Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 67 of 208
Found at i:19459383 original size:26 final size:26
Alignment explanation
Indices: 19459307--19459375 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
19459297 CCCAACAAAA
*
19459307 TTTTGACAATTTTACCCATGGTAAAG
1 TTTTGACGATTTTACCCATGGTAAAG
* * *
19459333 TTTTGATGATTTTACACGTGGTAAAG
1 TTTTGACGATTTTACCCATGGTAAAG
19459359 TTTTGACGATTTTACCC
1 TTTTGACGATTTTACCC
19459376 TTAGTAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (26 bp):
TTTTGACGATTTTACCCATGGTAAAG
Found at i:19463641 original size:27 final size:27
Alignment explanation
Indices: 19463603--19463664 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
19463593 ATAAACTATT
19463603 GGCCCGATTCTTTCAGTGATCTCATAC
1 GGCCCGATTCTTTCAGTGATCTCATAC
19463630 GGCCCGATTCTTTCAGTGATCTCATAC
1 GGCCCGATTCTTTCAGTGATCTCATAC
19463657 GGCCCGAT
1 GGCCCGAT
19463665 AAAATGCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.18, C:0.31, G:0.21, T:0.31
Consensus pattern (27 bp):
GGCCCGATTCTTTCAGTGATCTCATAC
Found at i:19467898 original size:3 final size:3
Alignment explanation
Indices: 19467890--19467991 Score: 134
Period size: 3 Copynumber: 34.0 Consensus size: 3
19467880 ACTGTTTCTC
*
19467890 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
19467938 ATT ACT ATT ATT ATT ATT ATT ATT ATC ATC ATT TTT GTT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
19467984 -TT ATT ATT
1 ATT ATT ATT
19467992 TATTTCATTT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.02
3 83 0.94
4 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19473623 original size:92 final size:87
Alignment explanation
Indices: 19473492--19473654 Score: 202
Period size: 92 Copynumber: 1.8 Consensus size: 87
19473482 CTGAAGATAG
* * ** * *
19473492 CAAATCTTATTTCCCTGAAGTTGCGATGGAGTAGATTAAAGCTATAAATTACAAATCTTATCTCT
1 CAAACCTTATCTCCCTGAAGTTGCGATGGAACAGATTAAA--AAT-AA--ACAAATCTTATCTCC
19473557 CTGAAGTTGCAGTAGAGCATATCATAT
61 CTGAAGTTGCAGTAGAGCATATCATAT
*
19473584 CAAACCTTATCTCCCTGAAGTTGC-AGTGGAACAGGTTAAAAATAAACAAATCTTATCTCCCTGA
1 CAAACCTTATCTCCCTGAAGTTGCGA-TGGAACAGATTAAAAATAAACAAATCTTATCTCCCTGA
19473648 AGTTGCA
65 AGTTGCA
19473655 ATGGAACAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
87 25 0.40
89 2 0.03
90 2 0.03
91 1 0.02
92 33 0.52
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (87 bp):
CAAACCTTATCTCCCTGAAGTTGCGATGGAACAGATTAAAAATAAACAAATCTTATCTCCCTGAA
GTTGCAGTAGAGCATATCATAT
Found at i:19473700 original size:49 final size:46
Alignment explanation
Indices: 19473584--19473886 Score: 290
Period size: 49 Copynumber: 6.5 Consensus size: 46
19473574 CATATCATAT
* * ***
19473584 CAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATAAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAAGCCA
* *
19473630 CAAATCTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGACAAGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATT-AA-A-AAGCCA
* * *
19473679 CATATCTTATCTCCCTGAAGTTGCAGTGAAATAGATT--AAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAAGCCA
* * * ***
19473723 CAAACCTTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAAGCCA
* * * * ** *
19473769 CCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGATGGGCTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATT-AA-A-AAGCCA
* *
19473818 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATT--AAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAAGCCA
*
19473862 CAAACCTTATCTCCCTGAAGTTGCA
1 CAAATCTTATCTCCCTGAAGTTGCA
19473887 TTAGAGCAGG
Statistics
Matches: 208, Mismatches: 41, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
44 62 0.30
45 2 0.01
46 68 0.33
47 4 0.02
48 2 0.01
49 70 0.34
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (46 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAAGCCA
Found at i:19473837 original size:95 final size:92
Alignment explanation
Indices: 19473589--19473886 Score: 266
Period size: 95 Copynumber: 3.2 Consensus size: 92
19473579 CATATCAAAC
* ** *** *
19473589 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAATAAACAAATCTTATCTCCCTGAAGTTGC
1 CTTATCTCCCTGAAGTTGCAGTGAAACAAATT--AAAGCCACAAATCTTATCTCCCTGAAGTTAC
* * * *
19473654 AATGGAACAGATTGAAGACAAGCTACATAT
64 AGTGGAACAGATTAAAAACAAAC-ACATAT
* * *
19473684 CTTATCTCCCTGAAGTTGCAGTGAAATAGATTAAAGCCACAAACCTTATCTCCCTGAAGTTACAG
1 CTTATCTCCCTGAAGTTGCAGTGAAACAAATTAAAGCCACAAATCTTATCTCCCTGAAGTTACAG
* *
19473749 TGGAACAGGTTAAAAATAAAC-CA-AT
66 TGGAACAGATTAAAAACAAACACATAT
* * * *
19473774 CTTATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGATGGGCTACAAATCTTATCTCCCTGAAGT
1 CTTATCTCCCTGAAGTTGCAGTGAAACAAATT-AA-A---GCCACAAATCTTATCTCCCTGAAGT
* * * *
19473839 TACAGTGGAGCAGATT-AAAGC---CACAAAC
61 TACAGTGGAACAGATTAAAAACAAACACATAT
19473867 CTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCA
19473887 TTAGAGCAGG
Statistics
Matches: 169, Mismatches: 27, Indels: 16
0.80 0.13 0.08
Matches are distributed among these distances:
90 29 0.17
91 5 0.03
92 3 0.02
93 63 0.37
94 3 0.02
95 66 0.39
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (92 bp):
CTTATCTCCCTGAAGTTGCAGTGAAACAAATTAAAGCCACAAATCTTATCTCCCTGAAGTTACAG
TGGAACAGATTAAAAACAAACACATAT
Found at i:19473894 original size:44 final size:44
Alignment explanation
Indices: 19473541--19473989 Score: 350
Period size: 44 Copynumber: 10.0 Consensus size: 44
19473531 AGCTATAAAT
* * * * *
19473541 TACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCATATCATA--
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * * **
19473583 T-CAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* *
19473626 TAAACAAATCTTATCTCCCTGAAGTTGCAATGGAACAGATTGAAGACAAGC
1 T--ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT----A-AAGC
* * **
19473677 TACATATCTTATCTCCCTGAAGTTGCAGTGAAATAGATTAAAGC
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * * * * **
19473721 CACAAACCTTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * *
19473765 TAAACCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGATGGGC
1 T--ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-A---GC
*
19473816 TACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGC
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * * * * * *
19473860 CACAAACCTTATCTCCCTGAAGTTGCATTAGAGCAGGTTGAAGA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
** * *
19473904 TACCTATCTTATCTCCCT-ACAGTTTCAGTGGAGCATATTAAAGC
1 TACAAATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTAAAGC
* * *
19473948 TACTAAT-TCTATCTCCCTGAAGTTGCAGTGCAGCGGATTAAA
1 TACAAATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
19473990 ACGATGAATC
Statistics
Matches: 322, Mismatches: 65, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
41 32 0.10
42 1 0.00
43 3 0.01
44 140 0.43
45 2 0.01
46 65 0.20
47 3 0.01
48 3 0.01
49 68 0.21
50 1 0.00
51 4 0.01
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (44 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
Found at i:19473897 original size:139 final size:136
Alignment explanation
Indices: 19473541--19473989 Score: 504
Period size: 139 Copynumber: 3.3 Consensus size: 136
19473531 AGCTATAAAT
* * * * * *
19473541 TACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCATATCATA---TCAAACCTTATCTCCCTGAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAA
* * * * *
19473603 GTTGCAGTGGAACAGGTTAAAAATAAACAAATCTTATCTCCCTGAAGTTGCAATGGAACAGATTG
66 GTTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTG
19473668 AAGACAAGC
131 AAG---AGC
* * **
19473677 TACATATCTTATCTCCCTGAAGTTGCAGTGAAATAGATTAAAGCCACAAACCTTATCTCCCTGAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAA
*
19473742 GTTACAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTG
66 GTTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTG
19473807 AAGATGGGC
131 AAGA---GC
*
19473816 TACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAA
* * * * * * *
19473881 GTTGCATTAGAGCAGGTTGAAGAT--ACCTATCTTATCTCCCT-ACAGTT-TCAGTGGAGCATAT
66 GTTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGA-AGTTGT-AGTGGAGCAAAT
19473942 T-AA-AGC
129 TGAAGAGC
* * *
19473948 TACTAAT-TCTATCTCCCTGAAGTTGCAGTGCAGCGGATTAAA
1 TACAAATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
19473990 ACGATGAATC
Statistics
Matches: 271, Mismatches: 33, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
131 1 0.00
132 38 0.14
135 1 0.00
136 38 0.14
137 32 0.12
139 161 0.59
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (136 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTGAA
GTTGCAGTGGAACAGGTTAAAAATAAACCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTG
AAGAGC
Found at i:19479368 original size:37 final size:36
Alignment explanation
Indices: 19479306--19479379 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
19479296 TGGATGGCAT
*
19479306 TAATATGTATGTTATATATATGTTATA-ATAATAAA
1 TAATATGAATGTTATATATATGTTATATATAATAAA
19479341 TAATATGAAATGTGTATATATATGTTATATTATAATAAA
1 TAATATG-AATGT-TATATATATGTTATA-TATAATAAA
19479380 AACAAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
35 7 0.21
36 4 0.12
37 15 0.44
39 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (36 bp):
TAATATGAATGTTATATATATGTTATATATAATAAA
Found at i:19496289 original size:13 final size:14
Alignment explanation
Indices: 19496258--19496289 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
19496248 TAGCCATTTT
19496258 TATTTTTCTTTTAA
1 TATTTTTCTTTTAA
19496272 TATTTTTCTTTTAA
1 TATTTTTCTTTTAA
19496286 -ATTT
1 TATTT
19496290 AATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTTTCTTTTAA
Found at i:19499509 original size:22 final size:23
Alignment explanation
Indices: 19499466--19499523 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
19499456 CTGAGTTGGT
*
19499466 AAACGGTAAGCTCTATCAAGCT-
1 AAACGGTAAGCTCCATCAAGCTA
* *
19499488 GAACGGTAAGCTCCGT-AGAGCTA
1 AAACGGTAAGCTCCATCA-AGCTA
19499511 AAACGGTAAGCTC
1 AAACGGTAAGCTC
19499524 ATAAGAGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 17 0.57
23 12 0.40
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.19
Consensus pattern (23 bp):
AAACGGTAAGCTCCATCAAGCTA
Found at i:19499530 original size:23 final size:22
Alignment explanation
Indices: 19499465--19499555 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
19499455 CCTGAGTTGG
*
19499465 TAAACGGTAAGCTCTATCA-AGC
1 TAAACGGTAAGCTC-ATAAGAGC
* *
19499487 TGAACGGTAAGCTCCGT-AGAGC
1 TAAACGGTAAGCT-CATAAGAGC
*
19499509 TAAAACGGTAAGCTCATAAGAGT
1 T-AAACGGTAAGCTCATAAGAGC
* *
19499532 TGAAACGATAAGCTCATACGAGC
1 T-AAACGGTAAGCTCATAAGAGC
19499555 T
1 T
19499556 GTGGTGGGTC
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.02
22 19 0.34
23 36 0.64
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (22 bp):
TAAACGGTAAGCTCATAAGAGC
Found at i:19502040 original size:17 final size:17
Alignment explanation
Indices: 19502018--19502052 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
19502008 GACCATGTTA
19502018 TAATTTCTTTGATATTT
1 TAATTTCTTTGATATTT
* *
19502035 TAATTTTTTTTATATTT
1 TAATTTCTTTGATATTT
19502052 T
1 T
19502053 TCAAAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TAATTTCTTTGATATTT
Found at i:19507378 original size:3 final size:3
Alignment explanation
Indices: 19507370--19507407 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
19507360 ATAAGGAAAC
19507370 AAT AAT AAT AA- AAT AAT AAT AAT AGATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT A
19507408 TTAAACTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 26 0.81
4 2 0.06
5 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19507384 original size:11 final size:12
Alignment explanation
Indices: 19507370--19507407 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
19507360 ATAAGGAAAC
19507370 AATAATAATAA-
1 AATAATAATAAT
19507381 AATAATAATAAT
1 AATAATAATAAT
19507393 AGATTAATAATAAT
1 A-A-TAATAATAAT
19507407 A
1 A
19507408 TTAAACTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 1 0.04
13 1 0.04
14 11 0.46
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AATAATAATAAT
Found at i:19507387 original size:14 final size:14
Alignment explanation
Indices: 19507370--19507407 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
19507360 ATAAGGAAAC
19507370 AATAATAATAAAAT
1 AATAATAATAAAAT
* *
19507384 AATAATAATAGATT
1 AATAATAATAAAAT
19507398 AATAATAATA
1 AATAATAATA
19507408 TTAAACTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:19508952 original size:50 final size:50
Alignment explanation
Indices: 19508897--19509305 Score: 378
Period size: 50 Copynumber: 8.2 Consensus size: 50
19508887 AACTTATTTA
*
19508897 ACTGCAATGTTGGGGAAGCAAGATTCGCAGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* ** * * * **
19508947 ACTGCACTACCT-GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTT
1 ACTGCAAT-GTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* * **
19508997 ACTGCAATGTCGGGGAAGCAAGATTCACCATTGTAGCTTCAAT-TAGTTCC
1 ACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCT-GTTCC
* * * * * * **
19509047 ACTGCACTGCCT-AGGAAGTAAGATTCGCTATTGTAGCTTCAATCTTTTTA
1 ACTGCAATG-TTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* *
19509097 ACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCC
1 ACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* * * * * * * **
19509147 ATTGTACT-TCCT-GGGAAGTAAGATTCGCTGTTGTAGCTTCATTATTTTTA
1 ACTGCAATGT--TGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* * * *
19509197 ACTACAATGTTGGGGAAGCAAGATTCACCGTTGTAGCTTCAACCTGTTCC
1 ACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* * *
19509247 ACTGTAATATGGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
*
19509297 ACTGTAATG
1 ACTGCAATG
19509306 CCAAAGAGAT
Statistics
Matches: 278, Mismatches: 71, Indels: 20
0.75 0.19 0.05
Matches are distributed among these distances:
49 3 0.01
50 272 0.98
51 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (50 bp):
ACTGCAATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
Found at i:19509017 original size:100 final size:100
Alignment explanation
Indices: 19508877--19509291 Score: 557
Period size: 100 Copynumber: 4.2 Consensus size: 100
19508867 GAGATAAGAC
*
19508877 TTGTAGCTTCAA-CTTATTTAACTGCAATGTTGGGGAAGCAAGATTCGCAGTTGTAGCTTCAATC
1 TTGTAGCTTCAATCTT-TTTAACTGCAATGTCGGGGAAGCAAGATTCGCAGTTGTAGCTTCAATC
19508941 TGTTCCACTGCACTACCTGGGAAGTAAGATTCGCTG
65 TGTTCCACTGCACTACCTGGGAAGTAAGATTCGCTG
* * *
19508977 TTGTAGCTTTAATCTTTTTTACTGCAATGTCGGGGAAGCAAGATTCACCA-TTGTAGCTTCAAT-
1 TTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTC-GCAGTTGTAGCTTCAATC
* * *
19509040 TAGTTCCACTGCACTGCCTAGGAAGTAAGATTCGCTA
65 T-GTTCCACTGCACTACCTGGGAAGTAAGATTCGCTG
*
19509077 TTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCAGTTGTAGCTTCAATCT
* * * *
19509142 ATTCCATTGTACTTCCTGGGAAGTAAGATTCGCTG
66 GTTCCACTGCACTACCTGGGAAGTAAGATTCGCTG
* * * * * * *
19509177 TTGTAGCTTCATTATTTTTAACTACAATGTTGGGGAAGCAAGATTCACCGTTGTAGCTTCAACCT
1 TTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCAGTTGTAGCTTCAATCT
* * *** *
19509242 GTTCCACTGTAATATGGGGGAAGCAAGATTCGCTG
66 GTTCCACTGCACTACCTGGGAAGTAAGATTCGCTG
19509277 TTGTAGCTTCAATCT
1 TTGTAGCTTCAATCT
19509292 GTTCCACTGT
Statistics
Matches: 276, Mismatches: 34, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
99 2 0.01
100 268 0.97
101 6 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (100 bp):
TTGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCAGTTGTAGCTTCAATCT
GTTCCACTGCACTACCTGGGAAGTAAGATTCGCTG
Found at i:19509322 original size:150 final size:149
Alignment explanation
Indices: 19508877--19509326 Score: 419
Period size: 150 Copynumber: 3.0 Consensus size: 149
19508867 GAGATAAGAC
19508877 TTGTAGCTTCA--ACTTATTTAACTGCAATGTTGGGGAAGCAAGATTCGCAGTTGTAGCTTCAAT
1 TTGTAGCTTCATTA-TT-TTTAACTGCAATGTTGGGGAAGCAAGATTCGCAGTTGTAGCTTCAAT
* * * * * * ** *
19508940 CTGTTCCACTGCACTACCTGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTTACTGCAAT
64 CTGTTCCACTGCAATATCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCACTGTAAT
* * * *
19509005 GTCGGGGAAGCA-AGATTCACCA
129 GCCAGGG-AG-ATAGATTCGCTA
* ** * * * *
19509027 TTGTAGCTTCAATTA-GTTCCACTGCACTGCCT-AGGAAGTAAGATTCGCTA-TTGTAGCTTCAA
1 TTGTAGCTTC-ATTATTTTTAACTGCAATG-TTGGGGAAGCAAGATTCGC-AGTTGTAGCTTCAA
* ** * * *
19509089 TCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCATTGTAC
63 TCTGTTCCACTGCAATATCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCACTGTAA
* * *
19509154 TTCCTGGGA-AGTAAGATTCGCTG
128 TGCCAGGGAGA-T-AGATTCGCTA
* * * *
19509177 TTGTAGCTTCATTATTTTTAACTACAATGTTGGGGAAGCAAGATTCACCGTTGTAGCTTCAACCT
1 TTGTAGCTTCATTATTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCAGTTGTAGCTTCAATCT
* * *
19509242 GTTCCACTGTAATATGGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGTAATGC
66 GTTCCACTGCAATATCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCACTGTAATGC
**
19509307 CAAAGAGATAGGATTCGCTA
131 CAGGGAGATA-GATTCGCTA
19509327 CCCACAGCTT
Statistics
Matches: 234, Mismatches: 53, Indels: 26
0.75 0.17 0.08
Matches are distributed among these distances:
147 1 0.00
149 7 0.03
150 221 0.94
151 4 0.02
153 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (149 bp):
TTGTAGCTTCATTATTTTTAACTGCAATGTTGGGGAAGCAAGATTCGCAGTTGTAGCTTCAATCT
GTTCCACTGCAATATCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTATTCCACTGTAATGC
CAGGGAGATAGATTCGCTA
Found at i:19517191 original size:3 final size:3
Alignment explanation
Indices: 19517183--19517223 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
19517173 ATAAGGAAAC
*
19517183 AAT AAT AAT AAT AA- AAT AAT AAT AAT -AT ATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19517224 TTAAACTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:19517203 original size:17 final size:17
Alignment explanation
Indices: 19517183--19517223 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
19517173 ATAAGGAAAC
19517183 AATAATAATA-ATAAAAT
1 AATAATAATATAT-AAAT
*
19517200 AATAATAATATATTAAT
1 AATAATAATATATAAAT
19517217 AATAATA
1 AATAATA
19517224 TTAAACTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAATAATATATAAAT
Found at i:19517224 original size:14 final size:14
Alignment explanation
Indices: 19517183--19517224 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
19517173 ATAAGGAAAC
*
19517183 AATAATAATAATAA
1 AATAATAATAATAT
19517197 AATAATAATAATAT
1 AATAATAATAATAT
*
19517211 ATTAATAATAATAT
1 AATAATAATAATAT
19517225 TAAACTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAATAATAATAT
Found at i:19521011 original size:30 final size:30
Alignment explanation
Indices: 19520977--19521037 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
19520967 ACATTTGAGG
* *
19520977 TAGATTCTTAAGTATTATGTGACACAGGTT
1 TAGATTCTCAAGTATTATGTGACAAAGGTT
19521007 TAGATTCTCAAGTATTATGTGACAAAGGTT
1 TAGATTCTCAAGTATTATGTGACAAAGGTT
19521037 T
1 T
19521038 GGCTCGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (30 bp):
TAGATTCTCAAGTATTATGTGACAAAGGTT
Found at i:19524077 original size:43 final size:43
Alignment explanation
Indices: 19524016--19524106 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
19524006 CATAGGATCT
* **
19524016 TCGATATGTGTTTTTGTGTAAGACCAC-GTTTGGGACTTTGGCA
1 TCGATATGTGTTTTTGTGTAAGACC-CTGTCTGGGACAGTGGCA
*
19524059 TCGATTTGTGTTTTTGTGTAAGACCCTGTCTGGGACAGTGGCA
1 TCGATATGTGTTTTTGTGTAAGACCCTGTCTGGGACAGTGGCA
19524102 TCGAT
1 TCGAT
19524107 CTATGAATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 1 0.02
43 42 0.98
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.38
Consensus pattern (43 bp):
TCGATATGTGTTTTTGTGTAAGACCCTGTCTGGGACAGTGGCA
Found at i:19526807 original size:36 final size:36
Alignment explanation
Indices: 19526760--19526837 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
19526750 TGTATTTTCT
*
19526760 ATATTGCTCTAAAATGAATTGAAACTTAATGGTTTG
1 ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
19526796 ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
1 ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
*
19526832 CTATTG
1 ATATTG
19526838 GAACGTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (36 bp):
ATATTGCTCTAAAATGAATTGAAACTTAATGGTATG
Found at i:19536949 original size:24 final size:24
Alignment explanation
Indices: 19536922--19536973 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
19536912 TTAGTAAGTC
*
19536922 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
19536946 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
19536970 AAAT
1 AAAT
19536974 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:19538846 original size:14 final size:14
Alignment explanation
Indices: 19538829--19538856 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19538819 CTCACATTTC
19538829 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
19538843 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
19538857 GATTTCTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:19538943 original size:18 final size:17
Alignment explanation
Indices: 19538920--19538955 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19538910 CTGTAAAATC
19538920 GATTTTGATTTTGATTTT
1 GATTTTG-TTTTGATTTT
*
19538938 GATTTTGTTTTGCTTTT
1 GATTTTGTTTTGATTTT
19538955 G
1 G
19538956 CTCTGCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.11, C:0.03, G:0.19, T:0.67
Consensus pattern (17 bp):
GATTTTGTTTTGATTTT
Found at i:19538957 original size:6 final size:6
Alignment explanation
Indices: 19538920--19538955 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
19538910 CTGTAAAATC
*
19538920 GATTTT GATTTT GATTTT GATTTT G-TTTT GCTTTT G
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT G
19538956 CTCTGCTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.11, C:0.03, G:0.19, T:0.67
Consensus pattern (6 bp):
GATTTT
Found at i:19540552 original size:17 final size:17
Alignment explanation
Indices: 19540532--19540566 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
19540522 ATATTAAGAA
19540532 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
19540549 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
19540566 T
1 T
19540567 AATAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:19540814 original size:34 final size:34
Alignment explanation
Indices: 19540751--19540817 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
19540741 CAAGAATACT
* *
19540751 ATTACGCCTCTGTTCCATTACATTCAACCAAACA
1 ATTACGCCTCTATTCCATTACATGCAACCAAACA
19540785 ATTACGCCTCTATTCCATTACA-GCGAACCAAAC
1 ATTACGCCTCTATTCCATTACATGC-AACCAAAC
19540818 GTGCCCTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 1 0.03
34 29 0.97
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.27
Consensus pattern (34 bp):
ATTACGCCTCTATTCCATTACATGCAACCAAACA
Found at i:19541345 original size:39 final size:40
Alignment explanation
Indices: 19541290--19541365 Score: 136
Period size: 39 Copynumber: 1.9 Consensus size: 40
19541280 TAAAATTATC
19541290 TTTTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTTTAG
1 TTTTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTTTAG
*
19541330 TTTTTTTTTT-TCTCTCATTTTATTTTCAAAGAGTTT
1 TTTTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTT
19541366 CCAAATATGC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 25 0.71
40 10 0.29
ACGTcount: A:0.17, C:0.13, G:0.07, T:0.63
Consensus pattern (40 bp):
TTTTTTTTTTCTCTCTCATTTTATTTCCAAAGAGTTTTAG
Found at i:19541517 original size:26 final size:25
Alignment explanation
Indices: 19541470--19541527 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
19541460 CGAACAAATT
* *
19541470 TATTTGACTCAACTCAATTCGAATA
1 TATTTCACTCAACTCAATTCGAAAA
*
19541495 TCATTTCACTCAACTTGAA-TCGAAAA
1 T-ATTTCACTCAAC-TCAATTCGAAAA
19541521 TATTTCA
1 TATTTCA
19541528 AATCAAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.25
26 18 0.64
27 3 0.11
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (25 bp):
TATTTCACTCAACTCAATTCGAAAA
Found at i:19547057 original size:50 final size:50
Alignment explanation
Indices: 19546961--19547195 Score: 197
Period size: 50 Copynumber: 4.6 Consensus size: 50
19546951 AGATCACATC
* * *
19546961 TAAGACCATGTCTGGGACATTGCATTGGCATCATTGAGGTTATGAGATGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATGAGAAGTCCCATG
* * **
19547017 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCCCATG
* * * *
19547067 TAAAACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCCCATG
* * * * * * * *
19547117 TAAGACCATATCTAGGATATGACATTGGTA--GTACAAGA-AACATCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAA-GTCCCATG
*
19547166 TAAGACCATGTCTGGGACATGGCTTTGGCA
1 TAAGACCATGTCTGGGACATGGCATTGGCA
19547196 TGTTATTATC
Statistics
Matches: 147, Mismatches: 30, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
48 3 0.02
49 35 0.24
50 77 0.52
52 1 0.01
53 2 0.01
55 1 0.01
56 28 0.19
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAAGTCCCATG
Found at i:19562351 original size:12 final size:12
Alignment explanation
Indices: 19562334--19562362 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
19562324 AAAAGGGGAC
19562334 AACAAACAAAAA
1 AACAAACAAAAA
19562346 AACAAACAAAAA
1 AACAAACAAAAA
19562358 AACAA
1 AACAA
19562363 GAGGACAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (12 bp):
AACAAACAAAAA
Found at i:19563342 original size:4 final size:4
Alignment explanation
Indices: 19563333--19563426 Score: 59
Period size: 4 Copynumber: 23.8 Consensus size: 4
19563323 TTTTCACTTG
* ** * * *
19563333 TTTA TTTA TTCA -TTA TTCC TTTTA TTTTA TTCA TTTA TTCA TTCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TT-TA TTTA TTTA TTTA TTTA TTTA
* * * *
19563382 CTTG TTTA TATA -TTA TTTA TTTA TTCA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
19563427 TAATCCTTCT
Statistics
Matches: 68, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
3 7 0.10
4 54 0.79
5 7 0.10
ACGTcount: A:0.23, C:0.09, G:0.01, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:19563363 original size:21 final size:21
Alignment explanation
Indices: 19563333--19563372 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
19563323 TTTTCACTTG
19563333 TTTATTTATTCA-TTATTCCT
1 TTTATTTATTCATTTATTCCT
19563353 TTTATTTTATTCATTTATTC
1 TTTA-TTTATTCATTTATTC
19563373 ATTCATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATTTATTCATTTATTCCT
Found at i:19563380 original size:21 final size:21
Alignment explanation
Indices: 19563337--19563380 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19563327 CACTTGTTTA
* *
19563337 TTTATTCATTATTCCTTTTAT
1 TTTATTCATTATTCCATTCAT
19563358 TTTATTCATTTATT-CATTCAT
1 TTTATTCA-TTATTCCATTCAT
19563379 TT
1 TT
19563381 ACTTGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTATTCATTATTCCATTCAT
Found at i:19563405 original size:35 final size:31
Alignment explanation
Indices: 19563333--19563416 Score: 91
Period size: 35 Copynumber: 2.6 Consensus size: 31
19563323 TTTTCACTTG
19563333 TTTATTTATTCATTA-TT-CCTTTTATTTTA
1 TTTATTTATTCATTATTTACCTTTTATTTTA
* *
19563362 TTCATTTATTCATTCATTTACTTGTTTATATATTA
1 TTTATTTATTCATT-ATTTACCT-TTTAT-T-TTA
19563397 TTTATTTATTCATTTATTTA
1 TTTATTTATTCA-TTATTTA
19563417 TTTATTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
29 13 0.29
30 1 0.02
31 2 0.04
32 2 0.04
33 5 0.11
34 1 0.02
35 19 0.42
36 2 0.04
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.65
Consensus pattern (31 bp):
TTTATTTATTCATTATTTACCTTTTATTTTA
Found at i:19566732 original size:5 final size:5
Alignment explanation
Indices: 19566724--19566786 Score: 58
Period size: 5 Copynumber: 12.8 Consensus size: 5
19566714 TTTTCTATTA
* * * *
19566724 AAAAT AAAAG AAACG AAAAG AAAA- TAAAG AAAAG AAAAT AAAAG AAAA-
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
*
19566772 AGAAG AAAAAG AAAA
1 AAAAG -AAAAG AAAA
19566787 AGGACAGGCC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
4 6 0.13
5 36 0.78
6 4 0.09
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:19566756 original size:24 final size:25
Alignment explanation
Indices: 19566729--19566786 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
19566719 TATTAAAAAT
*
19566729 AAAAGAAACGAAAAGAAAATA-AAG-
1 AAAAGAAAAGAAAAGAAAA-AGAAGA
*
19566753 AAAAGAAAATAAAAGAAAAAGAAGA
1 AAAAGAAAAGAAAAGAAAAAGAAGA
19566778 AAAAGAAAA
1 AAAAGAAAA
19566787 AGGACAGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 1 0.03
24 20 0.67
25 9 0.30
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (25 bp):
AAAAGAAAAGAAAAGAAAAAGAAGA
Found at i:19566777 original size:19 final size:18
Alignment explanation
Indices: 19566724--19566780 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
19566714 TTTTCTATTA
19566724 AAAATAAAAGAAACGAAAAG
1 AAAATAAAAGAAA--AAAAG
19566744 AAAAT-AAAG---AAAAG
1 AAAATAAAAGAAAAAAAG
19566758 AAAATAAAAGAAAAAGAAG
1 AAAATAAAAGAAAAA-AAG
19566777 AAAA
1 AAAA
19566781 AGAAAAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
14 10 0.31
15 4 0.12
18 2 0.06
19 11 0.34
20 5 0.16
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAATAAAAGAAAAAAAG
Found at i:19568064 original size:92 final size:92
Alignment explanation
Indices: 19567939--19568240 Score: 341
Period size: 92 Copynumber: 3.3 Consensus size: 92
19567929 CAGACTGAAG
* * * *
19567939 ATAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAACGGATTGAAGCTATAAATTGCAGATCTTAT
1 ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAACGGATTGAAGCTATAAATTGCAGATCTTAT
* * *
19568004 CTCTCTGAAGATGCAGTAGAGTAGATC
66 CTCTCTGAAGTTGCAATAGAGCAGATC
* * * *
19568031 ATAGCAAACCTTAGCTCCCTGAAGTTACAGTGGAGCAGG-TTGAAG-T-T--A-CG-AG-TCTTA
1 ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAAC-GGATTGAAGCTATAAATTGCAGATCTTA
* * *
19568088 TCTCCCTGAAGTTGCAATGGAGCAGACTGAAG
65 TCTCTCTGAAGTTGCAATAGAGCAGA-T---C
* * * *
19568120 ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACGGATTGAAGCTATAAATTACCGATCTTAT
1 ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAACGGATTGAAGCTATAAATTGCAGATCTTAT
19568185 CTCTCTGAAGTTGCAATAGAGCAGATC
66 CTCTCTGAAGTTGCAATAGAGCAGATC
19568212 ATAGCAAACCTTATCTCCCTGAAGTTGCA
1 ATAGCAAACCTTATCTCCCTGAAGTTGCA
19568241 ACGGAACAGG
Statistics
Matches: 170, Mismatches: 27, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
85 26 0.15
86 3 0.02
87 1 0.01
88 3 0.02
89 37 0.22
90 2 0.01
91 2 0.01
92 62 0.36
93 3 0.02
95 2 0.01
96 29 0.17
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (92 bp):
ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAACGGATTGAAGCTATAAATTGCAGATCTTAT
CTCTCTGAAGTTGCAATAGAGCAGATC
Found at i:19568075 original size:137 final size:137
Alignment explanation
Indices: 19567613--19568100 Score: 484
Period size: 137 Copynumber: 3.6 Consensus size: 137
19567603 GATGGATTGA
* * * *
19567613 AGATCATAGCAATCCTTATCTCCATGAAGTTGCAGTGGAGCAGACTAAAGATAGTGAATCTTATT
1 AGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATC
* * * *
19567678 TCCCTGAAGTTACAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTTTCTGAAGTTGCA
66 TCCCTAAAGTTACAGTGGAACGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCA
*
19567743 GTAGAGC
131 GTAGAGT
* * * ** * * * * *
19567750 AAATCATATCAAAACTTATCTCTTTGAAGTTGCAGTGGAACA-AGTTAAAAATAAACCAATCTTA
1 AGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAAGAT-AGCGAATCTTA
* * * *** *
19567814 TCTCCCTAAAGTTATAGTGGAGCAGG-TTGAAG--ACAGGCTACAAATCTTATCTC-CTTGAAGT
64 TCTCCCTAAAGTTACAGTGGAAC-GGATTGAAGCTATAAATTACAGATCTTATCTCTC-TGAAGT
*
19567875 TGCAGTGGAGT
127 TGCAGTAGAGT
* * * *
19567886 AGATTAAAGCCACAAACCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTT
1 AGATCATAG---CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTT
* * * *
19567951 ATTTCCCTAAAGTTGCAGTGGAACGGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGAT
63 ATCTCCCTAAAGTTACAGTGGAACGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTT
19568016 GCAGTAGAGT
128 GCAGTAGAGT
* * ** * * *
19568026 AGATCATAGCAAACCTTAGCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTA-CGAGTCTTATC
1 AGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATC
*
19568090 TCCCTGAAGTT
66 TCCCTAAAGTT
19568101 GCAATGGAGC
Statistics
Matches: 276, Mismatches: 63, Indels: 25
0.76 0.17 0.07
Matches are distributed among these distances:
135 1 0.00
136 55 0.20
137 81 0.29
138 66 0.24
139 34 0.12
140 38 0.14
141 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (137 bp):
AGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATC
TCCCTAAAGTTACAGTGGAACGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCA
GTAGAGT
Found at i:19568094 original size:44 final size:45
Alignment explanation
Indices: 19567618--19568467 Score: 300
Period size: 44 Copynumber: 18.8 Consensus size: 45
19567608 ATTGAAGATC
* *
19567618 ATAGC-AATCCTTATCTCCATGAAGTTGCAGTGGAGCAGACTAAAG
1 ATAGCAAAT-CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
** * * * * *
19567663 ATAGTGAATCTTATTTCCCTGAAGTTACAGTGGAACAGATTAAAG
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * ** * **
19567708 CTATAAATTACAGATCTTATCTTTCTGAAGTTGCAGTAGAGCA-A---ATC
1 --AT--A--GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * ** * * * *
19567755 ATATCAAAACTTATCTCTTTGAAGTTGCAGTGGAACA-AGTTAAAA
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAG
* * * ** **
19567800 ATAAACCAATCTTATCTCCCTAAAGTTATAGTGGAGCAGGTTGAAG
1 AT-AGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * * *
19567846 ACAGGCTACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAG
1 ATA-G---CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
** * *
19567895 CCA-CAAACCTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAG
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * * * *
19567939 ATAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAACGGATTGAAG
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * * * *
19567984 CTATAAATTGCAGATCTTATCTCTCTGAAGATGCAGTAGAGTAGA-T---C
1 --AT--A--GCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * **
19568031 ATAGCAAACCTTAGCTCCCTGAAGTTACAGTGGAGCAGGTTGAAG
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * *
19568076 TTA-CGAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAG
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * *
19568120 ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACGGATTGAAG
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * * *
19568165 CTATA-AATTACCGATCTTATCTCTCTGAAGTTGCAATAGAGCAGA-T---C
1 --ATAGCA--A---ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* ** * * * *
19568212 ATAGCAAACCTTATCTCCCTGAAGTTGCAACGGAACAG-GTTACAA
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA-AG
* * * * * *
19568257 ATA-AATCAATCTTATCTCCTTAAAGTTGCAGTAGAGAAGATTGAAG
1 ATAGCA--AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * *
19568303 ATAGGCTACAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAG
1 ATA-G---CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
** * * * * **
19568352 CGA-CCAACCTTATCTCCTTGAAGTTGTAGTGGAGCAGGTTGAAG
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* *
19568396 ATA-CCAATCTTATCTCCC------TG-AGTGGAGCAGATTGAAG
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* ** *
19568433 CTA-CAAATCCAATCTCCCTGAAGTTGTAGTGGAGC
1 ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
19568468 GGATTAAAAC
Statistics
Matches: 592, Mismatches: 156, Indels: 115
0.69 0.18 0.13
Matches are distributed among these distances:
37 30 0.05
38 2 0.00
41 82 0.14
42 1 0.00
43 4 0.01
44 129 0.22
45 118 0.20
46 64 0.11
47 10 0.02
48 1 0.00
49 71 0.12
50 3 0.01
51 77 0.13
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (45 bp):
ATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
Found at i:19568097 original size:181 final size:181
Alignment explanation
Indices: 19567903--19568237 Score: 580
Period size: 181 Copynumber: 1.9 Consensus size: 181
19567893 AGCCACAAAC
* *
19567903 CTTATCCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTAAAGTTGCA
1 CTTATCCCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTGCA
* * *
19567968 GTGGAACGGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGATGCAGTAGAGTAGATCAT
66 GTGGAACGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGATGCAATAGAGCAGATCAT
19568033 AGCAAACCTTAGCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACGAGT
131 AGCAAACCTTAGCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACGAGT
* *
19568084 CTTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
1 CTTATCCCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTGCA
* *
19568149 GTGGAACGGATTGAAGCTATAAATTACCGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCAT
66 GTGGAACGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGATGCAATAGAGCAGATCAT
*
19568214 AGCAAACCTTATCTCCCTGAAGTT
131 AGCAAACCTTAGCTCCCTGAAGTT
19568238 GCAACGGAAC
Statistics
Matches: 144, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
181 144 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (181 bp):
CTTATCCCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTGCA
GTGGAACGGATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGATGCAATAGAGCAGATCAT
AGCAAACCTTAGCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGTTACGAGT
Found at i:19568431 original size:37 final size:37
Alignment explanation
Indices: 19568379--19568453 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
19568369 TTGAAGTTGT
* * **
19568379 AGTGGAGCAGGTTGAAGATACCAATCTTATCTCCCTG
1 AGTGGAGCAGATTGAAGATACAAATCCAATCTCCCTG
*
19568416 AGTGGAGCAGATTGAAGCTACAAATCCAATCTCCCTG
1 AGTGGAGCAGATTGAAGATACAAATCCAATCTCCCTG
19568453 A
1 A
19568454 AGTTGTAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (37 bp):
AGTGGAGCAGATTGAAGATACAAATCCAATCTCCCTG
Found at i:19573427 original size:26 final size:27
Alignment explanation
Indices: 19573379--19573430 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
19573369 GAAACTTGTC
*
19573379 TTTTTTTTGTTATATTTATTATTTTAA
1 TTTTTTTTGTTATATTTACTATTTTAA
19573406 TTTTTTGTTG-TATATTT-CTATTTTA
1 TTTTTT-TTGTTATATTTACTATTTTA
19573431 CATACGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 13 0.57
28 3 0.13
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (27 bp):
TTTTTTTTGTTATATTTACTATTTTAA
Found at i:19574269 original size:20 final size:20
Alignment explanation
Indices: 19574244--19574281 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19574234 CATATATATA
19574244 TTTTTTACGAATATTTTCCT
1 TTTTTTACGAATATTTTCCT
*
19574264 TTTTTTATGAATATTTTC
1 TTTTTTACGAATATTTTC
19574282 ATATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTTACGAATATTTTCCT
Found at i:19587185 original size:26 final size:25
Alignment explanation
Indices: 19587139--19587188 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
19587129 GAAACTTGTC
*
19587139 TTTTTTGTTATATTTATTATTTTAA
1 TTTTTTGTTATATTTACTATTTTAA
19587164 TTTTTTGTTGTATATTT-CTATTTTA
1 TTTTTTG-T-TATATTTACTATTTTA
19587189 CATACGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 8 0.36
27 7 0.32
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (25 bp):
TTTTTTGTTATATTTACTATTTTAA
Found at i:19588027 original size:19 final size:19
Alignment explanation
Indices: 19588005--19588041 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19587995 TATATATATA
19588005 TTTTTTACGAATATTTTCC
1 TTTTTTACGAATATTTTCC
*
19588024 TTTTTTATGAATATTTTC
1 TTTTTTACGAATATTTTC
19588042 ATATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTTTACGAATATTTTCC
Found at i:19592521 original size:23 final size:23
Alignment explanation
Indices: 19592495--19592616 Score: 226
Period size: 23 Copynumber: 5.3 Consensus size: 23
19592485 ATAAGTGCCA
*
19592495 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
19592518 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
19592541 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
*
19592564 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
19592587 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
19592610 CACTGAT
1 CACTGAT
19592617 CAATAACACT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 96 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATACGTAGCCGAAGCTAC
Found at i:19592868 original size:18 final size:17
Alignment explanation
Indices: 19592842--19592880 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
19592832 ATTTTCCTTC
19592842 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
19592859 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
19592877 CACA
1 CACA
19592881 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:19606634 original size:20 final size:20
Alignment explanation
Indices: 19606609--19606648 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19606599 CGTAAAATGA
*
19606609 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
19606629 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
19606649 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:19606638 original size:34 final size:35
Alignment explanation
Indices: 19606594--19606660 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
19606584 CAGTAAAATA
*
19606594 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
19606628 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
19606661 CTGGTGTTTG
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:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:19606664 original size:14 final size:15
Alignment explanation
Indices: 19606588--19606664 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
19606578 GATTGCCAGT
* *
19606588 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
19606602 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
19606616 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
19606636 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
19606651 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
19606665 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:19607405 original size:23 final size:23
Alignment explanation
Indices: 19607374--19607423 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
19607364 TAAATAATAA
* *
19607374 TTGTTAATTTTATT-TATATATTT
1 TTGTAAATTTTATTAT-TACATTT
19607397 TTGTAAATTTTATTATTACATTT
1 TTGTAAATTTTATTATTACATTT
19607420 TTGT
1 TTGT
19607424 TATTTGTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (23 bp):
TTGTAAATTTTATTATTACATTT
Found at i:19617684 original size:72 final size:72
Alignment explanation
Indices: 19617589--19617780 Score: 330
Period size: 72 Copynumber: 2.7 Consensus size: 72
19617579 CAATGCTAAA
* *
19617589 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTTGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
19617654 GTGCAAT
66 GTGCAAT
*
19617661 CTAGTTTTATCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
19617726 GTGTAAT
66 GTGCAAT
* *
19617733 CTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTT
19617781 GTAACACCCC
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 113 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGCAAT
Found at i:19619117 original size:45 final size:45
Alignment explanation
Indices: 19619047--19619156 Score: 159
Period size: 45 Copynumber: 2.4 Consensus size: 45
19619037 ATAACGGTAG
* *
19619047 CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGT-GCTGAAT
1 CAGTAACAGTAACAGTAACAATATTCAACACACAAAGTATC-GAAT
* *
19619092 CTGTAACAGTAACAGTAACAATATTCGACACACAAAGTATCGAAT
1 CAGTAACAGTAACAGTAACAATATTCAACACACAAAGTATCGAAT
*
19619137 CAGTAACAGTAACAATAACA
1 CAGTAACAGTAACAGTAACA
19619157 GTAGTCGGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 57 0.98
46 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAATATTCAACACACAAAGTATCGAAT
Found at i:19619446 original size:39 final size:39
Alignment explanation
Indices: 19619362--19619447 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 39
19619352 TTCATTGCTT
* * *
19619362 CAGTATTTTCACAGTTCAATGCAGTACACATAACAATATT
1 CAGTATTTTCACAATTCAA-GCAGTACACAAAACAATATC
* *
19619402 AAGTATTTTCACAATTCACA-CAGTACTCAAAACAATATC
1 CAGTATTTTCACAATTCA-AGCAGTACACAAAACAATATC
19619441 CAGTATT
1 CAGTATT
19619448 CCATAATTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
39 22 0.56
40 16 0.41
41 1 0.03
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (39 bp):
CAGTATTTTCACAATTCAAGCAGTACACAAAACAATATC
Found at i:19622325 original size:21 final size:20
Alignment explanation
Indices: 19622297--19622335 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19622287 GCAGATTTTA
19622297 TGGAATATGA-AGATATTAAC
1 TGGAATATGAGA-ATATTAAC
19622317 TGGACATATGAGAATATTA
1 TGGA-ATATGAGAATATTA
19622336 TTGATTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (20 bp):
TGGAATATGAGAATATTAAC
Found at i:19622958 original size:13 final size:13
Alignment explanation
Indices: 19622942--19622979 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
19622932 CTTTTTCACG
19622942 GCACTTTCCAAAA
1 GCACTTTCCAAAA
19622955 GCACTTTCCAAAA
1 GCACTTTCCAAAA
*
19622968 GCA-TTGCCAAAA
1 GCACTTTCCAAAA
19622980 TAGCCCTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (13 bp):
GCACTTTCCAAAA
Found at i:19623452 original size:21 final size:22
Alignment explanation
Indices: 19623412--19623452 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19623402 GTCTTAACTT
*
19623412 ATTGCAATTTATTTTATCAATC
1 ATTGCAATATATTTTATCAATC
*
19623434 ATTGCAATAT-TTTTGTCAA
1 ATTGCAATATATTTTATCAA
19623453 ACTATATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTGCAATATATTTTATCAATC
Found at i:19628822 original size:14 final size:14
Alignment explanation
Indices: 19628803--19628832 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19628793 CTATTTGATA
*
19628803 GTAATTGACTTTTC
1 GTAATTGACTTGTC
19628817 GTAATTGACTTGTC
1 GTAATTGACTTGTC
19628831 GT
1 GT
19628833 GAAGAAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (14 bp):
GTAATTGACTTGTC
Found at i:19634300 original size:20 final size:20
Alignment explanation
Indices: 19634275--19634325 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
19634265 TCAACCTTTA
19634275 AATCAAGTTAAAATGGT-TTC
1 AATCAAGTTAAAAT-GTCTTC
* *
19634295 AATCAAGTTAGAATTTCTTC
1 AATCAAGTTAAAATGTCTTC
19634315 AATC-AGTTAAA
1 AATCAAGTTAAA
19634326 CTATTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
AATCAAGTTAAAATGTCTTC
Found at i:19639977 original size:35 final size:35
Alignment explanation
Indices: 19639926--19639996 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
19639916 TAATGTAAGG
* *
19639926 TGAGTTTGAAATGAGCATGGTGGGAGAGCTCTCAT
1 TGAGCTTGAAATGAGCATGATGGGAGAGCTCTCAT
19639961 TGAGCTTGAAATGAGCATGATGGGAGAGCTCTCAT
1 TGAGCTTGAAATGAGCATGATGGGAGAGCTCTCAT
19639996 T
1 T
19639997 CTTTTTGGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (35 bp):
TGAGCTTGAAATGAGCATGATGGGAGAGCTCTCAT
Found at i:19645273 original size:55 final size:55
Alignment explanation
Indices: 19645206--19645313 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
19645196 CTTAACTTGC
* *
19645206 AAACATTTTGATCTTGTAA-GAGTTATTTCATTGTTTGCTTATTTGTATCTCTTTG
1 AAACATTCTGATCTTGTAAGGA-TTATTACATTGTTTGCTTATTTGTATCTCTTTG
*
19645261 AAACATTCTGATCTTGTAAGGATTATTACTTTGTTTGCTTATTTGTATCTCTT
1 AAACATTCTGATCTTGTAAGGATTATTACATTGTTTGCTTATTTGTATCTCTT
19645314 ATAGAGGGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
55 47 0.96
56 2 0.04
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (55 bp):
AAACATTCTGATCTTGTAAGGATTATTACATTGTTTGCTTATTTGTATCTCTTTG
Found at i:19647989 original size:9 final size:9
Alignment explanation
Indices: 19647972--19648008 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
19647962 TATAGTTTGA
*
19647972 TATTTGAAT
1 TATTCGAAT
19647981 TATTCGAAT
1 TATTCGAAT
*
19647990 TATTCGAGT
1 TATTCGAAT
19647999 TATTCGAAT
1 TATTCGAAT
19648008 T
1 T
19648009 TGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19648078 original size:9 final size:9
Alignment explanation
Indices: 19648061--19648091 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
19648051 TCGAGTTGAT
19648061 TCGAATAAC
1 TCGAATAAC
*
19648070 TCGATTAAC
1 TCGAATAAC
19648079 TCGAATAAC
1 TCGAATAAC
19648088 TCGA
1 TCGA
19648092 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:19662299 original size:19 final size:19
Alignment explanation
Indices: 19662275--19662312 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19662265 TAGATAAGAT
19662275 TGAGGTGTTATAAGGTCGG
1 TGAGGTGTTATAAGGTCGG
19662294 TGAGGTGTTATAAGGTCGG
1 TGAGGTGTTATAAGGTCGG
19662313 GGTCTGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.42, T:0.32
Consensus pattern (19 bp):
TGAGGTGTTATAAGGTCGG
Found at i:19670625 original size:12 final size:13
Alignment explanation
Indices: 19670602--19670666 Score: 60
Period size: 13 Copynumber: 4.7 Consensus size: 13
19670592 TTATGACTAC
*
19670602 ATTATAATATTTT
1 ATTATTATATTTT
19670615 ATT-TTATATTTT
1 ATTATTATATTTT
*
19670627 ATTATTATTGTTATTAAT
1 ATTATTA----TATT-TT
19670645 ATTATTATATTTT
1 ATTATTATATTTT
19670658 ATTATTATA
1 ATTATTATA
19670667 GTGATATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 11 0.26
13 16 0.37
14 4 0.09
17 4 0.09
18 8 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (13 bp):
ATTATTATATTTT
Found at i:19670633 original size:3 final size:3
Alignment explanation
Indices: 19670609--19670665 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
19670599 TACATTATAA
* *
19670609 TAT T-T TAT T-T TA- TAT T-T TAT TAT TAT TGT TAT TAA TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19670652 TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT
19670666 AGTGATATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
2 12 0.27
3 32 0.73
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:19674581 original size:53 final size:53
Alignment explanation
Indices: 19674517--19674623 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
19674507 ATAAGGTATG
* * *
19674517 AAAGTTGATCATTCTCTTACTCTCCAAATTTGATTAACAACATTAAGGATAGA
1 AAAGTTCATCATTCTCTTACTCTCCAAATTCGATCAACAACATTAAGGATAGA
*
19674570 AAAGTTCATCATTCTCTTACTCTCTAAATTCGATCAACAACATTAAGGATAGA
1 AAAGTTCATCATTCTCTTACTCTCCAAATTCGATCAACAACATTAAGGATAGA
19674623 A
1 A
19674624 TATAATATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (53 bp):
AAAGTTCATCATTCTCTTACTCTCCAAATTCGATCAACAACATTAAGGATAGA
Found at i:19675505 original size:36 final size:36
Alignment explanation
Indices: 19675458--19675567 Score: 129
Period size: 36 Copynumber: 3.1 Consensus size: 36
19675448 ACAATTTTAA
19675458 TATTATTATTTAATGTAAATATAATATAAGTATTTT
1 TATTATTATTTAATGTAAATATAATATAAGTATTTT
*
19675494 TATTATAATTTAATGTAAATATAA-AT-A-TATTTT
1 TATTATTATTTAATGTAAATATAATATAAGTATTTT
* *
19675527 ATCATTTATTATTTAAT-TTAATATATATAAAAGTATTTT
1 -T-A-TTATTATTTAATGTAAATATA-ATATAAGTATTTT
19675566 TA
1 TA
19675568 ATGGGTCACT
Statistics
Matches: 63, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
33 6 0.10
34 2 0.03
35 10 0.16
36 35 0.56
37 2 0.03
38 2 0.03
39 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (36 bp):
TATTATTATTTAATGTAAATATAATATAAGTATTTT
Found at i:19675555 original size:39 final size:40
Alignment explanation
Indices: 19675489--19675565 Score: 97
Period size: 39 Copynumber: 1.9 Consensus size: 40
19675479 TAATATAAGT
19675489 ATTTTTATTATAATTTAATGTAAATATAAATA-TATTTTATC
1 ATTTTTATTATAATTTAA-GTAAATATAAA-AGTATTTTATC
*
19675530 ATTTATTATT-TAATTTAA-TATATATAAAAGTATTTT
1 ATTT-TTATTATAATTTAAGTAAATATAAAAGTATTTT
19675566 TAATGGGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
38 1 0.03
39 15 0.45
41 12 0.36
42 5 0.15
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (40 bp):
ATTTTTATTATAATTTAAGTAAATATAAAAGTATTTTATC
Found at i:19675685 original size:13 final size:13
Alignment explanation
Indices: 19675669--19675698 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19675659 GAAAAAGTAT
19675669 TTACCAAAATGGG
1 TTACCAAAATGGG
19675682 TTACCAAAATGGG
1 TTACCAAAATGGG
19675695 TTAC
1 TTAC
19675699 TTTTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (13 bp):
TTACCAAAATGGG
Found at i:19675774 original size:25 final size:26
Alignment explanation
Indices: 19675738--19675786 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
19675728 CCAATAAATT
*
19675738 TTTTTTTGAATAAAT-TTTTTTTATA
1 TTTTTTTAAATAAATGTTTTTTTATA
*
19675763 TTTTTTTAAATAATTGTTTTTTTA
1 TTTTTTTAAATAAATGTTTTTTTA
19675787 AAAAAATACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTTTTAAATAAATGTTTTTTTATA
Found at i:19675878 original size:27 final size:27
Alignment explanation
Indices: 19675848--19675909 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
19675838 CCTATCAGGT
19675848 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
19675875 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
19675902 AGGCGCCA
1 AGGCGCCA
19675910 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:19677164 original size:27 final size:28
Alignment explanation
Indices: 19677126--19677202 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
19677116 CCGGCCCGGC
*
19677126 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
19677153 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
19677180 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
19677203 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:19682315 original size:81 final size:81
Alignment explanation
Indices: 19682178--19682347 Score: 331
Period size: 81 Copynumber: 2.1 Consensus size: 81
19682168 TGCATAATCC
*
19682178 TCTGAACTCGTCTAAGTGTTGTGATGCCTGAGTCTTCCAATCCCTTATCTGTCAAGGCCTTACCC
1 TCTGAACTCGTCTAAGTGTTGTGATGCCTGAGTCTTCCAATCCCTTATCTGCCAAGGCCTTACCC
19682243 ACATCTGAACTATCTA
66 ACATCTGAACTATCTA
19682259 TCTGAACTCGTCTAAGTGTTGTGATGCCTGAGTCTTCCAATCCCTTATCTGCCAAGGCCTTACCC
1 TCTGAACTCGTCTAAGTGTTGTGATGCCTGAGTCTTCCAATCCCTTATCTGCCAAGGCCTTACCC
19682324 ACATCTGAACTATCTA
66 ACATCTGAACTATCTA
19682340 TCTGAACT
1 TCTGAACT
19682348 GTGGCCCGTT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 88 1.00
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (81 bp):
TCTGAACTCGTCTAAGTGTTGTGATGCCTGAGTCTTCCAATCCCTTATCTGCCAAGGCCTTACCC
ACATCTGAACTATCTA
Found at i:19693670 original size:6 final size:6
Alignment explanation
Indices: 19693661--19693686 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19693651 TAAGTCTAAG
19693661 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
19693687 TAAACTTAAT
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:19695405 original size:18 final size:18
Alignment explanation
Indices: 19695382--19695425 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
19695372 ATATATATAG
19695382 AACTAATAATAAACAATA-
1 AACTAATAA-AAACAATAT
*
19695400 AACTAAT-AAAATAATAT
1 AACTAATAAAAACAATAT
19695417 AACTAATAA
1 AACTAATAA
19695426 GAATAATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.30
17 8 0.35
18 8 0.35
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (18 bp):
AACTAATAAAAACAATAT
Found at i:19695409 original size:8 final size:8
Alignment explanation
Indices: 19695388--19695425 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
19695378 ATAGAACTAA
19695388 TAATAAAC
1 TAATAAAC
19695396 -AATAAAC
1 TAATAAAC
*
19695403 TAATAAAA
1 TAATAAAC
19695411 TAATATAAC
1 TAATA-AAC
19695420 TAATAA
1 TAATAA
19695426 GAATAATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 7 0.27
8 12 0.46
9 7 0.27
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (8 bp):
TAATAAAC
Found at i:19695430 original size:18 final size:16
Alignment explanation
Indices: 19695382--19695432 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 16
19695372 ATATATATAG
*
19695382 AACTAATAATAAACAATA
1 AACTAAT-A-AAATAATA
19695400 AACTAATAAAATAATA
1 AACTAATAAAATAATA
19695416 TAACTAATAAGAATAAT
1 -AACTAATAA-AATAAT
19695433 GGATAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 7 0.23
17 10 0.33
18 13 0.43
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (16 bp):
AACTAATAAAATAATA
Found at i:19696553 original size:115 final size:115
Alignment explanation
Indices: 19696344--19696555 Score: 266
Period size: 115 Copynumber: 1.8 Consensus size: 115
19696334 AAATTTTGGA
* * * * * *
19696344 AAAATTAAGTCTCAGGATCCATACGGCCAATGACATGCCTGTGTGTGCAAGCTGAGTGGGTCACA
1 AAAATTAAGTCTCAGGATCCACACGGCCAAGGACACGCCTGTGTGTCCAAACTCAGTGGGTCACA
* * *
19696409 TGGCCATGTCGCCAAGCCGTCTAACTCACTGTTGAATATGTTAAAATTTT
66 CGACCATGTCGCCAAGCCATCTAACTCACTGTTGAATATGTTAAAATTTT
*
19696459 AAAATTAAGTCTTAGGATCCACACGGCCAAGGACACGTCC-GTGTGTCCAAAC-CATGTGGGTCA
1 AAAATTAAGTCTCAGGATCCACACGGCCAAGGACACG-CCTGTGTGTCCAAACTCA-GTGGGTCA
* * * *
19696522 CACGACCATGTCGCTAGGCCATGTAAGTCACTGT
64 CACGACCATGTCGCCAAGCCATCTAACTCACTGT
19696556 CAAAACCCTT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
114 1 0.01
115 78 0.96
116 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (115 bp):
AAAATTAAGTCTCAGGATCCACACGGCCAAGGACACGCCTGTGTGTCCAAACTCAGTGGGTCACA
CGACCATGTCGCCAAGCCATCTAACTCACTGTTGAATATGTTAAAATTTT
Found at i:19700786 original size:26 final size:26
Alignment explanation
Indices: 19700757--19700818 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
19700747 GACTTGTGAC
19700757 AAGTGGTGAG-ACCGAAAGGGTATCTT
1 AAGTGGT-AGTACCGAAAGGGTATCTT
*
19700783 AAGTGGTAGTCCCGAAAGGGTATCTT
1 AAGTGGTAGTACCGAAAGGGTATCTT
19700809 AAGTGGTAGT
1 AAGTGGTAGT
19700819 CCTTAGTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (26 bp):
AAGTGGTAGTACCGAAAGGGTATCTT
Found at i:19700819 original size:26 final size:26
Alignment explanation
Indices: 19700768--19700820 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
19700758 AGTGGTGAGA
19700768 CCGAAAGGGTATCTTAAGTGGTAGTC
1 CCGAAAGGGTATCTTAAGTGGTAGTC
19700794 CCGAAAGGGTATCTTAAGTGGTAGTC
1 CCGAAAGGGTATCTTAAGTGGTAGTC
19700820 C
1 C
19700821 TTAGTGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (26 bp):
CCGAAAGGGTATCTTAAGTGGTAGTC
Found at i:19703494 original size:25 final size:25
Alignment explanation
Indices: 19703462--19703509 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
19703452 AATAAATAAT
*
19703462 ATAATTAATAATAAAAATTTAAAAA
1 ATAATTAATAATAAAAAGTTAAAAA
* *
19703487 ATAATTAATTATTAAAAGTTAAA
1 ATAATTAATAATAAAAAGTTAAA
19703510 TTTCTACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAATTAATAATAAAAAGTTAAAAA
Found at i:19706628 original size:31 final size:30
Alignment explanation
Indices: 19706580--19706641 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
19706570 GTGAAATTTA
**
19706580 ATCATTTTATTGAAATAATATTTTAATTAAT
1 ATCATTTTATTGAAATAA-ATGATAATTAAT
**
19706611 ATCATTTTATTTTAATAAATGATAATTAAT
1 ATCATTTTATTGAAATAAATGATAATTAAT
19706641 A
1 A
19706642 GACTTGCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (30 bp):
ATCATTTTATTGAAATAAATGATAATTAAT
Found at i:19709735 original size:468 final size:465
Alignment explanation
Indices: 19708844--19710214 Score: 1610
Period size: 468 Copynumber: 2.9 Consensus size: 465
19708834 TGGGTTGCAC
* * * * *
19708844 GAAGCAAGAGTTTGGTATGTGTAGAGTGAGGTTTCATTGCTATGGAACATGTGATTGAGTTGCTA
1 GAAGCAAGAGTTTGGGATGTGCAGAGCGAGATTTCATTGCTATGGAGCATGTGATTGAGTTGCTA
* * * *
19708909 GAAGTAGGAGTTTGCTATTATGAAGTAGGAATTC-ACATTA-TTCAGAGAAGGATTTCATTACTT
66 -AAGTAGGAGTTTGCTATTATAAAGTAGGAGTTCGA-ATTACTT-AGAGAAGGATTTCACTATTT
* * *
19708972 GGGTGGAAGCAAGA-CATTGGGTTAGGTGGAGGAAGATTTTATTGCTATGGAGTAAGAGTTCGGG
128 GGGTGGGAGCAAGAGC-TTGGG-TAGGTGGAGGAAGATTTTATTGTTATGGAGCAAGAGTTCGGG
* * * * *
19709036 TTTAGCAGAGTAGGAGTTCAAGCTATGCCGTGTAAGATTTCACTAATAAGAAGGAGTTTGGGTTA
191 TTTAGCAGAATAGGAGTTCAAACTATGTCGTGTAAGATTTCACTAATATGGAGGAGTTTGGG-T-
* * *
19709101 TATGG-AGTATGATTTTATCATTGTGGAGCAATAGTTGAAGATGCTTGGAGTAAGATTTAATTGT
254 TATGGAAGTAAGATTTTACCATTGTGGAGCAAGAGTTGAAGATGCTTGGAGTAAGATTTAATTGT
* * * **
19709165 TATGGAGCAGAAGTTTGCATTGCTCGGAGTAGGATTTATGGAGCAATAGTTTAGGCTATACGAAA
319 TATGGAGCAGAAGTTTGCATTGCTCGAAGTAGGATTTATGGAGCAAGAATTTAGGCTGCACGAAA
* * * * *
19709230 CAACATTTTACTATTATCGACCTATAATTTGGGTTGCATGAAGCAAGAGTTTAGGCTAGGCAAAC
384 TAACATTTCACTATTATGGACCTAGAATTTGGGTTGCATGAAGCAAGAGTTTAGGCTAGACAAAC
19709295 TA-GAATCTCATTGTTAT
449 TATG-ATCTCATTGTTAT
* * *
19709312 GAAGCAAGATTTTGGGATGTGCAGAGCGATATTTCATTGCTATGGAGCATGTGATTAAGTTGCTC
1 GAAGCAAGAGTTTGGGATGTGCAGAGCGAGATTTCATTGCTATGGAGCATGTGATTGAGTTGCT-
* * * * *
19709377 AAAGTAGGGGTTTGCCATTATTAAGTAGGAGTTCGAATTACTTAAAAAAGGATTTCACTATTTGG
65 AAAGTAGGAGTTTGCTATTATAAAGTAGGAGTTCGAATTACTTAGAGAAGGATTTCACTATTTGG
* * * **
19709442 GTGGGAGTAAGAGCTTGGGCTAGGTGGAGAAAGATTTTATTTTTATGGAGCAAGAGTTCGAATTT
130 GTGGGAGCAAGAGCTTGGG-TAGGTGGAGGAAGATTTTATTGTTATGGAGCAAGAGTTCGGGTTT
* * *
19709507 AGCAGAATAGGTGTTCAAACTATGTCGTGTAAGATTTCATTCATATGGAGGAGTTTGGGTTATGG
194 AGCAGAATAGGAGTTCAAACTATGTCGTGTAAGATTTCACTAATATGGAGGAGTTTGGGTTATGG
* * *** * *
19709572 AAAGTAAGATTTTACCACTATGGAGTTGGAGTAGAAGATGCTTGGAGTAAGATTTATTTGTTATG
259 -AAGTAAGATTTTACCATTGTGGAGCAAGAGTTGAAGATGCTTGGAGTAAGATTTAATTGTTATG
** * * * * *** *
19709637 GAGTGGAAGTTTGCATTGCTCGAAGTAGGATTTATAGAGCAAGAACTAAGGCTGCAAGGTGTAAG
323 GAGCAGAAGTTTGCATTGCTCGAAGTAGGATTTATGGAGCAAGAATTTAGGCTGCACGAAATAAC
* * * * *
19709702 ATTTCACTATTATGGACCTAGAATTTAGGTTGCATGAAGTAAGAGTTTGGGCTAGACGAAGTATG
388 ATTTCACTATTATGGACCTAGAATTTGGGTTGCATGAAGCAAGAGTTTAGGCTAGACAAACTATG
19709767 ATCTCATTGTTAT
453 ATCTCATTGTTAT
* ** * *
19709780 AAAGCAAGAGTTAAGGATGTGTC-GAACGAGATTTCATTGCTATAGAGCATGTGATTGAGTTGCT
1 GAAGCAAGAGTTTGGGATGTG-CAGAGCGAGATTTCATTGCTATGGAGCATGTGATTGAGTTGC-
* * * * * * *
19709844 TGAAGTAAGAGTCTGTTATTATAAAGTAGGAGTTCGCATTACTTAGAGAAGAATTTCACTGTTTG
64 TAAAGTAGGAGTTTGCTATTATAAAGTAGGAGTTCGAATTACTTAGAGAAGGATTTCACTATTTG
* * * * *
19709909 GGAGGGAACAAGAGCTTGGGTTGTGTGGAGGAAGATTTTATTGTTATAGAGCAAGAGTTTGGGTT
129 GGTGGGAGCAAGAGCTTGGGTAG-GTGGAGGAAGATTTTATTGTTATGGAGCAAGAGTTCGGGTT
* * * *
19709974 TAGCA-AAGTAGGAGTTCGATCTATGTCATGTAAGATTTCACTAATACT-GAGGAGTTTGGATTA
193 TAGCAGAA-TAGGAGTTCAAACTATGTCGTGTAAGATTTCACTAATA-TGGAGGAGTTTGGGTTA
* * * * * * *
19710037 -AG-ATTAGGATTTCACCATTGTGAAGCACGATTTGAAGATGCTTGGAGTAAGATTTAATTGTTA
256 TGGAAGTAAGATTTTACCATTGTGGAGCAAGAGTTGAAGATGCTTGGAGTAAGATTTAATTGTTA
* * * *
19710100 TGGAGCAGAAGTTTGCATTGCTCAAAGTAAGATTTATGGATCAAGATTTTAGGCTGCACGAAATA
321 TGGAGCAGAAGTTTGCATTGCTCGAAGTAGGATTTATGGAGCAAGAATTTAGGCTGCACGAAATA
* *
19710165 ATATTTCACTATTATGGACCTCGAATTTGGGTTGCATGAAGCAAGAGTTT
386 ACATTTCACTATTATGGACCTAGAATTTGGGTTGCATGAAGCAAGAGTTT
19710215 GGGATGTGCG
Statistics
Matches: 756, Mismatches: 135, Indels: 27
0.82 0.15 0.03
Matches are distributed among these distances:
465 147 0.19
466 5 0.01
467 6 0.01
468 589 0.78
469 9 0.01
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (465 bp):
GAAGCAAGAGTTTGGGATGTGCAGAGCGAGATTTCATTGCTATGGAGCATGTGATTGAGTTGCTA
AAGTAGGAGTTTGCTATTATAAAGTAGGAGTTCGAATTACTTAGAGAAGGATTTCACTATTTGGG
TGGGAGCAAGAGCTTGGGTAGGTGGAGGAAGATTTTATTGTTATGGAGCAAGAGTTCGGGTTTAG
CAGAATAGGAGTTCAAACTATGTCGTGTAAGATTTCACTAATATGGAGGAGTTTGGGTTATGGAA
GTAAGATTTTACCATTGTGGAGCAAGAGTTGAAGATGCTTGGAGTAAGATTTAATTGTTATGGAG
CAGAAGTTTGCATTGCTCGAAGTAGGATTTATGGAGCAAGAATTTAGGCTGCACGAAATAACATT
TCACTATTATGGACCTAGAATTTGGGTTGCATGAAGCAAGAGTTTAGGCTAGACAAACTATGATC
TCATTGTTAT
Found at i:19710457 original size:57 final size:57
Alignment explanation
Indices: 19710369--19710484 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 57
19710359 GAAATGAAAA
* * * *
19710369 ATCTTAACTAATATATAATATTAGTGTTTTAGGTAACTAATCTCCTAAGAATCAACT
1 ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAATCTCCTAAGAATCAACT
* *
19710426 ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAGTCTCCTAAGAATCAGCT
1 ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAATCTCCTAAGAATCAACT
19710483 AT
1 AT
19710485 ATAGTGTGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (57 bp):
ATCTTAACTAATATAGAATATCAATATTTTAGGTAACTAATCTCCTAAGAATCAACT
Found at i:19722669 original size:21 final size:21
Alignment explanation
Indices: 19722629--19722669 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
19722619 ATTTTTATTT
19722629 TTATTTTTTTATCCTTATGTAA
1 TTATTTTTTTAT-CTTATGTAA
19722651 TTATTATTTTTAT-TTATGT
1 TTATT-TTTTTATCTTATGT
19722670 TGGTATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (21 bp):
TTATTTTTTTATCTTATGTAA
Found at i:19729136 original size:138 final size:137
Alignment explanation
Indices: 19728813--19729203 Score: 424
Period size: 138 Copynumber: 2.8 Consensus size: 137
19728803 TTGAAGTAGT
* * * *
19728813 AGTGGGTCAGATTGAAACTAAAGTGACGAATCTTCTTTGCCTGAAGTTGTAGTGGAGCAAGATGA
1 AGTGGGTCAAAATGAAACTAAAGTGACGAATCTTATAT-CCTGAAGTTGTAGTGGAGCAAGATGA
* * * * * *
19728878 AACTATAAATCATATATCTCTGAAGTTGCAGTGGATCGGATTGAAGATACAATTCTTATACCCCT
65 AGCTACAAATCATATATCCCTGAAGTTGCAGTGGATCGGATTGAAGCTACAATTCCTATACACCT
*
19728943 GAAGTTGC
130 GAAGTTAC
* * * ** * * * *
19728951 AGTGGGTCGAAATGAAATTATAGTGGTGAATCTTATCTCCCTAAAGTTGCAGTGTAGCAAGATGA
1 AGTGGGTCAAAATGAAACTAAAGTGACGAATCTTATAT-CCTGAAGTTGTAGTGGAGCAAGATGA
* * * *
19729016 AGCTACAAATCCTATATCCCTGAAGTTACAGTGGATCAGATTGAAGCTACAATTCCTATACATCT
65 AGCTACAAATCATATATCCCTGAAGTTGCAGTGGATCGGATTGAAGCTACAATTCCTATACACCT
19729081 GAAGTTAC
130 GAAGTTAC
* * * *
19729089 AGTGGGTCAAAATGAAACTACAGTGACAAATCCTATATCTCTGAAGTTGTAGTGGATCAA-ATTG
1 AGTGGGTCAAAATGAAACTAAAGTGACGAATCTTATATC-CTGAAGTTGTAGTGGAGCAAGA-TG
* * * * * * *
19729153 AAGCTGCAAATCTTATAACCCTAAAGTTGCAATGGGTCGGATTGAATCTAC
64 AAGCTACAAATCATATATCCCTGAAGTTGCAGTGGATCGGATTGAAGCTAC
19729204 CATAGTGAGT
Statistics
Matches: 206, Mismatches: 45, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
137 2 0.01
138 204 0.99
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (137 bp):
AGTGGGTCAAAATGAAACTAAAGTGACGAATCTTATATCCTGAAGTTGTAGTGGAGCAAGATGAA
GCTACAAATCATATATCCCTGAAGTTGCAGTGGATCGGATTGAAGCTACAATTCCTATACACCTG
AAGTTAC
Found at i:19729189 original size:94 final size:94
Alignment explanation
Indices: 19729020--19729190 Score: 227
Period size: 94 Copynumber: 1.8 Consensus size: 94
19729010 AGATGAAGCT
* * * *
19729020 ACAAATCCTATATCCCTGAAGTTACAGTGGATCAGATTGAAGCTACAATTCCTATACATCTGAAG
1 ACAAATCCTATATCCCTGAAGTTACAGTGGATCAAATTGAAGCTACAAATCCTATACACCTAAAG
*
19729085 TTACAGTGGGTCAAAATGAAACTACAGTG
66 TTACAATGGGTCAAAATGAAACTACAGTG
* ** * *
19729114 ACAAATCCTATATCTCTGAAGTTGTAGTGGATCAAATTGAAGCTGCAAATCTTATA-ACCCTAAA
1 ACAAATCCTATATCCCTGAAGTTACAGTGGATCAAATTGAAGCTACAAATCCTATACA-CCTAAA
*
19729178 GTTGCAATGGGTC
65 GTTACAATGGGTC
19729191 GGATTGAATC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
93 1 0.02
94 64 0.98
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (94 bp):
ACAAATCCTATATCCCTGAAGTTACAGTGGATCAAATTGAAGCTACAAATCCTATACACCTAAAG
TTACAATGGGTCAAAATGAAACTACAGTG
Found at i:19729234 original size:94 final size:94
Alignment explanation
Indices: 19729057--19729707 Score: 621
Period size: 94 Copynumber: 6.9 Consensus size: 94
19729047 TGGATCAGAT
* ** * * * ** *
19729057 TGAAGCTACAATTCCTATACATCTGAAGTTACAGTGGGTCAAAATGAAACTA-CAGT-GACAAAT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGTTACCA-TAG-CGAAT
* * * * * *
19729120 CCTATATCTCTGAAGTTGTAGTGGATCAA-A
64 CTTATCTCCCTAAAGTTGTAGTAGAGCAAGA
* * * * * * * *
19729150 TTGAAGCTGCAAATCTTATAACCCTAAAGTTGCAATGGGTCGGATTGAA-TCTACCATAGTGAGT
1 -TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGT-TACCATAGCGAAT
* *
19729214 CTTATCTCCCTAAAGCTGTAGTGGAGCAAGA
64 CTTATCTCCCTAAAGTTGTAGTAGAGCAAGA
* * * *
19729245 TGGAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTTAGATTAAAGTTACCATAGCGAGTCT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCT
* *
19729310 TATCTCTCTAAAGTTGTAATAGAGCAAGA
66 TATCTCCCTAAAGTTGTAGTAGAGCAAGA
* * * * ** * * * *
19729339 TGAAGTTACAAATCCAATACCCTTTAAGTTATAGTAGGTCAGACTAAAGTTACCATAACGAATCT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCT
* * * * *
19729404 TATCCCCCTGAAGTT-AAGTGGAGTAAGA
66 TATCTCCCTAAAGTTGTAGTAGAGCAAGA
* **
19729432 TTG-AGCTACAAATCGTATACCCCTGAAGTTATAGTGGGTCAGATTGAAGTTACCATAGCGAATC
1 -TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATC
* *
19729496 TTATCTCCCTGAAGTTGTAGTAAAGCAAGA
65 TTATCTCCCTAAAGTTGTAGTAGAGCAAGA
* ** * * *
19729526 TGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAACTACAAATGGTGAATC
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGTTAC-CATAGCGAATC
* **
19729591 TTATCTCTCTAAAGTTACAGTAGAGCAAGA
65 TTATCTCCCTAAAGTTGTAGTAGAGCAAGA
* * *
19729621 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTAGGTCAGATTGAAATTACCATAGCGAAACT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCT
* *
19729686 TATCTCCCTGAAGTTGCAGTAG
66 TATCTCCCTAAAGTTGTAGTAG
19729708 GTCAGATTGA
Statistics
Matches: 457, Mismatches: 91, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
93 78 0.17
94 291 0.64
95 88 0.19
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (94 bp):
TGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCT
TATCTCCCTAAAGTTGTAGTAGAGCAAGA
Found at i:19729470 original size:187 final size:189
Alignment explanation
Indices: 19729213--19729701 Score: 610
Period size: 187 Copynumber: 2.6 Consensus size: 189
19729203 CCATAGTGAG
* * ** *
19729213 TCTTATCTCCCTAAAGCTGTAGTGGAGCAAGATGGAGCTACAAATCCTATACCCCTGAAGTTGCA
1 TCTTATCCCCCTAAAGTTACAGTGGAGCAAGATTGAGCTACAAATCCTATACCCCTGAAGTTGCA
* * * * *
19729278 GTGGGTTAGATTAAAGTTACCATAGCGAGTCTTATCTCTCTAAAGTTGTAATAGAGCAAGATGAA
66 GTGGGTCAGATTAAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGTAATAAAGCAAGATGAA
* * * * *
19729343 GTTACAAATCCAATACCCTTTAAGTTATAGTAGGTCAGACT-AAAGTTAC-CATAACGAA
131 GCTACAAATCCAATACCCCTGAAGTTATAGTAGGTCAGACTGAAA-CTACAAATAACGAA
* * * **
19729401 TCTTATCCCCCTGAAGTTA-AGTGGAGTAAGATTGAGCTACAAATCGTATACCCCTGAAGTTATA
1 TCTTATCCCCCTAAAGTTACAGTGGAGCAAGATTGAGCTACAAATCCTATACCCCTGAAGTTGCA
* *
19729465 GTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGTAGTAAAGCAAGATGAA
66 GTGGGTCAGATTAAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGTAATAAAGCAAGATGAA
* * * * ***
19729530 GCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAACTACAAATGGTGAA
131 GCTACAAATCCAATACCCCTGAAGTTATAGTAGGTCAGACTGAAACTACAAATAACGAA
* * *
19729589 TCTTATCTCTCTAAAGTTACAGTAGAGCAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTTGC
1 TCTTATCCCCCTAAAGTTACAGTGGAGCAAGATTG-AGCTACAAATCCTATACCCCTGAAGTTGC
* *
19729653 AGTAGGTCAGATTGAAA-TTACCATAGCGAAACTTATCTCCCTGAAGTTG
65 AGTGGGTCAGATT-AAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTG
19729702 CAGTAGGTCA
Statistics
Matches: 257, Mismatches: 39, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
187 135 0.53
188 41 0.16
189 79 0.31
190 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (189 bp):
TCTTATCCCCCTAAAGTTACAGTGGAGCAAGATTGAGCTACAAATCCTATACCCCTGAAGTTGCA
GTGGGTCAGATTAAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGTAATAAAGCAAGATGAA
GCTACAAATCCAATACCCCTGAAGTTATAGTAGGTCAGACTGAAACTACAAATAACGAA
Found at i:19729476 original size:43 final size:44
Alignment explanation
Indices: 19729013--19729582 Score: 163
Period size: 44 Copynumber: 12.3 Consensus size: 44
19729003 TGTAGCAAGA
* * * *
19729013 TGAAGCTACAAATCCTATATCCCTGAAGTTACAGTGGATCAGAT
1 TGAAGCTACAAATCTTATACCCCTGAAGTTATAGTGGGTCAGAT
* * ** * * *
19729057 TGAAGCTACAATTCCTATACATCTGAAGTTACAGTGGGTCAAAA
1 TGAAGCTACAAATCTTATACCCCTGAAGTTATAGTGGGTCAGAT
* * * * * * *
19729101 TGAAACTACAGTGACAAATCCTATATCTCTGAAGTTGTAGTGGATCAAAT
1 TG-AA--GC--T-ACAAATCTTATACCCCTGAAGTTATAGTGGGTCAGAT
* * * ** * *
19729151 TGAAGCTGCAAATCTTATAACCCTAAAGTTGCAATGGGTCGGAT
1 TGAAGCTACAAATCTTATACCCCTGAAGTTATAGTGGGTCAGAT
* * * *
19729195 TGAATCTACCATAGTGAGTCTTAT-CTCCCTAAAGCTGTAGTGGAG-CAAGA-
1 TGAAGCTA-CA-A---A-TCTTATAC-CCCTGAAGTTATAGTGG-GTC-AGAT
* * ** *
19729245 TGGAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTTAGAT
1 TGAAGCTACAAATCTTATACCCCTGAAGTTATAGTGGGTCAGAT
* * * * * * *
19729289 TAAAGTTACCATAGCGAGTCTTAT-CTCTCTAAAGTTGTAATAGAG-CAAGA-
1 TGAAGCTA-CA-A---A-TCTTATAC-CCCTGAAGTTATAGT-GGGTC-AGAT
* ** * * * *
19729339 TGAAGTTACAAATCCAATACCCTTTAAGTTATAGTAGGTCAGAC
1 TGAAGCTACAAATCTTATACCCCTGAAGTTATAGTGGGTCAGAT
* * * *
19729383 TAAAGTTACCATAACGAATCTTATCCCCCTGAAGTTA-AGTGGAGTAAGAT
1 TGAAG----C-T-ACAAATCTTATACCCCTGAAGTTATAGTGG-GTCAGAT
*
19729433 TG-AGCTACAAATCGTATACCCCTGAAGTTATAGTGGGTCAGAT
1 TGAAGCTACAAATCTTATACCCCTGAAGTTATAGTGGGTCAGAT
* * **
19729476 TGAAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGTAGTAAAG-CAAGA-
1 TGAAG----C-TA-CAAATCTTATAC-CCCTGAAGTTATAGT-GGGTC-AGAT
* *
19729526 TGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGAT
1 TGAAGCTACAAATCTTATACCCCTGAAGTTATAGTGGGTCAGAT
*
19729570 TGAAACTACAAAT
1 TGAAGCTACAAAT
19729583 GGTGAATCTT
Statistics
Matches: 389, Mismatches: 86, Indels: 102
0.67 0.15 0.18
Matches are distributed among these distances:
43 41 0.11
44 159 0.41
45 15 0.04
46 3 0.01
47 2 0.01
48 3 0.01
49 20 0.05
50 134 0.34
51 12 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (44 bp):
TGAAGCTACAAATCTTATACCCCTGAAGTTATAGTGGGTCAGAT
Found at i:19729579 original size:44 final size:44
Alignment explanation
Indices: 19728781--19729582 Score: 150
Period size: 44 Copynumber: 17.3 Consensus size: 44
19728771 AACAGATCGG
* * *
19728781 TGAAATCT-CAAATCCTATACCCTTGAAGTAGTAGTGGGTCAGAT
1 TGAAA-CTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
* * ***
19728825 TGAAACTAAAGTGACGAATCTTCTTTGCCTGAAGTTGTAGTGGAG-CAAGA-
1 TGAAAC-----T-ACAAATCTTATACCCCTGAAGTTGTAGTGG-GTC-AGAT
* * * * * * *
19728875 TGAAACTATAAATCATATATCTCTGAAGTTGCAGTGGATCGGAT
1 TGAAACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
* * *
19728919 TGAAGA-TACAATTCTTATACCCCTGAAGTTGCAGTGGGTC-GAAA
1 TGAA-ACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAG-AT
* * * * *
19728963 TGAAATTATAGTGGTGAATCTTAT-CTCCCTAAAGTTGCAGTGTAG-CAAGA-
1 TGAAACTACA------AATCTTATAC-CCCTGAAGTTGTAGTG-GGTC-AGAT
* * * ** *
19729013 TGAAGCTACAAATCCTATATCCCTGAAGTTACAGTGGATCAGAT
1 TGAAACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
* * * ** ** * *
19729057 TGAAGCTACAATTCCTATACATCTGAAGTTACAGTGGGTCAAAA
1 TGAAACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
* * * * *
19729101 TGAAACTACAGTGACAAATCCTATATCTCTGAAGTTGTAGTGGATCAAAT
1 TG-AA--AC--T-ACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
* * * * * * *
19729151 TGAAGCTGCAAATCTTATAACCCTAAAGTTGCAATGGGTCGGAT
1 TGAAACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
* * *
19729195 TGAATCTACCATAGTGAGTCTTAT-CTCCCTAAAGCTGTAGTGGAG-CAAGA-
1 TGAAACTA-CA-A---A-TCTTATAC-CCCTGAAGTTGTAGTGG-GTC-AGAT
* * * * *
19729245 TGGAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTTAGAT
1 TGAAACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
* * * * *
19729289 T-AAAGTTACCATAGCGAGTCTTAT-CTCTCTAAAGTTGTAATAGAG-CAAGA-
1 TGAAA-CTA-CA-A---A-TCTTATAC-CCCTGAAGTTGTAGT-GGGTC-AGAT
** ** * * * * *
19729339 TGAAGTTACAAATCCAATACCCTTTAAGTTATAGTAGGTCAGAC
1 TGAAACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
* * * * *
19729383 TAAAGTTACCATAACGAATCTTATCCCCCTGAAGTT-AAGTGGAGTAAGAT
1 TGAA---A-C-T-ACAAATCTTATACCCCTGAAGTTGTAGTGG-GTCAGAT
* * *
19729433 TG-AGCTACAAATCGTATACCCCTGAAGTTATAGTGGGTCAGAT
1 TGAAACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
* **
19729476 TGAAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGTAGTAAAG-CAAGA-
1 TGAA---A-C-TA-CAAATCTTATAC-CCCTGAAGTTGTAGT-GGGTC-AGAT
* *
19729526 TGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGAT
1 TGAAACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
19729570 TGAAACTACAAAT
1 TGAAACTACAAAT
19729583 GGTGAATCTT
Statistics
Matches: 548, Mismatches: 130, Indels: 160
0.65 0.16 0.19
Matches are distributed among these distances:
43 49 0.09
44 245 0.45
45 17 0.03
46 3 0.01
47 2 0.00
48 4 0.01
49 20 0.04
50 187 0.34
51 20 0.04
52 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
TGAAACTACAAATCTTATACCCCTGAAGTTGTAGTGGGTCAGAT
Found at i:19729697 original size:282 final size:282
Alignment explanation
Indices: 19729038--19729718 Score: 736
Period size: 282 Copynumber: 2.4 Consensus size: 282
19729028 TATATCCCTG
* * * ** * *
19729038 AAGTTACAGTGGATC-AGATTGAAGCTACAATTCCTATACATCTGAAGTTACAGTGGGTCAAAAT
1 AAGTTACAGTAGAGCAAGA-TGAAGCTACAAATCCTATACCCCTGAAGTTACAGTAGGTCAGAAT
* * * * * *
19729102 GAAACTA-CAGT-GAC-AAATCCTATATCTCTGAAGTTGTAGTGGATCAAATTGAAGCTGCAAAT
65 GAAATTACCA-TAG-CGAAA-CTTATCTCCCTGAAGTTGAAGTGGATCAAATTGAAGCTACAAAT
* * * * *
19729164 CTTATAACCCTAAAGTTGCAATGGGTCGGATTGAATCTACCATAGTGAGTCTTATCTCCCTAAAG
127 CGTATAACCCTAAAGTTACAATGGGTCAGATTGAATCTACCATAGCGAATCTTATCTCCCTAAAG
** * *
19729229 CTGTAGTGGAGCAAGATGGAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTTAGATTAAAG
192 CTGTAGTAAAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTAAAG
* * *
19729294 TTACCATAGCGAGTCTTATCTCTCTA
257 CTACAATAGCGAATCTTATCTCTCTA
** * * * * * * *
19729320 AAGTTGTAATAGAGCAAGATGAAGTTACAAATCCAATACCCTTTAAGTTATAGTAGGTCAGACT-
1 AAGTTACAGTAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTACAGTAGGTCAGAATG
* * *
19729384 AAAGTTACCATAACGAATCTTATCCCCCTGAAGTT-AAGTGGAGT-AAGATTG-AGCTACAAATC
66 AAA-TTACCATAGCGAAACTTATCTCCCTGAAGTTGAAGTGGA-TCAA-ATTGAAGCTACAAATC
* * * * *
19729446 GTATACCCCTGAAGTTATAGTGGGTCAGATTGAAGT-TACCATAGCGAATCTTATCTCCCTGAAG
128 GTATAACCCTAAAGTTACAATGGGTCAGATTGAA-TCTACCATAGCGAATCTTATCTCCCTAAAG
* *
19729510 TTGTAGTAAAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAA
192 CTGTAGTAAAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATT-AAA
* *
19729575 -CTACAAATGGTGAATCTTATCTCTCTA
256 GCTAC-AATAGCGAATCTTATCTCTCTA
* *
19729602 AAGTTACAGTAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTAGGTCAGATTG
1 AAGTTACAGTAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTACAGTAGGTCAGAATG
* *
19729667 AAATTACCATAGCGAAACTTATCTCCCTGAAGTTGCAGTAGG-TCAGATTGAA
66 AAATTACCATAGCGAAACTTATCTCCCTGAAGTTGAAGT-GGATCAAATTGAA
19729719 ATTACCATAG
Statistics
Matches: 323, Mismatches: 61, Indels: 29
0.78 0.15 0.07
Matches are distributed among these distances:
281 131 0.41
282 175 0.54
283 15 0.05
284 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (282 bp):
AAGTTACAGTAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTACAGTAGGTCAGAATG
AAATTACCATAGCGAAACTTATCTCCCTGAAGTTGAAGTGGATCAAATTGAAGCTACAAATCGTA
TAACCCTAAAGTTACAATGGGTCAGATTGAATCTACCATAGCGAATCTTATCTCCCTAAAGCTGT
AGTAAAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGATTAAAGCTAC
AATAGCGAATCTTATCTCTCTA
Found at i:19729769 original size:50 final size:50
Alignment explanation
Indices: 19729641--19729755 Score: 230
Period size: 50 Copynumber: 2.3 Consensus size: 50
19729631 AATCCTATAC
19729641 CCCTGAAGTTGCAGTAGGTCAGATTGAAATTACCATAGCGAAACTTATCT
1 CCCTGAAGTTGCAGTAGGTCAGATTGAAATTACCATAGCGAAACTTATCT
19729691 CCCTGAAGTTGCAGTAGGTCAGATTGAAATTACCATAGCGAAACTTATCT
1 CCCTGAAGTTGCAGTAGGTCAGATTGAAATTACCATAGCGAAACTTATCT
19729741 CCCTGAAGTTGCAGT
1 CCCTGAAGTTGCAGT
19729756 GGAACAAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (50 bp):
CCCTGAAGTTGCAGTAGGTCAGATTGAAATTACCATAGCGAAACTTATCT
Found at i:19729812 original size:144 final size:145
Alignment explanation
Indices: 19729533--19729847 Score: 350
Period size: 144 Copynumber: 2.2 Consensus size: 145
19729523 AGATGAAGCT
* * * * * *
19729533 ACAAATCCTATAC-CCCTGAAGTTGTAGTGGGTCAGATTGAAACTACAAATGGTGAATCTTATCT
1 ACAAATCTTAT-CTCCCTGAAGTTGCAGTAGGTCAGATTGAAACTACAAATAGCGAAACTTATCT
* * * * *
19729597 CTCTAAAGTTACAGTAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGCAGTAGGTCA
65 CCCTAAAGTTACAGTAGAACAAAATGAAACTACAAATCCTACACCCCTGAAGTTGCAGTAGGTCA
* * *
19729662 GATTGAAATTACCATA
130 GATTGAAACTACAACA
* * *
19729678 GCGAAA-CTTATCTCCCTGAAGTTGCAGTAGGTCAGATTGAAATTAC-CATAGCGAAACTTATCT
1 AC-AAATCTTATCTCCCTGAAGTTGCAGTAGGTCAGATTGAAACTACAAATAGCGAAACTTATCT
* * * * *
19729741 CCCTGAAGTTGCAGTGGAACAAAATGAAACTACAAATCCTACACCCCTGAAGTTGTA-TTGAGTC
65 CCCTAAAGTTACAGTAGAACAAAATGAAACTACAAATCCTACACCCCTGAAGTTGCAGTAG-GTC
* *
19729805 GGGTTGAAACTACAACA
129 AGATTGAAACTACAACA
*
19729822 ACAAATCTTATCTCCTTGAAGTTGCA
1 ACAAATCTTATCTCCCTGAAGTTGCA
19729848 ATAGAGCAAG
Statistics
Matches: 140, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
143 5 0.04
144 97 0.69
145 35 0.25
146 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (145 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTAGGTCAGATTGAAACTACAAATAGCGAAACTTATCTC
CCTAAAGTTACAGTAGAACAAAATGAAACTACAAATCCTACACCCCTGAAGTTGCAGTAGGTCAG
ATTGAAACTACAACA
Found at i:19737298 original size:3 final size:3
Alignment explanation
Indices: 19737290--19737318 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19737280 CAAGGATCCT
19737290 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
19737319 TCCTGCAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:19740476 original size:11 final size:11
Alignment explanation
Indices: 19740455--19740487 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19740445 ATTTATTTTG
19740455 AAATA-AAAAA
1 AAATATAAAAA
19740465 AAATATAAAAA
1 AAATATAAAAA
*
19740476 AAATTTAAAAA
1 AAATATAAAAA
19740487 A
1 A
19740488 TGGAGCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATATAAAAA
Found at i:19750650 original size:24 final size:24
Alignment explanation
Indices: 19750623--19750672 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
19750613 TCTACCAAAG
19750623 ATTTTAAAGCATGAAGTCAAAACA
1 ATTTTAAAGCATGAAGTCAAAACA
19750647 ATTTTAAAGCATGAAGTCAAAACA
1 ATTTTAAAGCATGAAGTCAAAACA
19750671 AT
1 AT
19750673 CACTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (24 bp):
ATTTTAAAGCATGAAGTCAAAACA
Found at i:19753121 original size:18 final size:18
Alignment explanation
Indices: 19753100--19753142 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
19753090 ATTTTACATA
*
19753100 TTTTAAATTATTCTAATT
1 TTTTAAATTATTATAATT
* *
19753118 TTTTAAGTTATTATTATT
1 TTTTAAATTATTATAATT
19753136 TTTTAAA
1 TTTTAAA
19753143 AATATATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTAAATTATTATAATT
Found at i:19753256 original size:25 final size:25
Alignment explanation
Indices: 19753228--19753276 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
19753218 TTTGAAAATA
19753228 TATAATTTATAAATATATAAAAACG
1 TATAATTTATAAATATATAAAAACG
* * *
19753253 TATAGTTTATAAATTTATATAAAC
1 TATAATTTATAAATATATAAAAAC
19753277 ACATAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (25 bp):
TATAATTTATAAATATATAAAAACG
Found at i:19754752 original size:32 final size:32
Alignment explanation
Indices: 19754711--19754779 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
19754701 TAAATGCTAT
* *
19754711 TTAAATAATTGACTATAATGATACATAAAATA
1 TTAAATAATTGAATATAATGATACAAAAAATA
* *
19754743 TTAAATAATTTAATATAATGATATAAAAAATA
1 TTAAATAATTGAATATAATGATACAAAAAATA
19754775 -TAAAT
1 TTAAAT
19754780 TAATCTAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 5 0.15
32 28 0.85
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (32 bp):
TTAAATAATTGAATATAATGATACAAAAAATA
Found at i:19755369 original size:17 final size:17
Alignment explanation
Indices: 19755349--19755387 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
19755339 ATAAAATTAT
19755349 TAAAAAATTAAAAAATA
1 TAAAAAATTAAAAAATA
* * *
19755366 TAAATATTTAGAAAATA
1 TAAAAAATTAAAAAATA
19755383 TAAAA
1 TAAAA
19755388 CCAAGAGGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
TAAAAAATTAAAAAATA
Found at i:19755373 original size:24 final size:26
Alignment explanation
Indices: 19755338--19755387 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
19755328 CAAGAAATGC
19755338 AATAAAATTA-TTAAAAAAT-TAAAA
1 AATAAAATTATTTAAAAAATATAAAA
*
19755362 AATATAAA-TATTTAGAAAATATAAAA
1 AATA-AAATTATTTAAAAAATATAAAA
19755388 CCAAGAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 6 0.27
25 11 0.50
26 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
AATAAAATTATTTAAAAAATATAAAA
Found at i:19766550 original size:24 final size:25
Alignment explanation
Indices: 19766490--19766559 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
19766480 AGCGTCCCGA
* *
19766490 TATATGGCTC-TCCAGAACTTCCTGT
1 TATATGGCTCTTAC-GAGCTTCCTGT
* *
19766515 TATATGGTTCTTGCGAGCTTCCTGT
1 TATATGGCTCTTACGAGCTTCCTGT
*
19766540 T-TATGGCTCTTATGAGCTTC
1 TATATGGCTCTTACGAGCTTC
19766560 TCGATAATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 16 0.42
25 20 0.53
26 2 0.05
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (25 bp):
TATATGGCTCTTACGAGCTTCCTGT
Found at i:19766574 original size:25 final size:24
Alignment explanation
Indices: 19766542--19766627 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 24
19766532 CTTCCTGTTT
19766542 ATGGCTCTTATGAGCTTCTCGATA
1 ATGGCTCTTATGAGCTTCTCGATA
19766566 ATTGGCTCTTCGGA-GAGCTTCTCGATA
1 A-TGGCTCTT---ATGAGCTTCTCGATA
*
19766593 ACTGACTCTTATGAGCTTC-CTGATTA
1 A-TGGCTCTTATGAGCTTCTC-GA-TA
19766619 ATGGCTCTT
1 ATGGCTCTT
19766628 CAAAGCTTCC
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
24 3 0.06
25 24 0.46
26 3 0.06
27 21 0.40
28 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (24 bp):
ATGGCTCTTATGAGCTTCTCGATA
Found at i:19766716 original size:25 final size:25
Alignment explanation
Indices: 19766676--19766734 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
19766666 TATGGCTCTT
**
19766676 ATGAGCTTCTTGTTATATAGCTCGA
1 ATGAGCTTCTCATTATATAGCTCGA
*
19766701 ATGAGCTTCTCATTATATGGCTCGA
1 ATGAGCTTCTCATTATATAGCTCGA
*
19766726 AAGAGCTTC
1 ATGAGCTTC
19766735 CCGTTTACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (25 bp):
ATGAGCTTCTCATTATATAGCTCGA
Found at i:19770478 original size:21 final size:21
Alignment explanation
Indices: 19770437--19770489 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
19770427 CTACAACTTA
* * *
19770437 AAGCGGAGGCAGCAGCGAGGG
1 AAGCAGAGGCAGCAACAAGGG
19770458 AAGCAGAGGCAGCAACAAGGG
1 AAGCAGAGGCAGCAACAAGGG
* *
19770479 CATCAGAGGCA
1 AAGCAGAGGCA
19770490 ACAAGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACAAGGG
Found at i:19770851 original size:43 final size:44
Alignment explanation
Indices: 19770803--19770900 Score: 135
Period size: 43 Copynumber: 2.2 Consensus size: 44
19770793 GTGTTTTCCC
* * *
19770803 ACAAACGCCATTATAGAACATGATCTTTAGTAGCGATTTTA-CT
1 ACAAACGCCACTAAAGAACATGATCTTTAGTAGCGATTCTAGCT
* * *
19770846 ACAAACGCCGCTAAAGAACATGATCTTTTGTGGCGATTCTAGCT
1 ACAAACGCCACTAAAGAACATGATCTTTAGTAGCGATTCTAGCT
19770890 ACAAACGCCAC
1 ACAAACGCCAC
19770901 AACATGCTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 35 0.74
44 12 0.26
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (44 bp):
ACAAACGCCACTAAAGAACATGATCTTTAGTAGCGATTCTAGCT
Found at i:19772215 original size:9 final size:9
Alignment explanation
Indices: 19772196--19772255 Score: 61
Period size: 9 Copynumber: 6.6 Consensus size: 9
19772186 TTTATATTTT
*
19772196 TAAAAAATA
1 TAAAAATTA
*
19772205 TAAATATTA
1 TAAAAATTA
19772214 TAAAAATTA
1 TAAAAATTA
19772223 TAAAGAATATA
1 TAAA-AAT-TA
19772234 TAAAAA-TA
1 TAAAAATTA
19772242 TTAAAAATTA
1 -TAAAAATTA
19772252 -AAAA
1 TAAAA
19772256 TTTTCTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
8 6 0.14
9 25 0.57
10 7 0.16
11 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:19772339 original size:23 final size:23
Alignment explanation
Indices: 19772313--19772357 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
19772303 CTTAAACTTT
* *
19772313 AAAAACCCTTACAAACCCTAAAC
1 AAAAACCCTTAAAAAACCTAAAC
19772336 AAAAACCCTTAAAAAACCTAAA
1 AAAAACCCTTAAAAAACCTAAA
19772358 ATCTTATCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.29, G:0.00, T:0.13
Consensus pattern (23 bp):
AAAAACCCTTAAAAAACCTAAAC
Found at i:19779383 original size:23 final size:22
Alignment explanation
Indices: 19779357--19779400 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19779347 ATACAAAAAC
*
19779357 AAGGGAACATTGCCTCGAGACAT
1 AAGGGAA-AATGCCTCGAGACAT
*
19779380 AAGGGAAAATGTCTCGAGACA
1 AAGGGAAAATGCCTCGAGACA
19779401 AAAATCCCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.16
Consensus pattern (22 bp):
AAGGGAAAATGCCTCGAGACAT
Found at i:19781235 original size:51 final size:51
Alignment explanation
Indices: 19781168--19781266 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 51
19781158 CTATTATTCA
* *
19781168 CTCAATTTCCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCCTATTTAAT
1 CTCAATTTCATCTCAATTTCCTCT-CAAATTTCTCTCAAACCCCTATTTAAT
* *
19781219 CTCAATTTGATCTCAATTTCCTCTCAAATTTCTCTTAAACCCCTATTT
1 CTCAATTTCATCTCAATTTCCTCTCAAATTTCTCTCAAACCCCTATTT
19781267 TTAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.43
Consensus pattern (51 bp):
CTCAATTTCATCTCAATTTCCTCTCAAATTTCTCTCAAACCCCTATTTAAT
Found at i:19781253 original size:11 final size:11
Alignment explanation
Indices: 19781168--19781250 Score: 52
Period size: 11 Copynumber: 7.8 Consensus size: 11
19781158 CTATTATTCA
19781168 CTCAATTTCCT
1 CTCAATTTCCT
19781179 CTCAATTTCCT
1 CTCAATTTCCT
19781190 -TCCAAATTT-CT
1 CT-C-AATTTCCT
*
19781201 CTCAA-ATCC-
1 CTCAATTTCCT
**
19781210 CT--ATTTAAT
1 CTCAATTTCCT
**
19781219 CTCAATTTGAT
1 CTCAATTTCCT
19781230 CTCAATTTCCT
1 CTCAATTTCCT
19781241 CTCAAATTTC
1 CTC-AATTTC
19781251 TCTTAAACCC
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 5 0.09
10 4 0.07
11 33 0.59
12 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.43
Consensus pattern (11 bp):
CTCAATTTCCT
Found at i:19791779 original size:15 final size:17
Alignment explanation
Indices: 19791759--19791795 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
19791749 ATAAATATGA
19791759 TATTTTT-ATTTCT-TT
1 TATTTTTAATTTCTGTT
*
19791774 TATTTTTAATTTTTGTT
1 TATTTTTAATTTCTGTT
19791791 TATTT
1 TATTT
19791796 ATTGTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 5 0.26
17 7 0.37
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (17 bp):
TATTTTTAATTTCTGTT
Done.