Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 76 of 310
Found at i:24285599 original size:6 final size:7
Alignment explanation
Indices: 24285573--24285598 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
24285563 AATATTTAAG
24285573 TTTTTTA
1 TTTTTTA
24285580 TTTTTTA
1 TTTTTTA
24285587 TTTTTTA
1 TTTTTTA
24285594 TTTTT
1 TTTTT
24285599 AAATTTTAAA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:24286768 original size:41 final size:41
Alignment explanation
Indices: 24286723--24286859 Score: 177
Period size: 41 Copynumber: 3.3 Consensus size: 41
24286713 GTTTATAACT
* *
24286723 TTTAGTGGCGTTTTACCAAAAGTGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
24286764 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
* * * * * * *
24286805 TTTAACGGCGTTTTAACAAAAAACGCCACTATTGCTC-AGTT
1 TTTAGCGGCGTTTT-ACCAAAAGCGCCGCTAATGCTCTGGTC
24286846 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
24286860 TGTTAAAATG
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 67 0.79
42 18 0.21
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGTC
Found at i:24290781 original size:51 final size:51
Alignment explanation
Indices: 24290702--24290811 Score: 166
Period size: 51 Copynumber: 2.2 Consensus size: 51
24290692 TTACTTGCAA
* * **
24290702 CAGCAACATTATCCACTCCATGTGATGTTGTAAAATCACAAACATATTCAT
1 CAGCAACATTATCCACTCCATCTAATGTTACAAAATCACAAACATATTCAT
* *
24290753 CAGCAACATTATCCACTCTATCTAATGTTACAAAATCACCAACATATTCAT
1 CAGCAACATTATCCACTCCATCTAATGTTACAAAATCACAAACATATTCAT
24290804 CAGCAACA
1 CAGCAACA
24290812 ACTTCACTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.27
Consensus pattern (51 bp):
CAGCAACATTATCCACTCCATCTAATGTTACAAAATCACAAACATATTCAT
Found at i:24290980 original size:33 final size:33
Alignment explanation
Indices: 24290941--24291018 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
24290931 TACCCCTCCT
* *
24290941 ACATCACCCTCCCCAACAGATTCTACCTTTTCT
1 ACATCACCCTCCCCAACAGATTCTACCTCTTCA
* ** * *
24290974 AGATCACATTCACCATCAGATTCTACCTCTTCA
1 ACATCACCCTCCCCAACAGATTCTACCTCTTCA
24291007 ACATCACCCTCC
1 ACATCACCCTCC
24291019 TCAGCAGTCA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.41, G:0.04, T:0.28
Consensus pattern (33 bp):
ACATCACCCTCCCCAACAGATTCTACCTCTTCA
Found at i:24291690 original size:117 final size:117
Alignment explanation
Indices: 24291484--24291694 Score: 359
Period size: 117 Copynumber: 1.8 Consensus size: 117
24291474 GGTAACAGAA
*
24291484 ATCAACAACATCGAGACCACTGTCACATCACAAATCGACAAAACAAACCCTATATTGTGGCACTG
1 ATCAACAACATCGAGACCACTGTCACATCACAAATCGACAAAACAAACCCTACATTGTGGCACTG
*
24291549 AAATTGCAATAATAAGTCACAAATAACCATATACAATTTTAACAACAACTTT
66 AAATTGCAATAATAAATCACAAATAACCATATACAATTTTAACAACAACTTT
* * * * *
24291601 ATCAACAACATTGGGACCATTGTCGCTTCACAAATCGACAAAACAAACCCTACATTGTGGCACTG
1 ATCAACAACATCGAGACCACTGTCACATCACAAATCGACAAAACAAACCCTACATTGTGGCACTG
24291666 AAATTGCAATAATAAATCACAAATAACCA
66 AAATTGCAATAATAAATCACAAATAACCA
24291695 ACAAACCAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 87 1.00
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.22
Consensus pattern (117 bp):
ATCAACAACATCGAGACCACTGTCACATCACAAATCGACAAAACAAACCCTACATTGTGGCACTG
AAATTGCAATAATAAATCACAAATAACCATATACAATTTTAACAACAACTTT
Found at i:24292393 original size:38 final size:38
Alignment explanation
Indices: 24292336--24292414 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
24292326 TAATAATTTC
24292336 CTTAACTTTTTACACTTTAACCAAAAGTAGTGAAAAAT
1 CTTAACTTTTTACACTTTAACCAAAAGTAGTGAAAAAT
* *
24292374 CTTAACTTTTTGCAGTTTAACCAAAAGTAGTGAAAAAT
1 CTTAACTTTTTACACTTTAACCAAAAGTAGTGAAAAAT
24292412 CTT
1 CTT
24292415 TCACTTTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (38 bp):
CTTAACTTTTTACACTTTAACCAAAAGTAGTGAAAAAT
Found at i:24298887 original size:15 final size:15
Alignment explanation
Indices: 24298867--24298920 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
24298857 ATACTACAAA
24298867 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
24298882 ATATTTATAATTGCAAT
1 ATATTTATTATT--AAT
*
24298899 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
24298916 ATATT
1 ATATT
24298921 AATATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 16 0.50
17 5 0.16
19 11 0.34
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:24299002 original size:16 final size:19
Alignment explanation
Indices: 24298977--24299032 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
24298967 TATAATTGAA
24298977 ATATTAAATAATTTATTAA-
1 ATATT-AATAATTTATTAAT
24298996 A-A-TAATAAATTATATTAATT
1 ATATTAAT-AATT-TATTAA-T
24299016 ATATTAATAATTTATTA
1 ATATTAATAATTTATTA
24299033 TATGACTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 5 0.16
18 7 0.23
19 1 0.03
20 6 0.19
21 5 0.16
22 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATTAATAATTTATTAAT
Found at i:24300666 original size:39 final size:39
Alignment explanation
Indices: 24300559--24300693 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
24300549 GACCTCGAGT
* * *
24300559 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
24300600 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
24300638 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
24300677 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
24300694 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:24308650 original size:372 final size:372
Alignment explanation
Indices: 24307959--24308710 Score: 1362
Period size: 372 Copynumber: 2.0 Consensus size: 372
24307949 TTAATTTTGA
24307959 TTAATT-TGACTATTTTCGACAGATTCGCGCAAAGGGCGAAAATTGGCTCGGCTGACACTGCTGA
1 TTAATTGTGACTATTTTCGACAGATTCGCGCAAAGGGCGAAAATTGGCTCGGCTGACACTGCTGA
* *
24308023 AAGCACAAAATCGAGAAGCAATTTGAAGTTTTGAGGCACATTAATTTCCAGCCTAAGACGATCCA
66 AAGCACAAAATCGAGAAGCAATTTGAAGTTTCGAGGCACATTAATTTCCAGCCTAAGACGACCCA
24308088 GAAATGTGTATTAATTCATAATTTAATTAATTTTAATTTATTCTACATTTAATTTGGGTTAAATA
131 GAAATGTGTATTAATTCATAATTTAATTAATTTTAATTTATTCTACATTTAATTTGGGTTAAATA
* * *
24308153 AATTATTTTTAATTAATTATGGAGAAAGGGTCTAATTGAACCGCGCCATTCGAACCATATTGAGT
196 AATTATTTTTAATTAATTATGGAGAAAGGGTCCAATTGAACCACACCATTCGAACCATATTGAGT
* *
24308218 GAACCGAACCAGCAACTAATTGGTCAGACCAGAACCGTCAGCATTTTAGATGATTAAATATGCTT
261 GAACCAAACCAACAACTAATTGGTCAGACCAGAACCGTCAGCATTTTAGATGATTAAATATGCTT
24308283 GCAAAAAGGCCCTTGAAGAACTATCAAAATGCATTCAAACCCCTCCT
326 GCAAAAAGGCCCTTGAAGAACTATCAAAATGCATTCAAACCCCTCCT
*
24308330 TTAATTGTGACTATTTTCGACAGATTCGCGCAAAGGGCGAAAATTGGCTTGGCTGACACTGCTGA
1 TTAATTGTGACTATTTTCGACAGATTCGCGCAAAGGGCGAAAATTGGCTCGGCTGACACTGCTGA
24308395 AAGCACAAAATCGAGAAGCAATTTGAAGTTTCGAGGCACATTAATTTCCAGCCTAAGACGACCCA
66 AAGCACAAAATCGAGAAGCAATTTGAAGTTTCGAGGCACATTAATTTCCAGCCTAAGACGACCCA
*
24308460 GAAATGTGTATTAATTCATAATTTAATTAATTTTAATTTATTCTCCATTTAATTTGGGTTAAATA
131 GAAATGTGTATTAATTCATAATTTAATTAATTTTAATTTATTCTACATTTAATTTGGGTTAAATA
*
24308525 AATTATTTTTAATTAATTATGGAGAAAGGGTCCAATTGAACCACACCGTTCGAACCATATTGAGT
196 AATTATTTTTAATTAATTATGGAGAAAGGGTCCAATTGAACCACACCATTCGAACCATATTGAGT
* ** *
24308590 GAACCAAACCAACAACTAATTGGTCAGCCCAGAATTGTCAGCATTTTAGCTGATTAAATATGCTT
261 GAACCAAACCAACAACTAATTGGTCAGACCAGAACCGTCAGCATTTTAGATGATTAAATATGCTT
*
24308655 GCAAAAAGGCCCTTGAAGAACTATCAAAATGCATTCAAGCCCCTCCT
326 GCAAAAAGGCCCTTGAAGAACTATCAAAATGCATTCAAACCCCTCCT
24308702 TTAATTGTG
1 TTAATTGTG
24308711 GCTTTATGAA
Statistics
Matches: 365, Mismatches: 15, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
371 6 0.02
372 359 0.98
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (372 bp):
TTAATTGTGACTATTTTCGACAGATTCGCGCAAAGGGCGAAAATTGGCTCGGCTGACACTGCTGA
AAGCACAAAATCGAGAAGCAATTTGAAGTTTCGAGGCACATTAATTTCCAGCCTAAGACGACCCA
GAAATGTGTATTAATTCATAATTTAATTAATTTTAATTTATTCTACATTTAATTTGGGTTAAATA
AATTATTTTTAATTAATTATGGAGAAAGGGTCCAATTGAACCACACCATTCGAACCATATTGAGT
GAACCAAACCAACAACTAATTGGTCAGACCAGAACCGTCAGCATTTTAGATGATTAAATATGCTT
GCAAAAAGGCCCTTGAAGAACTATCAAAATGCATTCAAACCCCTCCT
Found at i:24309035 original size:41 final size:40
Alignment explanation
Indices: 24308976--24309055 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 40
24308966 TTCTTCTCTA
*
24308976 GGGAAAGAGGCTCACATCAGCCATTTTGGAGCAGCAATNTT
1 GGGAAAGAGGCTCACATCAGCCATTTTGAAGCAGCAAT-TT
* *
24309017 GGGAAAGAGGCTCTCATCAGCCATTTTGAAGTAGCAATT
1 GGGAAAGAGGCTCACATCAGCCATTTTGAAGCAGCAATT
24309056 AAATGTTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 1 0.03
41 35 0.97
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (40 bp):
GGGAAAGAGGCTCACATCAGCCATTTTGAAGCAGCAATTT
Found at i:24319561 original size:40 final size:40
Alignment explanation
Indices: 24319506--24319608 Score: 109
Period size: 40 Copynumber: 2.6 Consensus size: 40
24319496 AACAAATTGA
* *
24319506 CTATATTTGGCACTTAGTGTGCG-TTTCGAGATAGCTTCAG
1 CTATATATGGCACTTAGTGTGCGAATTCGA-ATAGCTTCAG
* * * * *
24319546 CTATATATAGCACTTAGTATGCGAATTGGAATAGTTTCGG
1 CTATATATGGCACTTAGTGTGCGAATTCGAATAGCTTCAG
* *
24319586 CTATATGTGGCACTAAGTGTGCG
1 CTATATATGGCACTTAGTGTGCG
24319609 GTACTGAGAC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 47 0.92
41 4 0.08
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (40 bp):
CTATATATGGCACTTAGTGTGCGAATTCGAATAGCTTCAG
Found at i:24321316 original size:44 final size:44
Alignment explanation
Indices: 24321266--24321810 Score: 294
Period size: 44 Copynumber: 11.9 Consensus size: 44
24321256 CATCGTGGTG
* *
24321266 AATCTTATCTCCTTGAAGTTGCAGTGAAGCAGATTAAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGTTACA
** * * * *
24321310 AATCTTATCTCCCAAAAGTTGCAATGAAGCACATTGTAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGTTA-CA
* * * *
24321355 AAT-TTATCTCTCTGAAGTTGCAGT-AGAGTAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTGAAGTTACA
* * * *
24321398 TAA-CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATAGCG
1 -AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGTTA-CA
* *
24321443 AATCTTATTTCCCTGAAGTTGTAGTGGAA-CAGATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGATT---G----AAGTTACA
* * * * * *
24321494 AATCTTATCTCCCTGAAGATGCAGTTG-AGAAAATTGAAGATGCG
1 AATCTTATCTCCCTGAAGTTGCAG-TGAAGCAGATTGAAGTTACA
* * * *
24321538 CATCTTATTTCCCTAAAGTTGCAGTGGAA-CAGAGTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGT-GAAGCAGA-T-----T-GAAGTTACA
* * * * *
24321589 AATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAA-TATGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGT-TACA
* * * * ***
24321633 AATTTTATCTCCCTGAAATTGCAGTGAAGCAGGTTGAAGATGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGTTACA
* * * **
24321677 AATCTTATTTCCTTGAAGTTACAGTGAAATAGATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATT---G----AAGTTACA
* * * **
24321728 AATCTTATCTCCTTGAAATTGCAGTGGAGCAGATTGAAGTTATT
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGTTACA
* * * *
24321772 AATCTTATCTCCCTAAAGTTGCGGTGGAGTAGATTGAAG
1 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAG
24321811 CGACGAACCC
Statistics
Matches: 377, Mismatches: 88, Indels: 72
0.70 0.16 0.13
Matches are distributed among these distances:
43 5 0.01
44 229 0.61
45 36 0.10
46 2 0.01
47 1 0.00
48 3 0.01
50 5 0.01
51 90 0.24
52 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGTTACA
Found at i:24321625 original size:95 final size:96
Alignment explanation
Indices: 24321302--24321658 Score: 367
Period size: 95 Copynumber: 3.8 Consensus size: 96
24321292 AAGCAGATTA
* * * * *
24321302 AAGTTACAAATCTTATCTCCCAAAAGTTGCAATGAAGCACATTGTAGATAGCAAAT-TTATCTCT
1 AAGTTACAAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCC
* * **
24321366 CTGAAGTTGCAGTAGAGTAGATTAAAGCTAC
66 CTAAAGTTGCAGTGGAACAGATTAAAGCTAC
* * * * *
24321397 -A--T---AA-CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATAGCGAATCTTATTTCC
1 AAGTTACAAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCC
* *
24321455 CTGAAGTTGTAGTGGAACAGATTAAAGCTAC
66 CTAAAGTTGCAGTGGAACAGATTAAAGCTAC
* * * * * * ** *
24321486 AAGTTACAAATCTTATCTCCCTGAAGATGCAGTTGAGAAAATTGAAGAT-GCGCATCTTATTTCC
1 AAGTTACAAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCC
*
24321550 CTAAAGTTGCAGTGGAACAGAGTAAAGCTAC
66 CTAAAGTTGCAGTGGAACAGATTAAAGCTAC
* * *
24321581 AAGTTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAATAT-GCAAATTTTATCTCC
1 AAGTTACAAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCC
24321645 CTGAAA-TTGCAGTG
66 CT-AAAGTTGCAGTG
24321659 AAGCAGGTTG
Statistics
Matches: 218, Mismatches: 35, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
88 37 0.17
89 35 0.16
90 1 0.00
92 2 0.01
94 1 0.00
95 106 0.49
96 36 0.17
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGTTACAAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCC
CTAAAGTTGCAGTGGAACAGATTAAAGCTAC
Found at i:24321809 original size:139 final size:138
Alignment explanation
Indices: 24321492--24321810 Score: 374
Period size: 139 Copynumber: 2.3 Consensus size: 138
24321482 CTACAAGTTA
* * * * *
24321492 CAAATCTTATCTCCCTGAAGATGCAGTTGAGAAAATTGAAGATGCGCATCTTATTTCCCTAAAGT
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGATGCGAATCTTATTTCCCTAAAGT
* *
24321557 TGCAGTGGAACAGAGTAAAGCTACAAGTTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGA
66 TACAGTGAAACAGAGTAAAGCTACAAGTTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGA
24321622 TTGAATAT
131 TTGAATAT
* * * * * * *
24321630 GCAAATTTTATCTCCCTGAAA-TTGCAGTGAAGCAGGTTGAAGATGTGAATCTTATTTCCTTGAA
1 -CAAATCTTATCTCCCT-AAAGTTGCAGTGGAGAAGATTGAAGATGCGAATCTTATTTCCCTAAA
* * * * *
24321694 GTTACAGTGAAATAGATTAAAGCTACAAGTTACAAATCTTATCTCCTTGAAA-TTGCAGTGGAGC
64 GTTACAGTGAAACAGAGTAAAGCTACAAGTTACAAATCTTATCTCCCT-AAAGTTACAATGGAGC
24321758 AGATTGAAGTTAT
128 AGATTGAA--TAT
* * *
24321771 -TAATCTTATCTCCCTAAAGTTGCGGTGGAGTAGATTGAAG
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAG
24321811 CGACGAACCC
Statistics
Matches: 150, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
138 3 0.02
139 139 0.93
140 5 0.03
141 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.31
Consensus pattern (138 bp):
CAAATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGATGCGAATCTTATTTCCCTAAAGT
TACAGTGAAACAGAGTAAAGCTACAAGTTACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGA
TTGAATAT
Found at i:24326956 original size:43 final size:42
Alignment explanation
Indices: 24326909--24327026 Score: 116
Period size: 43 Copynumber: 2.7 Consensus size: 42
24326899 AGAAAAAGAC
24326909 CAAAAAAGGAAGCTACATGGAAGAAACCACA-AT-TGCATCCAAA
1 CAAAAAAGGAAGC-ACATGGAAGAAACCACATATATG--TCCAAA
* *
24326952 CAAAAAAGGAAGCA-ATGTGAAAGTAACCACATCTATGTCCAAA
1 CAAAAAAGGAAGCACATG-G-AAGAAACCACATATATGTCCAAA
* * *
24326995 CAAAAAAGGAAGCAACCTAGAAGCAACCACAT
1 CAAAAAAGGAAGC-ACATGGAAGAAACCACAT
24327027 TAGGACAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
41 3 0.05
42 2 0.03
43 53 0.83
44 3 0.05
45 3 0.05
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.12
Consensus pattern (42 bp):
CAAAAAAGGAAGCACATGGAAGAAACCACATATATGTCCAAA
Found at i:24333799 original size:6 final size:6
Alignment explanation
Indices: 24333788--24333813 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
24333778 AAAATAACAT
24333788 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
24333814 GAACACACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:24334685 original size:20 final size:21
Alignment explanation
Indices: 24334639--24334686 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
24334629 AATTATTTTA
*
24334639 AATTATAAATATTATAAATATT
1 AATTA-AAATATTATAAAGATT
*
24334661 -TTTAAAATATTA-AAAGATT
1 AATTAAAATATTATAAAGATT
24334680 AATTAAA
1 AATTAAA
24334687 TTTGACATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 6 0.27
20 13 0.59
21 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AATTAAAATATTATAAAGATT
Found at i:24339893 original size:30 final size:30
Alignment explanation
Indices: 24339857--24339916 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
24339847 TATTTTATTA
* *
24339857 TTAATTTTGTTATTATTTTAAAGGTATTTG
1 TTAATTTTATTATTATTCTAAAGGTATTTG
*
24339887 TTAATTTTATTATTATTCTAGAGGTATTTG
1 TTAATTTTATTATTATTCTAAAGGTATTTG
24339917 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTATTATTCTAAAGGTATTTG
Found at i:24342869 original size:12 final size:12
Alignment explanation
Indices: 24342852--24342887 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
24342842 AAGCATGTCA
24342852 TATCTGTATTTG
1 TATCTGTATTTG
24342864 TATCTGTATTCTG
1 TATCTGTATT-TG
24342877 TATCTGT-TTTG
1 TATCTGTATTTG
24342888 GGGAAGGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.09
12 12 0.52
13 9 0.39
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.58
Consensus pattern (12 bp):
TATCTGTATTTG
Found at i:24349139 original size:18 final size:18
Alignment explanation
Indices: 24349104--24349137 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24349094 CAAACCTGTC
*
24349104 ATTTTTCCTTTTCATTTG
1 ATTTTTCCTTCTCATTTG
24349122 ATTTTTCCTTCT-ATTT
1 ATTTTTCCTTCTCATTT
24349138 TGTTTCGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.18, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTTCCTTCTCATTTG
Found at i:24352029 original size:26 final size:26
Alignment explanation
Indices: 24351981--24352037 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
24351971 GATTTCATAA
** * *
24351981 GCCGAGGTCATTTTGGGCTATTTTGG
1 GCCGAGGTCATTTTGAACCATTTTAG
24352007 GCCGAGGTCATTTTGAACCATTTTAG
1 GCCGAGGTCATTTTGAACCATTTTAG
24352033 GCCGA
1 GCCGA
24352038 ACTGAGCCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (26 bp):
GCCGAGGTCATTTTGAACCATTTTAG
Found at i:24356597 original size:9 final size:9
Alignment explanation
Indices: 24356583--24356615 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
24356573 TTCTTATATT
24356583 TTTTTTTAC
1 TTTTTTTAC
24356592 TTTTTTTAC
1 TTTTTTTAC
24356601 -TTTTTTAC
1 TTTTTTTAC
24356609 TTTTTTT
1 TTTTTTT
24356616 CTTATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:24356604 original size:7 final size:8
Alignment explanation
Indices: 24356584--24356614 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
24356574 TCTTATATTT
24356584 TTTTTTAC
1 TTTTTTAC
24356592 TTTTTTTAC
1 -TTTTTTAC
24356601 TTTTTTAC
1 TTTTTTAC
24356609 TTTTTT
1 TTTTTT
24356615 TCTTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTAC
Found at i:24356764 original size:21 final size:21
Alignment explanation
Indices: 24356708--24356781 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
24356698 ATATTATTAA
* * * *
24356708 TTTTAAAAAATTTGTAATATA
1 TTTTTAAAATTTTATAATATT
*
24356729 TATTTAAAATGTTTTATAATATT
1 TTTTTAAAA--TTTTATAATATT
*
24356752 TTTTTAAAATTTTA-ATTATT
1 TTTTTAAAATTTTATAATATT
24356772 ATTTTTAAAA
1 -TTTTTAAAA
24356782 ATATTTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 5 0.12
21 21 0.49
23 17 0.40
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTTTAAAATTTTATAATATT
Found at i:24356782 original size:22 final size:23
Alignment explanation
Indices: 24356695--24356783 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 23
24356685 GCTTATTTAA
* *
24356695 TTTATATTATTAATTTTAAAAAA
1 TTTATATTATTATTTTTAAAAAT
* * * *
24356718 TTTGTAATA-TATATTTAAAATGT
1 TTTATATTATTATTTTTAAAA-AT
*
24356741 TTTATAATATT-TTTTT-AAAAT
1 TTTATATTATTATTTTTAAAAAT
24356762 TTTA-ATTATTATTTTTAAAAAT
1 TTTATATTATTATTTTTAAAAAT
24356784 ATTTTTTAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
20 5 0.10
21 10 0.19
22 17 0.33
23 19 0.37
24 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTATATTATTATTTTTAAAAAT
Found at i:24357067 original size:18 final size:18
Alignment explanation
Indices: 24357044--24357090 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
24357034 CTGACTATTA
24357044 ATAAATTTAAATATAAAT
1 ATAAATTTAAATATAAAT
*
24357062 ATAAATTTTAA-A-AAAT
1 ATAAATTTAAATATAAAT
*
24357078 ATATA-TTAAATAT
1 ATAAATTTAAATAT
24357091 TATTTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 1 0.04
18 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATTTAAATATAAAT
Found at i:24357298 original size:27 final size:26
Alignment explanation
Indices: 24357265--24357333 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
24357255 AAATTTTAAA
*
24357265 TATAATTTTTAAATACATTTAAAAAAT
1 TATAATTTTTAAATA-ATATAAAAAAT
* *
24357292 TATAATTTTTTAATAATATAAGAAAT
1 TATAATTTTTAAATAATATAAAAAAT
*
24357318 CATAATATTTTAAATA
1 TATAAT-TTTTAAATA
24357334 TTTTTTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 14 0.39
27 22 0.61
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (26 bp):
TATAATTTTTAAATAATATAAAAAAT
Found at i:24357317 original size:26 final size:27
Alignment explanation
Indices: 24357265--24357330 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
24357255 AAATTTTAAA
* *
24357265 TATAATTTTTAAATACATTTAAAAAAT
1 TATAATTTTTTAATACATATAAAAAAT
*
24357292 TATAATTTTTTAATA-ATATAAGAAAT
1 TATAATTTTTTAATACATATAAAAAAT
* *
24357318 CATAATATTTTAA
1 TATAATTTTTTAA
24357331 ATATTTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (27 bp):
TATAATTTTTTAATACATATAAAAAAT
Found at i:24357480 original size:23 final size:22
Alignment explanation
Indices: 24357426--24357500 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
24357416 TTATTATTAA
* *
24357426 TTTTAAATTTTTTTAATGTATAT
1 TTTTAAATTTTTATAATATAT-T
**
24357449 TTAAAAATTTTTATAATATATT
1 TTTTAAATTTTTATAATATATT
24357471 TTTTACAA-TTTTA-AATAT-TAT
1 TTTTA-AATTTTTATAATATAT-T
24357492 TTTTAAATT
1 TTTTAAATT
24357501 CTTTTTTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 3 0.07
21 12 0.28
22 9 0.21
23 19 0.44
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (22 bp):
TTTTAAATTTTTATAATATATT
Found at i:24357496 original size:21 final size:21
Alignment explanation
Indices: 24357457--24357500 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24357447 ATTTAAAAAT
24357457 TTTTATAATATATTTTTTACAA
1 TTTTATAATATATTTTTTA-AA
24357479 TTTTA-AATAT-TATTTTTAAA
1 TTTTATAATATAT-TTTTTAAA
24357499 TT
1 TT
24357501 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATAATATATTTTTTAAA
Found at i:24360552 original size:30 final size:30
Alignment explanation
Indices: 24360516--24360638 Score: 174
Period size: 30 Copynumber: 4.1 Consensus size: 30
24360506 GTCCCAGAGT
* *
24360516 AGTTCATATAACCCAGACATAGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
*
24360546 AGTTCATATCACCCGGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
24360576 AGTTCATATCACTCGGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* **
24360606 AGTTCATATCACCCGGATATAGGCAGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
24360636 AGT
1 AGT
24360639 CCATTTGACC
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATAGGTGGTTCG
Found at i:24364131 original size:33 final size:33
Alignment explanation
Indices: 24364037--24364162 Score: 114
Period size: 33 Copynumber: 3.7 Consensus size: 33
24364027 TAAAACTAAT
* * *
24364037 AATTTCAAAACTAATTTGAAAAATATATATTTAA
1 AATTTAAAAAATAATTTTAAAAATATATA-TTAA
* *
24364071 AATTTATAAAAAAATAATTTCACAAATATATATCT-A
1 AA-TT-T-AAAAAATAATTTTAAAAATATATAT-TAA
*
24364107 AAGTTAAAAAATAATTTTAAAAATA-ATAATTAA
1 AATTTAAAAAATAATTTTAAAAATATAT-ATTAA
*
24364140 AATTTAAAAAA-AATTGTAAAAAT
1 AATTTAAAAAATAATTTTAAAAAT
24364163 TAATAATATA
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
32 14 0.18
33 31 0.40
34 3 0.04
35 3 0.04
36 5 0.06
37 21 0.27
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (33 bp):
AATTTAAAAAATAATTTTAAAAATATATATTAA
Found at i:24364160 original size:32 final size:35
Alignment explanation
Indices: 24364110--24364174 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
24364100 ATATCTAAAG
*
24364110 TTAAAAAATAATTTTAAAAA-TAATAAT-TAAAAT
1 TTAAAAAATAATTGTAAAAATTAATAATATAAAAT
24364143 TTAAAAAA-AATTGTAAAAATTAATAATATAAA
1 TTAAAAAATAATTGTAAAAATTAATAATATAAA
24364175 TTACAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 10 0.34
33 15 0.52
34 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (35 bp):
TTAAAAAATAATTGTAAAAATTAATAATATAAAAT
Found at i:24364176 original size:33 final size:32
Alignment explanation
Indices: 24364079--24364176 Score: 94
Period size: 33 Copynumber: 3.0 Consensus size: 32
24364069 AAAATTTATA
* *
24364079 AAAAAATAATT-TCACAAAT-ATATATCTAAAGTT
1 AAAAAATAATTGT-AAAAATAATA-AT-TAAATTT
*
24364112 AAAAAATAATTTTAAAAATAATAATTAAAATTT
1 AAAAAATAATTGTAAAAATAATAATT-AAATTT
24364145 AAAAAA-AATTGTAAAAATTAATAATATAAATT
1 AAAAAATAATTGTAAAAA-TAATAAT-TAAATT
24364177 ACAATTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
32 11 0.19
33 41 0.72
34 5 0.09
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (32 bp):
AAAAAATAATTGTAAAAATAATAATTAAATTT
Found at i:24364214 original size:18 final size:18
Alignment explanation
Indices: 24364188--24364240 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
24364178 CAATTTTTTA
* *
24364188 AAATTAATAATATAAATT
1 AAATAAATAATATAAAAT
*
24364206 AAATAAATAAAATAAAAT
1 AAATAAATAATATAAAAT
24364224 AAGA-AAATAATATAAAA
1 AA-ATAAATAATATAAAA
24364241 CTTAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 29 0.97
19 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAATAATATAAAAT
Found at i:24364248 original size:18 final size:17
Alignment explanation
Indices: 24364193--24364263 Score: 54
Period size: 18 Copynumber: 4.0 Consensus size: 17
24364183 TTTTAAAATT
24364193 AATAATAT-AAATTAAATA
1 AATAATATAAAATT-AA-A
* *
24364211 AATAAAATAAAATAAGAA
1 AATAATATAAAATTA-AA
24364229 AATAATATAAAACTTAAA
1 AATAATATAAAA-TTAAA
* * *
24364247 AAAAAAAAAAAATTAAA
1 AATAATATAAAATTAAA
24364264 GAAAAAGACA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
17 5 0.12
18 31 0.72
19 7 0.16
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (17 bp):
AATAATATAAAATTAAA
Found at i:24364268 original size:18 final size:18
Alignment explanation
Indices: 24364201--24364269 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 18
24364191 TTAATAATAT
* *
24364201 AAATTAAATAAATAAAATA
1 AAATTAAAGAAA-AAAAAA
24364220 AAA-T-AAGAAAATAATATAA
1 AAATTAAAGAAAA-AA-A-AA
*
24364239 AACTTAAA-AAAAAAAAA
1 AAATTAAAGAAAAAAAAA
24364256 AAATTAAAGAAAAA
1 AAATTAAAGAAAAA
24364270 GACAAAATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
16 1 0.03
17 16 0.40
18 8 0.20
19 8 0.20
20 5 0.12
21 2 0.05
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATTAAAGAAAAAAAAA
Found at i:24364425 original size:14 final size:14
Alignment explanation
Indices: 24364408--24364460 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
24364398 ATTTTTTTAA
24364408 AATTTTAAAAAATT
1 AATTTTAAAAAATT
*
24364422 AA-TTTGAAAAA-T
1 AATTTTAAAAAATT
24364434 ACATTTTTAAAAAATT
1 A-A-TTTTAAAAAATT
*
24364450 AATTTGAAAAA
1 AATTTTAAAAA
24364461 TACATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 2 0.06
13 9 0.28
14 10 0.31
15 9 0.28
16 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (14 bp):
AATTTTAAAAAATT
Found at i:24364433 original size:13 final size:13
Alignment explanation
Indices: 24364415--24364461 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
24364405 TAAAATTTTA
24364415 AAAAATTAATTTG
1 AAAAATTAATTTG
*
24364428 AAAAA-TACATTTTTA
1 AAAAATTA-A--TTTG
24364443 AAAAATTAATTTG
1 AAAAATTAATTTG
24364456 AAAAAT
1 AAAAAT
24364462 ACATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.07
13 15 0.54
15 9 0.32
16 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (13 bp):
AAAAATTAATTTG
Found at i:24364441 original size:28 final size:28
Alignment explanation
Indices: 24364410--24364473 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
24364400 TTTTTTAAAA
24364410 TTTTAAAAAATTAATTTGAAAAATACAT
1 TTTTAAAAAATTAATTTGAAAAATACAT
24364438 TTTTAAAAAATTAATTTGAAAAATACAT
1 TTTTAAAAAATTAATTTGAAAAATACAT
24364466 TTTTAAAA
1 TTTTAAAA
24364474 TTTATAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (28 bp):
TTTTAAAAAATTAATTTGAAAAATACAT
Found at i:24364550 original size:22 final size:24
Alignment explanation
Indices: 24364523--24364610 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 24
24364513 TTAAAAAATA
24364523 TTTTTAAAAATAATAAT-TAAAA-
1 TTTTTAAAAATAATAATATAAAAC
*
24364545 TTTTT-AAAA-AATATTATAAAAC
1 TTTTTAAAAATAATAATATAAAAC
* * *
24364567 ATTTTAAATAT-AT-AT-TACAAAT
1 TTTTTAAAAATAATAATATA-AAAC
*
24364589 TTTTTAAAATTAATAATATAAA
1 TTTTTAAAAATAATAATATAAA
24364611 TTAAATAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
20 5 0.10
21 11 0.22
22 21 0.42
23 7 0.14
24 4 0.08
25 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTTAAAAATAATAATATAAAAC
Found at i:24364640 original size:36 final size:36
Alignment explanation
Indices: 24364600--24364672 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 36
24364590 TTTTAAAATT
*
24364600 AATAATAT-AAA-TTAAATAAGTAAAATAAATTAAGAA
1 AATAATATAAAACTTAAA-AAG-AAAAAAAATTAAGAA
24364636 AATAATATAAAACTTAAAAAGAAAAAAAATTAAGAA
1 AATAATATAAAACTTAAAAAGAAAAAAAATTAAGAA
24364672 A
1 A
24364673 GAGACAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 23 0.68
37 6 0.18
38 5 0.15
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (36 bp):
AATAATATAAAACTTAAAAAGAAAAAAAATTAAGAA
Found at i:24364645 original size:18 final size:18
Alignment explanation
Indices: 24364595--24364646 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
24364585 AAATTTTTTA
*
24364595 AAATTAATAATATAAATT
1 AAATAAATAATATAAATT
* *
24364613 AAATAAGTAAAATAAATT
1 AAATAAATAATATAAATT
24364631 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
24364647 ACTTAAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATAAATAATATAAATT
Found at i:24364702 original size:9 final size:9
Alignment explanation
Indices: 24364688--24364722 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
24364678 AAAATATAAG
24364688 AAAAAAAGT
1 AAAAAAAGT
24364697 AAAAAAAGT
1 AAAAAAAGT
*
24364706 AATAAAAGT
1 AAAAAAAGT
24364715 AATAAAAA
1 AA-AAAAA
24364723 AATATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:24369665 original size:35 final size:35
Alignment explanation
Indices: 24369550--24369671 Score: 172
Period size: 35 Copynumber: 3.5 Consensus size: 35
24369540 ATAAAGAAAA
* *
24369550 CCATAATGAGATGTGAAACGTAGGTATGACATTTT
1 CCATACTGAGTTGTGAAACGTAGGTATGACATTTT
* * *
24369585 CCATACCGAGTGGTGAAATGTAGGTATGACATTTT
1 CCATACTGAGTTGTGAAACGTAGGTATGACATTTT
* *
24369620 TCATACTGAGTTGTGAAACGTAGGTATGATATTTT
1 CCATACTGAGTTGTGAAACGTAGGTATGACATTTT
*
24369655 CCATATTGAGTTGTGAA
1 CCATACTGAGTTGTGAA
24369672 CTGTGGCACC
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 75 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
CCATACTGAGTTGTGAAACGTAGGTATGACATTTT
Found at i:24376939 original size:39 final size:40
Alignment explanation
Indices: 24376844--24377105 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
24376834 TTGAATGATG
*
24376844 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
24376882 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
24376923 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
24376962 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
24377001 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
24377040 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
24377079 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
24377106 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:24384302 original size:39 final size:40
Alignment explanation
Indices: 24384207--24384468 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
24384197 TTGAATGATG
*
24384207 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
24384245 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
24384286 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
24384325 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
24384364 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
24384403 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
24384442 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
24384469 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:24387853 original size:35 final size:35
Alignment explanation
Indices: 24387752--24387862 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
24387742 CATACTATGA
*
24387752 TGTGAAACGTAGGTAT-GTCATTTTCCATACCGAGT
1 TGTGAAACGTAGGTATGGT-ATTTTCCATACTGAGT
* * *
24387787 GGTGAAATGTAGGTATGGTATTTTTCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTTCCATACTGAGT
* *
24387822 TGTGAAACGTAGGTATGGTATTTTCCTTACTGAAT
1 TGTGAAACGTAGGTATGGTATTTTCCATACTGAGT
24387857 TGTGAA
1 TGTGAA
24387863 TTGTGGCACT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 64 0.97
36 2 0.03
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTTTCCATACTGAGT
Found at i:24393206 original size:148 final size:149
Alignment explanation
Indices: 24392938--24393233 Score: 558
Period size: 148 Copynumber: 2.0 Consensus size: 149
24392928 AAGCATATCC
*
24392938 ACACCTCTCAATAACCATATCCATACTAAATGATTATAACATTATGCTCAAACATATATAAGCCA
1 ACACCTCTCAATAACCATATCCATACCAAATGATTATAACATTATGCTCAAACATATATAAGCCA
24393003 TTTTCACATGGCTATCCAAAATTATACAAATCCAAAGGGTCCATGACCCACTAC-AAAAGGGTAG
66 TTTTCACATGGCTATCCAAAATTATACAAATCCAAAGGGTCCATGACCCACTACAAAAAGGGTAG
*
24393067 TCCTATACATGCCATTTTT
131 TCCTATACATGACATTTTT
24393086 ACACCTCTCAATAACCATATCCATACCAAATGATTATAACATTATGCTCAAACATATATAAGCCA
1 ACACCTCTCAATAACCATATCCATACCAAATGATTATAACATTATGCTCAAACATATATAAGCCA
*
24393151 TTTTCGCATGGCTATCCAAAATTATACAAATCCAAAGGGTCCATGACCCACTACAAAAAGGGTAG
66 TTTTCACATGGCTATCCAAAATTATACAAATCCAAAGGGTCCATGACCCACTACAAAAAGGGTAG
24393216 TCCTATACATGACATTTT
131 TCCTATACATGACATTTT
24393234 CAGAGTTCAA
Statistics
Matches: 144, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
148 117 0.81
149 27 0.19
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (149 bp):
ACACCTCTCAATAACCATATCCATACCAAATGATTATAACATTATGCTCAAACATATATAAGCCA
TTTTCACATGGCTATCCAAAATTATACAAATCCAAAGGGTCCATGACCCACTACAAAAAGGGTAG
TCCTATACATGACATTTTT
Found at i:24394091 original size:49 final size:49
Alignment explanation
Indices: 24393870--24394326 Score: 643
Period size: 49 Copynumber: 9.6 Consensus size: 49
24393860 CCCTTCGGGA
* * * *
24393870 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCAATCGGTC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGG-C
* *
24393918 C-TGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* * *
24393964 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
24394011 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
24394058 CTTATCACATATATATACACTTTCAAATTCATCAGATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
24394107 CTTATCACATATATATACACTTTCAAATTCATCAGATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
24394156 CTTATCACATATATATACACTTTCAAATTCATCAGATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
24394205 CTTATCACATATATATACACTTTCAAATTCATCAGATCGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
* *
24394254 CTTATCAC--ATATATACACTTTCACATTCATCACACCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
24394301 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
24394327 CACAATTATC
Statistics
Matches: 384, Mismatches: 18, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
46 3 0.01
47 179 0.47
48 1 0.00
49 201 0.52
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
Found at i:24402600 original size:18 final size:18
Alignment explanation
Indices: 24402539--24402620 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
24402529 TAACATTCAA
* *
24402539 TTATTTAGTAGCAATTAG
1 TTATTCAGTAGCAATCAG
* *
24402557 TTATTCAATAGCAATCAT
1 TTATTCAGTAGCAATCAG
**
24402575 TTGCTCAGTAGCAATCAG
1 TTATTCAGTAGCAATCAG
* * *
24402593 TTATTCAGTAACGATCAA
1 TTATTCAGTAGCAATCAG
24402611 TTATTCAGTA
1 TTATTCAGTA
24402621 ATAGTCAGTC
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (18 bp):
TTATTCAGTAGCAATCAG
Found at i:24402619 original size:36 final size:35
Alignment explanation
Indices: 24402527--24402638 Score: 98
Period size: 36 Copynumber: 3.1 Consensus size: 35
24402517 AGTTTCATTT
* *
24402527 AGTAACATTCAATTATTTAGTAGCAATTAGTTATTC
1 AGTAACA-TCAATTATTCAGTAGCAATCAGTTATTC
* * * **
24402563 AATAGCAATCATTTGCTCAGTAGCAATCAGTTATTC
1 AGTAAC-ATCAATTATTCAGTAGCAATCAGTTATTC
** * *
24402599 AGTAACGATCAATTATTCAGTAATAGTCAGTCATTC
1 AGTAAC-ATCAATTATTCAGTAGCAATCAGTTATTC
24402635 AGTA
1 AGTA
24402639 CTTTTATTTA
Statistics
Matches: 58, Mismatches: 17, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (35 bp):
AGTAACATCAATTATTCAGTAGCAATCAGTTATTC
Found at i:24404095 original size:28 final size:30
Alignment explanation
Indices: 24404055--24404125 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 30
24404045 ATAATTATTT
24404055 AATTAATAAATATCT-TTTACTT-AATAATA
1 AATTAATAAATATCTATTTACTTAAATAA-A
24404084 AA-TAATAAATATCTATTTACTTAAATAAA
1 AATTAATAAATATCTATTTACTTAAATAAA
24404113 AATTAATTAAATA
1 AATTAA-TAAATA
24404126 AATATATCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
28 12 0.32
29 12 0.32
30 8 0.21
31 6 0.16
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (30 bp):
AATTAATAAATATCTATTTACTTAAATAAA
Found at i:24405894 original size:17 final size:18
Alignment explanation
Indices: 24405872--24405911 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
24405862 ACTTATGTGT
24405872 ATATAAA-AATTAATAAA
1 ATATAAATAATTAATAAA
* *
24405889 ATATAAATGATTATTAAA
1 ATATAAATAATTAATAAA
24405907 ATATA
1 ATATA
24405912 TATTATGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
ATATAAATAATTAATAAA
Found at i:24407241 original size:10 final size:10
Alignment explanation
Indices: 24407226--24407252 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
24407216 TTTATAGCCG
24407226 AAAAATAAAT
1 AAAAATAAAT
24407236 AAAAATAAAT
1 AAAAATAAAT
24407246 AAAAATA
1 AAAAATA
24407253 GATTTCCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:24409602 original size:15 final size:13
Alignment explanation
Indices: 24409584--24409664 Score: 56
Period size: 16 Copynumber: 5.6 Consensus size: 13
24409574 CCTTTCCATG
24409584 TTCTTGTTTTCTTT
1 TTCTT-TTTTCTTT
24409598 CTTCTTCTTTTC-TT
1 -TTCTT-TTTTCTTT
* *
24409612 TTCTTTGTTATTT
1 TTCTTTTTTCTTT
24409625 CTTCTTTTTTTTCTTT
1 -TTC--TTTTTTCTTT
24409641 TTCTTTTCTTCCGTTT
1 TTCTTTT-TT-C-TTT
24409657 TTCTTTTT
1 TTCTTTTT
24409665 ACTTCGTTGC
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
12 3 0.06
13 11 0.20
14 7 0.13
15 15 0.28
16 18 0.33
ACGTcount: A:0.01, C:0.19, G:0.04, T:0.77
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:24409611 original size:11 final size:10
Alignment explanation
Indices: 24409590--24409650 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
24409580 CATGTTCTTG
24409590 TTTTC-TTTC
1 TTTTCTTTTC
24409599 TTCTTCTTTTC
1 TT-TTCTTTTC
24409610 TTTTCTTTGT-
1 TTTTCTTT-TC
24409620 TATTTC--TTC
1 T-TTTCTTTTC
24409629 TTTT-TTTTC
1 TTTTCTTTTC
24409638 TTTTTCTTTTC
1 -TTTTCTTTTC
24409649 TT
1 TT
24409651 CCGTTTTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
8 4 0.09
9 7 0.16
10 16 0.37
11 16 0.37
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTC
Found at i:24410813 original size:12 final size:12
Alignment explanation
Indices: 24410796--24410836 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
24410786 AGGAGATATT
24410796 TGATATGTTATA
1 TGATATGTTATA
* *
24410808 TGATATG--CTC
1 TGATATGTTATA
24410818 TGATATGTTATA
1 TGATATGTTATA
24410830 TGATATG
1 TGATATG
24410837 ATTCTGATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 8 0.35
12 15 0.65
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (12 bp):
TGATATGTTATA
Found at i:24410822 original size:22 final size:23
Alignment explanation
Indices: 24410796--24410881 Score: 104
Period size: 22 Copynumber: 3.8 Consensus size: 23
24410786 AGGAGATATT
*
24410796 TGATATGTTATATGATATG-CTC
1 TGATATGTTATATGATATGATTC
24410818 TGATATGTTATATGATATGATTC
1 TGATATGTTATATGATATGATTC
* * *
24410841 TGATA-GTTAAATAATATGATTT
1 TGATATGTTATATGATATGATTC
* *
24410863 TGATATGCTACATGATATG
1 TGATATGTTATATGATATG
24410882 GGAAATTCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
22 38 0.69
23 17 0.31
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (23 bp):
TGATATGTTATATGATATGATTC
Found at i:24414552 original size:10 final size:10
Alignment explanation
Indices: 24414522--24414555 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
24414512 AACCCTAATT
*
24414522 TTTTCTTTTCT
1 TTTTC-TTTCC
24414533 TTTTCTTTCC
1 TTTTCTTTCC
24414543 TTTTCTTTCC
1 TTTTCTTTCC
24414553 TTT
1 TTT
24414556 CTATTTCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTCTTTCC
Found at i:24414632 original size:3 final size:3
Alignment explanation
Indices: 24414614--24414661 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
24414604 TTCACTTTTA
*
24414614 ATT ATT A-T ATT A-T ATT ATT ATT A-T ATT -TT AGTA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
24414656 ATT ATT
1 ATT ATT
24414662 TACTTATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 8 0.21
3 28 0.74
4 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:24417334 original size:5 final size:5
Alignment explanation
Indices: 24417308--24417384 Score: 59
Period size: 5 Copynumber: 14.8 Consensus size: 5
24417298 CACATTCTTG
* * *
24417308 TTTCT TTTCT CCTTCT GTTCT TTTCT TTGT-T ATT-T TTTCTT TTTCT
1 TTTCT TTTCT -TTTCT TTTCT TTTCT TT-TCT TTTCT TTTC-T TTTCT
*
24417354 TTTCTT TTTCT TTTCT TTTGT TTTGCT TTTC
1 TTTC-T TTTCT TTTCT TTTCT TTT-CT TTTC
24417385 GCTTCATTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.07
5 36 0.61
6 19 0.32
ACGTcount: A:0.01, C:0.18, G:0.05, T:0.75
Consensus pattern (5 bp):
TTTCT
Found at i:24417352 original size:6 final size:6
Alignment explanation
Indices: 24417341--24417372 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
24417331 TCTTTGTTAT
24417341 TTTTTC TTTTTC -TTTTC TTTTTC -TTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
24417373 GTTTTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:24417358 original size:11 final size:11
Alignment explanation
Indices: 24417302--24417372 Score: 67
Period size: 11 Copynumber: 6.6 Consensus size: 11
24417292 TCTTTCCACA
24417302 TTCTTGTTTCTT
1 TTCTT-TTTCTT
** *
24417314 TTCTCCTTCTG
1 TTCTTTTTCTT
24417325 TTC-TTTTC-T
1 TTCTTTTTCTT
* *
24417334 TTGTTATT-TT
1 TTCTTTTTCTT
24417344 TTCTTTTTCTT
1 TTCTTTTTCTT
24417355 TTCTTTTTCTT
1 TTCTTTTTCTT
24417366 TTCTTTT
1 TTCTTTT
24417373 GTTTTGCTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
9 2 0.04
10 13 0.28
11 27 0.59
12 4 0.09
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:24417382 original size:11 final size:10
Alignment explanation
Indices: 24417308--24417384 Score: 59
Period size: 11 Copynumber: 7.4 Consensus size: 10
24417298 CACATTCTTG
24417308 TTTCTTTTCT
1 TTTCTTTTCT
* *
24417318 CCTTCTGTTCT
1 -TTTCTTTTCT
24417329 TTTCTTTGT-T
1 TTTCTTT-TCT
*
24417339 ATT-TTTTCTT
1 TTTCTTTTC-T
24417349 TTTCTTTTCTT
1 TTTCTTTTC-T
24417360 TTTCTTTTCT
1 TTTCTTTTCT
*
24417370 TTTGTTTTGCT
1 TTTCTTTT-CT
24417381 TTTC
1 TTTC
24417385 GCTTCATTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
8 1 0.02
9 3 0.06
10 19 0.36
11 30 0.57
ACGTcount: A:0.01, C:0.18, G:0.05, T:0.75
Consensus pattern (10 bp):
TTTCTTTTCT
Found at i:24418517 original size:5 final size:5
Alignment explanation
Indices: 24418497--24418562 Score: 53
Period size: 5 Copynumber: 12.2 Consensus size: 5
24418487 GTAGCGAATG
*
24418497 ATGAT AGGAT AT-AT ATGAT ATGTTAT ATGAT ATGTTAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATG--AT ATGAT ATG--AT ATGAT ATGAT
*
24418545 CTGAT ATGCTAT ATGAT A
1 ATGAT ATG--AT ATGAT A
24418563 CGATTCTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
4 4 0.08
5 31 0.62
7 15 0.30
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.42
Consensus pattern (5 bp):
ATGAT
Found at i:24418525 original size:12 final size:12
Alignment explanation
Indices: 24418508--24418562 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
24418498 TGATAGGATA
24418508 TATATGATATGT
1 TATATGATATGT
24418520 TATATGATATGT
1 TATATGATATGT
24418532 TATATGATATG-
1 TATATGATATGT
* *
24418543 -ATCTGATATGC
1 TATATGATATGT
24418554 TATATGATA
1 TATATGATA
24418563 CGATTCTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.23
12 30 0.77
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (12 bp):
TATATGATATGT
Found at i:24418529 original size:17 final size:17
Alignment explanation
Indices: 24418505--24418562 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
24418495 TGATGATAGG
24418505 ATAT-ATATGATATGTT
1 ATATGATATGATATGTT
* * *
24418521 ATATGATATGTTATATG
1 ATATGATATGATATGTT
* *
24418538 ATATGATCTGATATGCT
1 ATATGATATGATATGTT
24418555 ATATGATA
1 ATATGATA
24418563 CGATTCTAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
16 4 0.12
17 28 0.88
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (17 bp):
ATATGATATGATATGTT
Found at i:24420477 original size:5 final size:5
Alignment explanation
Indices: 24420451--24420527 Score: 59
Period size: 5 Copynumber: 14.8 Consensus size: 5
24420441 CACATTCTTG
* * *
24420451 TTTCT TTTCT CCTTCT GTTCT TTTCT TTGT-T ATT-T TTTCTT TTTCT
1 TTTCT TTTCT -TTTCT TTTCT TTTCT TT-TCT TTTCT TTTC-T TTTCT
*
24420497 TTTCTT TTTCT TTTCT TTTGT TTTGCT TTTC
1 TTTC-T TTTCT TTTCT TTTCT TTT-CT TTTC
24420528 GCTTCATTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.07
5 36 0.61
6 19 0.32
ACGTcount: A:0.01, C:0.18, G:0.05, T:0.75
Consensus pattern (5 bp):
TTTCT
Found at i:24420495 original size:6 final size:6
Alignment explanation
Indices: 24420484--24420515 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
24420474 TCTTTGTTAT
24420484 TTTTTC TTTTTC -TTTTC TTTTTC -TTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
24420516 GTTTTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:24420501 original size:11 final size:11
Alignment explanation
Indices: 24420445--24420515 Score: 67
Period size: 11 Copynumber: 6.6 Consensus size: 11
24420435 TCTTTCCACA
24420445 TTCTTGTTTCTT
1 TTCTT-TTTCTT
** *
24420457 TTCTCCTTCTG
1 TTCTTTTTCTT
24420468 TTC-TTTTC-T
1 TTCTTTTTCTT
* *
24420477 TTGTTATT-TT
1 TTCTTTTTCTT
24420487 TTCTTTTTCTT
1 TTCTTTTTCTT
24420498 TTCTTTTTCTT
1 TTCTTTTTCTT
24420509 TTCTTTT
1 TTCTTTT
24420516 GTTTTGCTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
9 2 0.04
10 13 0.28
11 27 0.59
12 4 0.09
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:24420525 original size:11 final size:10
Alignment explanation
Indices: 24420451--24420527 Score: 59
Period size: 11 Copynumber: 7.4 Consensus size: 10
24420441 CACATTCTTG
24420451 TTTCTTTTCT
1 TTTCTTTTCT
* *
24420461 CCTTCTGTTCT
1 -TTTCTTTTCT
24420472 TTTCTTTGT-T
1 TTTCTTT-TCT
*
24420482 ATT-TTTTCTT
1 TTTCTTTTC-T
24420492 TTTCTTTTCTT
1 TTTCTTTTC-T
24420503 TTTCTTTTCT
1 TTTCTTTTCT
*
24420513 TTTGTTTTGCT
1 TTTCTTTT-CT
24420524 TTTC
1 TTTC
24420528 GCTTCATTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
8 1 0.02
9 3 0.06
10 19 0.36
11 30 0.57
ACGTcount: A:0.01, C:0.18, G:0.05, T:0.75
Consensus pattern (10 bp):
TTTCTTTTCT
Found at i:24421660 original size:5 final size:5
Alignment explanation
Indices: 24421640--24421705 Score: 53
Period size: 5 Copynumber: 12.2 Consensus size: 5
24421630 GTAGCGAATG
*
24421640 ATGAT AGGAT AT-AT ATGAT ATGTTAT ATGAT ATGTTAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATG--AT ATGAT ATG--AT ATGAT ATGAT
*
24421688 CTGAT ATGCTAT ATGAT A
1 ATGAT ATG--AT ATGAT A
24421706 CGATTCTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
4 4 0.08
5 31 0.62
7 15 0.30
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.42
Consensus pattern (5 bp):
ATGAT
Found at i:24421668 original size:12 final size:12
Alignment explanation
Indices: 24421651--24421705 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
24421641 TGATAGGATA
24421651 TATATGATATGT
1 TATATGATATGT
24421663 TATATGATATGT
1 TATATGATATGT
24421675 TATATGATATG-
1 TATATGATATGT
* *
24421686 -ATCTGATATGC
1 TATATGATATGT
24421697 TATATGATA
1 TATATGATA
24421706 CGATTCTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.23
12 30 0.77
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (12 bp):
TATATGATATGT
Found at i:24421672 original size:17 final size:17
Alignment explanation
Indices: 24421648--24421705 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
24421638 TGATGATAGG
24421648 ATAT-ATATGATATGTT
1 ATATGATATGATATGTT
* * *
24421664 ATATGATATGTTATATG
1 ATATGATATGATATGTT
* *
24421681 ATATGATCTGATATGCT
1 ATATGATATGATATGTT
24421698 ATATGATA
1 ATATGATA
24421706 CGATTCTAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
16 4 0.12
17 28 0.88
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (17 bp):
ATATGATATGATATGTT
Found at i:24432548 original size:31 final size:32
Alignment explanation
Indices: 24432498--24432557 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
24432488 TTAAAAAATA
24432498 ATTAAAATAATATTTTTTTA-TAAAATAAACT
1 ATTAAAATAATATTTTTTTAGTAAAATAAACT
* *
24432529 ATTAAAAT-ATTTATTTTTTAGTATAATAA
1 ATTAAAATAATAT-TTTTTTAGTAAAATAA
24432558 CTTAATTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.12
31 15 0.60
32 7 0.28
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
ATTAAAATAATATTTTTTTAGTAAAATAAACT
Found at i:24432831 original size:26 final size:27
Alignment explanation
Indices: 24432791--24432849 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
24432781 ATAATTATTT
*
24432791 TTAAAAATTAGAAATTA-TTAAAATTA
1 TTAAAAAGTAGAAATTATTTAAAATTA
*
24432817 TTAAAAAGTATAAATTATTTTAAAATTA
1 TTAAAAAGTAGAAATTA-TTTAAAATTA
24432845 -TAAAA
1 TTAAAA
24432850 GTTTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 15 0.52
27 5 0.17
28 9 0.31
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (27 bp):
TTAAAAAGTAGAAATTATTTAAAATTA
Found at i:24432846 original size:18 final size:17
Alignment explanation
Indices: 24432797--24432848 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
24432787 ATTTTTAAAA
*
24432797 ATTAGAAATTATTAAAATT
1 ATTAAAAATTA-T-AAATT
*
24432816 ATTAAAAAGTATAAATT
1 ATTAAAAATTATAAATT
*
24432833 ATTTTAAAATTATAAA
1 A-TTAAAAATTATAAA
24432849 AGTTTTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 6 0.21
18 13 0.46
19 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
ATTAAAAATTATAAATT
Found at i:24435212 original size:6 final size:6
Alignment explanation
Indices: 24435196--24435226 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
24435186 CCTCCAAAGC
24435196 TTCTGGT TTCTGT TTCTGT TTCTGT TTCTGT
1 TTCT-GT TTCTGT TTCTGT TTCTGT TTCTGT
24435227 CTAGTCGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.00, C:0.16, G:0.19, T:0.65
Consensus pattern (6 bp):
TTCTGT
Found at i:24437536 original size:32 final size:33
Alignment explanation
Indices: 24437473--24437547 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
24437463 ATATAAATTC
* * *
24437473 AAAAAGTAAAAAAAAAGTTTTAGTTAATTTTTT
1 AAAAAATAAAAAAAAAGTCTAAGTTAATTTTTT
* * *
24437506 AAAAATTAAAAAAATAGTCTAAGTT-TTTTTTT
1 AAAAAATAAAAAAAAAGTCTAAGTTAATTTTTT
24437538 AAAAAATAAA
1 AAAAAATAAA
24437548 TTCTAGAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 15 0.42
33 21 0.58
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (33 bp):
AAAAAATAAAAAAAAAGTCTAAGTTAATTTTTT
Found at i:24439122 original size:4 final size:4
Alignment explanation
Indices: 24439113--24439161 Score: 89
Period size: 4 Copynumber: 12.2 Consensus size: 4
24439103 ACATGTTAAA
*
24439113 TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT GAGT
1 TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT TAGT
24439161 T
1 T
24439162 GTCATGCTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
TAGT
Found at i:24443422 original size:20 final size:22
Alignment explanation
Indices: 24443399--24443446 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
24443389 AGCACAATTA
24443399 GCAATCAGGG-GCAACAAA-AT
1 GCAATCAGGGAGCAACAAAGAT
* *
24443419 GCAATC-GGGAGCACCAAAGTT
1 GCAATCAGGGAGCAACAAAGAT
24443440 GCAATCA
1 GCAATCA
24443447 TGTACATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.13
20 13 0.57
21 7 0.30
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (22 bp):
GCAATCAGGGAGCAACAAAGAT
Found at i:24456314 original size:62 final size:62
Alignment explanation
Indices: 24456235--24456361 Score: 164
Period size: 62 Copynumber: 2.0 Consensus size: 62
24456225 TTCCAAATCT
* * ** * * *
24456235 AAAAATTCAACAAATTTAGCTCTTAATGTTTACAAAACTTGTCATTTTAGTTCTGATTCTAA
1 AAAAATTCAACAAATTTAGCCCTCAACATTTACAAAACTTGTCAATCTAGTTCTAATTCTAA
* * *
24456297 AAAAATTCAATATATTTAGCCCTCAACATTTACAAAATTTGTCAATCTAGTTCTAATTCTAA
1 AAAAATTCAACAAATTTAGCCCTCAACATTTACAAAACTTGTCAATCTAGTTCTAATTCTAA
24456359 AAA
1 AAA
24456362 TTCCAAATTA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (62 bp):
AAAAATTCAACAAATTTAGCCCTCAACATTTACAAAACTTGTCAATCTAGTTCTAATTCTAA
Found at i:24457830 original size:45 final size:45
Alignment explanation
Indices: 24457798--24458108 Score: 550
Period size: 45 Copynumber: 6.9 Consensus size: 45
24457788 TTATCTTCGA
* * * * * * *
24457798 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
24457844 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
24457889 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
24457934 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
24457979 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
24458024 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
24458069 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATT
24458109 TCATTTCAGA
Statistics
Matches: 258, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
45 225 0.87
46 33 0.13
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.41
Consensus pattern (45 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
Found at i:24463008 original size:48 final size:48
Alignment explanation
Indices: 24462895--24463112 Score: 243
Period size: 48 Copynumber: 4.6 Consensus size: 48
24462885 GGTATGATGT
* * * * *
24462895 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCCATCAAGT--
1 CGATGCCATGTCCCAGACATAGTCTTACACTAACACATCTAT-ACGTGC
* * *
24462942 CGATGCTATGTCCCAGACATAGTCTTACACTAACACCTCTATATGTGC
1 CGATGCCATGTCCCAGACATAGTCTTACACTAACACATCTATACGTGC
* * *
24462990 CGATGCCATGTCCCAGACATAGTCATACACTAACACCTCTATACATGC
1 CGATGCCATGTCCCAGACATAGTCTTACACTAACACATCTATACGTGC
* * *
24463038 CGATGCCATGTCCCAGACATGGTATTACACTGACACATC--T-CGTAGC
1 CGATGCCATGTCCCAGACATAGTCTTACACTAACACATCTATACGT-GC
24463084 CGATG-CATGTCCCAGACAT-GTCTTACACT
1 CGATGCCATGTCCCAGACATAGTCTTACACT
24463113 GGCTTACATC
Statistics
Matches: 150, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
44 9 0.06
45 16 0.11
46 11 0.07
47 36 0.24
48 78 0.52
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATAGTCTTACACTAACACATCTATACGTGC
Found at i:24463122 original size:46 final size:47
Alignment explanation
Indices: 24463039--24463251 Score: 183
Period size: 46 Copynumber: 4.6 Consensus size: 47
24463029 TATACATGCC
* * *
24463039 GATGCCATGTCCCAGACATGGTATTACACTGAC--ACATCTCGTA-GCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGTAGGCT
24463085 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCG-AGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTAGGCT
* * * *** * *
24463131 AATGCATGTCTCAGACATGTCTTACACTAGCTTTTGTCTC-AATGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTAGGCT
* * *
24463177 GATGCCATGTCCCAGATATGGTCTTACACCGGCTCT-CATAAT-GT-GGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGTAGGCT
24463225 GATGCATGT-CCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
24463252 AGCGCACAAA
Statistics
Matches: 136, Mismatches: 22, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
44 11 0.08
45 24 0.18
46 62 0.46
47 17 0.12
48 20 0.15
49 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (47 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGTAGGCT
Found at i:24463186 original size:93 final size:92
Alignment explanation
Indices: 24463085--24463254 Score: 238
Period size: 93 Copynumber: 1.8 Consensus size: 92
24463075 TCTCGTAGCC
* *
24463085 GATGCATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCTAATGCATGTCTCAGAC
1 GATGCATGTCCCAGACATGGTCTTACACCGGCTCT-CATAAT-GAGGCTAATGCATGTC-CAGAC
24463147 ATGTCTTACACTAGCTTTTGTCTCAATGCT
63 ATGTCTTACACTAGCTTTTGTCTCAATGCT
* * *
24463177 GATGCCATGTCCCAGATATGGTCTTACACCGGCTCTCATAATGTGGCTGATGCATGTCCAGACAT
1 GATG-CATGTCCCAGACATGGTCTTACACCGGCTCTCATAATGAGGCTAATGCATGTCCAGACAT
24463242 GTCTTACACTAGC
65 GTCTTACACTAGC
24463255 GCACAAATAA
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
92 4 0.06
93 33 0.48
94 30 0.43
95 2 0.03
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGGTCTTACACCGGCTCTCATAATGAGGCTAATGCATGTCCAGACATG
TCTTACACTAGCTTTTGTCTCAATGCT
Found at i:24467959 original size:42 final size:42
Alignment explanation
Indices: 24467912--24467997 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
24467902 TTTATTCTTA
* *
24467912 TTAATAATATTCAGTTTGAACATACTCTCATACATATACGCT
1 TTAATAATATTAAGTTTGAACATACTCTCATACATATACCCT
* *
24467954 TTAATAATATTAAGTTTGAACATGCTTTCATACATATACCCT
1 TTAATAATATTAAGTTTGAACATACTCTCATACATATACCCT
24467996 TT
1 TT
24467998 TCCCACAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (42 bp):
TTAATAATATTAAGTTTGAACATACTCTCATACATATACCCT
Found at i:24472371 original size:22 final size:22
Alignment explanation
Indices: 24472328--24472371 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
24472318 ATTTCCAAAT
* *
24472328 GAAATCTCATTCCTATTTATAG
1 GAAATCTCATGCCTATTCATAG
* *
24472350 GAAATTTCATGCCTCTTCATAG
1 GAAATCTCATGCCTATTCATAG
24472372 AGACTTCTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (22 bp):
GAAATCTCATGCCTATTCATAG
Found at i:24474366 original size:42 final size:42
Alignment explanation
Indices: 24474309--24474390 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
24474299 TATGATTTGT
* *
24474309 AGATTTTGTTATTTTTATTCTTAAAATCAAATTATGCTTAGA
1 AGATTATGTTATTTTTATTCTTAAAATCAAAATATGCTTAGA
* *
24474351 AGATTATGTTGTTTTTATTTTTAAAATCAAAATATGCTTA
1 AGATTATGTTATTTTTATTCTTAAAATCAAAATATGCTTA
24474391 TAGTTCCATA
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:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (42 bp):
AGATTATGTTATTTTTATTCTTAAAATCAAAATATGCTTAGA
Found at i:24476501 original size:18 final size:18
Alignment explanation
Indices: 24476478--24476516 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24476468 ATAATTGATA
*
24476478 TATTTT-AATTATGCTTAT
1 TATTTTGAATAATG-TTAT
24476496 TATTTTGAATAATGTTAT
1 TATTTTGAATAATGTTAT
24476514 TAT
1 TAT
24476517 ACAGAACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (18 bp):
TATTTTGAATAATGTTAT
Found at i:24477465 original size:20 final size:20
Alignment explanation
Indices: 24477442--24477506 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
24477432 TGTTTTGGAA
24477442 CACACGGTCGTGTCTGATAG
1 CACACGGTCGTGTCTGATAG
** ***
24477462 CACACTGGT-GTGTGAGACCT
1 CACAC-GGTCGTGTCTGATAG
* *
24477482 CACACGGCCGTGTCTGATGG
1 CACACGGTCGTGTCTGATAG
24477502 CACAC
1 CACAC
24477507 TGGCGTGTGA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 2 0.06
20 27 0.84
21 3 0.09
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (20 bp):
CACACGGTCGTGTCTGATAG
Found at i:24477486 original size:40 final size:41
Alignment explanation
Indices: 24477442--24477531 Score: 146
Period size: 40 Copynumber: 2.2 Consensus size: 41
24477432 TGTTTTGGAA
*
24477442 CACACGGTCGTGTCTGATAGCACACTGGTGTGTGAGA-CCT
1 CACACGGTCGTGTCTGATAGCACACTGGCGTGTGAGACCCT
* *
24477482 CACACGGCCGTGTCTGATGGCACACTGGCGTGTGAGACCCT
1 CACACGGTCGTGTCTGATAGCACACTGGCGTGTGAGACCCT
24477523 CACACGGTC
1 CACACGGTC
24477532 ATGTTTGCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 34 0.76
41 11 0.24
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.21
Consensus pattern (41 bp):
CACACGGTCGTGTCTGATAGCACACTGGCGTGTGAGACCCT
Found at i:24477513 original size:20 final size:20
Alignment explanation
Indices: 24477450--24477514 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
24477440 AACACACGGT
24477450 CGTGTCTGATAGCACACTGG
1 CGTGTCTGATAGCACACTGG
* ** ***
24477470 TGTGTGAGACCTCACAC-GG
1 CGTGTCTGATAGCACACTGG
*
24477489 CCGTGTCTGATGGCACACTGG
1 -CGTGTCTGATAGCACACTGG
24477510 CGTGT
1 CGTGT
24477515 GAGACCCTCA
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (20 bp):
CGTGTCTGATAGCACACTGG
Found at i:24479583 original size:51 final size:51
Alignment explanation
Indices: 24479502--24479604 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
24479492 AAAAACTACT
* *
24479502 TCTACAACATATAGAATATAAAACTATCGTATAAAAGATAAAGTCATAAAA
1 TCTAAAACATATAAAATATAAAACTATCGTATAAAAGATAAAGTCATAAAA
*
24479553 TCTAAAACATATAAAATTTAAAACTATCGTATAAAAGATAAAGTCATAAAA
1 TCTAAAACATATAAAATATAAAACTATCGTATAAAAGATAAAGTCATAAAA
24479604 T
1 T
24479605 TCATACTAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.55, C:0.11, G:0.07, T:0.27
Consensus pattern (51 bp):
TCTAAAACATATAAAATATAAAACTATCGTATAAAAGATAAAGTCATAAAA
Found at i:24479802 original size:5 final size:5
Alignment explanation
Indices: 24479792--24479828 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
24479782 ACCTCTGTGA
24479792 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
24479829 GAACACACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:24479812 original size:15 final size:14
Alignment explanation
Indices: 24479792--24479828 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
24479782 ACCTCTGTGA
24479792 AAAATAAAATAAAAT
1 AAAATAAAAT-AAAT
24479807 AAAATAAAATAAAT
1 AAAATAAAATAAAT
24479821 AAAATAAA
1 AAAATAAA
24479829 GAACACACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:24482078 original size:5 final size:5
Alignment explanation
Indices: 24482068--24482099 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
24482058 CAATTTATGA
24482068 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
24482100 GAACATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:24482093 original size:9 final size:9
Alignment explanation
Indices: 24482069--24482099 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
24482059 AATTTATGAA
24482069 AAATAAAAT
1 AAATAAAAT
24482078 AAAATAAAAT
1 -AAATAAAAT
24482088 AAATAAAAT
1 AAATAAAAT
24482097 AAA
1 AAA
24482100 GAACATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:24488325 original size:24 final size:24
Alignment explanation
Indices: 24488281--24488340 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
24488271 AGTAAAATTT
*
24488281 TATTTGTAATAAAATAGGTTAGCTG
1 TATTTGT-ATAAAATAGGTTAACTG
*
24488306 TATTTGTATAAATTTA-GTTAACTG
1 TATTTGTATAAA-ATAGGTTAACTG
24488330 TATTTGTATAA
1 TATTTGTATAA
24488341 GTTACTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (24 bp):
TATTTGTATAAAATAGGTTAACTG
Found at i:24489552 original size:15 final size:15
Alignment explanation
Indices: 24489534--24489566 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
24489524 AATAACTATG
24489534 TTCAAA-ATTATGAAT
1 TTCAAATATTAT-AAT
24489549 TTCAAATATTATAAT
1 TTCAAATATTATAAT
24489564 TTC
1 TTC
24489567 TAAACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (15 bp):
TTCAAATATTATAAT
Found at i:24491823 original size:13 final size:13
Alignment explanation
Indices: 24491786--24491841 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
24491776 AATAACAAAA
24491786 AGAAAATATATAAT
1 AGAAAATA-ATAAT
24491800 -GTAATAATAATAAT
1 AG-AA-AATAATAAT
24491814 AGAAAATAATAAT
1 AGAAAATAATAAT
24491827 A-AAAATAAATAAT
1 AGAAAAT-AATAAT
24491840 AG
1 AG
24491842 GGATAATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.14
13 18 0.49
14 9 0.24
15 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (13 bp):
AGAAAATAATAAT
Found at i:24491825 original size:19 final size:18
Alignment explanation
Indices: 24491801--24491873 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
24491791 ATATATAATG
24491801 TAATAATAATAATAGAAAA
1 TAATAATAATAATA-AAAA
*
24491820 TAATAATAAAAATAAATAA
1 TAATAATAATAATAAA-AA
*** *
24491839 TAGGGATAATAGTAAACAA
1 TAATAATAATAATAAA-AA
24491858 -AATAATAATAATAAAA
1 TAATAATAATAATAAAA
24491874 GACAAACAAC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
17 1 0.02
18 13 0.31
19 28 0.67
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (18 bp):
TAATAATAATAATAAAAA
Found at i:24491836 original size:16 final size:16
Alignment explanation
Indices: 24491802--24491840 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
24491792 TATATAATGT
*
24491802 AATAATAATAATAGAA
1 AATAATAATAATAAAA
24491818 AATAATAATAA-AAATA
1 AATAATAATAATAAA-A
24491834 AATAATA
1 AATAATA
24491841 GGGATAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AATAATAATAATAAAA
Found at i:24499760 original size:28 final size:28
Alignment explanation
Indices: 24499725--24499782 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
24499715 CTATATAGAT
*
24499725 AATAGATTTGAAAGGAAA-TATAAATATA
1 AATAGATTT-AAAAGAAATTATAAATATA
*
24499753 AATAGATTTAAAAGAAATTATATATATA
1 AATAGATTTAAAAGAAATTATAAATATA
24499781 AA
1 AA
24499783 ATAACATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (28 bp):
AATAGATTTAAAAGAAATTATAAATATA
Found at i:24499881 original size:23 final size:26
Alignment explanation
Indices: 24499855--24499909 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
24499845 ATTTAAATGA
24499855 AATAT-TATACAA-AA-TTTTAAAAC
1 AATATATATACAAGAAGTTTTAAAAC
*
24499878 AATATGATATACAAGAATGTTTTAAAAT
1 AATAT-ATATACAAGAA-GTTTTAAAAC
24499906 AATA
1 AATA
24499910 ATGATATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 5 0.19
25 7 0.27
26 2 0.08
28 12 0.46
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (26 bp):
AATATATATACAAGAAGTTTTAAAAC
Found at i:24500672 original size:13 final size:13
Alignment explanation
Indices: 24500654--24500680 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24500644 CATGCGAAAG
24500654 AGGAAAACTAAAA
1 AGGAAAACTAAAA
24500667 AGGAAAACTAAAA
1 AGGAAAACTAAAA
24500680 A
1 A
24500681 CATTTAGAAA
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:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (13 bp):
AGGAAAACTAAAA
Found at i:24503742 original size:26 final size:26
Alignment explanation
Indices: 24503712--24503923 Score: 352
Period size: 26 Copynumber: 8.2 Consensus size: 26
24503702 ACTTGATATC
24503712 TTAGGTAAATATTCCATGATAATGGG
1 TTAGGTAAATATTCCATGATAATGGG
* *
24503738 TTAGGTAAATGTTCCATGATAATGGA
1 TTAGGTAAATATTCCATGATAATGGG
24503764 TTAGGTAAATATTCCATGATAATGGG
1 TTAGGTAAATATTCCATGATAATGGG
* *
24503790 TTAGGTAAATGTTCCATGATAATGGA
1 TTAGGTAAATATTCCATGATAATGGG
24503816 TTAGGTAAATATTCCATGATAATGGG
1 TTAGGTAAATATTCCATGATAATGGG
* *
24503842 TTAGGTAAATGTTCCATGATAATGGA
1 TTAGGTAAATATTCCATGATAATGGG
24503868 TTAGGTAAATATTCCATGATAATGGG
1 TTAGGTAAATATTCCATGATAATGGG
* *
24503894 TTAGGTAAATGTTCCATGATAATGGT
1 TTAGGTAAATATTCCATGATAATGGG
24503920 TTAG
1 TTAG
24503924 ATACCATTGG
Statistics
Matches: 172, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 172 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (26 bp):
TTAGGTAAATATTCCATGATAATGGG
Found at i:24503780 original size:52 final size:52
Alignment explanation
Indices: 24503712--24503923 Score: 415
Period size: 52 Copynumber: 4.1 Consensus size: 52
24503702 ACTTGATATC
24503712 TTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGA
1 TTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGA
24503764 TTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGA
1 TTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGA
24503816 TTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGA
1 TTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGA
*
24503868 TTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGT
1 TTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGA
24503920 TTAG
1 TTAG
24503924 ATACCATTGG
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 159 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (52 bp):
TTAGGTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCATGATAATGGA
Found at i:24504437 original size:26 final size:26
Alignment explanation
Indices: 24504408--24504463 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
24504398 TGGTACAAAT
24504408 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
24504434 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
24504460 TGAT
1 TGAT
24504464 TGGCATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:24506102 original size:27 final size:27
Alignment explanation
Indices: 24506062--24506256 Score: 222
Period size: 27 Copynumber: 7.2 Consensus size: 27
24506052 AGGAAACGTC
*
24506062 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
24506089 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
24506115 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
24506143 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
24506169 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
* **
24506197 CTGGTGGCTCTACCAC-ATATATCTTTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* *
24506224 ATGGTGGCTCTGCCATAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
24506251 CTGGTG
1 CTGGTG
24506257 ACTTCGTCAC
Statistics
Matches: 143, Mismatches: 14, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
26 13 0.09
27 123 0.86
28 7 0.05
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:24506141 original size:54 final size:54
Alignment explanation
Indices: 24506059--24506256 Score: 326
Period size: 54 Copynumber: 3.7 Consensus size: 54
24506049 TGGAGGAAAC
24506059 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
24506113 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
*
24506167 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* ** * *
24506221 TTTATGGTGGCTCTGCCATAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
24506257 ACTTCGTCAC
Statistics
Matches: 137, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
53 6 0.04
54 131 0.96
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:24516859 original size:3 final size:3
Alignment explanation
Indices: 24516851--24516880 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
24516841 CTTTCAAAAA
*
24516851 ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24516881 TGCAATATAC
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:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:24524603 original size:25 final size:25
Alignment explanation
Indices: 24524544--24524603 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
24524534 AACCACGCCT
* *
24524544 TTGTGGTGAACTCTCTATAAAGCCC
1 TTGTGGCGAACTCTCTATAAAGCCA
* * * *
24524569 TTATGACGAACTCTCTGTAAAGTCA
1 TTGTGGCGAACTCTCTATAAAGCCA
24524594 TTGTGGCGAA
1 TTGTGGCGAA
24524604 TTCTTTGAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (25 bp):
TTGTGGCGAACTCTCTATAAAGCCA
Found at i:24526999 original size:21 final size:20
Alignment explanation
Indices: 24526956--24527008 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
24526946 AAATAATATT
24526956 AATATATAAATAGAAATAGA
1 AATATATAAATAGAAATAGA
24526976 AATATAATAAATAGAAAT-GTA
1 AATAT-ATAAATAGAAATAG-A
*
24526997 AATAGATAAATA
1 AATATATAAATA
24527009 ATAATAGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
AATATATAAATAGAAATAGA
Found at i:24528362 original size:44 final size:43
Alignment explanation
Indices: 24528286--24528456 Score: 146
Period size: 44 Copynumber: 3.9 Consensus size: 43
24528276 AAGAATTGCT
** * *
24528286 GCTTCAATCTGCTCCACTTTATCCTCAAGGAGATTAGACTCGTA
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATTAGACT-GTA
* * ** *
24528330 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATGGGA-TTTA
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATTAGACTGTA
* * * * *
24528372 CTGTCTTCAGTCTGCTCCGCTGTAACTTCAAGGAGATAAGACTGGTG
1 --G-CTTCAATCTGCTCCACTGCAACTTCAAGGAGATTAGACT-GTA
* *
24528419 GCTTCAATCTGTTCCACTGCAACTTCAAGAAGATTAGA
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATTAGA
24528457 TCCGCCATAA
Statistics
Matches: 98, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 62 0.63
45 31 0.32
46 1 0.01
47 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (43 bp):
GCTTCAATCTGCTCCACTGCAACTTCAAGGAGATTAGACTGTA
Found at i:24528589 original size:44 final size:44
Alignment explanation
Indices: 24528534--24528639 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
24528524 GTCTGCTCTG
*
24528534 CTGCAATTTCAGGGAGATGAGGCTATTGGCTTCAATCTACTCCA
1 CTGCAACTTCAGGGAGATGAGGCTATTGGCTTCAATCTACTCCA
* * ** *
24528578 CTGCAACTTCAGGGAGATGAGGTTGTTGGCTTTTATCTGCTCCA
1 CTGCAACTTCAGGGAGATGAGGCTATTGGCTTCAATCTACTCCA
* * *
24528622 CCGCAACTTTAGGAAGAT
1 CTGCAACTTCAGGGAGAT
24528640 AAGATCCGCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.30
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATGAGGCTATTGGCTTCAATCTACTCCA
Found at i:24528874 original size:45 final size:45
Alignment explanation
Indices: 24528799--24528966 Score: 171
Period size: 45 Copynumber: 3.8 Consensus size: 45
24528789 TTGTAGCTTT
*
24528799 AATCTGTTCCACTGCAA-TGTCAGGGAAATAAGATTCGCTGTCTTC
1 AATCTGCTCCACTGCAACT-TCAGGGAAATAAGATTCGCTGTCTTC
* * * ** * *
24528844 AGTTTGCTCCGCTGCAACTTCAGGGAAATAAGGCT-GGTGGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTGTCTTC
*
24528888 AATCTGCTCCACTGCAACTTCA-GGAAGATAAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAA-ATAAGATTCGCTGTCTTC
* * * * *
24528933 GATCTGCTCCATTGCAGCTTCAAGGAGATAAGAT
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGAT
24528967 CTACAACTTC
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
43 4 0.04
44 32 0.32
45 59 0.60
46 4 0.04
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTGTCTTC
Found at i:24528954 original size:89 final size:89
Alignment explanation
Indices: 24528794--24528964 Score: 213
Period size: 89 Copynumber: 1.9 Consensus size: 89
24528784 ATAATTTGTA
* * * * *
24528794 GCTTTAATCTGTTCCACTGCAATGTCAGGGAAATAAGATTCGCTGTCTTCAGTTTGCTCCGCTGC
1 GCTTCAATCTGCTCCACTGCAATGTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGC
*
24528859 AACTTCAGGGAAATAAGGCTGGTG
66 AACTTCAAGGAAATAAGGCTGGTG
*
24528883 GCTTCAATCTGCTCCACTGCAACT-TCA-GGAAGATAAGATTCGCTATCTTC-GATCTGCTCCAT
1 GCTTCAATCTGCTCCACTGCAA-TGTCAGGGAA-ATAAGATTCGCTATCTTCAG-TCTGCTCCAC
* *
24528945 TGCAGCTTCAAGGAGATAAG
63 TGCAACTTCAAGGAAATAAG
24528965 ATCTACAACT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
88 5 0.07
89 64 0.91
90 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (89 bp):
GCTTCAATCTGCTCCACTGCAATGTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGC
AACTTCAAGGAAATAAGGCTGGTG
Done.