Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 161 of 205
Found at i:48075553 original size:109 final size:109
Alignment explanation
Indices: 48075362--48075577 Score: 423
Period size: 109 Copynumber: 2.0 Consensus size: 109
48075352 TAGAATGTAA
*
48075362 AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACATGTTTGGAGGACAAAG
1 AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACACGTTTGGAGGACAAAG
48075427 AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTTGC
66 AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTTGC
48075471 AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACACGTTTGGAGGACAAAG
1 AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACACGTTTGGAGGACAAAG
48075536 AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTT
66 AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTT
48075578 ATGTTCTCTA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 106 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (109 bp):
AATTTACAAGAATTAAGATTGGTATACTGTATAAATACAAATTGGGACACGTTTGGAGGACAAAG
AGCCTTACCTCCTCTGCACGTAATGTCCAATATTGATCATTTGC
Found at i:48083695 original size:32 final size:32
Alignment explanation
Indices: 48083654--48083717 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
48083644 TAGAACAGCT
48083654 TCAAGGAGGGGCATAAAGTTTAAGACCACACC
1 TCAAGGAGGGGCATAAAGTTTAAGACCACACC
48083686 TCAAGGAGGGGCATAAAGTTTAAGACCACACC
1 TCAAGGAGGGGCATAAAGTTTAAGACCACACC
48083718 CCTTCTGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.16
Consensus pattern (32 bp):
TCAAGGAGGGGCATAAAGTTTAAGACCACACC
Found at i:48091792 original size:20 final size:20
Alignment explanation
Indices: 48091767--48091810 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
48091757 ACTCAGGGGG
* *
48091767 ACTTCTACCATTACAAGTCC
1 ACTTCTACCAATACAAGCCC
*
48091787 ACTTCTATCAATACAAGCCC
1 ACTTCTACCAATACAAGCCC
48091807 ACTT
1 ACTT
48091811 TTAACCATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.30
Consensus pattern (20 bp):
ACTTCTACCAATACAAGCCC
Found at i:48091820 original size:20 final size:20
Alignment explanation
Indices: 48091767--48091821 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
48091757 ACTCAGGGGG
*
48091767 ACTTCT-ACCATTACAAGTCC
1 ACTTCTAACCA-TACAAGCCC
* *
48091787 ACTTCTATCAATACAAGCCC
1 ACTTCTAACCATACAAGCCC
*
48091807 ACTTTTAACCATACA
1 ACTTCTAACCATACA
48091822 TTTTGTGAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.29
Consensus pattern (20 bp):
ACTTCTAACCATACAAGCCC
Found at i:48096413 original size:21 final size:21
Alignment explanation
Indices: 48096379--48096419 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
48096369 AAAAACCATG
* * *
48096379 CATTAATTATTTATGTTTAAA
1 CATTAATCAATTATGATTAAA
48096400 CATTAATCAATTATGATTAA
1 CATTAATCAATTATGATTAA
48096420 TATATGTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (21 bp):
CATTAATCAATTATGATTAAA
Found at i:48099054 original size:40 final size:39
Alignment explanation
Indices: 48098973--48099074 Score: 156
Period size: 40 Copynumber: 2.6 Consensus size: 39
48098963 ACAAATTTAA
*
48098973 TATTAAATTAA-ATTAAA-T-ACTTATCTTGATAATATTT
1 TATTAATTTAATATTAAAGTGA-TTATCTTGATAATATTT
48099010 TATTAATTTAATATTAAAGTGATTATCTTGATAAATATTT
1 TATTAATTTAATATTAAAGTGATTATCTTGAT-AATATTT
48099050 TATTAATTTAATATTAAAGTGATTA
1 TATTAATTTAATATTAAAGTGATTA
48099075 AGTTTAATCA
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
37 10 0.17
38 6 0.10
39 11 0.18
40 33 0.55
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (39 bp):
TATTAATTTAATATTAAAGTGATTATCTTGATAATATTT
Found at i:48110124 original size:20 final size:23
Alignment explanation
Indices: 48110091--48110136 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
48110081 TTTTAAAAAA
48110091 TTCAAATATTATAA-TAAAA-ATT
1 TTCAAATA-TATAATTAAAATATT
48110113 TTCAAATA-ATAATTAAAATATT
1 TTCAAATATATAATTAAAATATT
48110135 TT
1 TT
48110137 TAACTTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 5 0.23
22 13 0.59
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
TTCAAATATATAATTAAAATATT
Found at i:48110129 original size:21 final size:22
Alignment explanation
Indices: 48110083--48110136 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
48110073 ATATTAATTT
*
48110083 TTAAAAA-ATTCAAATATTATAA
1 TTAAAAATTTTCAAATA-TATAA
48110105 -TAAAAATTTTCAAATA-ATAA
1 TTAAAAATTTTCAAATATATAA
48110125 TTAAAATATTTT
1 TTAAAA-ATTTT
48110137 TAACTTACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.14
21 11 0.39
22 13 0.46
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAAAAATTTTCAAATATATAA
Found at i:48110443 original size:26 final size:26
Alignment explanation
Indices: 48110405--48110455 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
48110395 AATCCCCTAG
*
48110405 TTTTACCATTGTATTTTCTTTAACAC
1 TTTTACCACTGTATTTTCTTTAACAC
48110431 TTTTACCACTGTATTTTCTTTAACA
1 TTTTACCACTGTATTTTCTTTAACA
48110456 AAGATTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTTACCACTGTATTTTCTTTAACAC
Found at i:48114597 original size:58 final size:61
Alignment explanation
Indices: 48114532--48114666 Score: 163
Period size: 58 Copynumber: 2.3 Consensus size: 61
48114522 AGTTCAACGA
48114532 TGATTAAATTTAATCACTT-TA-ATATTAAATTAATAAAATAC-T-TA-ACAAGATAAATATT
1 TGATTAAATTTAAT-A-TTATATATATTAAATTAATAAAATACTTATATACAAGATAAATATT
* * *
48114590 TGATTAAATTTAATATTATATCTATTAAATTACTAGAATACTTATATACAAGATAAATATT
1 TGATTAAATTTAATATTATATATATTAAATTAATAAAATACTTATATACAAGATAAATATT
** *
48114651 AAATTAATTTTAATAT
1 TGATTAAATTTAATAT
48114667 GAAAATTATT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
56 2 0.03
57 3 0.05
58 31 0.47
59 1 0.02
60 2 0.03
61 27 0.41
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (61 bp):
TGATTAAATTTAATATTATATATATTAAATTAATAAAATACTTATATACAAGATAAATATT
Found at i:48114663 original size:61 final size:58
Alignment explanation
Indices: 48114554--48114666 Score: 154
Period size: 61 Copynumber: 1.9 Consensus size: 58
48114544 ATCACTTTAA
**
48114554 TATTAAATTAATAAAATACTTAACAAGATAAATATTTGATTAAATTTAATATTATATC
1 TATTAAATTAATAAAATACTTAACAAGATAAATATTAAATTAAATTTAATATTATATC
* * *
48114612 TATTAAATTACTAGAATACTTATATACAAGATAAATATTAAATTAATTTTAATAT
1 TATTAAATTAATAAAATAC-T-TA-ACAAGATAAATATTAAATTAAATTTAATAT
48114667 GAAAATTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 17 0.36
59 1 0.02
60 2 0.04
61 27 0.57
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (58 bp):
TATTAAATTAATAAAATACTTAACAAGATAAATATTAAATTAAATTTAATATTATATC
Found at i:48114677 original size:61 final size:58
Alignment explanation
Indices: 48114554--48114685 Score: 149
Period size: 61 Copynumber: 2.2 Consensus size: 58
48114544 ATCACTTTAA
** * *
48114554 TATTAAATTAATAAAATACTTAACAAGATAAATATTTGATTAAATTTAATATTATATC
1 TATTAAATTAATAAAATACTTAACAAGATAAATATTAAATTAAATTTAATATAAAATC
* * *
48114612 TATTAAATTACTAGAATACTTATATACAAGATAAATATTAAATTAATTTTAATATGAAAAT-
1 TATTAAATTAATAAAATAC-T-TA-ACAAGATAAATATTAAATTAAATTTAATAT-AAAATC
*
48114673 TATTAAAATAATA
1 TATTAAATTAATA
48114686 TTATTTTTGG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 17 0.28
59 1 0.02
60 2 0.03
61 38 0.62
62 3 0.05
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (58 bp):
TATTAAATTAATAAAATACTTAACAAGATAAATATTAAATTAAATTTAATATAAAATC
Found at i:48115135 original size:19 final size:19
Alignment explanation
Indices: 48115102--48115141 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
48115092 TTCAAATTAT
*
48115102 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
48115121 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
48115140 AT
1 AT
48115142 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:48121269 original size:19 final size:20
Alignment explanation
Indices: 48121233--48121270 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
48121223 TACACACAAC
*
48121233 TTTTTTTTATTAAAAAAATG
1 TTTTTTTTATAAAAAAAATG
48121253 TTTTTTTT-TAAAAAAAAT
1 TTTTTTTTATAAAAAAAAT
48121271 ACAAATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTTTTATAAAAAAAATG
Found at i:48125116 original size:44 final size:44
Alignment explanation
Indices: 48125053--48125253 Score: 330
Period size: 44 Copynumber: 4.6 Consensus size: 44
48125043 CATATCACAT
* * *
48125053 CACTTGTCATTTGTCACTGATAAGATAAGTGTAACTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
48125097 CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
*
48125141 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
* *
48125185 CACTAATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
* *
48125229 CACTAATCACTTGTTACTGATCAGA
1 CACTTATCACTTGTCACTGATCAGA
48125254 AGTACTCAAA
Statistics
Matches: 151, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 151 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTAC
Found at i:48149961 original size:61 final size:60
Alignment explanation
Indices: 48149896--48150034 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
48149886 ATCCTAAATA
* * ** *
48149896 TAAAATATTCAACAAATTTAGCCATCAATGTTTACAAAATTTGTCATTTTAGTT-TGAATTC
1 TAAAA-ATTCAATAAATTTAACCATCAACATTTACAAAATTTGTCAATTTAGTTCT-AATTC
* * *
48149957 TAAAAAATCAATAAATTTAACCTTCAACATTTACAAAGTTTGTCAATTTAGTTCTAATTC
1 TAAAAATTCAATAAATTTAACCATCAACATTTACAAAATTTGTCAATTTAGTTCTAATTC
48150017 TAAAAAATTCAATAAATT
1 T-AAAAATTCAATAAATT
48150035 AATTTTTGGT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 46 0.69
61 21 0.31
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (60 bp):
TAAAAATTCAATAAATTTAACCATCAACATTTACAAAATTTGTCAATTTAGTTCTAATTC
Found at i:48151575 original size:3 final size:3
Alignment explanation
Indices: 48151567--48151602 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
48151557 CCGAAAATGA
48151567 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
48151603 CTTGCTACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:48155555 original size:14 final size:14
Alignment explanation
Indices: 48155538--48155570 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
48155528 ACAATATCCA
48155538 AACAATAATAAAAT
1 AACAATAATAAAAT
*
48155552 AACAATAATATAAT
1 AACAATAATAAAAT
48155566 AACAA
1 AACAA
48155571 AACAACACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (14 bp):
AACAATAATAAAAT
Found at i:48155574 original size:33 final size:33
Alignment explanation
Indices: 48155508--48155575 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 33
48155498 TAGCAAAAGT
* * * * *
48155508 AATAATAAAATAAGATTTATACAATATCCAAAC
1 AATAATAAAATAACAATAATACAATAACAAAAC
*
48155541 AATAATAAAATAACAATAATATAATAACAAAAC
1 AATAATAAAATAACAATAATACAATAACAAAAC
48155574 AA
1 AA
48155576 CACCGCCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.65, C:0.10, G:0.01, T:0.24
Consensus pattern (33 bp):
AATAATAAAATAACAATAATACAATAACAAAAC
Found at i:48157675 original size:108 final size:106
Alignment explanation
Indices: 48157544--48157856 Score: 407
Period size: 108 Copynumber: 2.9 Consensus size: 106
48157534 AAGAAAAAGG
* **
48157544 AAAAAAAAAATTTGGGTATTGGTCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAATTTTC
1 AAAAAAAAATTTTGGGTGCTGGTCTGTCAATGGCCGGCACCCAGTACAA-TTTAAAAAAATTTTC
48157609 TTTTTTTTAATTGTTAGAATCAGATATCAGTATACGAAAAAAAT
65 TTTTTTTT--TTGTTAGAATCAGATATCAGTATACGAAAAAAAT
* * *
48157653 -AAAAAAAATTTTGGGTGCTGGTCTGTCAATGGTCGGCATCCAGTACAATTTAAAAAAA-ATTCT
1 AAAAAAAAATTTTGGGTGCTGGTCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAATTTTCT
* *
48157716 TTTTTTTTTGTGTCAAAATCAGATATCAGTATACGAAAAAAGT
66 TTTTTTTTTGT-T-AGAATCAGATATCAGTATACGAAAAAAAT
* * * *
48157759 AAAAAAAAATTTATGGGTGCTGGCCTGTCAATGGCTGGCACCCAGTATAATTT-AAAAATTTTTC
1 AAAAAAAAATTT-TGGGTGCTGGTCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAATTTTC
* * *
48157823 ATTTTTTTCTTGTAAGAATCAAATATCAGTATAC
65 -TTTTTTTTTTGTTAGAATCAGATATCAGTATAC
48157857 TTTTTTCATA
Statistics
Matches: 179, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
104 4 0.02
105 1 0.01
106 38 0.21
107 44 0.25
108 81 0.45
109 11 0.06
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (106 bp):
AAAAAAAAATTTTGGGTGCTGGTCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAATTTTCT
TTTTTTTTTGTTAGAATCAGATATCAGTATACGAAAAAAAT
Found at i:48157891 original size:20 final size:20
Alignment explanation
Indices: 48157866--48157903 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
48157856 CTTTTTTCAT
48157866 ATACTGATATCTGATTCTAA
1 ATACTGATATCTGATTCTAA
48157886 ATACTGATATCTGATTCT
1 ATACTGATATCTGATTCT
48157904 GACACGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
ATACTGATATCTGATTCTAA
Found at i:48159900 original size:15 final size:15
Alignment explanation
Indices: 48159880--48159929 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
48159870 CCTTGACACG
48159880 AATTCTCAACGAACA
1 AATTCTCAACGAACA
*
48159895 AATTCTTCATCG--CA
1 AATTC-TCAACGAACA
*
48159909 AACTCTCAACGAACA
1 AATTCTCAACGAACA
*
48159924 AGTTCT
1 AATTCT
48159930 TCACCTATTC
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 11 0.41
16 5 0.19
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (15 bp):
AATTCTCAACGAACA
Found at i:48160171 original size:32 final size:32
Alignment explanation
Indices: 48160130--48160195 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
48160120 TCTTGTAGCT
48160130 CAGATTGTTTATTGTCCATTTCCTTGGCATCC
1 CAGATTGTTTATTGTCCATTTCCTTGGCATCC
48160162 CAGATTGTTTATTGTCCATTTCCTTGGCATCC
1 CAGATTGTTTATTGTCCATTTCCTTGGCATCC
48160194 CA
1 CA
48160196 TTGAATCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.17, C:0.26, G:0.15, T:0.42
Consensus pattern (32 bp):
CAGATTGTTTATTGTCCATTTCCTTGGCATCC
Found at i:48167566 original size:3 final size:3
Alignment explanation
Indices: 48167496--48167553 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
48167486 GGAGCTCTTC
48167496 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
48167544 TAT TAT TAT T
1 TAT TAT TAT T
48167554 TAAACATATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:48176489 original size:14 final size:14
Alignment explanation
Indices: 48176470--48176507 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
48176460 ATGATATTAG
48176470 AATAAAAAAATAAA
1 AATAAAAAAATAAA
48176484 AATAAAAAAA-AAA
1 AATAAAAAAATAAA
*
48176497 CATAAAAAAAT
1 AATAAAAAAAT
48176508 TGTCATGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (14 bp):
AATAAAAAAATAAA
Found at i:48176651 original size:18 final size:19
Alignment explanation
Indices: 48176603--48176652 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
48176593 ATTACTACCC
*
48176603 TAATACTAAT-ATAAATAA
1 TAATAATAATAATAAATAA
* *
48176621 TAA-AAGAAAAATAAATAA
1 TAATAATAATAATAAATAA
48176639 -AATAATAATAATAA
1 TAATAATAATAATAA
48176653 CAAGGATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
TAATAATAATAATAAATAA
Found at i:48178325 original size:18 final size:18
Alignment explanation
Indices: 48178299--48178336 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
48178289 TTAATAAAAT
48178299 AAATGG-AAATGGAAATTG
1 AAATGGAAAAT-GAAATTG
*
48178317 AAATTGAAAATGAAATTG
1 AAATGGAAAATGAAATTG
48178335 AA
1 AA
48178337 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
AAATGGAAAATGAAATTG
Found at i:48178338 original size:5 final size:5
Alignment explanation
Indices: 48178330--48178374 Score: 81
Period size: 5 Copynumber: 9.0 Consensus size: 5
48178320 TTGAAAATGA
*
48178330 AATTG AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
48178375 TCCTTTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:48185214 original size:45 final size:45
Alignment explanation
Indices: 48185150--48185239 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
48185140 GTGGTTGGCA
48185150 GGAAATGTTGCATTATTTATATTTTGAAGAATTATAAAAGCATGT
1 GGAAATGTTGCATTATTTATATTTTGAAGAATTATAAAAGCATGT
*
48185195 GGAAATGTTGCATTATTTATATTTTGAAGAATTATAAAGGCATGT
1 GGAAATGTTGCATTATTTATATTTTGAAGAATTATAAAAGCATGT
48185240 TAATAATTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (45 bp):
GGAAATGTTGCATTATTTATATTTTGAAGAATTATAAAAGCATGT
Found at i:48185797 original size:18 final size:18
Alignment explanation
Indices: 48185771--48185808 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
48185761 TTAATAAAAT
48185771 AAATGG-AAATGGAAATTG
1 AAATGGAAAAT-GAAATTG
*
48185789 AAATTGAAAATGAAATTG
1 AAATGGAAAATGAAATTG
48185807 AA
1 AA
48185809 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
AAATGGAAAATGAAATTG
Found at i:48185810 original size:5 final size:5
Alignment explanation
Indices: 48185802--48185841 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
48185792 TTGAAAATGA
*
48185802 AATTG AATTT AATTT AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
48185842 TCCTTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:48187771 original size:29 final size:30
Alignment explanation
Indices: 48187734--48187853 Score: 85
Period size: 29 Copynumber: 4.1 Consensus size: 30
48187724 AAAAAATAGA
* *
48187734 AAAAT-TATA-AATATCGTAAAAAAATTAT
1 AAAATATATAGAAAATCATAAAAAAATTAT
* *
48187762 AAAATATATAG-AAAT-ATAACAAATTTAAT
1 AAAATATATAGAAAATCATAAAAAAATT-AT
* *
48187791 AAAGTCATA-AGAAAATTATAAAAAAATGTA-
1 AAAAT-ATATAGAAAATCATAAAAAAAT-TAT
*
48187821 AATAA-ATATA-AAAATCGTAAAAAAATTAT
1 AA-AATATATAGAAAATCATAAAAAAATTAT
48187850 AAAA
1 AAAA
48187854 ATTATCGTAC
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
28 17 0.24
29 34 0.47
30 10 0.14
31 10 0.14
32 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (30 bp):
AAAATATATAGAAAATCATAAAAAAATTAT
Found at i:48187850 original size:20 final size:20
Alignment explanation
Indices: 48187733--48187855 Score: 72
Period size: 20 Copynumber: 5.8 Consensus size: 20
48187723 GAAAAAATAG
*
48187733 AAAAATTATAAATATCGTAA
1 AAAAATTATAAAAATCGTAA
*
48187753 AAAAATTATAAAATATATAGAAATATA
1 AAAAATTAT-AAA-A-ATCG---TA-A
* *
48187780 ACAAATT-TAATAAAGTCATAA
1 AAAAATTATAA-AAA-TCGTAA
*
48187801 GAAAATTATAAAAAAAT-GTAA
1 AAAAATTAT--AAAAATCGTAA
*
48187822 ATAAA-TATAAAAATCGTAA
1 AAAAATTATAAAAATCGTAA
48187841 AAAAATTATAAAAAT
1 AAAAATTATAAAAAT
48187856 TATCGTACCA
Statistics
Matches: 78, Mismatches: 11, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
18 6 0.08
19 8 0.10
20 21 0.27
21 15 0.19
22 4 0.05
23 6 0.08
24 3 0.04
25 4 0.05
26 4 0.05
27 7 0.09
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAATTATAAAAATCGTAA
Found at i:48187853 original size:8 final size:9
Alignment explanation
Indices: 48187712--48187858 Score: 57
Period size: 9 Copynumber: 15.2 Consensus size: 9
48187702 AGTTTTAATA
48187712 ATAAAAATT
1 ATAAAAATT
* *
48187721 AGGAAAAAAT
1 A-TAAAAATT
*
48187731 AGAAAAATT
1 ATAAAAATT
*
48187740 ATAAATATCGT
1 ATAAAAAT--T
*
48187751 AAAAAAATT
1 ATAAAAATT
48187760 AT-AAAATAT
1 ATAAAAAT-T
*
48187769 ATAGAAA-T
1 ATAAAAATT
48187777 ATAACAAATT
1 ATAA-AAATT
*
48187787 -TAATAAAGTC
1 ATAA-AAA-TT
48187797 ATAAGAAAATT
1 AT-A-AAAATT
*
48187808 ATAAAAAAAT
1 AT-AAAAATT
* *
48187818 GTAAATAAAT
1 ATAAA-AATT
48187828 ATAAAAATCGT
1 ATAAAAAT--T
*
48187839 AAAAAAATT
1 ATAAAAATT
48187848 ATAAAAATT
1 ATAAAAATT
48187857 AT
1 AT
48187859 CGTACCAAAA
Statistics
Matches: 105, Mismatches: 19, Indels: 28
0.69 0.12 0.18
Matches are distributed among these distances:
8 9 0.09
9 44 0.42
10 26 0.25
11 21 0.20
12 4 0.04
13 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (9 bp):
ATAAAAATT
Found at i:48191793 original size:14 final size:15
Alignment explanation
Indices: 48191769--48191798 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
48191759 TATAAAGATA
48191769 ATTTAAAATTATAAT
1 ATTTAAAATTATAAT
48191784 ATTT-AAATTATAAT
1 ATTTAAAATTATAAT
48191798 A
1 A
48191799 CACCCTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAAAATTATAAT
Found at i:48194198 original size:10 final size:10
Alignment explanation
Indices: 48194139--48194198 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
48194129 AAAAATTGTG
*
48194139 AAAATCATTA
1 AAAATTATTA
*
48194149 AAAATGATTA
1 AAAATTATTA
48194159 AAAATTA-TA
1 AAAATTATTA
* *
48194168 AGAATTTTTTA
1 A-AAATTATTA
**
48194179 AAAAAAATTA
1 AAAATTATTA
48194189 AAAATTATTA
1 AAAATTATTA
48194199 TAACAAAGAG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
9 3 0.08
10 32 0.84
11 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (10 bp):
AAAATTATTA
Found at i:48194615 original size:21 final size:21
Alignment explanation
Indices: 48194583--48194634 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
48194573 AATTTTCCAA
*
48194583 ATAATGTTTTTTGCTAACTTTC
1 ATAAT-TTTTTTGATAACTTTC
* *
48194605 ATAATTTTTTTTATAACTTTT
1 ATAATTTTTTTGATAACTTTC
*
48194626 ACAATTTTT
1 ATAATTTTT
48194635 AATGATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.60
Consensus pattern (21 bp):
ATAATTTTTTTGATAACTTTC
Found at i:48201299 original size:18 final size:19
Alignment explanation
Indices: 48201252--48201312 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
48201242 ATTTATTTTA
48201252 AATTTTATTAAATCATATAT
1 AATTTTATTAAAT-ATATAT
48201272 AATTTTATTAAAT-TATAT
1 AATTTTATTAAATATATAT
*
48201290 -ATTTTAATTATAATATATTT
1 AATTTT-ATTA-AATATATAT
48201310 AAT
1 AAT
48201313 AATAATTATG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 5 0.14
18 9 0.25
19 3 0.08
20 17 0.47
21 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTTTATTAAATATATAT
Found at i:48201305 original size:16 final size:16
Alignment explanation
Indices: 48201286--48201331 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
48201276 TTATTAAATT
48201286 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
48201302 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
48201317 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
48201332 CATTTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:48201410 original size:61 final size:61
Alignment explanation
Indices: 48201345--48201532 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
48201335 TTATAGTATC
48201345 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
48201406 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
48201464 C
61 T
*
48201465 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
48201526 ATATATT
1 ATATATT
48201533 TTAATTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:48201414 original size:120 final size:120
Alignment explanation
Indices: 48201272--48201569 Score: 553
Period size: 120 Copynumber: 2.5 Consensus size: 120
48201262 AATCATATAT
48201272 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATCA-TT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTAT-ATTT
48201336 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
48201392 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
48201457 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
48201512 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
48201570 ATGATTAAAT
Statistics
Matches: 173, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
119 1 0.01
120 167 0.97
121 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:48201432 original size:15 final size:15
Alignment explanation
Indices: 48201397--48201448 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
48201387 TTAAGAATTT
*
48201397 TATTAAATTAT-ATA
1 TATTTAATTATAATA
48201411 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
48201425 TATTTAATAATAAT-
1 TATTTAATTATAATA
48201439 TATGTTAATT
1 TAT-TTAATT
48201449 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:48201547 original size:16 final size:16
Alignment explanation
Indices: 48201526--48201567 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
48201516 TTATTAAATT
*
48201526 ATATATTTTAATTATA
1 ATATATTTTAATAATA
48201542 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
48201557 AT-TATGTTTAA
1 ATATAT-TTTAA
48201568 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:48201552 original size:15 final size:15
Alignment explanation
Indices: 48201517--48201558 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48201507 TTAAGAATTT
*
48201517 TATTAAATTAT-ATA
1 TATTTAATTATAATA
48201531 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
48201545 TATTTAATAATAAT
1 TATTTAATTATAAT
48201559 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:48201757 original size:16 final size:16
Alignment explanation
Indices: 48201736--48201768 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
48201726 TAAGATTACT
48201736 ATTACGCCTCGATTCC
1 ATTACGCCTCGATTCC
*
48201752 ATTACGCCTCTATTCC
1 ATTACGCCTCGATTCC
48201768 A
1 A
48201769 ATACAGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.36, G:0.09, T:0.33
Consensus pattern (16 bp):
ATTACGCCTCGATTCC
Found at i:48202598 original size:40 final size:42
Alignment explanation
Indices: 48202554--48202645 Score: 152
Period size: 40 Copynumber: 2.2 Consensus size: 42
48202544 TTAAAAATAT
48202554 TTATATTAAAAAACACTACCAT-AATATAATAAAT-GTTTTA
1 TTATATTAAAAAACACTACCATAAATATAATAAATAGTTTTA
* *
48202594 TTATATCAAAAAACACTACCATAAATATAATAAATATTTTTA
1 TTATATTAAAAAACACTACCATAAATATAATAAATAGTTTTA
48202636 TTATATTAAA
1 TTATATTAAA
48202646 TATAAATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 21 0.45
41 12 0.26
42 14 0.30
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (42 bp):
TTATATTAAAAAACACTACCATAAATATAATAAATAGTTTTA
Found at i:48206674 original size:3 final size:3
Alignment explanation
Indices: 48206666--48206725 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
48206656 GTGGGTCAAA
48206666 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48206714 AAT AAT AAT AAT
1 AAT AAT AAT AAT
48206726 TTAAGTGAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:48214003 original size:18 final size:18
Alignment explanation
Indices: 48213961--48214006 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
48213951 GCATAAGAAT
48213961 ATAGATAA--TAAAATAA
1 ATAGATAATTTAAAATAA
** *
48213977 ATATTTAATTTAAACTAA
1 ATAGATAATTTAAAATAA
48213995 ATAGATAATTTA
1 ATAGATAATTTA
48214007 TTTATTTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
16 6 0.26
18 17 0.74
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (18 bp):
ATAGATAATTTAAAATAA
Found at i:48219694 original size:3 final size:3
Alignment explanation
Indices: 48219679--48219708 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
48219669 TTATTTTCTA
*
48219679 ATC ATC GTC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
48219709 TTATGATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:48222577 original size:2 final size:2
Alignment explanation
Indices: 48222572--48222608 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
48222562 AAAGAAAAAA
48222572 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
48222609 AACTGCTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48232920 original size:9 final size:9
Alignment explanation
Indices: 48232901--48232937 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
48232891 TGAGTTTTTA
48232901 AATTCGAAT
1 AATTCGAAT
48232910 AACTT-GAAT
1 AA-TTCGAAT
48232919 AATTCGAAT
1 AATTCGAAT
48232928 AATTCGAAT
1 AATTCGAAT
48232937 A
1 A
48232938 TTAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:48233983 original size:21 final size:21
Alignment explanation
Indices: 48233958--48234000 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
48233948 CGAAAATTTT
48233958 CGATTCGATCGAATGTTCACC
1 CGATTCGATCGAATGTTCACC
48233979 CGATTCGATCGAATGTTCACC
1 CGATTCGATCGAATGTTCACC
48234000 C
1 C
48234001 CTACTAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (21 bp):
CGATTCGATCGAATGTTCACC
Found at i:48236075 original size:22 final size:22
Alignment explanation
Indices: 48236050--48236094 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
48236040 ATGGAAATTG
48236050 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
48236072 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
48236094 T
1 T
48236095 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:48240679 original size:22 final size:22
Alignment explanation
Indices: 48240651--48240695 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
48240641 AGGGGGAGTG
48240651 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
48240673 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
48240695 T
1 T
48240696 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:48246863 original size:4 final size:4
Alignment explanation
Indices: 48246854--48246899 Score: 67
Period size: 4 Copynumber: 11.5 Consensus size: 4
48246844 ACCCTTGTTA
*
48246854 TTAT TTAT TTAT TTAT TTAT TT-T CTAT TTCAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TTAT TTAT TTAT TT
48246900 TAGTTTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 2 0.05
4 32 0.84
5 4 0.11
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:48246888 original size:24 final size:23
Alignment explanation
Indices: 48246855--48246900 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
48246845 CCCTTGTTAT
48246855 TATTTATTTATTTATTTATTTTC
1 TATTTATTTATTTATTTATTTTC
48246878 TATTTCATTTATTTATTTATTTT
1 TATTT-ATTTATTTATTTATTTT
48246901 AGTTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (23 bp):
TATTTATTTATTTATTTATTTTC
Found at i:48248818 original size:16 final size:16
Alignment explanation
Indices: 48248797--48248835 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
48248787 TTAGAAAATA
*
48248797 TAAAAATAAAATATTT
1 TAAAAATAAAATATAT
*
48248813 TAAAAAT-AATTATAT
1 TAAAAATAAAATATAT
48248828 TAAAAATA
1 TAAAAATA
48248836 TTATTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAAATAAAATATAT
Found at i:48250851 original size:3 final size:3
Alignment explanation
Indices: 48250843--48250871 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
48250833 CATCACTTCA
48250843 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
48250872 AGACTCAATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:48264647 original size:16 final size:16
Alignment explanation
Indices: 48264607--48264640 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48264597 AGGCTCGGAC
* *
48264607 CTAAAAACCCTAAATT
1 CTAAGAACCCCAAATT
48264623 CTAAGAACCCCAAATT
1 CTAAGAACCCCAAATT
48264639 CT
1 CT
48264641 CATAACCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.29, G:0.03, T:0.24
Consensus pattern (16 bp):
CTAAGAACCCCAAATT
Found at i:48266412 original size:23 final size:23
Alignment explanation
Indices: 48266386--48266483 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
48266376 ATAAGTGCCA
48266386 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48266409 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
48266432 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
48266454 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48266477 CACTGAT
1 CACTGAT
48266484 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:48266451 original size:45 final size:45
Alignment explanation
Indices: 48266393--48266481 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
48266383 CCACACTGAT
* *
48266393 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
48266438 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
48266482 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:48273784 original size:23 final size:23
Alignment explanation
Indices: 48273758--48273855 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
48273748 ATAAGTGCCA
48273758 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48273781 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
48273804 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
48273826 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48273849 CACTGAT
1 CACTGAT
48273856 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:48273823 original size:45 final size:45
Alignment explanation
Indices: 48273765--48273853 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
48273755 CCACACTGAT
* *
48273765 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
48273810 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
48273854 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:48278660 original size:56 final size:56
Alignment explanation
Indices: 48278574--48278805 Score: 446
Period size: 56 Copynumber: 4.1 Consensus size: 56
48278564 ACAAGGGATG
48278574 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
48278630 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
48278686 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
48278742 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
48278798 ATGGGCAA
1 ATGGGCAA
48278806 TAAACTAATA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 174 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:48285627 original size:13 final size:13
Alignment explanation
Indices: 48285609--48285634 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48285599 AATGCATTAA
48285609 AAACAACAAAAAC
1 AAACAACAAAAAC
48285622 AAACAACAAAAAC
1 AAACAACAAAAAC
48285635 CAAAGATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACAACAAAAAC
Found at i:48287388 original size:25 final size:25
Alignment explanation
Indices: 48287343--48287390 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
48287333 TACGAGTAAT
* *
48287343 TTTAAAAAATAATAATTTATTAAAA
1 TTTAAAAAAGAATAATCTATTAAAA
48287368 TTTAAAAAGAGAA-AATCTATTAA
1 TTTAAAAA-AGAATAATCTATTAA
48287391 CCTAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
TTTAAAAAAGAATAATCTATTAAAA
Found at i:48289899 original size:3 final size:3
Alignment explanation
Indices: 48289886--48289945 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
48289876 GGGTTCTCAC
* * * * *
48289886 ATG AAG ATG ATG ATG ATG ATG AAG ATG GTG ATG CTG ATA ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
*
48289934 ATG ATG GTG ATG
1 ATG ATG ATG ATG
48289946 GCAATGCAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:48292564 original size:22 final size:22
Alignment explanation
Indices: 48292538--48292614 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 22
48292528 ATATCCAAAC
48292538 AATAACAACAAAATAATAGCAA
1 AATAACAACAAAATAATAGCAA
* * * **
48292560 TATAATAACGAAATGGTAGCAA
1 AATAACAACAAAATAATAGCAA
* * * *
48292582 AACAACAACATAATAGTAACAA
1 AATAACAACAAAATAATAGCAA
* *
48292604 AACAATAACAA
1 AATAACAACAA
48292615 TTTTTTTTGT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.62, C:0.14, G:0.08, T:0.16
Consensus pattern (22 bp):
AATAACAACAAAATAATAGCAA
Found at i:48293683 original size:34 final size:33
Alignment explanation
Indices: 48293624--48293688 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
48293614 CAGTAAAATG
*
48293624 TTTTCCGAAAAATGATTTCTGGAAAATGATTTAC
1 TTTTCCGAAAAATGATTACTGGAAAAT-ATTTAC
*
48293658 TTTTCTGAAAAATGATTCACT-GAAAATATTT
1 TTTTCCGAAAAATGATT-ACTGGAAAATATTT
48293689 TCTGGTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 4 0.14
34 22 0.79
35 2 0.07
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (33 bp):
TTTTCCGAAAAATGATTACTGGAAAATATTTAC
Found at i:48293763 original size:20 final size:20
Alignment explanation
Indices: 48293738--48293776 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
48293728 GTTTTTACAT
48293738 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
48293758 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
48293777 TTTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:48293839 original size:18 final size:18
Alignment explanation
Indices: 48293816--48293851 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
48293806 GATTTATTTA
48293816 TAAATAGATAAATCAAAT
1 TAAATAGATAAATCAAAT
* *
48293834 TAAATATATCAATCAAAT
1 TAAATAGATAAATCAAAT
48293852 GGTTTAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAATAGATAAATCAAAT
Found at i:48294952 original size:31 final size:31
Alignment explanation
Indices: 48294914--48294975 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
48294904 AGGCAAATTA
48294914 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
48294945 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
48294976 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:48307680 original size:22 final size:22
Alignment explanation
Indices: 48307652--48307696 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
48307642 AGCATCAAGT
48307652 TAAAGTACCAAATTAAAAAAAA
1 TAAAGTACCAAATTAAAAAAAA
*
48307674 TAAAGTACCAAATTAAGAAAAA
1 TAAAGTACCAAATTAAAAAAAA
48307696 T
1 T
48307697 TGTGAAGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (22 bp):
TAAAGTACCAAATTAAAAAAAA
Found at i:48317109 original size:11 final size:10
Alignment explanation
Indices: 48317048--48317109 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 10
48317038 TTAATCAACC
*
48317048 ATTTTATATT
1 ATTTTATATA
*
48317058 ATATATATATTA
1 AT-TTTATA-TA
48317070 ATTTTGATATA
1 ATTTT-ATATA
*
48317081 ATTTT-TAAA
1 ATTTTATATA
48317090 ATTTTATATA
1 ATTTTATATA
48317100 ATTATTATAT
1 ATT-TTATAT
48317110 TATAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 8 0.19
10 8 0.19
11 20 0.48
12 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
ATTTTATATA
Found at i:48319174 original size:19 final size:19
Alignment explanation
Indices: 48319150--48319187 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
48319140 ATCTTATTAT
48319150 TAAATAAAATAATAAATAA
1 TAAATAAAATAATAAATAA
* *
48319169 TAAATAAATTTATAAATAA
1 TAAATAAAATAATAAATAA
48319188 ATACTGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAATAAAATAATAAATAA
Found at i:48319243 original size:27 final size:27
Alignment explanation
Indices: 48319194--48319246 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
48319184 ATAAATACTG
*
48319194 ATAATTTAATTTAAACATAATTAAAAA
1 ATAATTTAATTTAAACAAAATTAAAAA
*
48319221 ATAA-TTAATTTAAATAAATATTAAAA
1 ATAATTTAATTTAAACAAA-ATTAAAA
48319247 TCTTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
ATAATTTAATTTAAACAAAATTAAAAA
Found at i:48319756 original size:59 final size:59
Alignment explanation
Indices: 48319634--48319756 Score: 142
Period size: 57 Copynumber: 2.1 Consensus size: 59
48319624 TAACTTGGAC
* ** * * * *
48319634 AAAAAAAGTTTATGTCTCAATGTGAGAACAATTGTTAAGTTTAGAGTCTAACTTGAATA
1 AAAAAAAGTTTATATCTCAATACGAGAACAATTATTAAATTCAGAGTCTAACTTAAATA
* * *
48319693 AAAAAAAGTTTA-ATCTCAATACG-GAATAATTATTAAATTCAGAGTCTAATTTAAATT
1 AAAAAAAGTTTATATCTCAATACGAGAACAATTATTAAATTCAGAGTCTAACTTAAATA
48319750 AAAAAAA
1 AAAAAAA
48319757 TTATTAAACC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 34 0.63
58 8 0.15
59 12 0.22
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (59 bp):
AAAAAAAGTTTATATCTCAATACGAGAACAATTATTAAATTCAGAGTCTAACTTAAATA
Found at i:48327762 original size:12 final size:12
Alignment explanation
Indices: 48327747--48327779 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
48327737 TTTTCCATTC
48327747 TTTTTTATTTTA
1 TTTTTTATTTTA
48327759 TTTTTTA-TTTA
1 TTTTTTATTTTA
*
48327770 TTTTTAATTT
1 TTTTTTATTT
48327780 AAAATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:48327773 original size:22 final size:24
Alignment explanation
Indices: 48327723--48327780 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
48327713 AGGTGAATCG
*
48327723 TATTTTT-TTTCATTTTTTCCATTC
1 TATTTTTATTTTATTTTTT-CATTC
48327747 T-TTTTTATTTTATTTTTT-ATT-
1 TATTTTTATTTTATTTTTTCATTC
*
48327768 TATTTTTAATTTA
1 TATTTTTATTTTA
48327781 AAATATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 1 0.03
22 13 0.43
23 5 0.17
24 11 0.37
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (24 bp):
TATTTTTATTTTATTTTTTCATTC
Found at i:48328362 original size:3 final size:3
Alignment explanation
Indices: 48328356--48328404 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
48328346 TTTACTTTTG
* *
48328356 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA GTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
48328401 TTA T
1 TTA T
48328405 ACTTACATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:48330717 original size:7 final size:7
Alignment explanation
Indices: 48330705--48330730 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48330695 TCGAAGATCT
48330705 TAAACCC
1 TAAACCC
48330712 TAAACCC
1 TAAACCC
48330719 TAAACCC
1 TAAACCC
48330726 TAAAC
1 TAAAC
48330731 TCAAGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:48339442 original size:41 final size:41
Alignment explanation
Indices: 48339235--48339431 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
48339225 TTTATCGTTA
* * * *
48339235 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48339276 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48339317 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48339358 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
48339399 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
48339432 AAGAGCCGGT
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 143 0.97
42 2 0.01
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:48339704 original size:33 final size:32
Alignment explanation
Indices: 48339648--48339711 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
48339638 AGATATGTAT
48339648 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
48339680 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
48339712 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:48339728 original size:33 final size:33
Alignment explanation
Indices: 48339655--48339728 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
48339645 TATATATATA
* * **
48339655 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
48339687 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
48339720 TGTATGTAT
1 TATATGTAT
48339729 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:48346371 original size:41 final size:41
Alignment explanation
Indices: 48345836--48346360 Score: 973
Period size: 41 Copynumber: 12.8 Consensus size: 41
48345826 TTTATCGTTA
* * * *
48345836 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48345877 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48345918 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48345959 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48346000 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48346041 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48346082 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48346123 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48346164 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48346205 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48346246 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
48346287 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
48346328 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
48346361 AAGAGCCGGT
Statistics
Matches: 476, Mismatches: 4, Indels: 8
0.98 0.01 0.02
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 471 0.99
42 2 0.00
43 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:48346631 original size:33 final size:32
Alignment explanation
Indices: 48346575--48346638 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
48346565 ATAGATATGT
48346575 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
48346607 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
48346639 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:48346655 original size:33 final size:33
Alignment explanation
Indices: 48346582--48346655 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
48346572 TGTATATATA
* * **
48346582 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
48346614 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
48346647 TGTATGTAT
1 TATATGTAT
48346656 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:48355130 original size:43 final size:43
Alignment explanation
Indices: 48355083--48355245 Score: 218
Period size: 43 Copynumber: 3.8 Consensus size: 43
48355073 GCGTCGCTAA
* *** *
48355083 CTTTAGCGGCGTTTTTAGAAAAAACGCCGTTAAAGACCAGGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAGGAC
* *
48355126 CTTTAGCGGCGCTTTTCCCGAAAACGCTGCTAAAGACCAGGAC
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAGGAC
* * * *
48355169 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTGAAGACCAAGAA
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAGGAC
*
48355212 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAA
48355246 AACATGACTT
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 106 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCAGGAC
Found at i:48355468 original size:18 final size:18
Alignment explanation
Indices: 48355445--48355504 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
48355435 TTAAAACAAG
48355445 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
48355463 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
48355480 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
48355498 TTACATT
1 TTACATT
48355505 AGAATTACAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:48357914 original size:42 final size:41
Alignment explanation
Indices: 48357867--48358029 Score: 209
Period size: 42 Copynumber: 3.9 Consensus size: 41
48357857 CAAACAAAAA
* * * *
48357867 CGCCGCTAAAGATCGTGTTCTTTAGCGGTGTTTTTTCTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTC-TAAG
*
48357909 CGCCGCTAAAGAACATGGTCTTTAGCGGCATTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGC-GTTTTTTCTAAG
* *
48357951 CGTCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTAATAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT-CTAAG
**
48357993 CGTTGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTT
48358030 ACAAAAACGC
Statistics
Matches: 109, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
41 6 0.06
42 90 0.83
43 13 0.12
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCTAAG
Found at i:48358028 original size:84 final size:84
Alignment explanation
Indices: 48357870--48358029 Score: 230
Period size: 84 Copynumber: 1.9 Consensus size: 84
48357860 ACAAAAACGC
* * * * **
48357870 CGCTAAAGATCGTGTTCTTTAGCGGTGTTTTTTCTTAAGCGCCGCTAAAGAACATGGTCTTTAGC
1 CGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGGTCTTTAGC
*
48357935 GGCATTTTTTTCTAAGCGT
66 GGCACTTTTTTCTAAGCGT
**
48357954 CGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTAATAAGCGTTGCTAAAGAACATGGTCTTTAGC
1 CGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGGTCTTTAGC
*
48358019 GGCGCTTTTTT
66 GGCACTTTTTT
48358030 ACAAAAACGC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (84 bp):
CGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAAAGAACATGGTCTTTAGC
GGCACTTTTTTCTAAGCGT
Found at i:48358368 original size:21 final size:21
Alignment explanation
Indices: 48358343--48358392 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
48358333 TTTTGCTCTG
* *
48358343 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
48358364 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
48358385 ATCTGCTT
1 CTCTGCTT
48358393 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.04, C:0.42, G:0.18, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:48362917 original size:9 final size:9
Alignment explanation
Indices: 48362903--48363208 Score: 188
Period size: 9 Copynumber: 35.0 Consensus size: 9
48362893 ACTATAAATG
48362903 AGTTATGTA
1 AGTTATGTA
48362912 AGTTATGATA
1 AGTTATG-TA
* * *
48362922 TGATA-GGA
1 AGTTATGTA
48362930 AGGTTATGT-
1 A-GTTATGTA
48362939 A-TTATGTA
1 AGTTATGTA
*
48362947 AGTTATTTA
1 AGTTATGTA
*
48362956 AGTTATGCA
1 AGTTATGTA
* *
48362965 GGTTATTTA
1 AGTTATGTA
* *
48362974 ATTTATGGA
1 AGTTATGTA
48362983 AGTTATGTA
1 AGTTATGTA
48362992 AGTTATGTA
1 AGTTATGTA
* *
48363001 GGCTATGT-
1 AGTTATGTA
*
48363009 A-TTATCTA
1 AGTTATGTA
* *
48363017 AATAATGTA
1 AGTTATGTA
*
48363026 AGTTA-GGA
1 AGTTATGTA
48363034 AGGTTATGT-
1 A-GTTATGTA
48363043 A-TTATGTA
1 AGTTATGTA
*
48363051 AGTTATTTA
1 AGTTATGTA
*
48363060 AGTTATGCA
1 AGTTATGTA
* *
48363069 GGTTATTTA
1 AGTTATGTA
* *
48363078 ATTTATGGA
1 AGTTATGTA
48363087 AGTTATGTA
1 AGTTATGTA
48363096 AGTTATGTA
1 AGTTATGTA
* *
48363105 GGCTATGT-
1 AGTTATGTA
*
48363113 A-TTATCTA
1 AGTTATGTA
* *
48363121 AATAATGTA
1 AGTTATGTA
*
48363130 AGTTA-GGA
1 AGTTATGTA
48363138 AGGTTATGT-
1 A-GTTATGTA
48363147 A-TTATGTA
1 AGTTATGTA
*
48363155 AGTTATTTA
1 AGTTATGTA
*
48363164 AGTTATGCA
1 AGTTATGTA
* *
48363173 GGTTATTTA
1 AGTTATGTA
* *
48363182 ATTTATGGA
1 AGTTATGTA
48363191 AGTTATGTA
1 AGTTATGTA
48363200 AGTTATGTA
1 AGTTATGTA
48363209 GGCTATGTAT
Statistics
Matches: 216, Mismatches: 64, Indels: 34
0.69 0.20 0.11
Matches are distributed among these distances:
7 26 0.12
8 12 0.06
9 170 0.79
10 8 0.04
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (9 bp):
AGTTATGTA
Found at i:48363105 original size:104 final size:104
Alignment explanation
Indices: 48362925--48363247 Score: 628
Period size: 104 Copynumber: 3.1 Consensus size: 104
48362915 TATGATATGA
48362925 TAGGAAGGTTATGTATTATGTAAGTTATTTAAGTTATGCAGGTTATTTAATTTATGGAAGTTATG
1 TAGGAAGGTTATGTATTATGTAAGTTATTTAAGTTATGCAGGTTATTTAATTTATGGAAGTTATG
48362990 TAAGTTATGTAGGCTATGTATTATCTAAATAATGTAAGT
66 TAAGTTATGTAGGCTATGTATTATCTAAATAATGTAAGT
48363029 TAGGAAGGTTATGTATTATGTAAGTTATTTAAGTTATGCAGGTTATTTAATTTATGGAAGTTATG
1 TAGGAAGGTTATGTATTATGTAAGTTATTTAAGTTATGCAGGTTATTTAATTTATGGAAGTTATG
48363094 TAAGTTATGTAGGCTATGTATTATCTAAATAATGTAAGT
66 TAAGTTATGTAGGCTATGTATTATCTAAATAATGTAAGT
48363133 TAGGAAGGTTATGTATTATGTAAGTTATTTAAGTTATGCAGGTTATTTAATTTATGGAAGTTATG
1 TAGGAAGGTTATGTATTATGTAAGTTATTTAAGTTATGCAGGTTATTTAATTTATGGAAGTTATG
* *
48363198 TAAGTTATGTAGGCTATGTATAATCAAAATAATGTAAGT
66 TAAGTTATGTAGGCTATGTATTATCTAAATAATGTAAGT
48363237 TAGGAAGGTTA
1 TAGGAAGGTTA
48363248 AGTTATGTAA
Statistics
Matches: 217, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 217 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (104 bp):
TAGGAAGGTTATGTATTATGTAAGTTATTTAAGTTATGCAGGTTATTTAATTTATGGAAGTTATG
TAAGTTATGTAGGCTATGTATTATCTAAATAATGTAAGT
Found at i:48363238 original size:34 final size:34
Alignment explanation
Indices: 48362905--48363218 Score: 304
Period size: 34 Copynumber: 9.0 Consensus size: 34
48362895 TATAAATGAG
* * * *
48362905 TTATGTAAGTTATGATATGATAGGAAGGTTATGTA
1 TTATGTAAGTTATG-TAAGTTATGTAGGTTATGTA
* * *
48362940 TTATGTAAGTTATTTAAGTTATGCAGGTTATTTAA
1 TTATGTAAGTTATGTAAGTTATGTAGGTTATGT-A
* *
48362975 TTTATGGAAGTTATGTAAGTTATGTAGGCTATGTA
1 -TTATGTAAGTTATGTAAGTTATGTAGGTTATGTA
* * * * *
48363010 TTATCTAAATAATGTAAGTTAGGAAGGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTAGGTTATGTA
* * *
48363044 TTATGTAAGTTATTTAAGTTATGCAGGTTATTTAA
1 TTATGTAAGTTATGTAAGTTATGTAGGTTATGT-A
* *
48363079 TTTATGGAAGTTATGTAAGTTATGTAGGCTATGTA
1 -TTATGTAAGTTATGTAAGTTATGTAGGTTATGTA
* * * * *
48363114 TTATCTAAATAATGTAAGTTAGGAAGGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTAGGTTATGTA
* * *
48363148 TTATGTAAGTTATTTAAGTTATGCAGGTTATTTAA
1 TTATGTAAGTTATGTAAGTTATGTAGGTTATGT-A
* *
48363183 TTTATGGAAGTTATGTAAGTTATGTAGGCTATGTA
1 -TTATGTAAGTTATGTAAGTTATGTAGGTTATGTA
48363218 T
1 T
48363219 AATCAAAATA
Statistics
Matches: 224, Mismatches: 49, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
34 121 0.54
35 19 0.08
36 84 0.38
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.44
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAGTTATGTAGGTTATGTA
Found at i:48363294 original size:20 final size:20
Alignment explanation
Indices: 48363269--48363307 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
48363259 TCGAAATTTG
48363269 ATCTTAATATTATAAAAGTA
1 ATCTTAATATTATAAAAGTA
*
48363289 ATCTTAATATTATATAAGT
1 ATCTTAATATTATAAAAGT
48363308 TATGTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
ATCTTAATATTATAAAAGTA
Found at i:48363309 original size:57 final size:57
Alignment explanation
Indices: 48363246--48363906 Score: 563
Period size: 57 Copynumber: 11.7 Consensus size: 57
48363236 TTAGGAAGGT
* *
48363246 TAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCTTAATATTATA
1 TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAATCTTAATATTATA
* * * * **
48363303 TAAGTTATGTAATTCGGAATTTTA-CTTTAATATTGTATAAGTTAT-GTAAT-TTCGA
1 TAAGTTATGTAATTCGAAATTTTATC-TTAATATTATATAAGTAATCTTAATATTATA
* * * * * * ** * *
48363358 -AATTTTATCTTAATATTGTATAA-GTTAT-GTAAT-TCGA-A-ATTTTATCTTAATATTGTA
1 TAA-GTTAT-GTAAT-TCG-A-AATTTTATCTTAATAT-TATATAAGTAATCTTAATATTATA
* * * *
48363415 TAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGT--TATGAATATTATA
1 TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAATCTTAATATTATA
* * *
48363470 TAAGTTTTGTAATTAGAAATTTTATCTTAATATTATATAAGCAATCTTAATATTATA
1 TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAATCTTAATATTATA
* * * *
48363527 TAAGTTATGTAATTTGAAATTTGATCTTAATATTATAAAAGCAATCTTAATATTATA
1 TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAATCTTAATATTATA
* * * * * *
48363584 TAAGTTATGTAATTCGGAATTTTACCTTAATATTGTATAAGTTAT-GTAAT-TCGA-A
1 TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAATCTTAATAT-TATA
** * * * * * ** * *
48363639 -ATTTTATCTTAATATTGTATAA-GTTAT-GTAAT-TCGA-A-ATTTTATCTTAATATTGTA
1 TAAGTTAT-GTAAT-TCG-A-AATTTTATCTTAATAT-TATATAAGTAATCTTAATATTATA
* * *
48363695 TAAGTTATGTAATTCGATATTTTATCTTAACATTATATAAGCAATCTTAATATTATA
1 TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAATCTTAATATTATA
* *
48363752 TAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGCAATCTTAATATTATA
1 TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAATCTTAATATTATA
* * *
48363809 TAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAACCTTAATATTATA
1 TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAATCTTAATATTATA
*
48363866 TAAGTTATGTAATTCGAAATTTTATCTTAAT-TTGTATAAGT
1 TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGT
48363907 TATGTAATTC
Statistics
Matches: 476, Mismatches: 95, Indels: 67
0.75 0.15 0.11
Matches are distributed among these distances:
53 2 0.00
54 22 0.05
55 83 0.17
56 48 0.10
57 312 0.66
58 7 0.01
59 2 0.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (57 bp):
TAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTAATCTTAATATTATA
Found at i:48363342 original size:37 final size:37
Alignment explanation
Indices: 48363289--48363460 Score: 274
Period size: 37 Copynumber: 4.6 Consensus size: 37
48363279 TATAAAAGTA
* *
48363289 ATCTTAATATTATATAAGTTATGTAATTCGGAATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
48363326 A-CTTTAATATTGTATAAGTTATGTAATTTCGAAATTTT
1 ATC-TTAATATTGTATAAGTTATGTAA-TTCGAAATTTT
48363364 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
*
48363401 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
* *
48363438 ATCTTAACATTATATAAGTTATG
1 ATCTTAATATTGTATAAGTTATG
48363461 AATATTATAT
Statistics
Matches: 127, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
36 1 0.01
37 91 0.72
38 34 0.27
39 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (37 bp):
ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
Found at i:48363412 original size:75 final size:74
Alignment explanation
Indices: 48363289--48363735 Score: 307
Period size: 74 Copynumber: 6.2 Consensus size: 74
48363279 TATAAAAGTA
*
48363289 ATCTTAATATTATATAAGTTATGTAATTCGGAATTTTACTTTAATATTGTATAAGTTATGTAATT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTTACTTTAATATTGTATAAGTTATGTAA-T
48363354 TCGAAATTTT
65 TCGAAATTTT
*
48363364 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTTA-TCTTAATATTGTATAAGTTATGTAAT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTTACT-TTAATATTGTATAAGTTATGTAAT
*
48363428 TCGATATTTT
65 TCGAAATTTT
* * ** * * * * *
48363438 ATCTTAACATTATATAAGTTATGAATATTATATAAGTTT--TGTAAT-TAG-A-AATTTTATCTT
1 ATCTTAATATTATATAAGTTATGTA-ATTCGA-AATTTTACTTTAATATTGTATAA-GTTAT-GT
* ****
48363498 AATAT-TATATAAGCA
62 AAT-TCGA-A-ATTTT
* * * *
48363513 ATCTTAATATTATATAAGTTATGTAATTTGAAATTTGA-TCTTAATA-T-TATAA---AAGCAA-
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTTACT-TTAATATTGTATAAGTTATGTAAT
** *
48363571 TCTTAATATT
65 TCGAAATTTT
* * * * * * *
48363581 AT-ATAA-GTTATGTAA-TT-CGGAATT-T------TACCTTAATATTGTATAAGTTATGTAATT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTTACTTTAATATTGTATAAGTTATGTAATT
48363635 CGAAATTTT
66 CGAAATTTT
*
48363644 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTTA-TCTTAATATTGTATAAGTTATGTAAT
1 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTTACT-TTAATATTGTATAAGTTATGTAAT
*
48363708 TCGATATTTT
65 TCGAAATTTT
*
48363718 ATCTTAACATTATATAAG
1 ATCTTAATATTATATAAG
48363736 CAATCTTAAT
Statistics
Matches: 280, Mismatches: 59, Indels: 67
0.69 0.15 0.17
Matches are distributed among these distances:
57 7 0.03
58 1 0.00
59 5 0.02
62 4 0.01
63 9 0.03
64 8 0.03
65 8 0.03
66 9 0.03
67 8 0.03
68 3 0.01
69 2 0.01
70 1 0.00
71 4 0.01
72 6 0.02
73 11 0.04
74 94 0.34
75 93 0.33
76 7 0.03
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (74 bp):
ATCTTAATATTATATAAGTTATGTAATTCGAAATTTTACTTTAATATTGTATAAGTTATGTAATT
CGAAATTTT
Found at i:48363516 original size:20 final size:20
Alignment explanation
Indices: 48363493--48363587 Score: 90
Period size: 20 Copynumber: 4.9 Consensus size: 20
48363483 TAGAAATTTT
48363493 ATCTTAATATTATATAAGCA
1 ATCTTAATATTATATAAGCA
**
48363513 ATCTTAATATTATATAAGTT
1 ATCTTAATATTATATAAGCA
* * **
48363533 AT-GTAAT-TTGAAATTTG--
1 ATCTTAATATT-ATATAAGCA
*
48363550 ATCTTAATATTATAAAAGCA
1 ATCTTAATATTATATAAGCA
48363570 ATCTTAATATTATATAAG
1 ATCTTAATATTATATAAG
48363588 TTATGTAATT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
17 2 0.03
18 9 0.16
19 10 0.17
20 37 0.64
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.43
Consensus pattern (20 bp):
ATCTTAATATTATATAAGCA
Found at i:48363623 original size:37 final size:37
Alignment explanation
Indices: 48363570--48363735 Score: 278
Period size: 37 Copynumber: 4.5 Consensus size: 37
48363560 TATAAAAGCA
* *
48363570 ATCTTAATATTATATAAGTTATGTAATTCGGAATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
*
48363607 ACCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
48363644 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
*
48363681 ATCTTAATATTGTATAAGTTATGTAATTCGATATTTT
1 ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
* *
48363718 ATCTTAACATTATATAAG
1 ATCTTAATATTGTATAAG
48363736 CAATCTTAAT
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 122 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (37 bp):
ATCTTAATATTGTATAAGTTATGTAATTCGAAATTTT
Found at i:48363743 original size:20 final size:20
Alignment explanation
Indices: 48363718--48363755 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
48363708 TCGATATTTT
48363718 ATCTTAACATTATATAAGCA
1 ATCTTAACATTATATAAGCA
*
48363738 ATCTTAATATTATATAAG
1 ATCTTAACATTATATAAG
48363756 TTATGTAATT
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:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (20 bp):
ATCTTAACATTATATAAGCA
Found at i:48363798 original size:20 final size:20
Alignment explanation
Indices: 48363775--48363812 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
48363765 TAGAAATTTT
48363775 ATCTTAATATTATATAAGCA
1 ATCTTAATATTATATAAGCA
48363795 ATCTTAATATTATATAAG
1 ATCTTAATATTATATAAG
48363813 TTATGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
ATCTTAATATTATATAAGCA
Found at i:48363905 original size:36 final size:37
Alignment explanation
Indices: 48363854--48363986 Score: 205
Period size: 37 Copynumber: 3.6 Consensus size: 37
48363844 TAAAAGTAAC
*
48363854 CTTAATATTATATAAGTTATGTAATTCGAAATTTTAT
1 CTTAATATTATATAAGTTATGTAATTCGATATTTTAT
* *
48363891 CTTAAT-TTGTATAAGTTATGTAATTCGATATTTTAC
1 CTTAATATTATATAAGTTATGTAATTCGATATTTTAT
* *
48363927 CTTAATATTGTATAAGTTATGTAATTCGATTTTTTAT
1 CTTAATATTATATAAGTTATGTAATTCGATATTTTAT
*
48363964 CTTAACATTATATAAGTTATGTA
1 CTTAATATTATATAAGTTATGTA
48363987 TGTTATGTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
36 33 0.38
37 55 0.62
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.50
Consensus pattern (37 bp):
CTTAATATTATATAAGTTATGTAATTCGATATTTTAT
Found at i:48363914 original size:18 final size:18
Alignment explanation
Indices: 48363893--48363952 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
48363883 AATTTTATCT
48363893 TAATTTGTATAAGTTATG
1 TAATTTGTATAAGTTATG
* **
48363911 TAATTCG-ATATTTTACCT-
1 TAATTTGTATAAGTTA--TG
48363929 TAATATTGTATAAGTTATG
1 TAAT-TTGTATAAGTTATG
48363948 TAATT
1 TAATT
48363953 CGATTTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
17 6 0.19
18 12 0.39
19 7 0.23
20 6 0.19
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (18 bp):
TAATTTGTATAAGTTATG
Found at i:48364716 original size:156 final size:155
Alignment explanation
Indices: 48364503--48364815 Score: 549
Period size: 156 Copynumber: 2.0 Consensus size: 155
48364493 TTTAAAATAA
*
48364503 AATATTTTAATGTAATTCCGGTACAATTTAAACAATTGCTTCTATTTTGCTCAACATATATAACA
1 AATATTTTAATGTAATTCCAGTACAATTTAAACAATTGCTTCTATTTTGCTCAACATATATAACA
*
48364568 ATCGTTGATGGATAAT-ACAAGAAAACATAAGTCAGAAAAGTACATGGCAGTTGTAAAATAAGTA
66 ATCGTTGATGGATAATAAC-AGAAAACATAAGTCAGAAAAGTACATGGCAATTGTAAAATAAGTA
48364632 AAATGAAACATAAGCTAAAGGAAAAC
130 AAATGAAACATAAGCTAAAGGAAAAC
*
48364658 AATATTTTAATGTAATTCCCAGTACAATTTATTA-AATTGCTTCTATTTTGCTCAACATATATAA
1 AATATTTTAATGTAATT-CCAGTACAATTTA-AACAATTGCTTCTATTTTGCTCAACATATATAA
*
48364722 CAATCGTTGATGGATGATAACAGAAAACATAAGTCAGAAAAGTACATGGCAATTGTAAAATAAGT
64 CAATCGTTGATGGATAATAACAGAAAACATAAGTCAGAAAAGTACATGGCAATTGTAAAATAAGT
48364787 AAAATGAAACATAAGCTAAAGGAAAAC
129 AAAATGAAACATAAGCTAAAGGAAAAC
48364814 AA
1 AA
48364816 CCAAAACCAA
Statistics
Matches: 151, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
155 17 0.11
156 131 0.87
157 3 0.02
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (155 bp):
AATATTTTAATGTAATTCCAGTACAATTTAAACAATTGCTTCTATTTTGCTCAACATATATAACA
ATCGTTGATGGATAATAACAGAAAACATAAGTCAGAAAAGTACATGGCAATTGTAAAATAAGTAA
AATGAAACATAAGCTAAAGGAAAAC
Found at i:48366248 original size:19 final size:19
Alignment explanation
Indices: 48366224--48366265 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
48366214 GGACTACGTT
*
48366224 GGGGAACTGTTAGGGATTA
1 GGGGAAATGTTAGGGATTA
* *
48366243 GGGGAAATTTTAGGGATTT
1 GGGGAAATGTTAGGGATTA
48366262 GGGG
1 GGGG
48366266 GAGATGAGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.45, T:0.29
Consensus pattern (19 bp):
GGGGAAATGTTAGGGATTA
Found at i:48367335 original size:15 final size:15
Alignment explanation
Indices: 48367315--48367345 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
48367305 CTCAAACATT
*
48367315 AAACCCTAAACTCAA
1 AAACCCAAAACTCAA
48367330 AAACCCAAAACTCAA
1 AAACCCAAAACTCAA
48367345 A
1 A
48367346 CCACAAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.32, G:0.00, T:0.10
Consensus pattern (15 bp):
AAACCCAAAACTCAA
Found at i:48367664 original size:15 final size:16
Alignment explanation
Indices: 48367636--48367666 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
48367626 CCCTAACCCG
48367636 ACCCCTATAACCCTAA
1 ACCCCTATAACCCTAA
48367652 ACCCCTA-AACCCTAA
1 ACCCCTATAACCCTAA
48367667 GTCTTAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (16 bp):
ACCCCTATAACCCTAA
Found at i:48368615 original size:114 final size:110
Alignment explanation
Indices: 48368311--48368624 Score: 371
Period size: 114 Copynumber: 2.8 Consensus size: 110
48368301 AGGCACTTCC
*
48368311 TCAAAAACGCCGCTAAAGGCCCAAAAA-TAAAGAAAACGGCGTCGTTGGCCTTAGGTTTTTTTGC
1 TCAAAAACGCCGCTAAAGGCCCAAAAACT-CAG-AAACGGCGTCGTTGGCCTTAGG-TTTTTTGC
* * * * *
48368375 GGCGTTTTTAAGAAAACGCCGCTAAAGACAGGAGCATTAGCGGTGCTTT
63 GGCGCTTTTAATAAATCGCCGCT-AAGACACGAGCATTAGCGGCGCTTT
** * *
48368424 TCAAAAAGCGCCGC-AACAGGGACAAAAACTCAGAAACGACGTCGTTGGCATTAGGTTTTTTGCG
1 TCAAAAA-CGCCGCTAA-AGGCCCAAAAACTCAGAAACGGCGTCGTTGGCCTTAGGTTTTTTGCG
* * * *
48368488 GCGCTTTTTATAAATCGCCGCTAAGTCCCCCGAGCATTAGCGGCGTTTT
64 GCGCTTTTAATAAATCGCCGCTAAG--ACACGAGCATTAGCGGCGCTTT
* *
48368537 TCTAAAAATGCCGCTAAAGGCCCAAAAACTCAGTAAACGGCGTCGTTGGCCTTATGTTTTTTGCG
1 TC-AAAAACGCCGCTAAAGGCCCAAAAACTCAG-AAACGGCGTCGTTGGCCTTAGGTTTTTTGCG
*
48368602 GCGCTTTTCATAAATCGCCGCTA
64 GCGCTTTTAATAAATCGCCGCTA
48368625 TTGCTTATTA
Statistics
Matches: 172, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
111 3 0.02
112 27 0.16
113 67 0.39
114 74 0.43
115 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (110 bp):
TCAAAAACGCCGCTAAAGGCCCAAAAACTCAGAAACGGCGTCGTTGGCCTTAGGTTTTTTGCGGC
GCTTTTAATAAATCGCCGCTAAGACACGAGCATTAGCGGCGCTTT
Found at i:48368684 original size:40 final size:40
Alignment explanation
Indices: 48368635--48368726 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
48368625 TTGCTTATTA
*
48368635 TTAGCGGCGTTTTCGTAAATGTGCCGCTAAT-TCTCGATCT
1 TTAGCGGCGTTTTCGTAAATGCGCCGCTAATAT-TCGATCT
* * *
48368675 TTAGCGGCGTTTTTGTAGATGCGCCGCTAATATTCGATTT
1 TTAGCGGCGTTTTCGTAAATGCGCCGCTAATATTCGATCT
48368715 TTAGCGGCGTTT
1 TTAGCGGCGTTT
48368727 ATTGTCCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
40 46 0.98
41 1 0.02
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (40 bp):
TTAGCGGCGTTTTCGTAAATGCGCCGCTAATATTCGATCT
Found at i:48374801 original size:2 final size:2
Alignment explanation
Indices: 48374794--48374818 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48374784 CTAGCATAAA
48374794 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
48374819 TCTTGACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:48377158 original size:85 final size:84
Alignment explanation
Indices: 48377013--48377223 Score: 352
Period size: 85 Copynumber: 2.5 Consensus size: 84
48377003 TTGTTACACA
*
48377013 GTGGAATCAGCACTTAGCAATCACCTTATAA-TCAATGATACGGGGAATCAGCACATAGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTT-TAATTCAATGATACGGGGAATCAGCACATAGCAACCC
48377077 CTTTCACAGTCAAGGATACG
65 CTTTCACAGTCAAGGATACG
* *
48377097 GTGGAATCAGCACTTAGCAACCACCTTTAGATTCAATGATACGGGGAATCATCATATAGCAACCC
1 GTGGAATCAGCACTTAGCAACCACCTTTA-ATTCAATGATACGGGGAATCAGCACATAGCAACCC
48377162 CTTTCACAGTCAAGGATACG
65 CTTTCACAGTCAAGGATACG
*
48377182 GTGGAATCAGCACATAGCAACCACCTTTATATTCAATGATAC
1 GTGGAATCAGCACTTAGCAACCACCTTTA-ATTCAATGATAC
48377224 AGATTCACAT
Statistics
Matches: 120, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
83 2 0.02
84 27 0.22
85 91 0.76
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (84 bp):
GTGGAATCAGCACTTAGCAACCACCTTTAATTCAATGATACGGGGAATCAGCACATAGCAACCCC
TTTCACAGTCAAGGATACG
Found at i:48377223 original size:43 final size:43
Alignment explanation
Indices: 48377013--48377223 Score: 254
Period size: 43 Copynumber: 5.0 Consensus size: 43
48377003 TTGTTACACA
* *
48377013 GTGGAATCAGCACTTAGCAATCACCTTATA-A-TCAATGATACG
1 GTGGAATCAGCACATAGCAACCACCTT-TACAGTCAATGATACG
*
48377055 G-GGAATCAGCACATAGCAACC-CCTTTCACAGTCAAGGATACG
1 GTGGAATCAGCACATAGCAACCACCTTT-ACAGTCAATGATACG
* * *
48377097 GTGGAATCAGCACTTAGCAACCACCTTTAGATTCAATGATACG
1 GTGGAATCAGCACATAGCAACCACCTTTACAGTCAATGATACG
* * *
48377140 G-GGAATCATCATATAGCAACC-CCTTTCACAGTCAAGGATACG
1 GTGGAATCAGCACATAGCAACCACCTTT-ACAGTCAATGATACG
* *
48377182 GTGGAATCAGCACATAGCAACCACCTTTATATTCAATGATAC
1 GTGGAATCAGCACATAGCAACCACCTTTACAGTCAATGATAC
48377224 AGATTCACAT
Statistics
Matches: 143, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.01
40 5 0.03
41 24 0.17
42 42 0.29
43 61 0.43
44 10 0.07
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (43 bp):
GTGGAATCAGCACATAGCAACCACCTTTACAGTCAATGATACG
Found at i:48377286 original size:51 final size:51
Alignment explanation
Indices: 48377229--48377423 Score: 245
Period size: 51 Copynumber: 3.8 Consensus size: 51
48377219 GATACAGATT
* * * *
48377229 CACATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCTGATA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCATCACTATCTGGTA
*
48377280 CACATAGTAGCCTACACATAGTACTACACACGTGATCGA--AGCTATCTGGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGA-CCATCA-CTATCTGGTA
* * * *
48377331 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTA
1 CACATAGTAGCCTACACATAGTACTACACACGTGACC-ATCACTATCTGGTA
*
48377381 CACGTAGTAGCCTACACATAGTACTACACACGTGACCATCACT
1 CACATAGTAGCCTACACATAGTACTACACACGTGACCATCACT
48377424 TTCACTTTCA
Statistics
Matches: 123, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
49 4 0.03
50 42 0.34
51 74 0.60
52 2 0.02
53 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (51 bp):
CACATAGTAGCCTACACATAGTACTACACACGTGACCATCACTATCTGGTA
Found at i:48377408 original size:101 final size:102
Alignment explanation
Indices: 48377231--48377415 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
48377221 TACAGATTCA
*
48377231 CATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCTGATACACATAGTAGCCTACA
1 CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCTGATACACATAGTAGCCTACA
48377296 CATAGTACTACACACGTGATCGAAGCTATCTGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCTGGTACG
* * *
48377333 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
1 CATAGTAGCATGCACATAGTACTACACATGCGACC-ATCACTATCTGATACACATAGTAGCCTAC
48377396 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
48377416 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 40 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (102 bp):
CATAGTAGCATGCACATAGTACTACACATGCGACCATCACTATCTGATACACATAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGCTATCTGGTACG
Found at i:48379274 original size:33 final size:33
Alignment explanation
Indices: 48379232--48379297 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
48379222 TCGCACATGG
48379232 ATCCGTGGTTAGGATCGCCAGATTTTAATTTTT
1 ATCCGTGGTTAGGATCGCCAGATTTTAATTTTT
48379265 ATCCGTGGTTAGGATCGCCAGATTTTAATTTTT
1 ATCCGTGGTTAGGATCGCCAGATTTTAATTTTT
48379298 TTCGCTGTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (33 bp):
ATCCGTGGTTAGGATCGCCAGATTTTAATTTTT
Found at i:48380832 original size:78 final size:78
Alignment explanation
Indices: 48380703--48380859 Score: 260
Period size: 78 Copynumber: 2.0 Consensus size: 78
48380693 AAGATTTGAC
* *
48380703 AATGATATTGCATATTGCTTTTCTCACTTACCCCTCAATGTGCTTGAGGGTCCTTTCATAAGAAG
1 AATGATATTGCATATTGCTTTTCCCACTTACCCCTCAATGTGCTTAAGGGTCCTTTCATAAGAAG
48380768 ACTAATTTTTTAT
66 ACTAATTTTTTAT
* *
48380781 AATGATATTGCATATTGCTTTTCCCATTTACCCCTCCATGTGCTTAAGGGTCCTTTCATAAGAAG
1 AATGATATTGCATATTGCTTTTCCCACTTACCCCTCAATGTGCTTAAGGGTCCTTTCATAAGAAG
**
48380846 ACTTTTTTTTTAT
66 ACTAATTTTTTAT
48380859 A
1 A
48380860 TCGTGTTTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (78 bp):
AATGATATTGCATATTGCTTTTCCCACTTACCCCTCAATGTGCTTAAGGGTCCTTTCATAAGAAG
ACTAATTTTTTAT
Found at i:48383436 original size:21 final size:21
Alignment explanation
Indices: 48383407--48383519 Score: 86
Period size: 21 Copynumber: 5.4 Consensus size: 21
48383397 TTCCGTTTAG
* *
48383407 CTCTCATGAGCTTCTATTCAA
1 CTCTTATGAGCTTCTGTTCAA
* *
48383428 CTCTTATGAG-TTTTCGTTTAA
1 CTCTTATGAGCTTCT-GTTCAA
* *
48383449 CTCTTTTGAGCTTCTGTTTAA
1 CTCTTATGAGCTTCTGTTCAA
* * *
48383470 CCCTTAT-AGGTTTCCGTTCAA
1 CTCTTATGA-GCTTCTGTTCAA
* *
48383491 CTCTTATGAGCTTCCGTTTAA
1 CTCTTATGAGCTTCTGTTCAA
*
48383512 CCCTTATG
1 CTCTTATG
48383520 GGTTTATGTT
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
20 4 0.05
21 65 0.89
22 4 0.05
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (21 bp):
CTCTTATGAGCTTCTGTTCAA
Found at i:48383539 original size:42 final size:41
Alignment explanation
Indices: 48383401--48383550 Score: 138
Period size: 42 Copynumber: 3.6 Consensus size: 41
48383391 TTTTCTTTCC
* * * * * *
48383401 GTTTAGCTCTCATGAGCTTCTATTCAACTCTTATGAGTTTT
1 GTTTAACTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTT
* * *
48383442 CGTTTAACTCTTTTGAGCTTCTGTTTAACCCTTATAGGTTTCC
1 -GTTTAACTCTTATGAGCTTCTGTTTAACCCTTATGGGTTT-T
* *
48383485 GTTCAACTCTTATGAGCTTCCGTTTAACCCTTATGGGTTTAT
1 GTTTAACTCTTATGAGCTTCTGTTTAACCCTTATGGGTTT-T
* * * *
48383527 GTTTAGCACTTATGTGCTTTTGTT
1 GTTTAACTCTTATGAGCTTCTGTT
48383551 CAGCCTTAGG
Statistics
Matches: 86, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
42 86 1.00
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.47
Consensus pattern (41 bp):
GTTTAACTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTT
Done.