTACATATATTTTTTTTGTTCATTTTGGT
1 TTTTAGCCCATGAATTTGACAATTAGATCCATTTTGGTACATATATTTTTTTTGTTCATTTTGGT
36362283 ATATGAACTTAACAACTAACTTCA
66 ATATGAACTTAACAACTAACTTCA
36362307 TTTTAGCCCATGAATTTGACAATTAGATCCATTTTGGTACATATATTTTTTTTGTTCATTTTGGT
1 TTTTAGCCCATGAATTTGACAATTAGATCCATTTTGGTACATATATTTTTTTTGTTCATTTTGGT
36362372 ATATGAACTTAACAACTAACTTCA
66 ATATGAACTTAACAACTAACTTCA
* *
36362396 TTTTAGCCCTTGAACTTGA
1 TTTTAGCCCATGAATTTGA
36362415 ATTCCATTAA
Statistics
Matches: 284, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 284 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (89 bp):
TTTTAGCCCATGAATTTGACAATTAGATCCATTTTGGTACATATATTTTTTTTGTTCATTTTGGT
ATATGAACTTAACAACTAACTTCA
Found at i:36375949 original size:353 final size:341
Alignment explanation
Indices: 36375286--36375974 Score: 870
Period size: 353 Copynumber: 2.0 Consensus size: 341
36375276 GATGGCCTTG
* * *
36375286 TTTGAGGTACTCTTTAGTTACCCATCATTACTTGGTGTTTGTTTGCTGAGAAAGTAGTGGAAAAG
1 TTTGAGGTACTCTTTAATTACCCACCATTACTTGGTGTTTGTTTGCTGAGAAAGTAGAGGAAAAG
*
36375351 TTAACAATTTAACAAGGTTTATAAAAAATTTGAGCAAAGGGTATTTGAAAAAGTATTTTCTATGT
66 TTAACAAATTAACAAGGTTTATAAAAAATTT-AGCAAAGGGTATTTGAAAAAGTATTTTCTATGT
36375416 GTTTGAATTTAGAAATTGGGTCATTTTTTTGGCAGCTTTGGGTACTTCTTAATTACCCACCATTA
130 GTTTGAATTTAGAAATTGGGTCATTTTTTTGGCAGCTTTGGGTACTTCTTAATTACCCACCATTA
* **
36375481 CTTGGGGTTTGTTTTCTGAGAAAGTAGTCGGAAAAGTTGTTGAAAGTAATAAGGTTTAATCAAAA
195 CTTGGGGTTTGTTTCCTGAGAAAGTAGTCGGAAAAGTTGTAAAAAGTAATAAGGTTTAATCAAAA
* * * *
36375546 TTATACCAAGAATATTTGAAAAAGAATTTACTTTGTATTTTCTCTGTGTTTTAATTTAGAATTTG
260 TTATACAAAGAATATTTGAAAAAAAATTTACTTTGTATTTTCTATGTGTTTTAATTTAGAAATTG
*
36375611 GGTCGTTTTTTGGCAGT
325 GGTCATTTTTTGGCAGT
* ** *
36375628 TTTGTGGTACTCTTTAATTACCCACCATTACTTGGTGTTTGTTTGCTGAGAAAGTAGAGGGGAAT
1 TTTGAGGTACTCTTTAATTACCCACCATTACTTGGTGTTTGTTTGCTGAGAAAGTAGAGGAAAAG
* ** *
36375693 TTGTACAAATTAGTAAGGTTTATAAAATATTCT-GCAAAGGGTATTTGAAGAAGTGTTTACTTTG
66 TT-AACAAATTAACAAGGTTTATAAAAAATT-TAGCAAAGGGTATTTGAA-AA------A----G
* *
36375757 TATTTTTTATGTGTTTTAATTTAGAAATTGGGTCA-TTTTTTGGCAGCTTTGAGGTAC-TCTTTA
118 TATTTTCTATGTGTTTGAATTTAGAAATTGGGTCATTTTTTTGGCAGCTTTG-GGTACTTC-TTA
* * * * *
36375820 ATTACCCATCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGTGGGAAAGGTTG-AAAAATTAATA
181 ATTACCCACCATTACTTGGGGTTTGTTTCCTGAGAAAGTAGTCGGAAAAGTTGTAAAAAGTAATA
* **
36375884 AGGTTT-AT-AAAATAATGTACAAAGGGTATTTGAAAAAAAATGTTTACTTTGTA-TTTCTATGT
246 AGGTTTAATCAAAAT--TATACAAAGAATATTTGAAAAAAAA--TTTACTTTGTATTTTCTATGT
*
36375946 GTTTTAATTTATAAATTGGGTCATTTTTT
307 GTTTTAATTTAGAAATTGGGTCATTTTTT
36375975 ACAGCTTTGA
Statistics
Matches: 297, Mismatches: 31, Indels: 27
0.84 0.09 0.08
Matches are distributed among these distances:
342 76 0.26
343 25 0.08
344 1 0.00
349 1 0.00
350 5 0.02
351 2 0.01
352 52 0.18
353 124 0.42
354 11 0.04
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (341 bp):
TTTGAGGTACTCTTTAATTACCCACCATTACTTGGTGTTTGTTTGCTGAGAAAGTAGAGGAAAAG
TTAACAAATTAACAAGGTTTATAAAAAATTTAGCAAAGGGTATTTGAAAAAGTATTTTCTATGTG
TTTGAATTTAGAAATTGGGTCATTTTTTTGGCAGCTTTGGGTACTTCTTAATTACCCACCATTAC
TTGGGGTTTGTTTCCTGAGAAAGTAGTCGGAAAAGTTGTAAAAAGTAATAAGGTTTAATCAAAAT
TATACAAAGAATATTTGAAAAAAAATTTACTTTGTATTTTCTATGTGTTTTAATTTAGAAATTGG
GTCATTTTTTGGCAGT
Found at i:36375984 original size:176 final size:177
Alignment explanation
Indices: 36375403--36375984 Score: 743
Period size: 176 Copynumber: 3.3 Consensus size: 177
36375393 ATTTGAAAAA
*
36375403 GTATTTTCTATGTGTTTGAATTTAGAAATTGGGTCATTTTTTTGGCAGCTTTG-GGTACT-TCTT
1 GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCA-TTTTTTGGCAGCTTTGAGGTACTCT-TT
* * * ** *
36375466 AATTACCCACCATTACTTGGGGTTTGTTTTCTGAGAAAGTAGTCGGAAAAGTTGTTGAAAGTAAT
64 AATTACCCACCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGT-GGGAAAGTTGTAAAAATTAAT
* ** *
36375531 AAGGTTTAATCAAAAT-TATACCAAGAATATTTGAAAAAGAA--TTTACTTT
128 AAGGTTT-AT-AAAATATATACAAAGGGTATTTGAAAAAAAATGTTTACTTT
* * * * *
36375580 GTATTTTCTCTGTGTTTTAATTTAGAATTTGGGTCGTTTTTTGGCAGTTTTGTGGTACTCTTTAA
1 GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGAGGTACTCTTTAA
* * * * * *
36375645 TTACCCACCATTACTTGGTGTTTGTTTGCTGAGAAAGTAGAGGGGAATTTGTACAAATTAGTAAG
66 TTACCCACCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGTGGGAAAGTTGTAAAAATTAATAAG
* * * *
36375710 GTTTATAAAATATTCTGCAAAGGGTATTTG--AAGAAGTGTTTACTTT
131 GTTTATAAAATA-TATACAAAGGGTATTTGAAAAAAAATGTTTACTTT
*
36375756 GTATTTTTTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGAGGTACTCTTTAA
1 GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGAGGTACTCTTTAA
*
36375821 TTACCCATCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGTGGGAAAGGTTG-AAAAATTAATAA
66 TTACCCACCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGTGGGAAA-GTTGTAAAAATTAATAA
*
36375885 GGTTTATAAAATAATGTACAAAGGGTATTTGAAAAAAAATGTTTACTTT
130 GGTTTATAAAAT-ATATACAAAGGGTATTTGAAAAAAAATGTTTACTTT
* *
36375934 GTA-TTTCTATGTGTTTTAATTTATAAATTGGGTCATTTTTT-ACAGCTTTGA
1 GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGA
36375985 TATCGTACGT
Statistics
Matches: 352, Mismatches: 43, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
174 8 0.02
175 2 0.01
176 204 0.58
177 120 0.34
178 18 0.05
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (177 bp):
GTATTTTCTATGTGTTTTAATTTAGAAATTGGGTCATTTTTTGGCAGCTTTGAGGTACTCTTTAA
TTACCCACCATTACTTGGTGTTTGTTTCCTGAGAAAGTAGTGGGAAAGTTGTAAAAATTAATAAG
GTTTATAAAATATATACAAAGGGTATTTGAAAAAAAATGTTTACTTT
Found at i:36384286 original size:6 final size:7
Alignment explanation
Indices: 36384267--36384292 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
36384257 GAAATACATA
36384267 AATTTTT
1 AATTTTT
36384274 AATTTTT
1 AATTTTT
36384281 AATTTTT
1 AATTTTT
36384288 AATTT
1 AATTT
36384293 CATCAATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:36385988 original size:22 final size:22
Alignment explanation
Indices: 36385970--36386011 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
36385960 TTTATTTACT
36385970 TAAAAA-AATTT-AAACATTTA
1 TAAAAATAATTTGAAACATTTA
36385990 TAAAAATAATTTGAAAC-TTTA
1 TAAAAATAATTTGAAACATTTA
36386011 T
1 T
36386012 TGATTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAAAATAATTTGAAACATTTA
Found at i:36393237 original size:18 final size:16
Alignment explanation
Indices: 36393214--36393249 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
36393204 ATTTAAAATT
36393214 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
36393232 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
36393248 TT
1 TT
36393250 CTCATCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:36412621 original size:22 final size:21
Alignment explanation
Indices: 36412576--36412642 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 21
36412566 TATATTGTTG
36412576 TTTTGG-TGCTTTTTTTACTG-
1 TTTTGGTTG-TTTTTTTACTGT
36412596 TTTTGGTTGATTTTTTTACTGT
1 TTTTGGTTG-TTTTTTTACTGT
*
36412618 TTTTGAGTTGTTTTTTTATTGT
1 TTTTG-GTTGTTTTTTTACTGT
36412640 TTT
1 TTT
36412643 GATTGCTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.14
21 13 0.31
22 19 0.45
23 4 0.10
ACGTcount: A:0.07, C:0.04, G:0.18, T:0.70
Consensus pattern (21 bp):
TTTTGGTTGTTTTTTTACTGT
Found at i:36412644 original size:21 final size:21
Alignment explanation
Indices: 36412574--36412643 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
36412564 ATTATATTGT
*
36412574 TGTTTTGG-TGCTTTTTTTAC
1 TGTTTTGGTTGATTTTTTTAC
36412594 TGTTTTGGTTGATTTTTTTAC
1 TGTTTTGGTTGATTTTTTTAC
*
36412615 TGTTTTTGAGTTG-TTTTTTTAT
1 TG-TTTTG-GTTGATTTTTTTAC
36412637 TGTTTTG
1 TGTTTTG
36412644 ATTGCTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
20 8 0.18
21 18 0.40
22 15 0.33
23 4 0.09
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.69
Consensus pattern (21 bp):
TGTTTTGGTTGATTTTTTTAC
Found at i:36412654 original size:21 final size:21
Alignment explanation
Indices: 36412573--36412710 Score: 66
Period size: 21 Copynumber: 6.3 Consensus size: 21
36412563 AATTATATTG
* *
36412573 TTGTTTTG-GTGCTTTTTTTA
1 TTGTTTTGATTGCTATTTTTA
* * * *
36412593 CTGTTTTGGTTGATTTTTTTA
1 TTGTTTTGATTGCTATTTTTA
* *
36412614 CTGTTTTTGAGTTG-TTTTTTTA
1 TTG-TTTTGA-TTGCTATTTTTA
*
36412636 TTGTTTTGATTGCTATTTTCGTG
1 TTGTTTTGATTGCTATTTT--TA
* * *
36412659 TTATTTTTG-TTGTTATTTTTGT
1 TT-GTTTTGATTGCTATTTTT-A
*
36412681 TGCTGTTTTTATTGCTATTTTTA
1 T--TGTTTTGATTGCTATTTTTA
36412704 TTGTTTT
1 TTGTTTT
36412711 TAATGTTGTT
Statistics
Matches: 93, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
20 10 0.11
21 31 0.33
22 16 0.17
23 20 0.22
24 16 0.17
ACGTcount: A:0.09, C:0.05, G:0.17, T:0.69
Consensus pattern (21 bp):
TTGTTTTGATTGCTATTTTTA
Found at i:36412666 original size:12 final size:12
Alignment explanation
Indices: 36412639--36412764 Score: 66
Period size: 12 Copynumber: 10.8 Consensus size: 12
36412629 TTTTTTATTG
*
36412639 TTTTGATTGCTAT
1 TTTTG-TTGTTAT
*
36412652 TTTCG-TGTTAT
1 TTTTGTTGTTAT
36412663 TTTTGTTGTTAT
1 TTTTGTTGTTAT
* *
36412675 TTTTGTTGCTGT
1 TTTTGTTGTTAT
* *
36412687 TTTTATTGCTAT
1 TTTTGTTGTTAT
*
36412699 TTTTATTGTT-T
1 TTTTGTTGTTAT
*
36412710 TTAATGTTG----
1 TT-TTGTTGTTAT
**
36412719 TTTTACTGTTAT
1 TTTTGTTGTTAT
* ** *
36412731 TTTTGCTACTGT
1 TTTTGTTGTTAT
36412743 TTTTGTTGTTAT
1 TTTTGTTGTTAT
36412755 TTTTGTTGTT
1 TTTTGTTGTT
36412765 TGGATGTTAT
Statistics
Matches: 86, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
8 3 0.03
9 2 0.02
11 12 0.14
12 65 0.76
13 4 0.05
ACGTcount: A:0.10, C:0.06, G:0.16, T:0.68
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:36412729 original size:68 final size:68
Alignment explanation
Indices: 36412605--36412735 Score: 160
Period size: 68 Copynumber: 1.9 Consensus size: 68
36412595 GTTTTGGTTG
* *
36412605 ATTTTTTTACTGTTTTTGAGTTGTTTTTTTATTGTTTTGATTGCTATTTTCGTGTTATTTTTGTT
1 ATTTTTTTACTGTTTTTGAGTTGTATTTTTATTGTTTTGAATGCTATTTTCGTGTTATTTTTGTT
36412670 GTT
66 GTT
* * * *
36412673 ATTTTTGTTGCTGTTTTT-A-TTGCTATTTTTATTGTTTTTAATGTTGTTTTAC-TGTTATTTTT
1 ATTTTT-TTACTGTTTTTGAGTTG-TATTTTTATTGTTTTGAATGCTATTTT-CGTGTTATTTTT
36412735 G
63 G
36412736 CTACTGTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
67 3 0.06
68 40 0.74
69 11 0.20
ACGTcount: A:0.11, C:0.05, G:0.15, T:0.69
Consensus pattern (68 bp):
ATTTTTTTACTGTTTTTGAGTTGTATTTTTATTGTTTTGAATGCTATTTTCGTGTTATTTTTGTT
GTT
Found at i:36412758 original size:68 final size:68
Alignment explanation
Indices: 36412630--36412758 Score: 152
Period size: 68 Copynumber: 1.9 Consensus size: 68
36412620 TTGAGTTGTT
* * ** *
36412630 TTTTTATTGTTTTGATTGCTATTTTCGTGTTATTTTTGTTGTTATTTTTGTTGCTGTTTTTATTG
1 TTTTTATTGTTTTGAATGCTATTTTCGTGTTATTTTTGCTACTATTTTTGTTGCTATTTTTATTG
36412695 CTA
66 CTA
* * * * *
36412698 TTTTTATTGTTTTTAATGTTGTTTTAC-TGTTATTTTTGCTACTGTTTTTGTTGTTATTTTT
1 TTTTTATTGTTTTGAATGCTATTTT-CGTGTTATTTTTGCTACTATTTTTGTTGCTATTTTT
36412759 GTTGTTTGGA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
68 49 0.98
69 1 0.02
ACGTcount: A:0.11, C:0.05, G:0.15, T:0.69
Consensus pattern (68 bp):
TTTTTATTGTTTTGAATGCTATTTTCGTGTTATTTTTGCTACTATTTTTGTTGCTATTTTTATTG
CTA
Found at i:36425405 original size:19 final size:18
Alignment explanation
Indices: 36425381--36425427 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
36425371 ATTAAAATAA
*
36425381 TAAAAAATACTAATTTTCC
1 TAAAAAATA-TAATTTTAC
*
36425400 TAAAAATATATAATTTTAT
1 TAAAAA-ATATAATTTTAC
36425419 TAAAAAATA
1 TAAAAAATA
36425428 ACTTTTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.76
20 3 0.12
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAAATATAATTTTAC
Found at i:36428998 original size:16 final size:17
Alignment explanation
Indices: 36428977--36429009 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
36428967 GAAATTTTAC
*
36428977 CTTTAATAA-TTTAAAA
1 CTTTAAAAACTTTAAAA
36428993 CTTTAAAAACTTTAAAA
1 CTTTAAAAACTTTAAAA
36429010 GATCTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
CTTTAAAAACTTTAAAA
Found at i:36432937 original size:23 final size:23
Alignment explanation
Indices: 36432911--36433031 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
36432901 ACACTAGCGC
36432911 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
36432934 GCTCTCTGTTTAGCA-TGTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
36432957 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
36432982 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
36433005 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
36433028 GCTC
1 GCTC
36433032 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
22 5 0.06
23 61 0.71
24 1 0.01
25 15 0.17
26 4 0.05
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:36432980 original size:48 final size:46
Alignment explanation
Indices: 36432911--36433031 Score: 165
Period size: 48 Copynumber: 2.6 Consensus size: 46
36432901 ACACTAGCGC
* *
36432911 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCA-TGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACT-TCGT-GT
36432957 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
*
36433005 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
36433032 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
46 26 0.38
48 40 0.59
49 2 0.03
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
Found at i:36433060 original size:39 final size:39
Alignment explanation
Indices: 36432996--36433070 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
36432986 TCCGATTAGC
*
36432996 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
36433035 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
36433071 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:36433065 original size:23 final size:23
Alignment explanation
Indices: 36433035--36433124 Score: 87
Period size: 23 Copynumber: 3.9 Consensus size: 23
36433025 TGTGCTCAGT
36433035 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* *
36433058 ACTTTGTGTGCTCTCTGTTGCCCAGC
1 ACTTTGTGTACTCTCTGTT---TAGC
*
36433084 ACTTATGTG--CTCTCTGTTTAGT
1 ACTT-TGTGTACTCTCTGTTTAGC
*
36433106 ACTTCG-GTACTCTCTGTTT
1 ACTTTGTGTACTCTCTGTTT
36433125 GTTCCGTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.29
23 18 0.32
25 9 0.16
26 7 0.12
27 4 0.07
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:36444031 original size:28 final size:26
Alignment explanation
Indices: 36443980--36444063 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 26
36443970 TAAAAACTAA
*
36443980 AAAAAAAAAATTAGGAACCTTAAAAGTT
1 AAAAAAAAAATT--GAACCTTAAAAATT
* *
36444008 GATAAAAAAAATTTAACCTATAAAAATT
1 -AAAAAAAAAATTGAACCT-TAAAAATT
36444036 AAAAAAAAAATTGAACCCCTTAAAAATT
1 AAAAAAAAAATTGAA--CCTTAAAAATT
36444064 TAAACCCTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
27 18 0.38
28 15 0.32
29 14 0.30
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.24
Consensus pattern (26 bp):
AAAAAAAAAATTGAACCTTAAAAATT
Found at i:36454659 original size:53 final size:52
Alignment explanation
Indices: 36454546--36454660 Score: 169
Period size: 52 Copynumber: 2.2 Consensus size: 52
36454536 ACATTGATAG
* *
36454546 TCACCCAACCATTAATAATTTTTTCAGTCAACTAATTATACTTTTCTTTTTG
1 TCACCCAACTATTAATAATTTTTTCAGTCAACTAATTATACTTTTCTTTTTA
* *
36454598 CCATCCAACTATTAATAATTTTTTCAGTCAA-TCAATTATACTTTTTCTTTTTA
1 TCACCCAACTATTAATAATTTTTTCAGTCAACT-AATTATAC-TTTTCTTTTTA
36454651 TCACCCAACT
1 TCACCCAACT
36454661 GTTCAAAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 1 0.02
52 36 0.65
53 18 0.33
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.45
Consensus pattern (52 bp):
TCACCCAACTATTAATAATTTTTTCAGTCAACTAATTATACTTTTCTTTTTA
Found at i:36456661 original size:2 final size:2
Alignment explanation
Indices: 36456650--36456698 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
36456640 TTGTGTTGGC
36456650 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36456691 AT AT AT AT
1 AT AT AT AT
36456699 TGTTAGGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:36467364 original size:23 final size:25
Alignment explanation
Indices: 36467319--36467364 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
36467309 TATTAAAAAA
*
36467319 ATCATCCTCATAATTCAGGATGAAT
1 ATCATCCTCATAATTCAGAATGAAT
*
36467344 ATCATCC-CA-AATTCATAATGA
1 ATCATCCTCATAATTCAGAATGA
36467365 CATACCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 2 0.11
25 7 0.37
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (25 bp):
ATCATCCTCATAATTCAGAATGAAT
Found at i:36477445 original size:41 final size:41
Alignment explanation
Indices: 36477386--36477704 Score: 231
Period size: 41 Copynumber: 7.8 Consensus size: 41
36477376 GAAAGAAAAT
* *
36477386 GCCGCAAAAGGT-AAAGCAATAGCGGCGCTTATATAAAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATATAAAAGC
* * ****
36477426 ACCGCTAAAGGTCAGAGCAATAGCAGCGCTTATGGCCAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATATAAAAGC
* ****
36477467 GCCGCTAAAGGTC-GAAGCAATAGCGGCGTTTATGGGCAAGC
1 GCCGCTAAAGGTCAG-AGCAATAGCGGCGCTTATATAAAAGC
36477508 G-C-C--AAGGT-AGAGCAATAGCGGCGCTTATATAAAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATATAAAAGC
*
36477544 GCCGCTAAAGGTCGGAGCAATAGCGGCGCTTATGGCTTATATAAAAGC
1 GCCGCTAAAGGTCAGAGCAATAGC-G-GC-----GCTTATATAAAAGC
* * * ****
36477592 GCCGCTAAAGGTCGGAGCAATAGCGACGTTTATGGCTAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATATAAAAGC
* * * ****
36477633 GCCGCTAAATGTCGGAGCAATAACGGCGCTTATGGCCAAGC
1 GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATATAAAAGC
* *
36477674 GCCGCTAAAGGTC-GAAGTAATAGCGACGCTT
1 GCCGCTAAAGGTCAG-AGCAATAGCGGCGCTT
36477705 TCGCATAAGC
Statistics
Matches: 230, Mismatches: 33, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
36 22 0.10
37 7 0.03
38 1 0.00
39 1 0.00
40 18 0.08
41 138 0.60
42 1 0.00
43 2 0.01
46 1 0.00
47 1 0.00
48 38 0.17
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.18
Consensus pattern (41 bp):
GCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATATAAAAGC
Found at i:36477532 original size:77 final size:78
Alignment explanation
Indices: 36477433--36477578 Score: 222
Period size: 77 Copynumber: 1.9 Consensus size: 78
36477423 AGCACCGCTA
* ** *
36477433 AAGGTCAGAGCAATAGCAGCGCTTATGGCCAAGCGCCGCTAAAGGTCGAAGCAATAGCGGCGTTT
1 AAGGTCAGAGCAATAGCAGCGCTTATAGAAAAGCGCCGCTAAAGGTCGAAGCAATAGCGGCGCTT
36477498 ATGGGCAAGCGCC
66 ATGGGCAAGCGCC
* * *
36477511 AAGGT-AGAGCAATAGCGGCGCTTATATAAAAGCGCCGCTAAAGGTCGGAGCAATAGCGGCGCTT
1 AAGGTCAGAGCAATAGCAGCGCTTATAGAAAAGCGCCGCTAAAGGTCGAAGCAATAGCGGCGCTT
36477575 ATGG
66 ATGG
36477579 CTTATATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
77 56 0.92
78 5 0.08
ACGTcount: A:0.29, C:0.22, G:0.32, T:0.16
Consensus pattern (78 bp):
AAGGTCAGAGCAATAGCAGCGCTTATAGAAAAGCGCCGCTAAAGGTCGAAGCAATAGCGGCGCTT
ATGGGCAAGCGCC
Found at i:36477601 original size:48 final size:48
Alignment explanation
Indices: 36477530--36477668 Score: 193
Period size: 48 Copynumber: 3.0 Consensus size: 48
36477520 CAATAGCGGC
36477530 GCTTATATAAAAGCGCCGCTAAAGGTCGGAGCAATAGCGGCGCTTATG
1 GCTTATATAAAAGCGCCGCTAAAGGTCGGAGCAATAGCGGCGCTTATG
* *
36477578 GCTTATATAAAAGCGCCGCTAAAGGTCGGAGCAATAGCGACGTTTATG
1 GCTTATATAAAAGCGCCGCTAAAGGTCGGAGCAATAGCGGCGCTTATG
* *
36477626 GC-----T--AAGCGCCGCTAAATGTCGGAGCAATAACGGCGCTTATG
1 GCTTATATAAAAGCGCCGCTAAAGGTCGGAGCAATAGCGGCGCTTATG
36477667 GC
1 GC
36477669 CAAGCGCCGC
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
41 36 0.42
43 1 0.01
48 48 0.56
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.21
Consensus pattern (48 bp):
GCTTATATAAAAGCGCCGCTAAAGGTCGGAGCAATAGCGGCGCTTATG
Found at i:36477616 original size:24 final size:24
Alignment explanation
Indices: 36477541--36477616 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
36477531 CTTATATAAA
36477541 AGCGCCGCTAAAGGTCGGAGCAAT
1 AGCGCCGCTAAAGGTCGGAGCAAT
* * * ** ** *
36477565 AGCGGCGCTTATGG-CTTATATAAA
1 AGCGCCGCTAAAGGTCGGA-GCAAT
36477589 AGCGCCGCTAAAGGTCGGAGCAAT
1 AGCGCCGCTAAAGGTCGGAGCAAT
36477613 AGCG
1 AGCG
36477617 ACGTTTATGG
Statistics
Matches: 34, Mismatches: 16, Indels: 4
0.63 0.30 0.07
Matches are distributed among these distances:
23 2 0.06
24 30 0.88
25 2 0.06
ACGTcount: A:0.29, C:0.22, G:0.32, T:0.17
Consensus pattern (24 bp):
AGCGCCGCTAAAGGTCGGAGCAAT
Found at i:36477715 original size:41 final size:41
Alignment explanation
Indices: 36477588--36477723 Score: 175
Period size: 41 Copynumber: 3.3 Consensus size: 41
36477578 GCTTATATAA
*
36477588 AAGCGCCGCTAAAGGTCGGAGCAATAGCGACGTTTATGGCT
1 AAGCGCCGCTAAAGGTCGGAGCAATAGCGACGCTTATGGCT
* * * *
36477629 AAGCGCCGCTAAATGTCGGAGCAATAACGGCGCTTATGGCC
1 AAGCGCCGCTAAAGGTCGGAGCAATAGCGACGCTTATGGCT
* * *
36477670 AAGCGCCGCTAAAGGTCGAAGTAATAGCGACGCTT-TCGCAT
1 AAGCGCCGCTAAAGGTCGGAGCAATAGCGACGCTTATGGC-T
*
36477711 AAGCGCCGTTAAA
1 AAGCGCCGCTAAA
36477724 AGTCTAATTT
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 3 0.04
41 78 0.96
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCGGAGCAATAGCGACGCTTATGGCT
Found at i:36479931 original size:4 final size:4
Alignment explanation
Indices: 36479922--36479964 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
36479912 CGTCATCATG
* *
36479922 ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
36479965 GTAAGAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.44
Consensus pattern (4 bp):
ATGT
Found at i:36485992 original size:20 final size:20
Alignment explanation
Indices: 36485963--36486006 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
36485953 TTAATTTAAA
*
36485963 AAATTATAAAATAATTA-TT
1 AAATTATAAAAAAATTATTT
36485982 AAATTATTAAAAAAATTATTT
1 AAATTA-TAAAAAAATTATTT
36486003 AAAT
1 AAAT
36486007 CATTGATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTATAAAAAAATTATTT
Found at i:36489095 original size:22 final size:22
Alignment explanation
Indices: 36489052--36489095 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
36489042 TTTATAGTAC
* *
36489052 TTTTACAAAAAATTATACAATT
1 TTTTACAAAAAAATATAAAATT
36489074 TTTTA-AAAAAAATACTAAAATT
1 TTTTACAAAAAAATA-TAAAATT
36489096 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTTACAAAAAAATATAAAATT
Found at i:36489156 original size:3 final size:3
Alignment explanation
Indices: 36489148--36489177 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
36489138 ATTTTATATA
*
36489148 TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36489178 GTCAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:36490315 original size:21 final size:21
Alignment explanation
Indices: 36490276--36490315 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
36490266 ATCGAATTGA
* *
36490276 TTCAAATTAAACAATTATATT
1 TTCAAAATAAACAAGTATATT
*
36490297 TTCAAAATAAATAAGTATA
1 TTCAAAATAAACAAGTATA
36490316 GACAGATCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (21 bp):
TTCAAAATAAACAAGTATATT
Found at i:36490795 original size:35 final size:36
Alignment explanation
Indices: 36490736--36490804 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
36490726 TTATGTCAGG
* *
36490736 GTGTTTGATAATTTATTAAGTATTTTATTGAACTAA
1 GTGTTTGATAATTTATTAAATATTTAATTGAACTAA
36490772 GTGTTTGATAA-TTATTAAATATTTAATTGAACT
1 GTGTTTGATAATTTATTAAATATTTAATTGAACT
36490805 GAAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (36 bp):
GTGTTTGATAATTTATTAAATATTTAATTGAACTAA
Found at i:36502352 original size:17 final size:17
Alignment explanation
Indices: 36502318--36502352 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
36502308 AATTTAAATA
*
36502318 TGAATTGTTAAATTTCT
1 TGAATTGTTAAATCTCT
*
36502335 TGAATTGTTGAATCTCT
1 TGAATTGTTAAATCTCT
36502352 T
1 T
36502353 AAATATAACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (17 bp):
TGAATTGTTAAATCTCT
Found at i:36503114 original size:9 final size:9
Alignment explanation
Indices: 36503100--36503126 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
36503090 TACTATATGG
36503100 GCAAAATAT
1 GCAAAATAT
36503109 GCAAAATAT
1 GCAAAATAT
36503118 GCAAAATAT
1 GCAAAATAT
36503127 ACAATGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (9 bp):
GCAAAATAT
Found at i:36509316 original size:15 final size:15
Alignment explanation
Indices: 36509296--36509325 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36509286 AACTTGAAAG
36509296 GCAAAGAAGCTACAA
1 GCAAAGAAGCTACAA
36509311 GCAAAGAAGCTACAA
1 GCAAAGAAGCTACAA
36509326 ATGAGGGAGA
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:0.53, C:0.20, G:0.20, T:0.07
Consensus pattern (15 bp):
GCAAAGAAGCTACAA
Found at i:36514754 original size:12 final size:12
Alignment explanation
Indices: 36514737--36514771 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
36514727 GGATAATACA
36514737 TATCTATATATC
1 TATCTATATATC
*
36514749 TATCTATCTATC
1 TATCTATATATC
*
36514761 TATATATATAT
1 TATCTATATAT
36514772 ATACTCTCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (12 bp):
TATCTATATATC
Found at i:36518305 original size:29 final size:29
Alignment explanation
Indices: 36518272--36518330 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
36518262 TATGTTTTGG
** *
36518272 ATTATTAAATTATTTTAAAGTTTTTATTT
1 ATTATTAAATTATTCGAAACTTTTTATTT
* *
36518301 ATTATTGAATTCTTCGAAACTTTTTATTT
1 ATTATTAAATTATTCGAAACTTTTTATTT
36518330 A
1 A
36518331 AGTTGTTGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (29 bp):
ATTATTAAATTATTCGAAACTTTTTATTT
Found at i:36519976 original size:6 final size:6
Alignment explanation
Indices: 36519965--36519993 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
36519955 ACCTCTTAAT
36519965 ACAGGA ACAGGA ACAGGA ACAGGA ACAGG
1 ACAGGA ACAGGA ACAGGA ACAGGA ACAGG
36519994 TAGGAGAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.34, T:0.00
Consensus pattern (6 bp):
ACAGGA
Found at i:36524200 original size:18 final size:17
Alignment explanation
Indices: 36524173--36524209 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
36524163 AATTTTTAAC
*
36524173 TTTTTATATTATGTTAT
1 TTTTTATATTATGTAAT
36524190 TTTTATATATTATGTAAT
1 TTTT-TATATTATGTAAT
36524208 TT
1 TT
36524210 ATGACTCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTTATATTATGTAAT
Found at i:36547214 original size:18 final size:17
Alignment explanation
Indices: 36547174--36547216 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
36547164 TTACAATTTT
36547174 TTTTAAAAAATTCAAAA
1 TTTTAAAAAATTCAAAA
**
36547191 TATTTACAAAAATTTTAAA
1 T-TTTA-AAAAATTCAAAA
36547210 TTTTAAA
1 TTTTAAA
36547217 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.14
18 8 0.36
19 11 0.50
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAAAAAATTCAAAA
Found at i:36547227 original size:45 final size:45
Alignment explanation
Indices: 36547172--36547267 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 45
36547162 AATTACAATT
* * *
36547172 TTTTTTAAAAAATTCA-AAATATTTACAAAAATTTTAA-ATTTTAAA
1 TTTTTTAAAAAATT-ATAAAAATATACAAAAA-GTTAAGATTTTAAA
*
36547217 TTTTTTAAAAAATTATAAAAATATATAAAAAGTTAAGATTTTAAA
1 TTTTTTAAAAAATTATAAAAATATACAAAAAGTTAAGATTTTAAA
36547262 TTTTTT
1 TTTTTT
36547268 CTAAAATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 5 0.11
45 40 0.89
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (45 bp):
TTTTTTAAAAAATTATAAAAATATACAAAAAGTTAAGATTTTAAA
Found at i:36553078 original size:31 final size:31
Alignment explanation
Indices: 36553035--36553115 Score: 153
Period size: 31 Copynumber: 2.6 Consensus size: 31
36553025 AATTCCCAAA
*
36553035 TTACACATAAACTTTGATTCAATGTGCAATG
1 TTACGCATAAACTTTGATTCAATGTGCAATG
36553066 TTACGCATAAACTTTGATTCAATGTGCAATG
1 TTACGCATAAACTTTGATTCAATGTGCAATG
36553097 TTACGCATAAACTTTGATT
1 TTACGCATAAACTTTGATT
36553116 TTTGTATACA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (31 bp):
TTACGCATAAACTTTGATTCAATGTGCAATG
Found at i:36554655 original size:21 final size:21
Alignment explanation
Indices: 36554631--36554670 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
36554621 AAAACAATAA
* *
36554631 TAAAATTATATTTTAATCTCT
1 TAAAAATATAGTTTAATCTCT
*
36554652 TAAAAATATAGTTTCATCT
1 TAAAAATATAGTTTAATCT
36554671 AGGACCTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (21 bp):
TAAAAATATAGTTTAATCTCT
Found at i:36556541 original size:15 final size:15
Alignment explanation
Indices: 36556523--36556568 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
36556513 ATATTATAAT
36556523 AAATAATATAATTAA
1 AAATAATATAATTAA
* *
36556538 AAAT-ATATTATTTA
1 AAATAATATAATTAA
36556552 AAA-AAT-TAATTAA
1 AAATAATATAATTAA
36556565 AAAT
1 AAAT
36556569 TAAATGCGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
13 8 0.32
14 13 0.52
15 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAATATAATTAA
Found at i:36556561 original size:27 final size:29
Alignment explanation
Indices: 36556511--36556568 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
36556501 ATTCTTTACT
*
36556511 ATATATTATAATAAATAATATAATTAAAA
1 ATATATTATAATAAAAAATATAATTAAAA
*
36556540 ATATATTAT-TTAAAAAAT-TAATTAAAA
1 ATATATTATAATAAAAAATATAATTAAAA
36556567 AT
1 AT
36556569 TAAATGCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 11 0.41
28 7 0.26
29 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
ATATATTATAATAAAAAATATAATTAAAA
Found at i:36562515 original size:2 final size:2
Alignment explanation
Indices: 36562508--36562539 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36562498 ATGTTTGATA
36562508 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
36562540 TTGGTGAATA
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:36574263 original size:20 final size:20
Alignment explanation
Indices: 36574223--36574263 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
36574213 ATTTTTTAAG
* * *
36574223 TTTATTTATATTATGTTATT
1 TTTATATATATTATATAATT
36574243 TTTATATATATTATATAATT
1 TTTATATATATTATATAATT
36574263 T
1 T
36574264 ATAATACATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTATATATATTATATAATT
Found at i:36575873 original size:16 final size:16
Alignment explanation
Indices: 36575846--36575884 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
36575836 TAGCAAAACC
* *
36575846 AAATGTTCCGAATTTG
1 AAATGATCCGAACTTG
*
36575862 AATTGATCCGAACTTG
1 AAATGATCCGAACTTG
36575878 AAATGAT
1 AAATGAT
36575885 TAGAAAAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (16 bp):
AAATGATCCGAACTTG
Found at i:36584675 original size:47 final size:47
Alignment explanation
Indices: 36584606--36584699 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
36584596 AGCGGAGACA
36584606 GCTTCAGCATTATAAAAAAAGTAAAAAAGAAAATAAAGGTAAAGATT
1 GCTTCAGCATTATAAAAAAAGTAAAAAAGAAAATAAAGGTAAAGATT
*
36584653 GCTTCAGCATTATAAAGAAAGTAAAAAAGAAAATAAAGGTAAAGATT
1 GCTTCAGCATTATAAAAAAAGTAAAAAAGAAAATAAAGGTAAAGATT
36584700 CCAATTTTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.21
Consensus pattern (47 bp):
GCTTCAGCATTATAAAAAAAGTAAAAAAGAAAATAAAGGTAAAGATT
Found at i:36585018 original size:18 final size:16
Alignment explanation
Indices: 36584986--36585021 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
36584976 ATGGAACGAG
36584986 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
36585002 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
36585020 AA
1 AA
36585022 ATTTTAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Done.