Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 108 of 141
Found at i:31013370 original size:12 final size:13
Alignment explanation
Indices: 31013343--31013374 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
31013333 TATTTTGATG
31013343 TTTTGTCATAATT
1 TTTTGTCATAATT
31013356 TTTTGTCATAATT
1 TTTTGTCATAATT
31013369 TTTTGT
1 TTTTGT
31013375 TGGAATTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.66
Consensus pattern (13 bp):
TTTTGTCATAATT
Found at i:31017390 original size:20 final size:20
Alignment explanation
Indices: 31017365--31017402 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31017355 GAAAAATTAC
31017365 TTTT-GGAAAATCTAATTGAT
1 TTTTGGGAAAAT-TAATTGAT
31017385 TTTTGGGAAAATTAATTG
1 TTTTGGGAAAATTAATTG
31017403 TCAAGTCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (20 bp):
TTTTGGGAAAATTAATTGAT
Found at i:31017833 original size:16 final size:16
Alignment explanation
Indices: 31017768--31017836 Score: 61
Period size: 16 Copynumber: 4.2 Consensus size: 16
31017758 AAAAAAATAT
*
31017768 TATTTTAATAGATTTAA
1 TATTTTATTA-ATTTAA
*
31017785 TATTTAATTTAATTTAA
1 TATTTTA-TTAATTTAA
* *
31017802 TA-CTTATCTAA-ATAA
1 TATTTTAT-TAATTTAA
31017817 TATTTTATTAATTTAA
1 TATTTTATTAATTTAA
31017833 TATT
1 TATT
31017837 AAGTGATTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
15 9 0.22
16 16 0.39
17 14 0.34
18 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (16 bp):
TATTTTATTAATTTAA
Found at i:31051726 original size:15 final size:15
Alignment explanation
Indices: 31051703--31051742 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
31051693 GATATTTTTC
*
31051703 TAATCTCATGTTGTG
1 TAATATCATGTTGTG
31051718 TAATATCATGTTGTG
1 TAATATCATGTTGTG
*
31051733 TACTATCATG
1 TAATATCATG
31051743 GCTATTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (15 bp):
TAATATCATGTTGTG
Found at i:31051972 original size:47 final size:47
Alignment explanation
Indices: 31051914--31052035 Score: 167
Period size: 47 Copynumber: 2.6 Consensus size: 47
31051904 ATAATATGCA
*
31051914 AATTTTGGTGGCTTGACCACAACTATGTGCATTGGCAGCTTGTCTAC
1 AATTTTGGTGGCTTGTCCACAACTATGTGCATTGGCAGCTTGTCTAC
* * * *
31051961 AATTTTAGTGGCTTGTCCACAACTATGCGTATTGGCAGCTTGTCTGC
1 AATTTTGGTGGCTTGTCCACAACTATGTGCATTGGCAGCTTGTCTAC
**
31052008 AAAATTGGTGGCTTGTCCAC-A-TATGTGC
1 AATTTTGGTGGCTTGTCCACAACTATGTGC
31052036 TGGTGTGTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 5 0.08
46 1 0.02
47 59 0.91
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (47 bp):
AATTTTGGTGGCTTGTCCACAACTATGTGCATTGGCAGCTTGTCTAC
Found at i:31055948 original size:40 final size:40
Alignment explanation
Indices: 31055002--31055915 Score: 1717
Period size: 40 Copynumber: 22.9 Consensus size: 40
31054992 GGATATAGCT
* * *
31055002 ACTCGTTCAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTA
1 ACTCGTACAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTA
* **
31055042 ACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTTAGTA
1 ACTCGTACAAATGCCTTC-GGATCTTAGTCCGGATTTAGTA
*
31055082 ACTCGCACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055122 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055162 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055202 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055242 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055282 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055322 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055362 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055402 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055442 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055482 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055522 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055562 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055602 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055642 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055682 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055722 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055762 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055802 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055842 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
31055882 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGAT
1 ACTCGTACAAATGCCTTCGGATCTTAGTCCGGAT
31055916 ATGGTCACCT
Statistics
Matches: 865, Mismatches: 7, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
39 3 0.00
40 860 0.99
41 2 0.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (40 bp):
ACTCGTACAAATGCCTTCGGATCTTAGTCCGGATTTAGTA
Found at i:31062448 original size:16 final size:15
Alignment explanation
Indices: 31062427--31062463 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
31062417 TAGCTTCTTC
31062427 TTTTTTTCACGAAATT
1 TTTTTTTCACG-AATT
31062443 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
31062458 TTTTTT
1 TTTTTT
31062464 CAACTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.19, C:0.11, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:31062519 original size:12 final size:12
Alignment explanation
Indices: 31062502--31062560 Score: 93
Period size: 12 Copynumber: 5.0 Consensus size: 12
31062492 AAAGGAAACC
31062502 TTTTTTTTTGAA
1 TTTTTTTTTGAA
31062514 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
31062526 TTTTTTTTCGAA
1 TTTTTTTTTGAA
*
31062538 -TTTTTTTTCAA
1 TTTTTTTTTGAA
31062549 TTTTTTTTTGAA
1 TTTTTTTTTGAA
31062561 GAAACTACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.21
12 33 0.79
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:31062533 original size:23 final size:23
Alignment explanation
Indices: 31062502--31062556 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
31062492 AAAGGAAACC
* *
31062502 TTTTTTTTTGAATTTTTTTTTGAA
1 TTTTTTTTCGAA-TTTTTTTTCAA
31062526 TTTTTTTTCGAATTTTTTTTCAA
1 TTTTTTTTCGAATTTTTTTTCAA
31062549 TTTTTTTT
1 TTTTTTTT
31062557 TGAAGAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.15, C:0.04, G:0.05, T:0.76
Consensus pattern (23 bp):
TTTTTTTTCGAATTTTTTTTCAA
Found at i:31069502 original size:15 final size:15
Alignment explanation
Indices: 31069484--31069515 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31069474 CATTTCACTA
31069484 TTATGTATTTTATAT
1 TTATGTATTTTATAT
*
31069499 TTATGTCTTTTATAT
1 TTATGTATTTTATAT
31069514 TT
1 TT
31069516 TTCTTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTATTTTATAT
Found at i:31077438 original size:36 final size:36
Alignment explanation
Indices: 31077398--31077499 Score: 111
Period size: 36 Copynumber: 2.8 Consensus size: 36
31077388 TAATACATAA
*
31077398 GTATGTATATATATAAATAAGTTAAAAAATATGTAC
1 GTATGTATATATATATATAAGTTAAAAAATATGTAC
* *
31077434 GTATGT-TAGA-AT-TATAAAGTATATAAAAATATGTAT
1 GTATGTATATATATATAT-AAGT-TA-AAAAATATGTAC
* *
31077470 GTATGTATGTATATATATAAGCTAAAAAAT
1 GTATGTATATATATATATAAGTTAAAAAAT
31077500 GTTTATGAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
33 2 0.04
34 6 0.11
35 5 0.09
36 29 0.54
37 4 0.07
38 5 0.09
39 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (36 bp):
GTATGTATATATATATATAAGTTAAAAAATATGTAC
Found at i:31079936 original size:19 final size:19
Alignment explanation
Indices: 31079912--31079951 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
31079902 GAGTGATAGA
31079912 TAGCGTACACTAAAGAGTC
1 TAGCGTACACTAAAGAGTC
*
31079931 TAGCGTACACTATAGAGTC
1 TAGCGTACACTAAAGAGTC
31079950 TA
1 TA
31079952 AGCGGCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (19 bp):
TAGCGTACACTAAAGAGTC
Found at i:31085636 original size:49 final size:49
Alignment explanation
Indices: 31085509--31085971 Score: 848
Period size: 49 Copynumber: 9.6 Consensus size: 49
31085499 CCCTTCGGGA
* * *
31085509 CTTATCACAT-T-TATACACTTTCACATCCATCACATCGGGCATTTGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31085556 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31085603 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31085652 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31085701 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31085750 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31085799 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31085848 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31085897 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31085946 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
31085972 CACAATTATC
Statistics
Matches: 407, Mismatches: 5, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
46 1 0.00
47 54 0.13
49 352 0.86
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31088776 original size:27 final size:26
Alignment explanation
Indices: 31088741--31088837 Score: 119
Period size: 25 Copynumber: 3.8 Consensus size: 26
31088731 TGTTCTGACC
* *
31088741 CACAACTCGTGTGAGCA-AGCCCAATTT
1 CACAGCTCGTGTGAGCATA--CCGATTT
* *
31088768 CATAGCTCGTGAGAGCATACCGATTT
1 CACAGCTCGTGTGAGCATACCGATTT
31088794 -ACAGCTCGTGTGAGCATACCGA-TT
1 CACAGCTCGTGTGAGCATACCGATTT
31088818 CACAGCTCGTGTGAGCATAC
1 CACAGCTCGTGTGAGCATAC
31088838 ATGTACATGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.03
25 39 0.63
26 6 0.10
27 14 0.23
28 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCATACCGATTT
Found at i:31089946 original size:20 final size:20
Alignment explanation
Indices: 31089913--31089951 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31089903 GCCACATGGT
*
31089913 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATAGTATC
31089933 TTGG-TTGTGATTATAGTAT
1 TTGGCTTGTG-TTATAGTAT
31089952 TTTGAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.15, C:0.05, G:0.28, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATAGTATC
Found at i:31090685 original size:12 final size:12
Alignment explanation
Indices: 31090668--31090697 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31090658 TCAGTGAGTT
31090668 ACACGAGCACGG
1 ACACGAGCACGG
*
31090680 ACACGAGCTCGG
1 ACACGAGCACGG
31090692 ACACGA
1 ACACGA
31090698 CCCTATGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.33, G:0.30, T:0.03
Consensus pattern (12 bp):
ACACGAGCACGG
Found at i:31091227 original size:75 final size:75
Alignment explanation
Indices: 31091101--31091241 Score: 219
Period size: 75 Copynumber: 1.9 Consensus size: 75
31091091 AAAAACCAGA
**
31091101 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAATTAATTACATTCATTCCAAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATTACATTCATTCCAAA
31091166 AGGATATAGG
66 AGGATATAGG
* ** * *
31091176 ATTATTCCCTTATTAATAGATAAGGTAAATGGAAAGTTAGAAAAAGGAATTATATTCTTTCCAAA
1 ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATTACATTCATTCCAAA
31091241 A
66 A
31091242 TAATATTAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 59 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (75 bp):
ATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATTACATTCATTCCAAA
AGGATATAGG
Found at i:31091349 original size:17 final size:17
Alignment explanation
Indices: 31091316--31091350 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31091306 GGGTTTAAGG
31091316 TTTTAATTAATATAATT
1 TTTTAATTAATATAATT
31091333 TTTTATATTAATA-AATT
1 TTTTA-ATTAATATAATT
31091350 T
1 T
31091351 GGTAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAATTAATATAATT
Found at i:31091506 original size:44 final size:44
Alignment explanation
Indices: 31091442--31091527 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
31091432 AGTTTGTACA
31091442 TATAATGTGTTTAATGTTTAACCATCAAATTAAAT-TAATTCACT
1 TATAATGTGTTTAATGTTTAACCATCAAATT-AATGTAATTCACT
* **
31091486 TATAATGTGTTTAATTTTTAAGTATCAAATTAATGTAATTCA
1 TATAATGTGTTTAATGTTTAACCATCAAATTAATGTAATTCA
31091528 ATAATTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 3 0.08
44 35 0.92
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (44 bp):
TATAATGTGTTTAATGTTTAACCATCAAATTAATGTAATTCACT
Found at i:31111908 original size:21 final size:22
Alignment explanation
Indices: 31111874--31111915 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
31111864 TCAATTTCTC
*
31111874 AATCCAATATATATATTTCAAT
1 AATCCAATATATATAATTCAAT
*
31111896 AATCTAATA-ATATAATTCAA
1 AATCCAATATATATAATTCAA
31111916 GTTACACGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
AATCCAATATATATAATTCAAT
Found at i:31115912 original size:28 final size:27
Alignment explanation
Indices: 31115894--31115995 Score: 107
Period size: 28 Copynumber: 3.7 Consensus size: 27
31115884 TCAAAGTTTG
31115894 CCACAAAGGCTATTTTTTTAAGAGTTCA
1 CCACAAAGGCTATTTTTTTAA-AGTTCA
* * *
31115922 CCATACAA-GTTATTCTTTTTAGAGTTCA
1 CCACA-AAGGCTATT-TTTTTAAAGTTCA
* * *
31115950 CCACAAAGGCTATTCTTTTCATAGTTCG
1 CCACAAAGGCTATT-TTTTTAAAGTTCA
31115978 CCACAAAGGCTATTTTTT
1 CCACAAAGGCTATTTTTT
31115996 AATGTCGTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
27 6 0.10
28 49 0.78
29 8 0.13
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (27 bp):
CCACAAAGGCTATTTTTTTAAAGTTCA
Found at i:31122073 original size:16 final size:15
Alignment explanation
Indices: 31122052--31122091 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
31122042 TTTTGTATTT
31122052 TTTTAATATTAAATAA
1 TTTTAATATTAAA-AA
*
31122068 TTTTAAGATTAAAAA
1 TTTTAATATTAAAAA
*
31122083 TATTAATAT
1 TTTTAATAT
31122092 AATCGATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTTAATATTAAAAA
Found at i:31128274 original size:19 final size:18
Alignment explanation
Indices: 31128220--31128268 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
31128210 TAGTAATTTT
*
31128220 TATAATTTGTCTATATTT-C
1 TATAATTT-TATA-ATTTAC
31128239 TATAATTTTATAATTTAC
1 TATAATTTTATAATTTAC
31128257 TATAAGTTTTAT
1 TATAA-TTTTAT
31128269 TTTTTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
19 14 0.52
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (18 bp):
TATAATTTTATAATTTAC
Found at i:31129991 original size:39 final size:39
Alignment explanation
Indices: 31129948--31130024 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
31129938 ACGAAAATGC
*
31129948 GTTTTCAGCAAATTGACAGGAAAATCCTTCTAACTAGAA
1 GTTTTCAGCAAATTGACAAGAAAATCCTTCTAACTAGAA
* * ** *
31129987 GTTTTTAGCAGATTGGTAAGAAAATGCTTCTAACTAGA
1 GTTTTCAGCAAATTGACAAGAAAATCCTTCTAACTAGA
31130025 CGCGTTTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (39 bp):
GTTTTCAGCAAATTGACAAGAAAATCCTTCTAACTAGAA
Found at i:31130213 original size:93 final size:93
Alignment explanation
Indices: 31130054--31130239 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
31130044 CATTGAAAAC
31130054 GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTT
1 GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTT
31130119 TTGTTAAAGTAGGGTTATGGTTAGGTTT
66 TTGTTAAAGTAGGGTTATGGTTAGGTTT
31130147 GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTT
1 GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTT
31130212 TTGTTAAAGTAGGGTTATGGTTAGGTTT
66 TTGTTAAAGTAGGGTTATGGTTAGGTTT
31130240 TGTATGTTTT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (93 bp):
GCTTTTGGTTGGAAGCGTTTTCTTTTTACTAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTT
TTGTTAAAGTAGGGTTATGGTTAGGTTT
Found at i:31130229 original size:45 final size:45
Alignment explanation
Indices: 31130083--31130229 Score: 129
Period size: 45 Copynumber: 3.2 Consensus size: 45
31130073 TTCTTTTTAC
31130083 TAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTTTTGTTAAAG
1 TAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTTTTGTTAAAG
* * * ** * * ** *
31130128 TAGGGTTATGGTTAGGTTT--GCTTTTGGTTGGAAGCGTTTTCT-TTTTAC
1 TAGGGTTAT-TTTA-TTTTAGGGTTAAGGTT--TAG-ATTTT-TGTTAAAG
31130176 TAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTTTTGTTAAAG
1 TAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTTTTGTTAAAG
31130221 TAGGGTTAT
1 TAGGGTTAT
31130230 GGTTAGGTTT
Statistics
Matches: 73, Mismatches: 20, Indels: 18
0.66 0.18 0.16
Matches are distributed among these distances:
44 1 0.01
45 32 0.44
46 8 0.11
47 8 0.11
48 23 0.32
49 1 0.01
ACGTcount: A:0.20, C:0.03, G:0.27, T:0.50
Consensus pattern (45 bp):
TAGGGTTATTTTATTTTAGGGTTAAGGTTTAGATTTTTGTTAAAG
Found at i:31135245 original size:18 final size:18
Alignment explanation
Indices: 31135222--31135265 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31135212 CATTATTTGT
**
31135222 ATAAAATAATTCTAAAAA
1 ATAAAATAATTAAAAAAA
*
31135240 ATAAAAAAATTAAAAAAA
1 ATAAAATAATTAAAAAAA
31135258 ATTAAAAT
1 A-TAAAAT
31135266 TAAAATTAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
ATAAAATAATTAAAAAAA
Found at i:31135254 original size:6 final size:6
Alignment explanation
Indices: 31135245--31135290 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
31135235 AAAAAATAAA
*
31135245 AAAATT AAAA-- AAAATT AAAATT AAAATT AGAAATAT GAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT A-AAAT-T AAAATT AAAA
31135291 AAATTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.12
6 21 0.62
7 8 0.24
8 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (6 bp):
AAAATT
Found at i:31135255 original size:16 final size:16
Alignment explanation
Indices: 31135234--31135298 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
31135224 AAAATAATTC
31135234 TAAAAAATAA-AAAAAT
1 TAAAAAA-AATAAAAAT
*
31135250 TAAAAAAAATTAAAAT
1 TAAAAAAAATAAAAAT
*
31135266 TAAAATTAGAAATATGAAAT
1 TAAAA--A-AAATA-AAAAT
*
31135286 TAAAAAAATTAAA
1 TAAAAAAAATAAA
31135299 TTTATCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
15 2 0.05
16 18 0.46
17 4 0.10
18 2 0.05
19 4 0.10
20 9 0.23
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
TAAAAAAAATAAAAAT
Found at i:31137439 original size:43 final size:43
Alignment explanation
Indices: 31137378--31137619 Score: 378
Period size: 43 Copynumber: 5.6 Consensus size: 43
31137368 GTTCCAATAT
31137378 CGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAGCAC
1 CGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAGCAC
31137421 CGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAGCAC
1 CGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAGCAC
31137464 CGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAGCAC
1 CGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAGCAC
* *
31137507 CGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATT-GACAT
1 CGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAG-CAC
* * * *
31137550 CGATTTGAGATTTCGTGTAAGACCATAGTTGGGCTATTGGCAT
1 CGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAGCAC
** *
31137593 CGATACGAGATTTCCATGTAAGACCAT
1 CGATTTGAGATTT-CGTGTAAGACCAT
31137620 GTCTGGGGCA
Statistics
Matches: 190, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
42 1 0.01
43 176 0.93
44 13 0.07
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (43 bp):
CGATTTGAGATTTCGTGTAAGACCATAGCTGAGCTATTAGCAC
Found at i:31142083 original size:27 final size:27
Alignment explanation
Indices: 31142025--31142091 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
31142015 AGAGAGTCCA
* *
31142025 TTGGGACATTAAATACAGGGTAATCTG
1 TTGGGACAATAAACACAGGGTAATCTG
* * *
31142052 CTGGGACAGTAAACACAGGGTAGT-TCG
1 TTGGGACAATAAACACAGGGTAATCT-G
31142079 TTGGGACAATAAA
1 TTGGGACAATAAA
31142092 AATGGGTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.24
Consensus pattern (27 bp):
TTGGGACAATAAACACAGGGTAATCTG
Found at i:31144485 original size:12 final size:12
Alignment explanation
Indices: 31144463--31144497 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
31144453 AGTAACCTCA
31144463 CAGGCCCGTGTGC
1 CAGG-CCGTGTGC
31144476 CAGGCCGTGTGC
1 CAGGCCGTGTGC
*
31144488 TAGGCCGTGT
1 CAGGCCGTGT
31144498 AATAGCCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.09, C:0.31, G:0.40, T:0.20
Consensus pattern (12 bp):
CAGGCCGTGTGC
Found at i:31146246 original size:25 final size:24
Alignment explanation
Indices: 31146218--31146299 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 24
31146208 GTATGTTTTC
31146218 ACGAGCTGTAAATCAGTAAGCTCAT
1 ACGAGCTG-AAATCAGTAAGCTCAT
*
31146243 ACGAGCTGAGAATCGGTAAGCTC-T
1 ACGAGCTGA-AATCAGTAAGCTCAT
* *
31146267 CACGAGCTACAAATCAATAAGCTCAT
1 -ACGAGCT-GAAATCAGTAAGCTCAT
31146293 ACGAGCT
1 ACGAGCT
31146300 ATGGTGTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 2 0.04
25 45 0.92
26 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (24 bp):
ACGAGCTGAAATCAGTAAGCTCAT
Found at i:31146270 original size:50 final size:50
Alignment explanation
Indices: 31146187--31146302 Score: 153
Period size: 50 Copynumber: 2.3 Consensus size: 50
31146177 ATACATGTAT
* * * * ** *
31146187 GCTCATACGAGCTATGAATTGGTATGTTTTCACGAGCTGTAAATCAGTAA
1 GCTCATACGAGCTATGAATCGGTAAGCTCTCACGAGCTACAAATCAATAA
31146237 GCTCATACGAGCTGA-GAATCGGTAAGCTCTCACGAGCTACAAATCAATAA
1 GCTCATACGAGCT-ATGAATCGGTAAGCTCTCACGAGCTACAAATCAATAA
31146287 GCTCATACGAGCTATG
1 GCTCATACGAGCTATG
31146303 GTGTATCCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.02
50 55 0.96
51 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (50 bp):
GCTCATACGAGCTATGAATCGGTAAGCTCTCACGAGCTACAAATCAATAA
Found at i:31150513 original size:101 final size:101
Alignment explanation
Indices: 31150387--31150773 Score: 686
Period size: 101 Copynumber: 3.8 Consensus size: 101
31150377 AAAGTGATGG
31150387 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
31150452 AATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
66 AATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
31150488 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
31150553 AATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
66 AATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
31150589 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
31150654 AATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
66 AATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
* * * * *
31150690 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGG-ATGGTAATGGTCACATGTGCAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
* *
31150754 ACTATGTGCAGGCTAGTATG
64 ACAATGTGCAGGCTACTATG
31150774 TGAACCAGAC
Statistics
Matches: 277, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
100 4 0.01
101 242 0.87
102 31 0.11
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
AATGTGCAGGCTACTATGCGTACCGAATAGTTTCGA
Found at i:31150514 original size:51 final size:50
Alignment explanation
Indices: 31150385--31150775 Score: 421
Period size: 51 Copynumber: 7.7 Consensus size: 50
31150375 TGAAAGTGAT
* *
31150385 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATGTATA
* * * * *
31150435 GGTCGCATGTGTAGTACAATGTGCAGGCTACTATGCGTACCGAATAGTTTC
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAAT-GTATA
* * *
31150486 GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATGTATA
* * * * *
31150536 GGTCGCATGTGTAGTACAATGTGCAGGCTACTATGCGTACCGAATAGTTTC
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAAT-GTATA
* * *
31150587 GATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATGTATA
* * * * *
31150637 GGTCGCATGTGTAGTACAATGTGCAGGCTACTATGCGTACCGAATAGTTTC
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAAT-GTATA
* * * *
31150688 GATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATGGTA-A
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAAT-GTATA
* *
31150738 TGGTCACATGTGCAGTACTATGTGCAGGCTAGTATGTG
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
31150776 AACCAGACAT
Statistics
Matches: 279, Mismatches: 53, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
49 12 0.04
50 111 0.40
51 148 0.53
52 8 0.03
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (50 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATGTATA
Found at i:31169002 original size:18 final size:18
Alignment explanation
Indices: 31168959--31168995 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
31168949 GCACTCTTTC
*
31168959 TTTTCT-TTCTTCAATCT
1 TTTTCTCTTATTCAATCT
31168976 TTTTCTCTTATTCAAT-T
1 TTTTCTCTTATTCAATCT
31168993 TTT
1 TTT
31168996 GTTTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCTCTTATTCAATCT
Found at i:31170979 original size:20 final size:20
Alignment explanation
Indices: 31170954--31170991 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
31170944 TAACATCTAC
31170954 TGGCCTTTAATTCAACTTGT
1 TGGCCTTTAATTCAACTTGT
31170974 TGGCCTTTAATTCAACTT
1 TGGCCTTTAATTCAACTT
31170992 CATAACAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (20 bp):
TGGCCTTTAATTCAACTTGT
Found at i:31171251 original size:19 final size:19
Alignment explanation
Indices: 31171224--31171262 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
31171214 TTATTCCAAC
* *
31171224 AACTTAATTACCTAAGATG
1 AACTCAATTAACTAAGATG
31171243 AACTCAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
31171262 A
1 A
31171263 GTAATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.28
Consensus pattern (19 bp):
AACTCAATTAACTAAGATG
Found at i:31177156 original size:25 final size:25
Alignment explanation
Indices: 31177122--31177171 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
31177112 GATTTTCATT
31177122 CTATGTTAAAGGTGCTTCAAGAAAG
1 CTATGTTAAAGGTGCTTCAAGAAAG
31177147 CTATGTTAAAGGTGCTTCAAGAAAG
1 CTATGTTAAAGGTGCTTCAAGAAAG
31177172 ACATTCTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (25 bp):
CTATGTTAAAGGTGCTTCAAGAAAG
Found at i:31180305 original size:49 final size:48
Alignment explanation
Indices: 31180228--31180520 Score: 174
Period size: 50 Copynumber: 5.8 Consensus size: 48
31180218 TGATAATACA
* * * *
31180228 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTTCTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTATCT-TAC
* * * *
31180277 TGCCAATGCCATATCCCAGAAATGGTCTTACATGGGA-GTTCTCATATC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTATCTTA-C
* ** * * * *
31180325 GGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 --TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTATCTTAC
* * * ***
31180377 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTATCTTAC
* * * * * * *
31180427 TGCCAACGTCATGTCCCAAACATGGTCTTAAATGAGACCTCTCATAATCTCAAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA--TGT--T-ATCT-TAC
*
31180481 GATGCCAATGCCATGTCCCAGACATGGTCTTACATCGGAT
1 --TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
31180521 CTCATTCCCT
Statistics
Matches: 195, Mismatches: 37, Indels: 19
0.78 0.15 0.08
Matches are distributed among these distances:
47 2 0.01
48 6 0.03
49 32 0.16
50 115 0.59
53 8 0.04
54 1 0.01
56 31 0.16
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTATCTTAC
Found at i:31180345 original size:50 final size:50
Alignment explanation
Indices: 31180277--31180515 Score: 271
Period size: 50 Copynumber: 4.7 Consensus size: 50
31180267 TTTTCTGTAC
* * **
31180277 TGCCAATGCCATATCCCAGAAATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** * *
31180327 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
31180377 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * *
31180427 TGCCAACGTCATGTCCCAAACATGGTCTTAAATGAGACCTCTCATAATCTCAACGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T---CGG
31180483 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
31180516 CGGATCTCAT
Statistics
Matches: 159, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
50 127 0.80
53 1 0.01
56 31 0.19
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:31180410 original size:100 final size:104
Alignment explanation
Indices: 31180277--31180515 Score: 306
Period size: 100 Copynumber: 2.3 Consensus size: 104
31180267 TTTTCTGTAC
* * * ** * *
31180277 TGCCAATGCCATATCCCAGAAATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATGTC
* ** *
31180342 CCAGACATGGTCTTACGGGGGACCTCTC-ATCTC-A-G-
66 CCAAACATGGTCTTAAAGGAGACCTCTCAATCTCAACGA
* *
31180377 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGTCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATGTC
*
31180442 CCAAACATGGTCTTAAATGAGACCTCTCATAATCTCAACGA
66 CCAAACATGGTCTTAAAGGAGACCTCTC--AATCTCAACGA
31180483 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
31180516 CGGATCTCAT
Statistics
Matches: 119, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
100 79 0.66
103 5 0.04
104 1 0.01
105 1 0.01
106 33 0.28
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26
Consensus pattern (104 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCCATGTC
CCAAACATGGTCTTAAAGGAGACCTCTCAATCTCAACGA
Found at i:31184294 original size:51 final size:50
Alignment explanation
Indices: 31184208--31184406 Score: 195
Period size: 51 Copynumber: 3.9 Consensus size: 50
31184198 TGCCTATAAA
* * * *
31184208 CACGTATGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGA-AGATAATGGT
* * * * **
31184259 AACATGTGTAGTACTATGTGCAAGCTACTATGTGTACCGGAAGGTTTTGGT
1 CACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACC-GAAGATAATGGT
* * * * *
31184310 CGCGTGTGTAGTACTATGTGCAAGCTACTACGTGAACCGAAAAGT-TTGAT
1 CACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGAAGA-TAATGGT
* *
31184360 CACGTGTGTAGTACTATGTG-AAGCTACTATGTGTATCGAATGATAAT
1 CACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGAA-GATAAT
31184407 AATTACACGG
Statistics
Matches: 120, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
49 18 0.15
50 28 0.23
51 72 0.60
52 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGAAGATAATGGT
Found at i:31194390 original size:45 final size:45
Alignment explanation
Indices: 31194276--31194502 Score: 349
Period size: 45 Copynumber: 5.2 Consensus size: 45
31194266 CATGAAATTA
*
31194276 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
31194321 AGG-A--A---GACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
31194360 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
31194405 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
* * * *
31194450 AGGAAGCATTTGGCCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
31194495 AGGAAGCA
1 AGGAAGCA
31194503 CCATGGCTGA
Statistics
Matches: 169, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
39 37 0.22
40 1 0.01
42 2 0.01
44 1 0.01
45 128 0.76
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:31197518 original size:79 final size:81
Alignment explanation
Indices: 31197407--31197590 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
31197397 GCTACTCGTT
* *
31197407 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATC-TAACCC
* *
31197470 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
31197487 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTAACCCGG
* *
31197550 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
31197566 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31197591 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 25 0.27
79 51 0.56
80 15 0.16
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTAACCCGG
ATATAGTAACTTAGCA
Found at i:31197590 original size:40 final size:40
Alignment explanation
Indices: 31197388--31197590 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
31197378 CGGAATTTAA
** *
31197388 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31197428 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
31197468 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31197507 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGA-TCTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACT-TAGC
* * *
31197546 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
31197586 CCGGA
1 CCGGA
31197591 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 3 0.02
39 51 0.37
40 84 0.60
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:31203038 original size:50 final size:50
Alignment explanation
Indices: 31202966--31203205 Score: 257
Period size: 50 Copynumber: 4.7 Consensus size: 50
31202956 TTTGTACTGT
* * **
31202966 CAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
* * *
31203016 CCATGCCATGTCCTAGACATGGTCTTACGA-GGGACCTCTCATCTCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATATCGGTGC
* * * *
31203066 CAACGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
* * * *
31203116 CAATGCCATGTCTCAGACATAGTCTTAAATGGGACCTCTCATAATCTTAATGATGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATC-----GGTGC
**
31203172 CAATGCCATGTCCCAGGTATGGTCTTACATGGGA
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGA
31203206 TCTTATTCCC
Statistics
Matches: 157, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.01
50 121 0.77
51 2 0.01
56 33 0.21
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
Found at i:31207221 original size:50 final size:50
Alignment explanation
Indices: 31207108--31207356 Score: 227
Period size: 50 Copynumber: 4.9 Consensus size: 50
31207098 GACATTGGGG
**
31207108 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGA
* *
31207159 GGTTATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 -G--ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** * *
31207212 GATGAGAGGTCCCCCGTAAGACCATGTCTGAGACATGGCATGGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * * * *
31207262 TATGAGAGCTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-A
* * * ** * *
31207311 CAGGAAACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
31207357 TGTTATTATC
Statistics
Matches: 167, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 39 0.23
50 82 0.49
52 2 0.01
53 3 0.02
54 6 0.04
56 34 0.20
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:31207927 original size:28 final size:30
Alignment explanation
Indices: 31207895--31207968 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 30
31207885 AGGTGATAAC
*
31207895 ATATATATATATATATTATTAATATTAT-TT
1 ATATATATATATA-ATAATTAATATTATATT
* *
31207925 ATAAATAT-TATAATAATTTATATTATATT
1 ATATATATATATAATAATTAATATTATATT
*
31207954 AT-TAT-GATATAATAA
1 ATATATATATATAATAA
31207969 AACATTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 22 0.59
29 8 0.22
30 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
ATATATATATATAATAATTAATATTATATT
Found at i:31209276 original size:16 final size:16
Alignment explanation
Indices: 31209255--31209286 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31209245 GTTTTGTTGC
*
31209255 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
31209271 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
31209287 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:31209568 original size:51 final size:51
Alignment explanation
Indices: 31209510--31209704 Score: 252
Period size: 51 Copynumber: 3.8 Consensus size: 51
31209500 GATACCAGTT
* *
31209510 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTA
* *
31209561 CACATAGTAGCCTGCACATAGTACTACACACGTGATCA-AAGCTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCA-CTATCCGGTA
* * ** *
31209612 CGCATAGTAGCCTGCACATAGTACTACACATGCAACCTATCA-T-TCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTA
* *
31209662 CACGTAGTAGCCTACACATAGTACTACACACGTGACCATCACT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
31209705 TTCAATTTCA
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
49 4 0.03
50 39 0.32
51 78 0.63
52 1 0.01
53 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTA
Found at i:31209691 original size:101 final size:102
Alignment explanation
Indices: 31209512--31209696 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
31209502 TACCAGTTCA
** *
31209512 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACATAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCAACCATCACTATCCGATACACATAGTAGCCTACA
31209577 CATAGTACTACACACGTGATCAAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCAAAGCTATCCGGTACG
* * *
31209614 CATAGTAGCCTGCACATAGTACTACACATGCAACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
1 CATAGTAGCCTGCACATAGTACTACACATGCAACC-ATCACTATCCGATACACATAGTAGCCTAC
31209677 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
31209697 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 38 0.50
102 34 0.45
103 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.23
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCAACCATCACTATCCGATACACATAGTAGCCTACA
CATAGTACTACACACGTGATCAAAGCTATCCGGTACG
Found at i:31209719 original size:101 final size:102
Alignment explanation
Indices: 31209506--31209730 Score: 267
Period size: 101 Copynumber: 2.2 Consensus size: 102
31209496 TAATGATACC
**
31209506 AGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACATAGTAG
1 AGTTCACATAGTAGCCTGCACATAGTACTACACATGCAACCATCACTATCCGATACACATAGTAG
* * *
31209571 CCTGCACATAGTACTACACACGTGATCAAAGCTATCC
66 CCTACACATAGTACTACACACGTGACCAAAGCTATCA
* * * * * *
31209608 GGTACGCATAGTAGCCTGCACATAGTACTACACATGCAACCTATCA-T-TCTGGTACACGTAGTA
1 AGTTCACATAGTAGCCTGCACATAGTACTACACATGCAACC-ATCACTATCCGATACACATAGTA
* *
31209671 GCCTACACATAGTACTACACACGTGACCATCA-CTTTCA
65 GCCTACACATAGTACTACACACGTGACCA-AAGCTATCA
* * *
31209709 ATTTCACATAGTGGCCTACACA
1 AGTTCACATAGTAGCCTGCACA
31209731 CAGTCCATGC
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
101 60 0.59
102 38 0.37
103 4 0.04
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (102 bp):
AGTTCACATAGTAGCCTGCACATAGTACTACACATGCAACCATCACTATCCGATACACATAGTAG
CCTACACATAGTACTACACACGTGACCAAAGCTATCA
Found at i:31225968 original size:27 final size:26
Alignment explanation
Indices: 31225938--31226006 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
31225928 GTTATGATCG
*
31225938 AAATATCCCCATAGGGTAGAATGACCA
1 AAATA-CCCCATAGGGTAAAATGACCA
**
31225965 AAATACCCCCATAGGGTAAAATGACTG
1 AAATA-CCCCATAGGGTAAAATGACCA
31225992 AAATACCCCTATAGG
1 AAATACCCC-ATAGG
31226007 AGATGAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 4 0.11
27 33 0.89
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (26 bp):
AAATACCCCATAGGGTAAAATGACCA
Found at i:31228162 original size:24 final size:25
Alignment explanation
Indices: 31228135--31228181 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
31228125 ACTGGTCATA
*
31228135 GAGAGAATTGAGGA-AGGATATTTG
1 GAGAGAATTGAGGAGAGAATATTTG
*
31228159 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAGAGAATATT
31228182 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.26
Consensus pattern (25 bp):
GAGAGAATTGAGGAGAGAATATTTG
Found at i:31239065 original size:30 final size:30
Alignment explanation
Indices: 31239017--31239088 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
31239007 ATGGGCATAT
** * *
31239017 GGAGCTGAATTAATGCATGAATATGTTTAA
1 GGAGCTGAATGGAGGCATGAATATATTTAA
* * *
31239047 GGAGCTGAATGGAGGCATGCATGTATTTAG
1 GGAGCTGAATGGAGGCATGAATATATTTAA
*
31239077 GGAGCTAAATGG
1 GGAGCTGAATGG
31239089 GGATGCTAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.32, T:0.28
Consensus pattern (30 bp):
GGAGCTGAATGGAGGCATGAATATATTTAA
Found at i:31245680 original size:15 final size:15
Alignment explanation
Indices: 31245668--31245697 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31245658 CGTATTTCTT
*
31245668 TCAAATTTTTTTCAC
1 TCAAAATTTTTTCAC
31245683 TCAAAATTTTTTCAC
1 TCAAAATTTTTTCAC
31245698 GAATGAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (15 bp):
TCAAAATTTTTTCAC
Found at i:31245695 original size:26 final size:26
Alignment explanation
Indices: 31245647--31245696 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
31245637 TTTGCTTGAT
**
31245647 TTTTTTTCACTCGTATTTCTTTCAAA
1 TTTTTTTCACTCAAATTTCTTTCAAA
31245673 TTTTTTTCACTCAAAATTT-TTTCA
1 TTTTTTTCACTC-AAATTTCTTTCA
31245697 CGAATGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.22, C:0.18, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTTTTCACTCAAATTTCTTTCAAA
Found at i:31246157 original size:21 final size:21
Alignment explanation
Indices: 31246131--31246173 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31246121 GCCACATGAA
**
31246131 GCCATAATGATGTTCACACAT
1 GCCATAAACATGTTCACACAT
31246152 GCCATAAACATGTTCACACAT
1 GCCATAAACATGTTCACACAT
31246173 G
1 G
31246174 GAATTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (21 bp):
GCCATAAACATGTTCACACAT
Found at i:31247738 original size:19 final size:19
Alignment explanation
Indices: 31247714--31247750 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
31247704 GCAGATCATT
31247714 AAACAAAGATGCATTTAAA
1 AAACAAAGATGCATTTAAA
31247733 AAACAAAGATGCATTTAA
1 AAACAAAGATGCATTTAA
31247751 CAAATAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.22
Consensus pattern (19 bp):
AAACAAAGATGCATTTAAA
Found at i:31252507 original size:21 final size:21
Alignment explanation
Indices: 31252483--31252555 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
31252473 AGGTGAATAG
*
31252483 CCTCATTGTGGAGGTAAACGT
1 CCTCATTGTGGAGGTAAACGA
* *** *
31252504 CCTCGTTGTGGTTCTAAGCGA
1 CCTCATTGTGGAGGTAAACGA
* * *
31252525 GCTCGTTGTGGAGGTGAACGA
1 CCTCATTGTGGAGGTAAACGA
31252546 CCTCATTGTG
1 CCTCATTGTG
31252556 CTCTCCCCTC
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
CCTCATTGTGGAGGTAAACGA
Found at i:31253113 original size:19 final size:18
Alignment explanation
Indices: 31253072--31253110 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31253062 ACTTTTTTTA
* *
31253072 CAATTTTTTTTTCAACTT
1 CAATTTTTCTTTCAACCT
*
31253090 CAATTTTTCTTTCAGCCT
1 CAATTTTTCTTTCAACCT
31253108 CAA
1 CAA
31253111 ATTGTTGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (18 bp):
CAATTTTTCTTTCAACCT
Found at i:31256206 original size:24 final size:25
Alignment explanation
Indices: 31256179--31256226 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
31256169 ATTATACACT
*
31256179 ACACACACATA-CAATTTAATTAAA
1 ACACACAAATACCAATTTAATTAAA
*
31256203 ACACATAAATACTCAATTTAATTA
1 ACACACAAATAC-CAATTTAATTA
31256227 CACGAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
26 11 0.55
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (25 bp):
ACACACAAATACCAATTTAATTAAA
Found at i:31271466 original size:29 final size:29
Alignment explanation
Indices: 31271419--31271730 Score: 354
Period size: 29 Copynumber: 10.8 Consensus size: 29
31271409 ATCGATTAAA
* ** *
31271419 GAAAAGGAATGGTTTCGACCATTGAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
*
31271448 GAAAAGGGATGGTGACGACCATCAAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
* * *
31271477 GAGAAGGGATAGTGACGACCATCGAATAA
1 GAAAAGGGATGGTGACGACCATCGAATAT
** **
31271506 GAAAAGGGATGGTTTCGACCATAAAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
* * *
31271535 GGAAAGGGATGGTGATGACCATCGAATAA
1 GAAAAGGGATGGTGACGACCATCGAATAT
** * *
31271564 GAAAAGGGATGGTTTCGACTATCTAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
* *
31271593 GAAAAGGGATGGTAACAACCATCGAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
*
31271622 GAAAAGGGATGGTGACGACCATCAAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
* *
31271651 GAAAAGGAAAGGTGACGACCATCGAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
* * *
31271680 GAAATGGGATGGTGACAACCATCGAATAC
1 GAAAAGGGATGGTGACGACCATCGAATAT
* **
31271709 GTAAAGGGATGGTTTCGACCAT
1 GAAAAGGGATGGTGACGACCAT
31271731 TGTTTAGCAC
Statistics
Matches: 232, Mismatches: 51, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 232 1.00
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (29 bp):
GAAAAGGGATGGTGACGACCATCGAATAT
Found at i:31273145 original size:42 final size:41
Alignment explanation
Indices: 31273094--31273176 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 41
31273084 ATATTTTATT
*
31273094 TTATTTTTTAGTAATTTATTAGAATAAGGGAATTATTTTCCC
1 TTATCTTTTAGTAATTTATTAGAATAA-GGAATTATTTTCCC
*
31273136 TTATCTTTTAGTAGTTTATTAGAATAAGGAATTATTTTCCC
1 TTATCTTTTAGTAATTTATTAGAATAAGGAATTATTTTCCC
31273177 AATTAGGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 14 0.36
42 25 0.64
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAATTTATTAGAATAAGGAATTATTTTCCC
Found at i:31280670 original size:40 final size:40
Alignment explanation
Indices: 31280477--31280700 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
31280467 TTGAATGATG
* * * *
31280477 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* *
31280517 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31280557 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
31280597 TCCGGGTTTAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31280637 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
31280678 -CCGGGCT--GTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31280701 AACGAGTAGC
Statistics
Matches: 168, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
38 16 0.10
39 1 0.01
40 141 0.84
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31282878 original size:18 final size:17
Alignment explanation
Indices: 31282852--31282899 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
31282842 ATAATAAGAA
31282852 AACATTTTGAAATTGAAT
1 AACATTTTGAAA-TGAAT
*
31282870 AACAATTTGTAAATGAAT
1 AACATTTTG-AAATGAAT
*
31282888 AATATTTTGAAA
1 AACATTTTGAAA
31282900 ACAAACGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (17 bp):
AACATTTTGAAATGAAT
Found at i:31295570 original size:18 final size:19
Alignment explanation
Indices: 31295549--31295587 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
31295539 TACTAAGAAA
31295549 CTAT-GATATAGCAAA-AAT
1 CTATAGATAT-GCAAACAAT
31295567 CTATAGATATGCAAACAAT
1 CTATAGATATGCAAACAAT
31295586 CT
1 CT
31295588 TGGGTAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.28
Consensus pattern (19 bp):
CTATAGATATGCAAACAAT
Found at i:31296503 original size:26 final size:26
Alignment explanation
Indices: 31296469--31296534 Score: 98
Period size: 26 Copynumber: 2.5 Consensus size: 26
31296459 AAACTCTTTT
*
31296469 AAAAGAAAACTCAAGAGAA-ATTCTTA
1 AAAAGAAAACTCAAGAGAAGA-ACTTA
*
31296495 AAAAGAAAACTCAAGATAAGAACTTA
1 AAAAGAAAACTCAAGAGAAGAACTTA
31296521 AAAAGAAAACTCAA
1 AAAAGAAAACTCAA
31296535 AGATCATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 36 0.97
27 1 0.03
ACGTcount: A:0.62, C:0.12, G:0.11, T:0.15
Consensus pattern (26 bp):
AAAAGAAAACTCAAGAGAAGAACTTA
Found at i:31297933 original size:56 final size:56
Alignment explanation
Indices: 31297868--31297987 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
31297858 ACAAGGGATG
31297868 ATGGGCAAAACATGTCATGAAACATCATGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATCATGTGTTAATGGAAGAATAAAATAAGAAGC
31297924 ATGGGCAAAACATGTCATGAAACATCATGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATCATGTGTTAATGGAAGAATAAAATAAGAAGC
31297980 ATGGGCAA
1 ATGGGCAA
31297988 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.21
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATCATGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:31303257 original size:40 final size:40
Alignment explanation
Indices: 31303202--31303412 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
31303192 ATTTGAATGA
*
31303202 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
31303242 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
31303282 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
31303322 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
31303362 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
31303402 TATCC-GGCTAA
1 TATCCGGGCTAA
31303413 ATTCCGAAGA
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.04
40 146 0.94
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:31312991 original size:26 final size:26
Alignment explanation
Indices: 31312917--31312993 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
31312907 ACACAAATAT
* * *
31312917 CGCAGCAAAGCTGCCAGTAATAATGA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
*
31312943 TGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
*
31312969 CGCATCAAAGCTGCCAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAACAGTA
31312994 TATGTGGCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:31313189 original size:27 final size:28
Alignment explanation
Indices: 31313159--31313235 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
31313149 TCAACTCCTA
**
31313159 GGGGTATAACAGTCATTTTACCCTAT-G
1 GGGGTATTTCAGTCATTTTACCCTATCG
*
31313186 GGGGTATTTCAGTCTTTTTA-CCTATCG
1 GGGGTATTTCAGTCATTTTACCCTATCG
* *
31313213 AGGGTATTTCGGTCATTTTACCC
1 GGGGTATTTCAGTCATTTTACCC
31313236 ATCCAAGGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.12
27 35 0.83
28 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (28 bp):
GGGGTATTTCAGTCATTTTACCCTATCG
Found at i:31313245 original size:27 final size:27
Alignment explanation
Indices: 31313188--31313257 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
31313178 ACCCTATGGG
* * * * *
31313188 GGTATTTCAGTCTTTTTACCTATCGAG
1 GGTATTTCGGTCATTTTACCCATCCAA
31313215 GGTATTTCGGTCATTTTACCCATCCAA
1 GGTATTTCGGTCATTTTACCCATCCAA
*
31313242 GGTATTTCGATCATTT
1 GGTATTTCGGTCATTT
31313258 GCCCACAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (27 bp):
GGTATTTCGGTCATTTTACCCATCCAA
Found at i:31317686 original size:22 final size:23
Alignment explanation
Indices: 31317647--31317689 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
31317637 TAGGGGCACG
*
31317647 TAATATCCCGAAAATTACTACTT
1 TAATACCCCGAAAATTACTACTT
31317670 TAATACCCCG-AAATTACTAC
1 TAATACCCCGAAAATTACTAC
31317690 AGTAAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.30
Consensus pattern (23 bp):
TAATACCCCGAAAATTACTACTT
Found at i:31320237 original size:219 final size:220
Alignment explanation
Indices: 31319856--31320293 Score: 725
Period size: 219 Copynumber: 2.0 Consensus size: 220
31319846 GATGAATTTA
** *
31319856 AAGAATAAACTGTACTTATTGGCTATGCTAAAAATTTTGAAAATTTTATGGTAAGAAGATATGTG
1 AAGAATAAACTGTACTTATTGGCTAAACTAAAAATTCTGAAAATTTTATGGTAAGAAGATATGTG
* * ** *
31319921 ATTTTAGTTTCAGAAAAAATTTTTGGATCTTAATTCGGAGTTCTATAGCTCAAGATATAATTAAT
66 AGTCTAGTTTCAGAAAAAATTTGAGGATCTTAATTCGGAGTTCTATAGCTCAAGATATAAATAAT
* *
31319986 TTTGTGACAATGACTCAAGTGGACAGCTTTGAATGAACAAATAAATAAATAGTGAAATTAT-GAT
131 TTTGTGACAATGACGCAAGTGGACAACTTTGAATGAACAAATAAATAAATAGTGAAATTATAGAT
*
31320050 AATGTTACCTATAAGCATGTTATAC
196 AATGTTACATATAAGCATGTTATAC
31320075 AAGAATAAACTGTACTTATTGGCTAAACTAAAAATTCTGAAAATTTTATGGTAAGAAGATATGTG
1 AAGAATAAACTGTACTTATTGGCTAAACTAAAAATTCTGAAAATTTTATGGTAAGAAGATATGTG
* ** * *
31320140 AGTCTAGTTTCAGAGAAAATTTGAGGATCTTAATTTTGAGTTTTGTAGCTCAAGATATAAATAAT
66 AGTCTAGTTTCAGAAAAAATTTGAGGATCTTAATTCGGAGTTCTATAGCTCAAGATATAAATAAT
31320205 TTTGTGACAATGACGCAAGTGGACAACTTTGAATGAACAAATAAATAAATAGTGAAATTATAGAT
131 TTTGTGACAATGACGCAAGTGGACAACTTTGAATGAACAAATAAATAAATAGTGAAATTATAGAT
31320270 AATGTTACATATAAGCATGTTATA
196 AATGTTACATATAAGCATGTTATA
31320294 TACATTAAGG
Statistics
Matches: 202, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
219 176 0.87
220 26 0.13
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (220 bp):
AAGAATAAACTGTACTTATTGGCTAAACTAAAAATTCTGAAAATTTTATGGTAAGAAGATATGTG
AGTCTAGTTTCAGAAAAAATTTGAGGATCTTAATTCGGAGTTCTATAGCTCAAGATATAAATAAT
TTTGTGACAATGACGCAAGTGGACAACTTTGAATGAACAAATAAATAAATAGTGAAATTATAGAT
AATGTTACATATAAGCATGTTATAC
Found at i:31320624 original size:96 final size:96
Alignment explanation
Indices: 31320504--31320694 Score: 346
Period size: 96 Copynumber: 2.0 Consensus size: 96
31320494 TTAATAAATT
*
31320504 GAATGAAATATTAATTTATATCAAGATTTAGTGGAAATTCGAGGAAAATAGAAAATTACCAAAAT
1 GAATGAAATATTAATTTATATCAAGATTGAGTGGAAATTCGAGGAAAATAGAAAATTACCAAAAT
* *
31320569 GTTCCTGAATTTTGGTATTTCTGCAATTTAA
66 ATCCCTGAATTTTGGTATTTCTGCAATTTAA
*
31320600 GAATGAAATATTAATTTATATCAAGATTGAGTGGAAATTCGAGGAAAATAGAAAATTACTAAAAT
1 GAATGAAATATTAATTTATATCAAGATTGAGTGGAAATTCGAGGAAAATAGAAAATTACCAAAAT
31320665 ATCCCTGAATTTTGGTATTTCTGCAATTTA
66 ATCCCTGAATTTTGGTATTTCTGCAATTTA
31320695 GCCTGGTAAG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (96 bp):
GAATGAAATATTAATTTATATCAAGATTGAGTGGAAATTCGAGGAAAATAGAAAATTACCAAAAT
ATCCCTGAATTTTGGTATTTCTGCAATTTAA
Found at i:31321433 original size:14 final size:14
Alignment explanation
Indices: 31321414--31321455 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
31321404 GTTTGATTGG
31321414 CAGTAAAATGTTTT
1 CAGTAAAATGTTTT
*
31321428 CAGTAAAATGATTT
1 CAGTAAAATGTTTT
* *
31321442 CTGGAAAATGTTTT
1 CAGTAAAATGTTTT
31321456 ACTTTTCTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (14 bp):
CAGTAAAATGTTTT
Found at i:31321464 original size:20 final size:20
Alignment explanation
Indices: 31321439--31321478 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31321429 AGTAAAATGA
*
31321439 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
31321459 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
31321479 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:31321468 original size:34 final size:35
Alignment explanation
Indices: 31321424--31321490 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
31321414 CAGTAAAATG
*
31321424 TTTTCAGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCAGTAAAATGATTTACTGGAAAATATTTTAC
*
31321458 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCAGTAAAATGATTTACTGGAAAATATTTT
31321491 CTGTTGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCAGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:31321555 original size:32 final size:32
Alignment explanation
Indices: 31321480--31321556 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
31321470 TGATTTACTG
* *
31321480 GAAAATATTTTCTGTTGTTTAATTGAATCTGT
1 GAAAATATTTTCTGTTGTTTAATAGAATCTAT
* *
31321512 GTAAAATATTTTCTGTTGTTTGATAG-ATTTCAT
1 G-AAAATATTTTCTGTTGTTTAATAGAATCT-AT
31321545 GAAAATATTTTC
1 GAAAATATTTTC
31321557 CGAAAAAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 15 0.38
33 24 0.62
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.49
Consensus pattern (32 bp):
GAAAATATTTTCTGTTGTTTAATAGAATCTAT
Found at i:31324192 original size:28 final size:27
Alignment explanation
Indices: 31324156--31324235 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
31324146 CATGCAGTAG
* *
31324156 CAGTTTGGGCTTGAGCCCTATACAGCAA
1 CAGTGTGGGCTT-AGCCCAATACAGCAA
*
31324184 CAGTGTGGGCCTTAGCCCAATACAGTAA
1 CAGTGTGGG-CTTAGCCCAATACAGCAA
**
31324212 CAGTGTGGGCCTTAAACCAATACA
1 CAGTGTGGG-CTTAGCCCAATACA
31324236 ATAACAGTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 43 0.93
29 3 0.07
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (27 bp):
CAGTGTGGGCTTAGCCCAATACAGCAA
Found at i:31324240 original size:28 final size:28
Alignment explanation
Indices: 31324182--31324243 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
31324172 CCTATACAGC
** *
31324182 AACAGTGTGGGCCTTAGCCCAATACAGT
1 AACAGTGTGGGCCTTAAACCAATACAAT
31324210 AACAGTGTGGGCCTTAAACCAATACAAT
1 AACAGTGTGGGCCTTAAACCAATACAAT
31324238 AACAGT
1 AACAGT
31324244 ACAATGCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (28 bp):
AACAGTGTGGGCCTTAAACCAATACAAT
Found at i:31324380 original size:26 final size:26
Alignment explanation
Indices: 31324351--31324410 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
31324341 ACCAATATCA
* * * *
31324351 CAGCAAAGGTGCCAGTAATAATGACG
1 CAGCAAAGGTACCAATAACAATAACG
*
31324377 CAGCAAAGGTACCAATAACATTAACG
1 CAGCAAAGGTACCAATAACAATAACG
31324403 CAGCAAAG
1 CAGCAAAG
31324411 CCGCTAGTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (26 bp):
CAGCAAAGGTACCAATAACAATAACG
Found at i:31324630 original size:27 final size:27
Alignment explanation
Indices: 31324600--31324688 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 27
31324590 GAGTTGTAAT
31324600 AGTCATTTTACCCTAT-GAGGGTATTTC
1 AGTCATTTTACCC-ATCGAGGGTATTTC
31324627 AGTCATTTTACCCATCGAGGGTATTTC
1 AGTCATTTTACCCATCGAGGGTATTTC
* * * *
31324654 GGTCATCTTACCCATCCAAGGTATTTC
1 AGTCATTTTACCCATCGAGGGTATTTC
31324681 AGTCATTT
1 AGTCATTT
31324689 GTCCACAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 2 0.04
27 53 0.96
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.38
Consensus pattern (27 bp):
AGTCATTTTACCCATCGAGGGTATTTC
Found at i:31330696 original size:24 final size:25
Alignment explanation
Indices: 31330650--31330711 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
31330640 AAATAAGAAT
*
31330650 AAAT-AATAAAACAAATGACAAT-AA
1 AAATAAATAAAA-AAAGGACAATAAA
* *
31330674 GAATAAATAAAAAAAGGATAATAAA
1 AAATAAATAAAAAAAGGACAATAAA
*
31330699 AAATATATAAAAA
1 AAATAAATAAAAA
31330712 TAATAATAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (25 bp):
AAATAAATAAAAAAAGGACAATAAA
Found at i:31331912 original size:18 final size:18
Alignment explanation
Indices: 31331889--31331931 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
31331879 AATTTTTGTC
31331889 ATAAAATAATTAACTTTT
1 ATAAAATAATTAACTTTT
*
31331907 ATAAAATAATTAATTTTT
1 ATAAAATAATTAACTTTT
31331925 ATTAAAA
1 A-TAAAA
31331932 ATTTGAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAAATAATTAACTTTT
Found at i:31346978 original size:32 final size:32
Alignment explanation
Indices: 31346937--31347003 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
31346927 GAACCATTAG
*
31346937 TATAATATCGGATACTTAGGAATTTCACACAC
1 TATAATATCGGATACTTAGGAATCTCACACAC
* *
31346969 TATAATATCGGATACTTGGGAGTCTCACACAC
1 TATAATATCGGATACTTAGGAATCTCACACAC
31347001 TAT
1 TAT
31347004 GTGCTAACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (32 bp):
TATAATATCGGATACTTAGGAATCTCACACAC
Found at i:31352188 original size:15 final size:15
Alignment explanation
Indices: 31352148--31352188 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
31352138 ATCTATATAA
*
31352148 TCAAATTTAACTCAT
1 TCAAATTTAATTCAT
31352163 TCAAATTTAATTCTAT
1 TCAAATTTAATTC-AT
31352179 TC-AATTTAAT
1 TCAAATTTAAT
31352189 CCAAAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (15 bp):
TCAAATTTAATTCAT
Found at i:31367355 original size:21 final size:22
Alignment explanation
Indices: 31367331--31367378 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
31367321 GTTCGGGATC
*
31367331 GCACTCTGGTGCCTCTA-AATT
1 GCACTCTGATGCCTCTATAATT
* *
31367352 GCACTTTGATGCCTCTATATTT
1 GCACTCTGATGCCTCTATAATT
31367374 GCACT
1 GCACT
31367379 ACAGTTCCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.38
Consensus pattern (22 bp):
GCACTCTGATGCCTCTATAATT
Found at i:31377504 original size:40 final size:40
Alignment explanation
Indices: 31377420--31377603 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
31377410 TTGAATGCTG
* * * *
31377420 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
31377459 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
31377500 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
31377540 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
*
31377580 TCCGGGTTCAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
31377604 GTATGAGTTA
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 2 0.02
40 112 0.90
41 10 0.08
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:31377557 original size:80 final size:81
Alignment explanation
Indices: 31377420--31377600 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
31377410 TTGAATGCTG
* *
31377420 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
31377484 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
31377500 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
31377561 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
*
31377580 TCCGGGTTCAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
31377601 ATTGTATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:31377624 original size:39 final size:38
Alignment explanation
Indices: 31377421--31377640 Score: 165
Period size: 40 Copynumber: 5.6 Consensus size: 38
31377411 TGAATGCTGT
* * * * *
31377421 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTA-AA
** * *
31377461 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAATT
1 CCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
31377501 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAA-A
*
31377541 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACT-AAA
* **
31377580 TCCGGGTTCAGTCCCGAAGGCATTGTATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTA-AA
* *
31377620 CCGGGCTATGTCCCGAAGGCA
1 CCGGGTTAAGTCCCGAAGGCA
31377641 CTTGAACGAG
Statistics
Matches: 149, Mismatches: 21, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
39 32 0.21
40 109 0.73
41 8 0.05
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:31387109 original size:50 final size:50
Alignment explanation
Indices: 31386998--31387244 Score: 248
Period size: 50 Copynumber: 4.8 Consensus size: 50
31386988 ATTTGGATAA
*
31386998 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
31387054 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
31387104 AGAGGTCCCCTGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * *
31387154 AGA-ACTCCCATGTAAGACCATATATGGGATATGTCATTGGCA--GTACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
31387203 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
31387245 TGTTATTATC
Statistics
Matches: 164, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 37 0.23
50 82 0.50
53 3 0.02
55 1 0.01
56 40 0.24
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:31389343 original size:20 final size:21
Alignment explanation
Indices: 31389300--31389343 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31389290 CGTAAGCATG
*
31389300 TAGAAATTATATGTGAACCTT
1 TAGAAATTATATGTCAACCTT
*
31389321 TAGAAATTATATG-CAATCTT
1 TAGAAATTATATGTCAACCTT
31389341 TAG
1 TAG
31389344 TTGCTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
TAGAAATTATATGTCAACCTT
Found at i:31392431 original size:33 final size:34
Alignment explanation
Indices: 31392367--31392433 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
31392357 AGTAGTTATG
*
31392367 CAGTATCAGTCTGGGCCTGAACCCTATACAGTAA
1 CAGTATCAGTCTGGGCCTGAACCCTAAACAGTAA
* *
31392401 CAGTAT-AGTGTGGGCCT-TACCCTAAAACAGTAA
1 CAGTATCAGTCTGGGCCTGAACCCT-AAACAGTAA
31392434 TAATGTGGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 5 0.17
33 18 0.62
34 6 0.21
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (34 bp):
CAGTATCAGTCTGGGCCTGAACCCTAAACAGTAA
Found at i:31392443 original size:28 final size:28
Alignment explanation
Indices: 31392399--31392481 Score: 125
Period size: 28 Copynumber: 3.0 Consensus size: 28
31392389 CCTATACAGT
31392399 AACAGT-ATAGTGTGGGCCTTA-CCCTAA
1 AACAGTAATAGTGTGGGCCTTAGCCC-AA
* *
31392426 AACAGTAATAATGTGGGCCTTAGCCCAT
1 AACAGTAATAGTGTGGGCCTTAGCCCAA
31392454 AACAGTAATAGTGTGGGCCTTAGCCCAA
1 AACAGTAATAGTGTGGGCCTTAGCCCAA
31392482 TACAATAACC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 6 0.12
28 41 0.82
29 3 0.06
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (28 bp):
AACAGTAATAGTGTGGGCCTTAGCCCAA
Found at i:31395272 original size:40 final size:40
Alignment explanation
Indices: 31395218--31395303 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 40
31395208 ACCCATACCG
* * *
31395218 AATCC-TTCTTAGTAGGCGTTAAGGGCAGCCCACTCACAA
1 AATCCATTCTTAGTAGGCATTAAGAGCAACCCACTCACAA
31395257 AATCCATTCTTAGTAGGCATTAAGAGCAACCCACTCACAA
1 AATCCATTCTTAGTAGGCATTAAGAGCAACCCACTCACAA
31395297 AATCCAT
1 AATCCAT
31395304 GGTTACTCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
39 5 0.12
40 38 0.88
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (40 bp):
AATCCATTCTTAGTAGGCATTAAGAGCAACCCACTCACAA
Found at i:31398600 original size:29 final size:28
Alignment explanation
Indices: 31398559--31398613 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
31398549 GTGTGGAAGT
*
31398559 AAAAAAATAAATTGAGATTAAAAAAAGA
1 AAAAAAACAAATTGAGATTAAAAAAAGA
*
31398587 AAAACAAACAAATTGTGATTAAAAAAA
1 AAAA-AAACAAATTGAGATTAAAAAAA
31398614 AGTCTGGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (28 bp):
AAAAAAACAAATTGAGATTAAAAAAAGA
Found at i:31399790 original size:12 final size:12
Alignment explanation
Indices: 31399768--31399839 Score: 51
Period size: 12 Copynumber: 6.0 Consensus size: 12
31399758 AAGAGTGTGT
*
31399768 GAAAAAAGAAAA
1 GAAAGAAGAAAA
*
31399780 GAAAGATGAAAAA
1 GAAAGAAG-AAAA
*
31399793 GAAA-AAGAAATT
1 GAAAGAAGAAA-A
*
31399805 GAAAGAAAAAAA
1 GAAAGAAGAAAA
*
31399817 GAAAGTGAGAAAA
1 GAAAG-AAGAAAA
31399830 -AAAG-AGAAAA
1 GAAAGAAGAAAA
31399840 AGAATTTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
10 6 0.12
11 3 0.06
12 21 0.44
13 18 0.38
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (12 bp):
GAAAGAAGAAAA
Found at i:31399797 original size:24 final size:23
Alignment explanation
Indices: 31399770--31399843 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
31399760 GAGTGTGTGA
31399770 AAAAAGAAAAGAAAGATGAAAAAG
1 AAAAAGAAAAGAAAGA-GAAAAAG
* *
31399794 AAAAAGAAATTGAAAGAAAAAAAG
1 AAAAAGAAA-AGAAAGAGAAAAAG
*
31399818 AAAGTGAGAAAA-AAAGAGAAAAAG
1 AAA--AAGAAAAGAAAGAGAAAAAG
31399842 AA
1 AA
31399844 TTTCTAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
24 31 0.74
25 6 0.14
26 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.05
Consensus pattern (23 bp):
AAAAAGAAAAGAAAGAGAAAAAG
Found at i:31399832 original size:19 final size:19
Alignment explanation
Indices: 31399749--31399832 Score: 73
Period size: 19 Copynumber: 4.4 Consensus size: 19
31399739 AAAGAACATG
* ** *
31399749 GAAAAGAAAAAGAGTGTGT
1 GAAAAAAAAAAGAAAGTGA
31399768 GAAAAAAGAAAAGAAAGATGA
1 GAAAAAA-AAAAGAAAG-TGA
* *
31399789 -AAAAGAAAAAGAAATTGA
1 GAAAAAAAAAAGAAAGTGA
*
31399807 -AAGAAAAAAAGAAAGTGA
1 GAAAAAAAAAAGAAAGTGA
31399825 GAAAAAAA
1 GAAAAAAA
31399833 GAGAAAAAGA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
18 18 0.35
19 20 0.38
20 12 0.23
21 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (19 bp):
GAAAAAAAAAAGAAAGTGA
Found at i:31399837 original size:18 final size:17
Alignment explanation
Indices: 31399766--31399838 Score: 83
Period size: 18 Copynumber: 4.0 Consensus size: 17
31399756 AAAAGAGTGT
31399766 GTGAAAAAAGAAAAGAAA
1 GTGAAAAAA-AAAAGAAA
31399784 GATGAAAAAGAAAAAGAAA
1 G-TGAAAAA-AAAAAGAAA
*
31399803 TTGAAAGAAAAAAAGAAA
1 GTGAAA-AAAAAAAGAAA
*
31399821 GTGAGAAAAAAAGAGAAA
1 GTGA-AAAAAAAAAGAAA
31399839 AAGAATTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 28 0.58
19 19 0.40
20 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (17 bp):
GTGAAAAAAAAAAGAAA
Found at i:31401596 original size:26 final size:26
Alignment explanation
Indices: 31401560--31401610 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
31401550 GGATAAAAAG
31401560 GGGTCGCTAAGTGCAGATTCCCCGAT
1 GGGTCGCTAAGTGCAGATTCCCCGAT
* *
31401586 GGGTTGCTAAGTGCTGATTCCCCGA
1 GGGTCGCTAAGTGCAGATTCCCCGA
31401611 ATTATTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.25
Consensus pattern (26 bp):
GGGTCGCTAAGTGCAGATTCCCCGAT
Found at i:31401634 original size:42 final size:42
Alignment explanation
Indices: 31401587--31401809 Score: 150
Period size: 43 Copynumber: 5.3 Consensus size: 42
31401577 TTCCCCGATG
* *
31401587 GGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAAAAGT
1 GGTTGCTAAGTGCTGATTCCCCGTATTATTGATTATAAAAGT
* * *
31401629 GGTTGCTAAGTGCTGATTCCACCGTA-TATTTGATTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGTATTA-TTGATTATAAAAGT
* * * * * * *
31401672 GGTTTC-AATGTGTTGATTCCCCGTATCACTAAATATAAAGGT
1 GGTTGCTAA-GTGCTGATTCCCCGTATTATTGATTATAAAAGT
* * * *
31401714 GGTTGCTAAGTGTTGATTCCACCGTATCT-TTGATTGTGAAAGC
1 GGTTGCTAAGTGCTGATTCC-CCGTAT-TATTGATTATAAAAGT
* * * * * * *
31401757 GGTTGTTATGTGTTGATTCTCCGTATCACTGAATT-T-AAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATTATTG-ATTATAAAAGT
31401798 GGTTGCTAAGTG
1 GGTTGCTAAGTG
31401810 TTGAATCCAC
Statistics
Matches: 140, Mismatches: 32, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
41 13 0.09
42 61 0.44
43 66 0.47
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGTATTATTGATTATAAAAGT
Found at i:31401731 original size:85 final size:84
Alignment explanation
Indices: 31401622--31401821 Score: 294
Period size: 85 Copynumber: 2.4 Consensus size: 84
31401612 TTATTGATTC
* * *
31401622 TAAAAGTGGTTGCTAAGTGCTGATTCCACCGTATATTTGATTGTGAAAGGGGTT-TCAATGTGTT
1 TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATATTTGATTGTGAAAGCGGTTGT-AATGTGTT
31401686 GATTCCCCGTATCACTAAAT
65 GATTCCCCGTATCACTAAAT
* *
31401706 ATAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCTTTGATTGTGAAAGCGGTTGTTATGTGTT
1 -TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATATTTGATTGTGAAAGCGGTTGTAATGTGTT
* *
31401771 GATTCTCCGTATCACTGAAT
65 GATTCCCCGTATCACTAAAT
* *
31401791 TTAAGGTGGTTGCTAAGTGTTGAATCCACCG
1 TAAAGGTGGTTGCTAAGTGTTGATTCCACCG
31401822 AGTAACGGAT
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
84 29 0.28
85 75 0.71
86 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (84 bp):
TAAAGGTGGTTGCTAAGTGTTGATTCCACCGTATATTTGATTGTGAAAGCGGTTGTAATGTGTTG
ATTCCCCGTATCACTAAAT
Found at i:31404625 original size:21 final size:21
Alignment explanation
Indices: 31404596--31404636 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31404586 TGAAACAACG
*
31404596 AGTTGAATCGGTCTAAAAACC
1 AGTTAAATCGGTCTAAAAACC
31404617 AGTTAAATCGGTCTAAAAAC
1 AGTTAAATCGGTCTAAAAAC
31404637 TGATTGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (21 bp):
AGTTAAATCGGTCTAAAAACC
Found at i:31408076 original size:28 final size:27
Alignment explanation
Indices: 31408013--31408164 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
31408003 ATATTAAGTC
* * *
31408013 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
31408040 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
31408068 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
31408095 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
31408123 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
31408150 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31408165 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:31408097 original size:55 final size:55
Alignment explanation
Indices: 31408013--31408164 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
31408003 ATATTAAGTC
* * *
31408013 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
31408068 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
31408123 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
31408165 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:31413305 original size:16 final size:16
Alignment explanation
Indices: 31413265--31413297 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31413255 TTATAACTAA
31413265 TCTTAATTAATTAATT
1 TCTTAATTAATTAATT
*
31413281 TCTTCATTAATTAATT
1 TCTTAATTAATTAATT
31413297 T
1 T
31413298 TGTAATTAGG
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:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (16 bp):
TCTTAATTAATTAATT
Found at i:31415999 original size:17 final size:17
Alignment explanation
Indices: 31415977--31416009 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31415967 GACAATGGCA
31415977 TGGTTAGTGAAAACGTT
1 TGGTTAGTGAAAACGTT
31415994 TGGTTAGTGAAAACGT
1 TGGTTAGTGAAAACGT
31416010 GAAGGTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (17 bp):
TGGTTAGTGAAAACGTT
Found at i:31416699 original size:27 final size:26
Alignment explanation
Indices: 31416668--31416722 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
31416658 TAACTAAAAT
31416668 TAAATTAAATTAGAGAAATATATTAAA
1 TAAATTAAATTAGAG-AATATATTAAA
** *
31416695 TAAATTGGATTTGAGAATATATTAAA
1 TAAATTAAATTAGAGAATATATTAAA
31416721 TA
1 TA
31416723 TTAATGAGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (26 bp):
TAAATTAAATTAGAGAATATATTAAA
Found at i:31430538 original size:22 final size:19
Alignment explanation
Indices: 31430507--31430553 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
31430497 AAAGATGATA
31430507 ATTATTAATATATAATTATATCT
1 ATTA-TAATATAT-ATTA-AT-T
31430530 ATTATAATATATATTAATT
1 ATTATAATATATATTAATT
31430549 ATTAT
1 ATTAT
31430554 CTACTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 4 0.17
22 8 0.33
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATAATATATATTAATT
Found at i:31430549 original size:16 final size:15
Alignment explanation
Indices: 31430509--31430550 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
31430499 AGATGATAAT
31430509 TATTAATATATAATTA
1 TATTAAT-TATAATTA
31430525 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
31430541 TATTAATTAT
1 TATTAATTAT
31430551 TATCTACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:31431166 original size:25 final size:25
Alignment explanation
Indices: 31431106--31431166 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
31431096 CTCTTAAATT
*
31431106 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
* *
31431131 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
31431156 TTAATTAAATT
1 TTAATTAAATT
31431167 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:31431728 original size:76 final size:76
Alignment explanation
Indices: 31431595--31431743 Score: 271
Period size: 76 Copynumber: 2.0 Consensus size: 76
31431585 CTTGATGAGA
* *
31431595 AATATAGAGTCTGAAAATTTGCAAGAAATTCTCGAGGAACTTACAGTTCTAAGTTCTAAGTGGAC
1 AATATAGAGTCTGAAAATTTGCAAGAAATTCTCGAGGAACTCACAGTTCCAAGTTCTAAGTGGAC
31431660 TATGTCAAGGG
66 TATGTCAAGGG
*
31431671 AATATAGAGTCTGAAAATTTGCAAGAAATTCTCGAGGAACTCACAGTTCCAATTTCTAAGTGGAC
1 AATATAGAGTCTGAAAATTTGCAAGAAATTCTCGAGGAACTCACAGTTCCAAGTTCTAAGTGGAC
31431736 TATGTCAA
66 TATGTCAA
31431744 AGCAAGAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (76 bp):
AATATAGAGTCTGAAAATTTGCAAGAAATTCTCGAGGAACTCACAGTTCCAAGTTCTAAGTGGAC
TATGTCAAGGG
Found at i:31433914 original size:43 final size:43
Alignment explanation
Indices: 31433844--31433926 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
31433834 TAATACCGCT
*
31433844 AAACGCCGCTAAAGATCATGACCTTTAGCGACGCTTCTACCAC
1 AAACACCGCTAAAGATCATGACCTTTAGCGACGCTTCTACCAC
* *
31433887 AAACACCGTTAAAGATGATGACCTTTAGCGACGCTTCTAC
1 AAACACCGCTAAAGATCATGACCTTTAGCGACGCTTCTAC
31433927 AACCAACGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACACCGCTAAAGATCATGACCTTTAGCGACGCTTCTACCAC
Found at i:31438037 original size:21 final size:21
Alignment explanation
Indices: 31437981--31438042 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 21
31437971 CACATACACC
31437981 AATGCATACAAAATAAAAACTT
1 AATGC-TACAAAATAAAAACTT
* *
31438003 AACGCTAC---A-GAAAACTT
1 AATGCTACAAAATAAAAACTT
31438020 AATGCTACAAAATAAAAACTT
1 AATGCTACAAAATAAAAACTT
31438041 AA
1 AA
31438043 GCTTCCAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
17 14 0.44
18 1 0.03
20 1 0.03
21 12 0.38
22 4 0.12
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.21
Consensus pattern (21 bp):
AATGCTACAAAATAAAAACTT
Found at i:31440116 original size:13 final size:14
Alignment explanation
Indices: 31440085--31440275 Score: 50
Period size: 14 Copynumber: 13.4 Consensus size: 14
31440075 ACTAGTTAAT
*
31440085 CTAAACCCTAAACC
1 CTAAACCATAAACC
* *
31440099 ATAAACC-TAAACT
1 CTAAACCATAAACC
* * *
31440112 TTAAAACCCTAAGCC
1 CT-AAACCATAAACC
*
31440127 CTTAACACAT-AACC
1 CTAAAC-CATAAACC
*
31440141 TCTAAACCTTAAACC
1 -CTAAACCATAAACC
* * *
31440156 C-CAGCCTTTAAACC
1 CTAAACC-ATAAACC
* *
31440170 ATAAACCAAAAACC
1 CTAAACCATAAACC
* ** *
31440184 ATAGCCCCTAAACC
1 CTAAACCATAAACC
*
31440198 CATAATCCATAAACC
1 C-TAAACCATAAACC
*
31440213 TTAAA--ATAGTAACTC
1 CTAAACCATA--AAC-C
* *
31440228 CTAAACCTTAAACT
1 CTAAACCATAAACC
* *
31440242 CTAAACCGTATACC
1 CTAAACCATAAACC
*
31440256 CTAAACCAAAAACC
1 CTAAACCATAAACC
*
31440270 TTAAAC
1 CTAAAC
31440276 TATGGGATAA
Statistics
Matches: 126, Mismatches: 38, Indels: 26
0.66 0.20 0.14
Matches are distributed among these distances:
12 3 0.02
13 9 0.07
14 75 0.60
15 37 0.29
17 2 0.02
ACGTcount: A:0.45, C:0.32, G:0.03, T:0.20
Consensus pattern (14 bp):
CTAAACCATAAACC
Done.