Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015188.1 Kokia drynarioides strain JFW-HI SEQ_130232, whole genome shotgun sequence
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: 508151
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 585 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3325 original size:69 final size:69
Alignment explanation
Indices: 3214--3353 Score: 226
Period size: 69 Copynumber: 2.0 Consensus size: 69
3204 TTGCGCTAGA
* * *
3214 GATCTGTCCGCAAGCTATAATGTCACCGCAGTAGGCTTCATTGATCCTATTCCTAATTTCCTGAA
1 GATCTGTCCGCAAGCTACAATGTCACCACAGTAGGCTTCATTGATCCTAATCCTAATTTCCTGAA
3279 TGTG
66 TGTG
* * *
3283 GATCTGTCCGCAAGCTGCAATGTCATCACAGTAGGCTTCATTGATCCTAATCCTGATTTCCTGAA
1 GATCTGTCCGCAAGCTACAATGTCACCACAGTAGGCTTCATTGATCCTAATCCTAATTTCCTGAA
3348 TGTG
66 TGTG
3352 GA
1 GA
3354 CAAAGGCATG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (69 bp):
GATCTGTCCGCAAGCTACAATGTCACCACAGTAGGCTTCATTGATCCTAATCCTAATTTCCTGAA
TGTG
Found at i:11115 original size:21 final size:20
Alignment explanation
Indices: 11089--11140 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 20
11079 GTATTAAGGC
11089 AGAAGAAAAAGAAAGAAAAGA
1 AGAAGAAAAAGAAA-AAAAGA
11110 AGAAG--AAA-AAAAAAAGA
1 AGAAGAAAAAGAAAAAAAGA
11127 AGGAAGAAAAAGAA
1 A-GAAGAAAAAGAA
11141 GATGTTACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 3 0.11
20 3 0.11
21 7 0.26
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (20 bp):
AGAAGAAAAAGAAAAAAAGA
Found at i:21658 original size:50 final size:50
Alignment explanation
Indices: 21574--21690 Score: 162
Period size: 50 Copynumber: 2.3 Consensus size: 50
21564 CAAAATAACC
*
21574 AATCTTATACCCCTAAAGCTGTAAAGGAACAGATTGAAGCCGTAATGGAA
1 AATCTTATACCCCTAAAGCTGTAAAGGAACAGATTGAAGCCGTAAGGGAA
* * * *** *
21624 AATCTCATACACCTAAAGCTGTAGAGGGGTAGATTGAAGCCGTAAGGGCA
1 AATCTTATACCCCTAAAGCTGTAAAGGAACAGATTGAAGCCGTAAGGGAA
21674 AATCTTATACCCCTAAA
1 AATCTTATACCCCTAAA
21691 ATTATAGAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (50 bp):
AATCTTATACCCCTAAAGCTGTAAAGGAACAGATTGAAGCCGTAAGGGAA
Found at i:22190 original size:101 final size:100
Alignment explanation
Indices: 22016--22198 Score: 260
Period size: 101 Copynumber: 1.8 Consensus size: 100
22006 AATGAAGCTA
* * *
22016 CCTATACCCCTGAAGTTGCAGTGGGTCGGATAAAGTCATGAAAGCGAATCATTATCTTTCTAAAG
1 CCTATACCCCTGAAGTTGCAGTGGGTCGGATAAAGACATGAAAGCAAATCATTATCTCTCTAAAG
22081 TTACAGTGGAGAAAGATAAAGTTACCACACAAAAT
66 TTACAGTGGAGAAAGATAAAGTTACCACACAAAAT
* * * *
22116 CCTATACTCCTGAAGTTGTAGTGGGTCGGATTAAAGACATGAAAGCAAATCTTTATCTC-CTTGA
1 CCTATACCCCTGAAGTTGCAGTGGGTCGGA-TAAAGACATGAAAGCAAATCATTATCTCTC-TAA
* *
22180 AGTTGCAGTGGAGCAAGAT
64 AGTTACAGTGGAGAAAGAT
22199 GAAGCTACAA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
100 29 0.40
101 43 0.60
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (100 bp):
CCTATACCCCTGAAGTTGCAGTGGGTCGGATAAAGACATGAAAGCAAATCATTATCTCTCTAAAG
TTACAGTGGAGAAAGATAAAGTTACCACACAAAAT
Found at i:22219 original size:101 final size:100
Alignment explanation
Indices: 22016--22236 Score: 257
Period size: 101 Copynumber: 2.2 Consensus size: 100
22006 AATGAAGCTA
* * * * *
22016 CCTATACCCCTGAAGTTGCAGTGGGTCGGATAAAGTCATGAAAGCGAATCATTATCTTTCTAAAG
1 CCTATACTCCTGAAGTTGTAGTGGGTCGGATAAAGACATGAAAGCAAATCATTATCTCTCTAAAG
* *
22081 TTACAGTGGAGAAAGATAAAGTTACCACACAAAAT
66 TTACAGTGGAGAAAGATAAAGCTACAACACAAAAT
* *
22116 CCTATACTCCTGAAGTTGTAGTGGGTCGGATTAAAGACATGAAAGCAAATCTTTATCTC-CTTGA
1 CCTATACTCCTGAAGTTGTAGTGGGTCGGA-TAAAGACATGAAAGCAAATCATTATCTCTC-TAA
* * * * * *
22180 AGTTGCAGTGGAGCAAGATGAAGCTACAATACTAGAT
64 AGTTACAGTGGAGAAAGATAAAGCTACAACACAAAAT
*
22217 CCTAT-CTTCCTAAAGTTGTA
1 CCTATAC-TCCTGAAGTTGTA
22237 ATGAAGCGGA
Statistics
Matches: 102, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
100 30 0.29
101 72 0.71
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (100 bp):
CCTATACTCCTGAAGTTGTAGTGGGTCGGATAAAGACATGAAAGCAAATCATTATCTCTCTAAAG
TTACAGTGGAGAAAGATAAAGCTACAACACAAAAT
Found at i:25933 original size:24 final size:24
Alignment explanation
Indices: 25884--25934 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
25874 TCTAAATTTG
* * *
25884 AAATTTAATCTTTTTTTAATTCAA
1 AAATTTAATCTTATTTGAATTAAA
*
25908 AAATTTAATCTTATTTGATTTAAA
1 AAATTTAATCTTATTTGAATTAAA
25932 AAA
1 AAA
25935 ATAAAATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATTTAATCTTATTTGAATTAAA
Found at i:29341 original size:29 final size:30
Alignment explanation
Indices: 29297--29362 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
29287 TAGTTTAATG
* * *
29297 TGCAATTGTATGCATG-AATTTTGATTTTA
1 TGCAATTGTATACATGAAATTTCGATTTGA
*
29326 TGCAATTTTATACATGAAATTTCGATTTGA
1 TGCAATTGTATACATGAAATTTCGATTTGA
*
29356 TCCAATT
1 TGCAATT
29363 CATACAAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (30 bp):
TGCAATTGTATACATGAAATTTCGATTTGA
Found at i:30246 original size:15 final size:15
Alignment explanation
Indices: 30219--30259 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
30209 GAACTGACAA
30219 AATTATATTAAATTT
1 AATTATATTAAATTT
30234 AATTA-ATTCAAATTT
1 AATTATATT-AAATTT
30249 AATT-TATTAAA
1 AATTATATTAAA
30260 AAATTCCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTATATTAAATTT
Found at i:31560 original size:12 final size:13
Alignment explanation
Indices: 31532--31579 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
31522 TAAACCAAAT
*
31532 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
31545 TTTTCAAAA-CAC
1 TTTTCAAAAGCAC
*
31557 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
*
31570 TTCTCAAAAG
1 TTTTCAAAAG
31580 TAATGCTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:32813 original size:3 final size:3
Alignment explanation
Indices: 32805--32849 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
32795 ACTCCTAAAT
32805 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32850 GATACAAGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:33462 original size:27 final size:27
Alignment explanation
Indices: 33429--33484 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
33419 AATAAATAAT
* *
33429 TTAAAAATTATAAAAA-TATTCAAACAA
1 TTAAAAATTA-AAAAAGTATTAAAAAAA
33456 TTAAAAATTAAAAAAGTATTAAAAAAA
1 TTAAAAATTAAAAAAGTATTAAAAAAA
33483 TT
1 TT
33485 CTTAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (27 bp):
TTAAAAATTAAAAAAGTATTAAAAAAA
Found at i:34753 original size:77 final size:77
Alignment explanation
Indices: 34626--34779 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
34616 ATAATGAATG
* *
34626 AGGCACGTTATCACGAAAGTTTGCCCCCATTGTAATTAGCTTCAATTTGATGATCACCAACGTTC
1 AGGCACGTTATAACCAAAGTTTGCCCCCATTGTAATTAGCTTCAATTTGATGATCACCAACGTTC
34691 AACCCAGTGTCT
66 AACCCAGTGTCT
*
34703 AGGCACGTTATAACCAAAGTTTGCCCCCATTGTAATTAGCTTCAATTTGATGATCGCCAACGTTC
1 AGGCACGTTATAACCAAAGTTTGCCCCCATTGTAATTAGCTTCAATTTGATGATCACCAACGTTC
34768 AACCCAGTGTCT
66 AACCCAGTGTCT
34780 TGTTTGATGA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (77 bp):
AGGCACGTTATAACCAAAGTTTGCCCCCATTGTAATTAGCTTCAATTTGATGATCACCAACGTTC
AACCCAGTGTCT
Found at i:35569 original size:40 final size:40
Alignment explanation
Indices: 35492--35601 Score: 109
Period size: 40 Copynumber: 2.7 Consensus size: 40
35482 AAACAATAGT
*
35492 AAAAAC-GT-ACAAAAATAACATCCAAATAACCAAAATAACAATC
1 AAAAACAGTAACAAAAATAACA-GC-AA-AA-CAAAATAACAA-C
** *
35535 -AAAACAGTAGTAAAAATAATAGCAAAACAAAATAACAAC
1 AAAAACAGTAACAAAAATAACAGCAAAACAAAATAACAAC
*
35574 AAAAATAGTAACAAAAATAACAGCAAAA
1 AAAAACAGTAACAAAAATAACAGCAAAA
35602 ATAGCAACAA
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
39 1 0.02
40 34 0.61
41 2 0.04
42 7 0.12
43 3 0.05
44 9 0.16
ACGTcount: A:0.66, C:0.15, G:0.05, T:0.13
Consensus pattern (40 bp):
AAAAACAGTAACAAAAATAACAGCAAAACAAAATAACAAC
Found at i:35593 original size:24 final size:24
Alignment explanation
Indices: 35552--35625 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
35542 TAGTAAAAAT
*
35552 AATAGCAAAACAAAATAACAACAAA
1 AATAGCAACA-AAAATAACAACAAA
* *
35577 AATAGTAACAAAAATAACAGCAAA
1 AATAGCAACAAAAATAACAACAAA
*
35601 AATAGCAACAAAAATAACATCAAA
1 AATAGCAACAAAAATAACAACAAA
35625 A
1 A
35626 CAGTAAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 36 0.82
25 8 0.18
ACGTcount: A:0.69, C:0.15, G:0.05, T:0.11
Consensus pattern (24 bp):
AATAGCAACAAAAATAACAACAAA
Found at i:35612 original size:12 final size:12
Alignment explanation
Indices: 35552--35616 Score: 76
Period size: 12 Copynumber: 5.3 Consensus size: 12
35542 TAGTAAAAAT
*
35552 AATAGCAAAACAA
1 AATAGCAACA-AA
*
35565 AATAACAACAAA
1 AATAGCAACAAA
*
35577 AATAGTAACAAA
1 AATAGCAACAAA
* *
35589 AATAACAGCAAA
1 AATAGCAACAAA
35601 AATAGCAACAAA
1 AATAGCAACAAA
35613 AATA
1 AATA
35617 ACATCAAAAC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
12 35 0.81
13 8 0.19
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.11
Consensus pattern (12 bp):
AATAGCAACAAA
Found at i:35624 original size:12 final size:12
Alignment explanation
Indices: 35563--35625 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
35553 ATAGCAAAAC
35563 AAAATAACAACA
1 AAAATAACAACA
**
35575 AAAATAGTAACA
1 AAAATAACAACA
*
35587 AAAATAACAGCA
1 AAAATAACAACA
*
35599 AAAATAGCAACA
1 AAAATAACAACA
*
35611 AAAATAACATCA
1 AAAATAACAACA
35623 AAA
1 AAA
35626 CAGTAAAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.11
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:35634 original size:32 final size:32
Alignment explanation
Indices: 35592--35667 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
35582 TAACAAAAAT
* * *
35592 AACAGCAAAAATAGCAACAAAAATAAC-ATCAA
1 AACAGTAAAAAGAGC-ACAAAAACAACAATCAA
*
35624 AACAGTAAAAAAGAGCACCAAAACAACAATCAA
1 AACAGT-AAAAAGAGCACAAAAACAACAATCAA
35657 AACAGTAAAAA
1 AACAGTAAAAA
35668 AAAATAACAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 19 0.50
33 19 0.50
ACGTcount: A:0.66, C:0.18, G:0.08, T:0.08
Consensus pattern (32 bp):
AACAGTAAAAAGAGCACAAAAACAACAATCAA
Found at i:35635 original size:33 final size:33
Alignment explanation
Indices: 35598--35668 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
35588 AAATAACAGC
* *
35598 AAAAATAGCAACAAAAATAAC-ATCAAAACAGTA
1 AAAAAGAGC-ACAAAAACAACAATCAAAACAGTA
*
35631 AAAAAGAGCACCAAAACAACAATCAAAACAGTA
1 AAAAAGAGCACAAAAACAACAATCAAAACAGTA
35664 AAAAA
1 AAAAA
35669 AAATAACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 9 0.26
33 25 0.74
ACGTcount: A:0.68, C:0.17, G:0.07, T:0.08
Consensus pattern (33 bp):
AAAAAGAGCACAAAAACAACAATCAAAACAGTA
Found at i:35679 original size:36 final size:36
Alignment explanation
Indices: 35611--35721 Score: 103
Period size: 36 Copynumber: 3.3 Consensus size: 36
35601 AATAGCAACA
* *
35611 AAAATAAC-ATCAAAACAGT---AAAAAAGAGCACC
1 AAAACAACAATCAAAACAGTAAAAAAAAAGAACACC
*
35643 AAAACAACAATCAAAACAGTAAAAAAAAATAACACC
1 AAAACAACAATCAAAACAGTAAAAAAAAAGAACACC
* * * *
35679 AAAACAGCAACCAAAATAAT-AAAAAAAAG--CACC
1 AAAACAACAATCAAAACAGTAAAAAAAAAGAACACC
35712 -AAACAACAAT
1 AAAACAACAAT
35722 ATAATTTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
32 15 0.23
33 15 0.23
35 8 0.12
36 27 0.42
ACGTcount: A:0.67, C:0.20, G:0.05, T:0.08
Consensus pattern (36 bp):
AAAACAACAATCAAAACAGTAAAAAAAAAGAACACC
Found at i:35712 original size:33 final size:36
Alignment explanation
Indices: 35629--35721 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 36
35619 ATCAAAACAG
*
35629 TAAAAAAGAGCACCAAAACAACAATCAAAACAGTAA
1 TAAAAAAAAGCACCAAAACAACAATCAAAACAGTAA
* * *
35665 -AAAAAAATAACACCAAAACAGCAA-CCAAA-A-TAA
1 TAAAAAAA-AGCACCAAAACAACAATCAAAACAGTAA
35698 TAAAAAAAAGCACC-AAACAACAAT
1 TAAAAAAAAGCACCAAAACAACAAT
35722 ATAATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
32 8 0.17
33 8 0.17
34 8 0.17
35 10 0.21
36 14 0.29
ACGTcount: A:0.67, C:0.20, G:0.05, T:0.08
Consensus pattern (36 bp):
TAAAAAAAAGCACCAAAACAACAATCAAAACAGTAA
Found at i:37667 original size:9 final size:9
Alignment explanation
Indices: 37653--37678 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
37643 TCGTTATATT
37653 AATAAAATG
1 AATAAAATG
37662 AATAAAATG
1 AATAAAATG
37671 AATAAAAT
1 AATAAAAT
37679 TATCTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (9 bp):
AATAAAATG
Found at i:44607 original size:41 final size:41
Alignment explanation
Indices: 44553--44638 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
44543 TAGAGTTGGC
**
44553 CATTCACAATCGATTATGGACCTATAAGACTTGAGCAAATT
1 CATTCACAATCGATTATAAACCTATAAGACTTGAGCAAATT
* * * *
44594 CATTCACCATCGATTATAAACCTGTAAGACTTGGGCAATTT
1 CATTCACAATCGATTATAAACCTATAAGACTTGAGCAAATT
44635 CATT
1 CATT
44639 TTAACCCAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (41 bp):
CATTCACAATCGATTATAAACCTATAAGACTTGAGCAAATT
Found at i:45177 original size:6 final size:7
Alignment explanation
Indices: 45159--45186 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
45149 TGCTCTGCTT
45159 GTTTTTA
1 GTTTTTA
45166 GTTTTTA
1 GTTTTTA
45173 GTTTTTA
1 GTTTTTA
45180 GTTTTTA
1 GTTTTTA
45187 CCGCCGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (7 bp):
GTTTTTA
Found at i:49457 original size:97 final size:97
Alignment explanation
Indices: 49341--49540 Score: 240
Period size: 97 Copynumber: 2.1 Consensus size: 97
49331 NNNNNNNNAA
* ** * *
49341 AAAAAAAAAAAAAAACAATTAAGCCCCTCCTTTTTTTTTGCACTCAATTAAGCACTTGAACTTTC
1 AAAAAAAAAAAAAAACAATTAAGCCCCTCCTTTATTTTCCCACTCAATTAAGCACTTAAACTTTA
* *
49406 AAAATGTATCAAAAAAG-CTCTCAAACTTCTTC
66 AAAATGCAT-AAAAAAGACTCTCAAAATTCTTC
*** * ** *
49438 AAAAAAAAAAAAGCGCAATTAAGCCCCTGCTTTATTTTCCCACTCAATTGGGTACTTAAACTTTA
1 AAAAAAAAAAAAAAACAATTAAGCCCCTCCTTTATTTTCCCACTCAATTAAGCACTTAAACTTTA
* *
49503 AAAATGCATAAAAAAGACTTTCAAAATTTTTC
66 AAAATGCATAAAAAAGACTCTCAAAATTCTTC
49535 AAAAAA
1 AAAAAA
49541 GCAATTAAAC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
96 7 0.08
97 79 0.92
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (97 bp):
AAAAAAAAAAAAAAACAATTAAGCCCCTCCTTTATTTTCCCACTCAATTAAGCACTTAAACTTTA
AAAATGCATAAAAAAGACTCTCAAAATTCTTC
Found at i:49610 original size:18 final size:17
Alignment explanation
Indices: 49579--49634 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 17
49569 TTAGAAAAAA
*
49579 AAATTATAAAAAATAAT
1 AAATTTTAAAAAATAAT
*
49596 AAATTTTAGAAAAATTATT
1 AAATTTTA-AAAAA-TAAT
49615 AAATTTTAATAAAAT-AT
1 AAATTTTAA-AAAATAAT
49632 AAA
1 AAA
49635 AAAAATTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 11 0.33
18 7 0.21
19 15 0.45
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATTTTAAAAAATAAT
Found at i:49893 original size:11 final size:11
Alignment explanation
Indices: 49864--49897 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
49854 GATAAAAAAT
*
49864 AAAAATTA-AT
1 AAAAATTATAG
49874 AAAAATTATAG
1 AAAAATTATAG
49885 AAAAATTATAG
1 AAAAATTATAG
49896 AA
1 AA
49898 TGCTTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (11 bp):
AAAAATTATAG
Found at i:49961 original size:19 final size:17
Alignment explanation
Indices: 49939--50014 Score: 53
Period size: 20 Copynumber: 3.9 Consensus size: 17
49929 TTACAAAATT
49939 TATATTTCTTTACATTTTA
1 TATATTT-TTTA-ATTTTA
49958 TATAATTTTCTTAGGATTTTA
1 TAT-ATTTT-TTA--ATTTTA
*
49979 TAATATTTTTTGTATTTTTA
1 T-ATA-TTTTT-TAATTTTA
*
49999 TATATTTTATAATTTT
1 TATATTTTTTAATTTT
50015 TTACGATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
17 6 0.13
18 4 0.09
19 7 0.15
20 13 0.28
21 9 0.19
22 8 0.17
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (17 bp):
TATATTTTTTAATTTTA
Found at i:50025 original size:19 final size:19
Alignment explanation
Indices: 50003--50043 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
49993 TTTTTATATA
** *
50003 TTTTATAATTTTTTACGAT
1 TTTTATAAAATTTTACAAT
50022 TTTTATAAAATTTTACAAT
1 TTTTATAAAATTTTACAAT
50041 TTT
1 TTT
50044 ACAATTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTATAAAATTTTACAAT
Found at i:50248 original size:87 final size:89
Alignment explanation
Indices: 50132--50302 Score: 249
Period size: 87 Copynumber: 1.9 Consensus size: 89
50122 TAAAAGCAAT
50132 GGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTC-TTTTTGATGCATTTTAAAAGTTCAAACAC
1 GGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGG-CATTTTTGATGCATTTTAAAAGTTCAAACAC
*
50196 CCAATTGAGTG-AAAAAAAAGTAGG
65 CCAAATGAGTGCAAAAAAAAGTAGG
* * * * **
50220 GGCTTAATTGC-TTTTTTGAAAAGGTTTGAGGGCATTTTTTATGTATTTTGAAAGTTCAAGTACC
1 GGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCATTTTTGATGCATTTTAAAAGTTCAAACACC
50284 CAAATGAGTGCAAAAAAAA
66 CAAATGAGTGCAAAAAAAA
50303 AAGAAAAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
86 1 0.01
87 54 0.73
88 19 0.26
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (89 bp):
GGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCATTTTTGATGCATTTTAAAAGTTCAAACACC
CAAATGAGTGCAAAAAAAAGTAGG
Found at i:54602 original size:71 final size:71
Alignment explanation
Indices: 54485--54901 Score: 541
Period size: 71 Copynumber: 5.9 Consensus size: 71
54475 TTTCACATAT
* * * * *
54485 AGTGACTCATGATGCTATAGAGAATCCGCAACAAATGCAGGATCTCAACCATCGGACTAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGCCATCAGACTAGTTTCA
54550 CTTTAC
66 CTTTAC
* * *
54556 AGTGACTCACGATGCTGTAGAGAATCCGTAACAAATGCAAGGTCTCAACCATCAGACTAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGCCATCAGACTAGTTTCA
* *
54621 CTGTAA
66 CTTTAC
* * * * **
54627 AGTGACTCACGATGCTGTATAGAATTCGCAAGAAATGCAAGATCTCATCCATTGGACTAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGCCATCAGACTAGTTTCA
54692 CTTTAC
66 CTTTAC
* * * * *
54698 AGTGACTCATGATACTGTAGAGAATCC-CTAACAAATGCAAGATCTCAGCCATCGGACCAGTTTT
1 AGTGACTCACGATGCTGTAGAGAATCCGC-AACAAATGCAAGATCTCAGCCATCAGACTAGTTTC
54762 ACTTTAC
65 ACTTTAC
* * * * *
54769 AGTGACTCACGATGCTATAAAGAATCCGCAACACATGCAAGATCTCAGCCATCAGACCAATTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGCCATCAGACTAGTTTCA
54834 CTTTAC
66 CTTTAC
* * * *
54840 AATGACTCACGATGCTGTAAAGAATCCACAACAAATGCAATATCTCAGCCATCAGACT-GTTT
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGCCATCAGACTAGTTT
54902 TTTATCTTTG
Statistics
Matches: 302, Mismatches: 42, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
70 4 0.01
71 297 0.98
72 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (71 bp):
AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAGCCATCAGACTAGTTTCA
CTTTAC
Found at i:55372 original size:16 final size:16
Alignment explanation
Indices: 55348--55379 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55338 TCCTTACAAA
*
55348 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
55364 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
55380 AAAAATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:56995 original size:55 final size:55
Alignment explanation
Indices: 56931--57190 Score: 306
Period size: 55 Copynumber: 4.7 Consensus size: 55
56921 TCTATAGTTA
*
56931 GGGTAGAGCTTTGGTTTGCTTACATCTCGGTTAGAGCGTAAAACTATCATAGCTC
1 GGGTAGAGCTTTGGTTTGCTTACGTCTCGGTTAGAGCGTAAAACTATCATAGCTC
* *
56986 GGGTAGAGCTTTGGTTTGCTTACGTCTTGGTTAGAGCATAAAACTATCATAGCTC
1 GGGTAGAGCTTTGGTTTGCTTACGTCTCGGTTAGAGCGTAAAACTATCATAGCTC
* * * * *
57041 AGGTAGAGC-TTGGTTTGCTTACGTCTCGATTAGAGTGTAAAGCTATTATAGCTC
1 GGGTAGAGCTTTGGTTTGCTTACGTCTCGGTTAGAGCGTAAAACTATCATAGCTC
*** * * * *
57095 GGGTAGAGCTTTGAACTCCTTACGTCTCAGTTAGAGCGTAAAGCTATGATAGCTC
1 GGGTAGAGCTTTGGTTTGCTTACGTCTCGGTTAGAGCGTAAAACTATCATAGCTC
* * * * * * **
57150 GGTTAGATCTTTGATCTGCTTTCATCTCAATTAGAGCGTAA
1 GGGTAGAGCTTTGGTTTGCTTACGTCTCGGTTAGAGCGTAA
57191 GGTTGTTTCG
Statistics
Matches: 178, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
54 47 0.26
55 131 0.74
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (55 bp):
GGGTAGAGCTTTGGTTTGCTTACGTCTCGGTTAGAGCGTAAAACTATCATAGCTC
Found at i:57068 original size:109 final size:110
Alignment explanation
Indices: 56932--57190 Score: 324
Period size: 109 Copynumber: 2.4 Consensus size: 110
56922 CTATAGTTAG
*
56932 GGTAGAGCTTTGGTTTGCTTACATCTCGGTTAGAGCGTAAAACTATCATAGCTCGGGTAGAGCTT
1 GGTAGAGCTTTGGTTTGCTTACATCTCGATTAGAGCGTAAAACTATCATAGCTCGGGTAGAGCTT
*** * **
56997 TGGTTTGCTTACGTCTTGGTTAGAGCATAAAACTATCATAGCTCA
66 TGAACTCCTTACGTCTCAGTTAGAGCATAAAACTATCATAGCTCA
* * * *
57042 GGTAGAGC-TTGGTTTGCTTACGTCTCGATTAGAGTGTAAAGCTATTATAGCTCGGGTAGAGCTT
1 GGTAGAGCTTTGGTTTGCTTACATCTCGATTAGAGCGTAAAACTATCATAGCTCGGGTAGAGCTT
* * *
57106 TGAACTCCTTACGTCTCAGTTAGAGCGTAAAGCTATGATAGCTC-
66 TGAACTCCTTACGTCTCAGTTAGAGCATAAAACTATCATAGCTCA
* * * * *
57150 GGTTAGATCTTTGATCTGCTTTCATCTCAATTAGAGCGTAA
1 GG-TAGAGCTTTGGTTTGCTTACATCTCGATTAGAGCGTAA
57191 GGTTGTTTCG
Statistics
Matches: 126, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
108 2 0.02
109 91 0.72
110 33 0.26
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (110 bp):
GGTAGAGCTTTGGTTTGCTTACATCTCGATTAGAGCGTAAAACTATCATAGCTCGGGTAGAGCTT
TGAACTCCTTACGTCTCAGTTAGAGCATAAAACTATCATAGCTCA
Found at i:57640 original size:22 final size:23
Alignment explanation
Indices: 57593--57647 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
57583 TGCCACTTTC
57593 ATATGTGAAATTGTATGTTTTATG
1 ATATGTGAAATTGTATG-TTTATG
57617 ATATGTGAAATTGTATG-TTATG
1 ATATGTGAAATTGTATGTTTATG
*
57639 ATAAGTGAA
1 ATATGTGAA
57648 TGGTATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 13 0.43
24 17 0.57
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.44
Consensus pattern (23 bp):
ATATGTGAAATTGTATGTTTATG
Found at i:58954 original size:30 final size:30
Alignment explanation
Indices: 58920--58986 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 30
58910 GTTTGGGGAT
58920 TAAATTAG-AATTTTAGT-GACATTTAAGGAC
1 TAAATT-GTAATTTTAGTGGA-ATTTAAGGAC
*
58950 TAAATTGTAATTTTAGTGGAATTTGAGGAC
1 TAAATTGTAATTTTAGTGGAATTTAAGGAC
58980 TAAATTG
1 TAAATTG
58987 GGTTTTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.03
30 31 0.91
31 2 0.06
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.39
Consensus pattern (30 bp):
TAAATTGTAATTTTAGTGGAATTTAAGGAC
Found at i:59857 original size:26 final size:25
Alignment explanation
Indices: 59828--59876 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
59818 GTTGACTTTT
59828 ACTTTAACCGTTGAC-TTTTTCGACCA
1 ACTTTAA-C-TTGACATTTTTCGACCA
*
59854 ACTTTGACTTGACATTTTTCGAC
1 ACTTTAACTTGACATTTTTCGAC
59877 GTCTTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 10 0.48
26 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.41
Consensus pattern (25 bp):
ACTTTAACTTGACATTTTTCGACCA
Found at i:73602 original size:21 final size:21
Alignment explanation
Indices: 73577--73635 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
73567 TAGTTGCATG
*
73577 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAAGAGTC
* **
73598 TCTTGTATCGGTAGAATTGTC
1 ACTTGTATCGGTAGAAGAGTC
73619 ACTTGTATCGGTAGAAG
1 ACTTGTATCGGTAGAAG
73636 TCTGCACTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.36
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGAGTC
Found at i:74566 original size:40 final size:40
Alignment explanation
Indices: 74493--74580 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
74483 AATTTTCAAG
**** *
74493 TGGTGAAACCCTTGCCATTCTCCTTTTTTTTAATATTCTT
1 TGGTGAAACCCTTGCCATTCTCCTTCGAGTTAATATTATT
*
74533 TGGTGAAA-CCTCTGCCATTCTCCTTCGAGTTAATCTTATT
1 TGGTGAAACCCT-TGCCATTCTCCTTCGAGTTAATATTATT
74573 TGGT-AAAC
1 TGGTGAAAC
74581 TTTTTTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 6 0.15
40 34 0.85
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (40 bp):
TGGTGAAACCCTTGCCATTCTCCTTCGAGTTAATATTATT
Found at i:75859 original size:26 final size:25
Alignment explanation
Indices: 75824--75883 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
75814 TCAAGATTAC
*
75824 TATATAAAAAATTTTAATAAATAAAAA
1 TATAT-AAAAATATTAA-AAATAAAAA
* *
75851 TATATAAAAATATTAAATATTAAAA
1 TATATAAAAATATTAAAAATAAAAA
75876 TAATATAA
1 T-ATATAA
75884 TATATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 8 0.28
26 16 0.55
27 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TATATAAAAATATTAAAAATAAAAA
Found at i:77261 original size:20 final size:20
Alignment explanation
Indices: 77236--77277 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
77226 CGAATTATTT
77236 ATTCAACTCGATTCGAAAAA
1 ATTCAACTCGATTCGAAAAA
* *
77256 ATTCAATTCGATTTGAAAAA
1 ATTCAACTCGATTCGAAAAA
77276 AT
1 AT
77278 CAAGTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTCAACTCGATTCGAAAAA
Found at i:77337 original size:56 final size:56
Alignment explanation
Indices: 77227--77380 Score: 236
Period size: 56 Copynumber: 2.7 Consensus size: 56
77217 TTTGAAATTC
* ** * *
77227 GAATTATTTATTCAACTCGATTCGAAAAAATTCAATTCGATTTGAAAAAATCAAGTT
1 GAATTATTTATTCAACTCGACTC-AAAAAAACCAACTCGAATTGAAAAAATCAAGTT
*
77284 GAATTATTTATTCAACTCAACTCAAAAAAACCAACTCGAATTGAAAAAATCAAGTT
1 GAATTATTTATTCAACTCGACTCAAAAAAACCAACTCGAATTGAAAAAATCAAGTT
*
77340 GAATTATTTATTCAACTCGACTCAGAAAAACCAACTCGAAT
1 GAATTATTTATTCAACTCGACTCAAAAAAACCAACTCGAAT
77381 AATCCCTTTG
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
56 68 0.76
57 21 0.24
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (56 bp):
GAATTATTTATTCAACTCGACTCAAAAAAACCAACTCGAATTGAAAAAATCAAGTT
Found at i:77467 original size:17 final size:17
Alignment explanation
Indices: 77447--77484 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
77437 AAAATTACAA
77447 AAAATCAAAATAATTT-T
1 AAAATCAAAAT-ATTTAT
*
77464 AAAATCCAAATATTTAT
1 AAAATCAAAATATTTAT
77481 AAAA
1 AAAA
77485 ATTCCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATCAAAATATTTAT
Found at i:77473 original size:18 final size:17
Alignment explanation
Indices: 77447--77505 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 17
77437 AAAATTACAA
77447 AAAAT-CAAAATAATTTT
1 AAAATCCAAAAT-ATTTT
77464 AAAATCC-AAATATTTAT
1 AAAATCCAAAATATTT-T
77481 AAAAATTCCAAAATTTATTTT
1 -AAAA-TCCAAAA--TATTTT
77502 AAAA
1 AAAA
77506 AATTATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
16 4 0.11
17 10 0.29
18 5 0.14
19 3 0.09
20 7 0.20
21 1 0.03
22 5 0.14
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATCCAAAATATTTT
Found at i:77530 original size:11 final size:10
Alignment explanation
Indices: 77497--77527 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
77487 TCCAAAATTT
77497 ATTTTAAAAA
1 ATTTTAAAAA
*
77507 ATTATAAAAA
1 ATTTTAAAAA
77517 ATTTTAAAAA
1 ATTTTAAAAA
77527 A
1 A
77528 ATTCTAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:77683 original size:16 final size:16
Alignment explanation
Indices: 77662--77692 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
77652 TTTAAAAAAT
77662 TTTCAAATATATATAA
1 TTTCAAATATATATAA
*
77678 TTTCAAATTTATATA
1 TTTCAAATATATATA
77693 CCCAAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATAA
Found at i:78627 original size:5 final size:5
Alignment explanation
Indices: 78617--78653 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
78607 TCCTTTTTCA
* *
78617 TTTAT TTTAT TTTAT TTTAT TTTAC TTTAC TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
78654 GTTAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:78829 original size:29 final size:27
Alignment explanation
Indices: 78790--78847 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
78780 CTTTCTTATT
78790 TTATTTCAATAAATCATTATACTTTTA
1 TTATTTCAATAAATCATTATACTTTTA
* **
78817 TTATATTCAAATAACTTGTTATACTTTTA
1 TTAT-TTC-AATAAATCATTATACTTTTA
78846 TT
1 TT
78848 GCATTGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.15
28 3 0.12
29 19 0.73
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.53
Consensus pattern (27 bp):
TTATTTCAATAAATCATTATACTTTTA
Found at i:90029 original size:30 final size:30
Alignment explanation
Indices: 89967--90060 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 30
89957 GAAACACCAT
* ** *
89967 CACACAACAAA-ACATAGCACAAACAAAAA
1 CACACAACAAATATATAGCACGGACAAAGA
* * *
89996 CACACAGCAAATATGTAGCACGGACAGAGA
1 CACACAACAAATATATAGCACGGACAAAGA
*
90026 CACACAACAAATATATAGCACGGATAAAGA
1 CACACAACAAATATATAGCACGGACAAAGA
90056 CACAC
1 CACAC
90061 CTGAAGCGAA
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
29 10 0.19
30 43 0.81
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.09
Consensus pattern (30 bp):
CACACAACAAATATATAGCACGGACAAAGA
Found at i:94810 original size:22 final size:22
Alignment explanation
Indices: 94784--94825 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
94774 AGGAAAAAAA
94784 ACTTGGAG-TTTGACGAGGAACT
1 ACTTGG-GTTTTGACGAGGAACT
*
94806 ACTTGGGTTTTTACGAGGAA
1 ACTTGGGTTTTGACGAGGAA
94826 AACTTTGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (22 bp):
ACTTGGGTTTTGACGAGGAACT
Found at i:104296 original size:20 final size:20
Alignment explanation
Indices: 104254--104297 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
104244 ATTTAATTTG
* *
104254 AATTCGATTTTTTCACATGA
1 AATTCGATTTTTTCAAATCA
104274 AATTCG-TTTTATTCAAATCA
1 AATTCGATTTT-TTCAAATCA
104294 AATT
1 AATT
104298 GAATGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (20 bp):
AATTCGATTTTTTCAAATCA
Found at i:104348 original size:3 final size:3
Alignment explanation
Indices: 104340--104364 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
104330 TCCTAATAGA
104340 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
104365 GATAAAGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:109247 original size:11 final size:11
Alignment explanation
Indices: 109203--109276 Score: 64
Period size: 11 Copynumber: 6.7 Consensus size: 11
109193 TTCTGACTTG
109203 TATGTTGTG-TT
1 TATGTTG-GCTT
109214 T-TGTTGGCTT
1 TATGTTGGCTT
* **
109224 TATGATGATTT
1 TATGTTGGCTT
109235 TATGTCT-GCTT
1 TATGT-TGGCTT
109246 TATGTTGGCTT
1 TATGTTGGCTT
109257 TAATGTTGGCTT
1 T-ATGTTGGCTT
*
109269 TATATTGG
1 TATGTTGG
109277 ATGTTGTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
9 1 0.02
10 9 0.18
11 29 0.57
12 12 0.24
ACGTcount: A:0.14, C:0.07, G:0.24, T:0.55
Consensus pattern (11 bp):
TATGTTGGCTT
Found at i:109264 original size:12 final size:12
Alignment explanation
Indices: 109242--109270 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
109232 TTTTATGTCT
109242 GCTTT-ATGTTG
1 GCTTTAATGTTG
109253 GCTTTAATGTTG
1 GCTTTAATGTTG
109265 GCTTTA
1 GCTTTA
109271 TATTGGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (12 bp):
GCTTTAATGTTG
Found at i:109268 original size:23 final size:23
Alignment explanation
Indices: 109215--109278 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
109205 TGTTGTGTTT
* *
109215 TGTTGGCTTTATGAT-GATTTTA
1 TGTTGGCTTTATGTTGGATTTAA
*
109237 TGTCT-GCTTTATGTTGGCTTTAA
1 TGT-TGGCTTTATGTTGGATTTAA
*
109260 TGTTGGCTTTATATTGGAT
1 TGTTGGCTTTATGTTGGAT
109279 GTTGTTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.16, C:0.08, G:0.23, T:0.53
Consensus pattern (23 bp):
TGTTGGCTTTATGTTGGATTTAA
Found at i:110002 original size:21 final size:21
Alignment explanation
Indices: 109954--110004 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
109944 GTGAGGATTC
**
109954 CAACTCAACAAGTGAGCAGCA
1 CAACTCAGTAAGTGAGCAGCA
*
109975 CATCTCAGTAAGTGAGCAGCA
1 CAACTCAGTAAGTGAGCAGCA
*
109996 TAACTCAGT
1 CAACTCAGT
110005 TGCAAATGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (21 bp):
CAACTCAGTAAGTGAGCAGCA
Found at i:111159 original size:3 final size:3
Alignment explanation
Indices: 111151--111215 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
111141 AATCTCCATT
111151 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
111198 TTC -TA TTC TT- TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TT
111216 AAACCCTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 5 0.09
3 52 0.91
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:111458 original size:3 final size:3
Alignment explanation
Indices: 111450--111484 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
111440 TAATTTACCC
111450 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
111485 TTGTCACAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:125419 original size:16 final size:16
Alignment explanation
Indices: 125373--125419 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
125363 AAAATATATT
125373 TATATTATTTTATTTTA
1 TATATT-TTTTATTTTA
* *
125390 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
125406 TATATTTTTTATTT
1 TATATTTTTTATTT
125420 ATTGAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:126220 original size:20 final size:21
Alignment explanation
Indices: 126195--126234 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
126185 AAAAACGCAT
*
126195 AAAAATAAC-ATCAAAACAAC
1 AAAAATAACAACCAAAACAAC
126215 AAAAATAACAACCAAAACAA
1 AAAAATAACAACCAAAACAA
126235 AAGTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.72, C:0.20, G:0.00, T:0.07
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:126224 original size:12 final size:12
Alignment explanation
Indices: 126209--126290 Score: 51
Period size: 12 Copynumber: 6.8 Consensus size: 12
126199 ATAACATCAA
126209 AACAACAAAAAT
1 AACAACAAAAAT
* *
126221 AACAACCAAAAC
1 AACAACAAAAAT
*
126233 AA-AAGTAAAAAT
1 AACAA-CAAAAAT
* *
126245 AATAGC-AAAAT
1 AACAACAAAAAT
* *
126256 AAAAAATAAAAAT
1 -AACAACAAAAAT
*
126269 AACAATAAAAAT
1 AACAACAAAAAT
*
126281 AACAGCAAAA
1 AACAACAAAA
126291 GCAACATCAA
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
11 7 0.13
12 40 0.75
13 6 0.11
ACGTcount: A:0.73, C:0.12, G:0.04, T:0.11
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:126278 original size:24 final size:23
Alignment explanation
Indices: 126215--126279 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
126205 TCAAAACAAC
* *
126215 AAAAATAACAACCAAAACAAAAGT
1 AAAAATAACAA-CAAAAAAAAAAT
* *
126239 AAAAATAATAGCAAAATAAAAAAT
1 AAAAATAACAACAAAA-AAAAAAT
*
126263 AAAAATAACAATAAAAA
1 AAAAATAACAACAAAAA
126280 TAACAGCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 6 0.18
24 27 0.82
ACGTcount: A:0.75, C:0.09, G:0.03, T:0.12
Consensus pattern (23 bp):
AAAAATAACAACAAAAAAAAAAT
Found at i:126332 original size:22 final size:22
Alignment explanation
Indices: 126307--126354 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
126297 TCAAAACAGT
*
126307 AAAAAAGAATCAAAACAACAAA
1 AAAAAAGAACCAAAACAACAAA
* * *
126329 AAAATAGCACCAAAACAGCAAA
1 AAAAAAGAACCAAAACAACAAA
126351 AAAA
1 AAAA
126355 TACACCAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.73, C:0.17, G:0.06, T:0.04
Consensus pattern (22 bp):
AAAAAAGAACCAAAACAACAAA
Found at i:126355 original size:22 final size:22
Alignment explanation
Indices: 126317--126381 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
126307 AAAAAAGAAT
*
126317 CAAAACAACAAAAAAATAGCAC
1 CAAAACAGCAAAAAAATAGCAC
126339 CAAAACAGCAAAAAAATA-CAC
1 CAAAACAGCAAAAAAATAGCAC
* * *
126360 CAGAAATAGTAAACAAATAGCA
1 CA-AAACAGCAAAAAAATAGCA
126382 ATATTTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 5 0.14
22 30 0.81
23 2 0.05
ACGTcount: A:0.65, C:0.20, G:0.08, T:0.08
Consensus pattern (22 bp):
CAAAACAGCAAAAAAATAGCAC
Found at i:128710 original size:16 final size:16
Alignment explanation
Indices: 128689--128739 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
128679 ATATCCGTAA
128689 GGATATCATTGAAAAG
1 GGATATCATTGAAAAG
* *
128705 GGATATC--CG-TAA-
1 GGATATCATTGAAAAG
128717 GGATATCATTGAAAAG
1 GGATATCATTGAAAAG
128733 GGATATC
1 GGATATC
128740 CGTAAGGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 2 0.07
15 2 0.07
16 14 0.52
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (16 bp):
GGATATCATTGAAAAG
Found at i:128711 original size:28 final size:28
Alignment explanation
Indices: 128679--128900 Score: 293
Period size: 28 Copynumber: 7.9 Consensus size: 28
128669 ATTGATTTCT
128679 ATATCCGTAAGGATATCATTGAAAAGGG
1 ATATCCGTAAGGATATCATTGAAAAGGG
128707 ATATCCGTAAGGATATCATTGAAAAGGG
1 ATATCCGTAAGGATATCATTGAAAAGGG
* *
128735 ATATCCGTAAGGATATCATCGAAAAGGTT
1 ATATCCGTAAGGATATCATTGAAAAGG-G
*
128764 ATATCCTTAAGGATAT-ATTTTGAAAAGGG
1 ATATCCGTAAGGATATCA--TTGAAAAGGG
*
128793 ATACCCGTAAGGATATCATTGAAAAGGG
1 ATATCCGTAAGGATATCATTGAAAAGGG
*** *
128821 ATATCTACAATGATATCATTGAAAAGGG
1 ATATCCGTAAGGATATCATTGAAAAGGG
** * *
128849 ATATCCACAAAGATATCATTGAAAAAGG
1 ATATCCGTAAGGATATCATTGAAAAGGG
*
128877 ATATCCGCAAGGATATCATTGAAA
1 ATATCCGTAAGGATATCATTGAAA
128901 CATTTGAAAA
Statistics
Matches: 173, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
28 135 0.78
29 29 0.17
30 9 0.05
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (28 bp):
ATATCCGTAAGGATATCATTGAAAAGGG
Found at i:128824 original size:16 final size:16
Alignment explanation
Indices: 128803--128853 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
128793 ATACCCGTAA
128803 GGATATCATTGAAAAG
1 GGATATCATTGAAAAG
*
128819 GGATATC--T-ACAA-
1 GGATATCATTGAAAAG
*
128831 TGATATCATTGAAAAG
1 GGATATCATTGAAAAG
128847 GGATATC
1 GGATATC
128854 CACAAAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
12 6 0.22
13 3 0.11
14 2 0.07
15 3 0.11
16 13 0.48
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (16 bp):
GGATATCATTGAAAAG
Found at i:128881 original size:16 final size:16
Alignment explanation
Indices: 128801--128881 Score: 52
Period size: 16 Copynumber: 5.6 Consensus size: 16
128791 GGATACCCGT
128801 AAGGATATCATTGAAA
1 AAGGATATCATTGAAA
* *
128817 AGGGATATC--T--AC
1 AAGGATATCATTGAAA
*
128829 AATGATATCATTGAAA
1 AAGGATATCATTGAAA
* * *
128845 AGGGATATC---CACA
1 AAGGATATCATTGAAA
128858 AA-GATATCATTGAAA
1 AAGGATATCATTGAAA
128873 AAGGATATC
1 AAGGATATC
128882 CGCAAGGATA
Statistics
Matches: 45, Mismatches: 12, Indels: 16
0.62 0.16 0.22
Matches are distributed among these distances:
12 14 0.31
13 3 0.07
14 2 0.04
15 4 0.09
16 22 0.49
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.25
Consensus pattern (16 bp):
AAGGATATCATTGAAA
Found at i:139175 original size:30 final size:30
Alignment explanation
Indices: 139141--139232 Score: 121
Period size: 30 Copynumber: 3.1 Consensus size: 30
139131 TAATCTCTTG
*
139141 AACATATATCTATGACAATTCAAACGATTA
1 AACATATACCTATGACAATTCAAACGATTA
* * *
139171 AACATATACCTATGCCAATTTAAACTATTA
1 AACATATACCTATGACAATTCAAACGATTA
* * *
139201 AACATATACCTCTGTCAATTCAAATGATTA
1 AACATATACCTATGACAATTCAAACGATTA
139231 AA
1 AA
139233 TTAATATTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (30 bp):
AACATATACCTATGACAATTCAAACGATTA
Found at i:142209 original size:27 final size:27
Alignment explanation
Indices: 142179--142321 Score: 184
Period size: 27 Copynumber: 5.3 Consensus size: 27
142169 AGTCGTGTAC
142179 AGAGTATCGTTCATTTGAGCCAGAAAT
1 AGAGTATCGTTCATTTGAGCCAGAAAT
* *
142206 AGAGTAT-GTTTAATTGAGCCAGAAAT
1 AGAGTATCGTTCATTTGAGCCAGAAAT
*
142232 AGAGTATTGTTCATTTGAGCCAGAAAT
1 AGAGTATCGTTCATTTGAGCCAGAAAT
* * *
142259 AGAGTACCGCTC-TTTCGAGCCAGAAAC
1 AGAGTATCGTTCATTT-GAGCCAGAAAT
*
142286 AGAGTATCGCTC-TTTCGAGCCAGAAAT
1 AGAGTATCGTTCATTT-GAGCCAGAAAT
142313 AGAGTATCG
1 AGAGTATCG
142322 CCTTCTGCTT
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
26 27 0.26
27 77 0.74
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (27 bp):
AGAGTATCGTTCATTTGAGCCAGAAAT
Found at i:152801 original size:25 final size:25
Alignment explanation
Indices: 152772--152820 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
152762 TCTCGATAAA
152772 AGGGGAAAC-TAATCTTAGAAGATTG
1 AGGGGAAACAT-ATCTTAGAAGATTG
* *
152797 AGGGGAATCATATCTTATAAGATT
1 AGGGGAAACATATCTTAGAAGATT
152821 AGATTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (25 bp):
AGGGGAAACATATCTTAGAAGATTG
Found at i:154084 original size:29 final size:30
Alignment explanation
Indices: 154050--154110 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
154040 AGTAAATTTG
*
154050 AAATTTACTTTTTGTATTTTT-ATTTTTAA
1 AAATTTACTTTTTGTATTTTTAAATTTTAA
* *
154079 AAATTTATTTTTTTTATTTTTAAATTTTAA
1 AAATTTACTTTTTGTATTTTTAAATTTTAA
154109 AA
1 AA
154111 TTCAAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (30 bp):
AAATTTACTTTTTGTATTTTTAAATTTTAA
Found at i:154111 original size:29 final size:29
Alignment explanation
Indices: 154042--154112 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
154032 ATCTTTCTAG
*
154042 TAAA-TTTGAAATTTACTTTTTGTATTTT
1 TAAATTTTAAAATTTACTTTTTGTATTTT
* * *
154070 T-ATTTTTAAAAATTTATTTTTTTTATTTT
1 TAAATTTT-AAAATTTACTTTTTGTATTTT
154099 TAAATTTTAAAATT
1 TAAATTTTAAAATT
154113 CAAATTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 4 0.11
29 25 0.71
30 5 0.14
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.63
Consensus pattern (29 bp):
TAAATTTTAAAATTTACTTTTTGTATTTT
Found at i:154380 original size:38 final size:38
Alignment explanation
Indices: 154338--154414 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
154328 TAGCATATTT
154338 TAATCTTATATATTAAACATGGTCAAATACAAGTAATC
1 TAATCTTATATATTAAACATGGTCAAATACAAGTAATC
154376 TAATCTTATATATTAAACATGGTCAAATACAAGTAATC
1 TAATCTTATATATTAAACATGGTCAAATACAAGTAATC
154414 T
1 T
154415 CCCAATTCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (38 bp):
TAATCTTATATATTAAACATGGTCAAATACAAGTAATC
Found at i:155560 original size:49 final size:49
Alignment explanation
Indices: 155483--155581 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
155473 CTGAGCTTTC
*
155483 ATAGTTCACTCCCCTTATTTTTCCATCTTTTCAGATAACCTTGCAAACT
1 ATAGCTCACTCCCCTTATTTTTCCATCTTTTCAGATAACCTTGCAAACT
* *
155532 ATAGCTCACTCCTCTTATTTTTCCATCTTTTCCGATAACCTTGCAAACT
1 ATAGCTCACTCCCCTTATTTTTCCATCTTTTCAGATAACCTTGCAAACT
155581 A
1 A
155582 GGACGTGGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.40
Consensus pattern (49 bp):
ATAGCTCACTCCCCTTATTTTTCCATCTTTTCAGATAACCTTGCAAACT
Found at i:155906 original size:17 final size:17
Alignment explanation
Indices: 155886--155938 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 17
155876 ATGTTAGTCT
*
155886 TAAATAGATAAA-ATAAA
1 TAAATA-ATAAACAAAAA
155903 TAAATAATAAACAAAAA
1 TAAATAATAAACAAAAA
155920 T-AA-AATAAACAAAAA
1 TAAATAATAAACAAAAA
155935 -AAAT
1 TAAAT
155939 CCTTTAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.44
16 7 0.22
17 11 0.34
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (17 bp):
TAAATAATAAACAAAAA
Found at i:156227 original size:23 final size:24
Alignment explanation
Indices: 156200--156252 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
156190 AAGCAACCTG
156200 CAAAATAG-AGAAGAGCAAA-GCAA
1 CAAAATAGCAGAAGA-CAAATGCAA
156223 CAAAA-AGCTAGAAGACAAATGCAA
1 CAAAATAGC-AGAAGACAAATGCAA
156247 -AAAATA
1 CAAAATA
156253 AAATACCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 2 0.08
23 13 0.50
24 11 0.42
ACGTcount: A:0.62, C:0.13, G:0.17, T:0.08
Consensus pattern (24 bp):
CAAAATAGCAGAAGACAAATGCAA
Found at i:157316 original size:29 final size:29
Alignment explanation
Indices: 157267--157330 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
157257 TTTATTTTGG
* *
157267 CCCTTTTGTTCTGTTTCTTTTTAATCAAA
1 CCCTTTTGTTCTATTTCTTTTAAATCAAA
* **
157296 CCCTTTTGTTTTAATTT-TTTTAAATTTAA
1 CCCTTTTGTTCT-ATTTCTTTTAAATCAAA
157325 CCCTTT
1 CCCTTT
157331 CATTTAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.58
Consensus pattern (29 bp):
CCCTTTTGTTCTATTTCTTTTAAATCAAA
Found at i:157458 original size:24 final size:25
Alignment explanation
Indices: 157389--157458 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 25
157379 CCTTCTATTT
*
157389 TTTTTATATTTAAATCCTTTTGTATC
1 TTTTTA-AATTAAATCCTTTTGTATC
* *
157415 TTTTT-AATCAAATCCTTTTTTATCC
1 TTTTTAAATTAAATCCTTTTGTAT-C
157440 TTTTTAAATTAAA-CCTTTT
1 TTTTTAAATTAAATCCTTTT
157459 ATTTTTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 15 0.39
25 12 0.32
26 11 0.29
ACGTcount: A:0.26, C:0.14, G:0.01, T:0.59
Consensus pattern (25 bp):
TTTTTAAATTAAATCCTTTTGTATC
Found at i:159489 original size:18 final size:17
Alignment explanation
Indices: 159466--159500 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
159456 CTTTTTAAAG
159466 AGGTTGATGAACATACTC
1 AGGTTGATGAACA-ACTC
159484 AGGTTGATGAACAACTC
1 AGGTTGATGAACAACTC
159501 TTTTGAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (17 bp):
AGGTTGATGAACAACTC
Found at i:161275 original size:30 final size:30
Alignment explanation
Indices: 161240--161300 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
161230 TCCATCGGGG
*
161240 CAACACCTTTCTCATTGGAATGAAAGCAAT
1 CAACACCTTTCTCATTGGAAAGAAAGCAAT
161270 CAACACCTTTCTCATTGGAAAGAAAGCAAT
1 CAACACCTTTCTCATTGGAAAGAAAGCAAT
161300 C
1 C
161301 CTCCCCATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (30 bp):
CAACACCTTTCTCATTGGAAAGAAAGCAAT
Found at i:162820 original size:98 final size:98
Alignment explanation
Indices: 162713--163161 Score: 413
Period size: 98 Copynumber: 4.6 Consensus size: 98
162703 GGAGGGATTA
* * * * * ***
162713 AAGCCGCAATGGCGAATCTTGTACCTTAGAGATATGGAAGGAAAGGTTGAAGCCATAACGGTGTA
1 AAGCCGTAATGGCGAACCTTGTACCTTAGAGATATGGAGGGAAAAGTTGAAGCCACAACGGCAAA
* *
162778 CCTTATACCCTAGAGATGTGGAGGGAAAGGTTG
66 CCTTATACCTTAGAGATATGGAGGGAAAGGTTG
* * * * * * *
162811 AAGCTGCAATGGCGAACCTTGTACCTTAAAGATAT-GATGGGAAAAATTAAAGCCGCAACAGCAA
1 AAGCCGTAATGGCGAACCTTGTACCTTAGAGATATGGA-GGGAAAAGTTGAAGCCACAACGGCAA
* * * *
162875 ATCTTCTACCTTAAAGATAT-GATGGGAAAGATTG
65 ACCTTATACCTTAGAGATATGGA-GGGAAAGGTTG
** * * * *
162909 AAGCCGTAA-CACGAATCTTGTACCCTAGAGATATGGAGGGAAAAGTTGAAGCTGA-AACGGTAA
1 AAGCCGTAATGGCGAACCTTGTACCTTAGAGATATGGAGGGAAAAGTTGAAGC-CACAACGGCAA
* *
162972 ACCTTACACCTTAGAGATGTGGAGGGAAAGGTTG
65 ACCTTATACCTTAGAGATATGGAGGGAAAGGTTG
* * * * * * * *
163006 AAGCCGTAATGGCGAACCTCGTACCTTAGAGATAT-TATGGAAAAAATTGATGCCACAAAGACGA
1 AAGCCGTAATGGCGAACCTTGTACCTTAGAGATATGGA-GGGAAAAGTTGAAGCCACAACGGCAA
* *
163070 ATCTTTTACCTTAGAGATATGGAGGGAAAGGTTG
65 ACCTTATACCTTAGAGATATGGAGGGAAAGGTTG
* * * * * * *
163104 AAGCCGTAATGACGAACCTTCTACCCTAGAAATGTGGAGGGAAAGGTTGAAGCTACAA
1 AAGCCGTAATGGCGAACCTTGTACCTTAGAGATATGGAGGGAAAAGTTGAAGCCACAA
163162 GGATGAACCT
Statistics
Matches: 274, Mismatches: 68, Indels: 18
0.76 0.19 0.05
Matches are distributed among these distances:
97 79 0.29
98 194 0.71
99 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.22
Consensus pattern (98 bp):
AAGCCGTAATGGCGAACCTTGTACCTTAGAGATATGGAGGGAAAAGTTGAAGCCACAACGGCAAA
CCTTATACCTTAGAGATATGGAGGGAAAGGTTG
Found at i:163149 original size:49 final size:49
Alignment explanation
Indices: 162652--163156 Score: 340
Period size: 49 Copynumber: 10.3 Consensus size: 49
162642 GAAGATGTGA
* * * * * * * **
162652 AGGGAAAGATTGAAACTGCAATGGCGAATCTTATACTTTAGAGATGTAA
1 AGGGAAAGGTTGAAGCCGCAATGGCGAACCTTCTACCTTAGAGATATGG
* * * *
162701 AGGG-AGGGATTAAAGCCGCAATGGCGAATCTTGTACCTTAGAGATATGG
1 AGGGAAAGG-TTGAAGCCGCAATGGCGAACCTTCTACCTTAGAGATATGG
* ** * * * * * *
162750 AAGGAAAGGTTGAAGCCATAACGGTGTACCTTATACCCTAGAGATGTGG
1 AGGGAAAGGTTGAAGCCGCAATGGCGAACCTTCTACCTTAGAGATATGG
* * *
162799 AGGGAAAGGTTGAAGCTGCAATGGCGAACCTTGTACCTTAAAGATAT-G
1 AGGGAAAGGTTGAAGCCGCAATGGCGAACCTTCTACCTTAGAGATATGG
** * ** * * *
162847 ATGGGAAAAATTAAAGCCGCAACAGCAAATCTTCTACCTTAAAGATAT-G
1 A-GGGAAAGGTTGAAGCCGCAATGGCGAACCTTCTACCTTAGAGATATGG
* * ** * * *
162896 ATGGGAAAGATTGAAGCCGTAA-CACGAATCTTGTACCCTAGAGATATGG
1 A-GGGAAAGGTTGAAGCCGCAATGGCGAACCTTCTACCTTAGAGATATGG
* * * * ** *
162945 AGGGAAAAGTTGAAGCTGAAACGGTAAACCTTAC-ACCTTAGAGATGTGG
1 AGGGAAAGGTTGAAGCCGCAATGGCGAACCTT-CTACCTTAGAGATATGG
* *
162994 AGGGAAAGGTTGAAGCCGTAATGGCGAACC-TCGTACCTTAGAGATAT-T
1 AGGGAAAGGTTGAAGCCGCAATGGCGAACCTTC-TACCTTAGAGATATGG
* ** * * * * * *
163042 ATGGAAAAAATTGATGCCACAAAGACGAATCTTTTACCTTAGAGATATGG
1 A-GGGAAAGGTTGAAGCCGCAATGGCGAACCTTCTACCTTAGAGATATGG
* * * * *
163092 AGGGAAAGGTTGAAGCCGTAATGACGAACCTTCTACCCTAGAAATGTGG
1 AGGGAAAGGTTGAAGCCGCAATGGCGAACCTTCTACCTTAGAGATATGG
163141 AGGGAAAGGTTGAAGC
1 AGGGAAAGGTTGAAGC
163157 TACAAGGATG
Statistics
Matches: 351, Mismatches: 94, Indels: 22
0.75 0.20 0.05
Matches are distributed among these distances:
47 1 0.00
48 41 0.12
49 304 0.87
50 5 0.01
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (49 bp):
AGGGAAAGGTTGAAGCCGCAATGGCGAACCTTCTACCTTAGAGATATGG
Found at i:163268 original size:49 final size:49
Alignment explanation
Indices: 163215--163437 Score: 198
Period size: 49 Copynumber: 4.6 Consensus size: 49
163205 GAAGGAAATG
* *
163215 TTGAAGCCGCAACAGA-GAACCTTGTACCTTAGAGATATGATGGGAAAGA
1 TTGAAGCCGCAAC-GATAAACCTTATACCTTAGAGATATGATGGGAAAGA
* * * * * *
163264 TTGAAGCTGCAACGACAAATCTTGTACCTTAAAGATATTATGGGAAAGA
1 TTGAAGCCGCAACGATAAACCTTATACCTTAGAGATATGATGGGAAAGA
* * * ** *
163313 TTGAAGCCGCAACGATGAATCTTATACCCTAGAGATGGGA-GGGAAATA
1 TTGAAGCCGCAACGATAAACCTTATACCTTAGAGATATGATGGGAAAGA
* ** * * * * *
163361 TTAAAGATGTAACAATAAACCTTATACCTTAGAGATGTGAAGAGAAAGA
1 TTGAAGCCGCAACGATAAACCTTATACCTTAGAGATATGATGGGAAAGA
* * *
163410 TTGAAGTCGCAACGATGAATCTTATACC
1 TTGAAGCCGCAACGATAAACCTTATACC
163438 CTAAAAATAA
Statistics
Matches: 139, Mismatches: 33, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
48 40 0.29
49 99 0.71
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (49 bp):
TTGAAGCCGCAACGATAAACCTTATACCTTAGAGATATGATGGGAAAGA
Found at i:163288 original size:114 final size:115
Alignment explanation
Indices: 163069--163295 Score: 271
Period size: 114 Copynumber: 2.0 Consensus size: 115
163059 CACAAAGACG
* * * *
163069 AATCTTTTACCTTAGAGATATGGAGGGAAAGGTTGAAGCCGTAATGACGAACCTTCTACCCTAGA
1 AATCTTTTACCCTAGAGATATGGAAGGAAAGGTTGAAGCCGCAAAGACGAACCTTCTACCCTAGA
* * * **
163134 AATGTGGAGGGAAAGGTTGAAGCTACAAGGATGAACCTTGTACCTTAACC
66 AATATGGAGGGAAAGATTGAAGCTACAACGACAAACCTTGTACCTTAACC
* * * *
163184 AATC-TTTACCCTAGAGATGTGGAAGGAAATGTTGAAGCCGCAACAGA-GAACCTTGTACCTTAG
1 AATCTTTTACCCTAGAGATATGGAAGGAAAGGTTGAAGCCGCAA-AGACGAACCTTCTACCCTAG
* * *
163247 AGATAT-GATGGGAAAGATTGAAGCTGCAACGACAAATCTTGTACCTTAA
65 AAATATGGA-GGGAAAGATTGAAGCTACAACGACAAACCTTGTACCTTAA
163296 AGATATTATG
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
113 2 0.02
114 86 0.91
115 6 0.06
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (115 bp):
AATCTTTTACCCTAGAGATATGGAAGGAAAGGTTGAAGCCGCAAAGACGAACCTTCTACCCTAGA
AATATGGAGGGAAAGATTGAAGCTACAACGACAAACCTTGTACCTTAACC
Found at i:163410 original size:97 final size:97
Alignment explanation
Indices: 163190--163440 Score: 265
Period size: 97 Copynumber: 2.6 Consensus size: 97
163180 AACCAATCTT
* * * * *
163190 TACCCTAGAGATGTGGAAGGAAATG-TTGAAGCCGCAACAGA-GAACCTTGTACCTTAGAGATAT
1 TACCTTAGAGATGT-GAAGGAAA-GATTGAAGCCGCAAC-GATGAATCTTATACCCTAGAGATAG
* * * * *
163253 GATGGGAAAGATTGAAGCTGCAACGACAAATCTTG
63 GATGGGAAAGATTAAAGATGCAACAACAAACCTTA
* * * * *
163288 TACCTTAAAGATATTATGGGAAAGATTGAAGCCGCAACGATGAATCTTATACCCTAGAGATGGGA
1 TACCTTAGAGATGTGA-AGGAAAGATTGAAGCCGCAACGATGAATCTTATACCCTAGAGATAGGA
* * *
163353 -GGGAAATATTAAAGATGTAACAATAAACCTTA
65 TGGGAAAGATTAAAGATGCAACAACAAACCTTA
*
163385 TACCTTAGAGATGTGAAGAGAAAGATTGAAGTCGCAACGATGAATCTTATACCCTA
1 TACCTTAGAGATGTGAAG-GAAAGATTGAAGCCGCAACGATGAATCTTATACCCTA
163441 AAAATAAGGA
Statistics
Matches: 126, Mismatches: 23, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
96 1 0.01
97 77 0.61
98 48 0.38
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (97 bp):
TACCTTAGAGATGTGAAGGAAAGATTGAAGCCGCAACGATGAATCTTATACCCTAGAGATAGGAT
GGGAAAGATTAAAGATGCAACAACAAACCTTA
Found at i:163460 original size:146 final size:146
Alignment explanation
Indices: 163184--163480 Score: 318
Period size: 146 Copynumber: 2.0 Consensus size: 146
163174 TACCTTAACC
* * * * *
163184 AATCTTTACCCTAGAGATGTGGAAGGAAATGTTGAAGCCGCAACAGAGAACCTTGTACCTTAGAG
1 AATCTTTACCCTAGAGATGTGGAAGGAAATATTAAAGACGCAACAGAAAACCTTATACCTTAGAG
* * * * * *
163249 ATATGATGGGAAAGATTGAAGCTGCAACGACAAATCTTGTACCTTAAAGATATTATGGGAAAGAT
66 ATATGAAGAGAAAGATTGAAGCTGCAACGACAAATCTTATACCCTAAAGATATTAAGGAAAAGAT
* *
163314 TGAAGCCGCAACGATG
131 TGAAGCCACAAAGATG
* * *
163330 AATCTTATACCCTAGAGATG-GGAGGGAAATATTAAAGATGTAACA-ATAAACCTTATACCTTAG
1 AATCTT-TACCCTAGAGATGTGGAAGGAAATATTAAAGACGCAACAGA-AAACCTTATACCTTAG
* **
163393 AGATGTGAAGAGAAAGATTGAAG-TCGCAACGATGAATCTTATACCCTAAA-A-A-TAAGGAAAA
64 AGATATGAAGAGAAAGATTGAAGCT-GCAACGACAAATCTTATACCCTAAAGATATTAAGG-AAA
*
163454 GTAGATTGAAGCCACAAAGGTG
127 --AGATTGAAGCCACAAAGATG
163476 AATCT
1 AATCT
163481 CAAAACTGTA
Statistics
Matches: 125, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
143 4 0.03
144 3 0.02
145 3 0.02
146 102 0.82
147 13 0.10
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (146 bp):
AATCTTTACCCTAGAGATGTGGAAGGAAATATTAAAGACGCAACAGAAAACCTTATACCTTAGAG
ATATGAAGAGAAAGATTGAAGCTGCAACGACAAATCTTATACCCTAAAGATATTAAGGAAAAGAT
TGAAGCCACAAAGATG
Found at i:164231 original size:24 final size:24
Alignment explanation
Indices: 164197--164246 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
164187 AGCAACCTGC
164197 AAAACAGAGAAGAGCAAA-GCAACAA
1 AAAACAGAGAAGA-CAAATGCAA-AA
164222 AAAACA-AGAAGACAAATGCAAAA
1 AAAACAGAGAAGACAAATGCAAAA
164245 AA
1 AA
164247 CAAAATACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.33
24 10 0.42
25 6 0.25
ACGTcount: A:0.68, C:0.14, G:0.16, T:0.02
Consensus pattern (24 bp):
AAAACAGAGAAGACAAATGCAAAA
Found at i:165331 original size:24 final size:25
Alignment explanation
Indices: 165297--165351 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
165287 CTTTTATTTT
*
165297 ATTTTTGTTAAAATTTAACCCTTTC
1 ATTTTTGTTAAAAATTAACCCTTTC
*
165322 ATTTTT-TTAAAAATTAATCCTTTC
1 ATTTTTGTTAAAAATTAACCCTTTC
165346 ATTTTT
1 ATTTTT
165352 ATTTCTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 22 0.79
25 6 0.21
ACGTcount: A:0.29, C:0.13, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTTTTGTTAAAAATTAACCCTTTC
Found at i:165436 original size:24 final size:26
Alignment explanation
Indices: 165383--165436 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
165373 TTATCTTGTT
*
165383 TTTTATATCTAAATCCTTTTGTATAT
1 TTTTATATCTAAATCCTTTTGTATAC
* *
165409 TTTTA-ATC-AAATCCTTTTTTATCC
1 TTTTATATCTAAATCCTTTTGTATAC
165433 TTTT
1 TTTT
165437 TAAATTAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.24, C:0.15, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTTATATCTAAATCCTTTTGTATAC
Found at i:165436 original size:25 final size:25
Alignment explanation
Indices: 165382--165451 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
165372 TTTATCTTGT
165382 TTTTTATATCTAAATCCTTTTGTATA
1 TTTTTA-ATCTAAATCCTTTTGTATA
* *
165408 TTTTTAATC-AAATCCTTTTTTATCC
1 TTTTTAATCTAAATCCTTTTGTAT-A
165433 TTTTTAAAT-T-AATCCTTTT
1 TTTTT-AATCTAAATCCTTTT
165452 ATTTTGTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 13 0.33
25 17 0.44
26 9 0.23
ACGTcount: A:0.26, C:0.14, G:0.01, T:0.59
Consensus pattern (25 bp):
TTTTTAATCTAAATCCTTTTGTATA
Found at i:167739 original size:4 final size:4
Alignment explanation
Indices: 167724--167769 Score: 67
Period size: 4 Copynumber: 11.5 Consensus size: 4
167714 TAATAAATAT
*
167724 ATAC ATAT ATAC ATAC ATGA- ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC AT-AC ATAC ATAC ATAC ATAC ATAC ATAC AT
167770 GATATAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 1 0.03
4 36 0.95
5 1 0.03
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:167741 original size:12 final size:11
Alignment explanation
Indices: 167719--167766 Score: 60
Period size: 12 Copynumber: 4.1 Consensus size: 11
167709 TTTACTAATA
*
167719 AATATATACAT
1 AATACATACAT
167730 ATATACATACAT
1 A-ATACATACAT
167742 GAATACATACAT
1 -AATACATACAT
167754 ACATACATACAT
1 A-ATACATACAT
167766 A
1 A
167767 CATGATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
11 2 0.06
12 30 0.91
13 1 0.03
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (11 bp):
AATACATACAT
Found at i:168367 original size:2 final size:2
Alignment explanation
Indices: 168360--168389 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
168350 ATTTATCCTC
168360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
168390 TCATTTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:169206 original size:117 final size:117
Alignment explanation
Indices: 169064--169311 Score: 329
Period size: 117 Copynumber: 2.1 Consensus size: 117
169054 AGCATTGCAT
* * *
169064 TGTTT-TAGTGTCACTGCCAGTTCAGTATAGTATTACGGTGTTTACAATGTCACCGTCAGTTCAG
1 TGTTTATAGTGTCACCGCCAGTTCAGTACAGTATTACGGTGTTTACAATGTCACCGTCAGTTCAA
* * * *
169128 TGCTGTATTGCT-GTGTTTACAGTGTCATTGCTAGTTCAGTACAGTATTACGG
66 TGCTGTATT-ATAGTGTTTACAGTGTCACTGCCAGTTCAGTACAGTATTACGC
** * * *
169180 TGTTTATAGTGTCACCGTTAGTTCAGTACATTATTACGGTGTTTATAGTGTCACCGTCAGTTCAA
1 TGTTTATAGTGTCACCGCCAGTTCAGTACAGTATTACGGTGTTTACAATGTCACCGTCAGTTCAA
** *
169245 TTTTGTATTATAGTGTTTACAGTGTCACTGCCAGTTCAGTACGGTATTACGC
66 TGCTGTATTATAGTGTTTACAGTGTCACTGCCAGTTCAGTACAGTATTACGC
*
169297 TGTTTACAGTGTCAC
1 TGTTTATAGTGTCAC
169312 TTTCAGTTAA
Statistics
Matches: 114, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
116 6 0.05
117 108 0.95
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (117 bp):
TGTTTATAGTGTCACCGCCAGTTCAGTACAGTATTACGGTGTTTACAATGTCACCGTCAGTTCAA
TGCTGTATTATAGTGTTTACAGTGTCACTGCCAGTTCAGTACAGTATTACGC
Found at i:169319 original size:39 final size:39
Alignment explanation
Indices: 169070--169324 Score: 260
Period size: 39 Copynumber: 6.5 Consensus size: 39
169060 GCATTGTTTT
* *
169070 AGTGTCACTGCCAGTTCAGTATAGTATTACGGTGTTTAC
1 AGTGTCACTGTCAGTTCAGTACAGTATTACGGTGTTTAC
* * * * * *
169109 AATGTCACCGTCAGTTCAGTGCTGTATTGCTGTGTTTAC
1 AGTGTCACTGTCAGTTCAGTACAGTATTACGGTGTTTAC
* *
169148 AGTGTCATTG-CTAGTTCAGTACAGTATTACGGTGTTTAT
1 AGTGTCACTGTC-AGTTCAGTACAGTATTACGGTGTTTAC
* * * *
169187 AGTGTCACCGTTAGTTCAGTACATTATTACGGTGTTTAT
1 AGTGTCACTGTCAGTTCAGTACAGTATTACGGTGTTTAC
* * *** **
169226 AGTGTCACCGTCAGTTCAATTTTGTATTATAGTGTTTAC
1 AGTGTCACTGTCAGTTCAGTACAGTATTACGGTGTTTAC
* * *
169265 AGTGTCACTGCCAGTTCAGTACGGTATTACGCTGTTTAC
1 AGTGTCACTGTCAGTTCAGTACAGTATTACGGTGTTTAC
* *
169304 AGTGTCACTTTCAGTTAAGTA
1 AGTGTCACTGTCAGTTCAGTA
169325 ATTTGATAAC
Statistics
Matches: 173, Mismatches: 41, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
38 1 0.01
39 172 0.99
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (39 bp):
AGTGTCACTGTCAGTTCAGTACAGTATTACGGTGTTTAC
Found at i:172271 original size:31 final size:31
Alignment explanation
Indices: 172233--172293 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
172223 AATTCACATA
172233 CAATTAAGCCCATGCCATTAACTAAAATAAT
1 CAATTAAGCCCATGCCATTAACTAAAATAAT
172264 CAATTAAGCCCATGCCATTAACTAAAATAA
1 CAATTAAGCCCATGCCATTAACTAAAATAA
172294 ATTAAGCCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.25
Consensus pattern (31 bp):
CAATTAAGCCCATGCCATTAACTAAAATAAT
Found at i:172436 original size:19 final size:20
Alignment explanation
Indices: 172404--172454 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
172394 ATTTTCTCAT
*
172404 AAAATAATTAAAAAATCATAA
1 AAAATAA-TAAAAAGTCATAA
*
172425 AAAATAATAAAAAGT-AT-T
1 AAAATAATAAAAAGTCATAA
172443 AAAATAATAAAA
1 AAAATAATAAAA
172455 TTGGTATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 12 0.43
19 2 0.07
20 7 0.25
21 7 0.25
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATAATAAAAAGTCATAA
Found at i:172445 original size:10 final size:10
Alignment explanation
Indices: 172404--172452 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
172394 ATTTTCTCAT
172404 AAAATAATTAA
1 AAAATAA-TAA
*
172415 AAAATCATAA
1 AAAATAATAA
172425 AAAATAATAA
1 AAAATAATAA
* *
172435 AAAGTATTAA
1 AAAATAATAA
172445 AATAATAA
1 AA-AATAA
172453 AATTGGTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (10 bp):
AAAATAATAA
Found at i:172536 original size:18 final size:16
Alignment explanation
Indices: 172490--172539 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
172480 AAAAATAATA
*
172490 AAAACATATCAATATTAT
1 AAAA-ATATAAAT-TTAT
172508 AAAAATATAAATTTAT
1 AAAAATATAAATTTAT
172524 AATAAATTATAAATTT
1 AA-AAA-TATAAATTT
172540 TTTTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 6 0.21
17 10 0.34
18 13 0.45
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATATAAATTTAT
Found at i:172686 original size:29 final size:28
Alignment explanation
Indices: 172635--172716 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 28
172625 ACTTTAATAT
*
172635 AAACTTATAAAATTATTAAAAAAAATCATAA
1 AAACTTATAAAATTA-T-AAAAAACT-ATAA
172666 AAACTTATAAAAGTTATAAAAAACTATAA
1 AAACTTATAAAA-TTATAAAAAACTATAA
*
172695 AAATCTAAT-AAATTATAAAAAA
1 AAA-CTTATAAAATTATAAAAAA
172717 ATTATAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
28 10 0.21
29 10 0.21
30 11 0.23
31 13 0.28
32 3 0.06
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.28
Consensus pattern (28 bp):
AAACTTATAAAATTATAAAAAACTATAA
Found at i:172717 original size:29 final size:29
Alignment explanation
Indices: 172635--172724 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 29
172625 ACTTTAATAT
*
172635 AAACTTATAAAATTATTAAAAAAAATCATAA
1 AAACTAATAAAATTA-TAAAAAAAAT-ATAA
* *
172666 AAACTTATAAAAGTTAT-AAAAAACTATAA
1 AAACTAATAAAA-TTATAAAAAAAATATAA
*
172695 AAATCTAAT-AAATTATAAAAAAATTATAA
1 AAA-CTAATAAAATTATAAAAAAAATATAA
172724 A
1 A
172725 TTAATAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
28 4 0.08
29 22 0.42
30 11 0.21
31 13 0.25
32 3 0.06
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.29
Consensus pattern (29 bp):
AAACTAATAAAATTATAAAAAAAATATAA
Found at i:172815 original size:49 final size:50
Alignment explanation
Indices: 172708--172815 Score: 125
Period size: 49 Copynumber: 2.2 Consensus size: 50
172698 TCTAATAAAT
**
172708 TATAAAAAAATTATAAATTAATAAAATATGTTTAAAATTTTATAAAAACA
1 TATAAAAAAATTATAAATTAATAAAATATGTTTAAAAAATTATAAAAACA
* * *
172758 TAGAAAAAACTTGTAAA-TAATATAAA-AT-TTTAAATAAATTATAAAAA-A
1 TATAAAAAAATTATAAATTAATA-AAATATGTTTAAA-AAATTATAAAAACA
172806 TATAAAAAAA
1 TATAAAAAAA
172816 AGTCATACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
48 15 0.31
49 17 0.35
50 17 0.35
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (50 bp):
TATAAAAAAATTATAAATTAATAAAATATGTTTAAAAAATTATAAAAACA
Found at i:172956 original size:3 final size:3
Alignment explanation
Indices: 172948--172999 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
172938 TTATTTGTGA
*
172948 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
172996 ATT A
1 ATT A
173000 AAATTTTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:173466 original size:19 final size:20
Alignment explanation
Indices: 173417--173469 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
173407 CAAGATTTTA
173417 TTTTATGAT-TTTTATATAT
1 TTTTATGATATTTTATATAT
* *
173436 TTATATCA-ATTTTA-ATAT
1 TTTTATGATATTTTATATAT
173454 TTTTATGATATTTTAT
1 TTTTATGATATTTTAT
173470 GATTTCTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTATGATATTTTATATAT
Found at i:173469 original size:10 final size:10
Alignment explanation
Indices: 173415--173472 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
173405 TTCAAGATTT
173415 TATTTTATGA
1 TATTTTATGA
173425 T-TTTTAT-A
1 TATTTTATGA
*
173433 TATTTATATCA
1 TATTT-TATGA
173444 -ATTTTA--A
1 TATTTTATGA
173451 TATTTTTATGA
1 TA-TTTTATGA
173462 TATTTTATGA
1 TATTTTATGA
173472 T
1 T
173473 TTCTTATAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
7 1 0.02
8 3 0.07
9 16 0.39
10 17 0.41
11 4 0.10
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (10 bp):
TATTTTATGA
Found at i:179298 original size:18 final size:17
Alignment explanation
Indices: 179271--179326 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 17
179261 TCCTGTCAGG
179271 TTTT-TTTTTTTTTAAA
1 TTTTATTTTTTTTTAAA
*
179287 TTTTA-ATTTTTTTACTAA
1 TTTTATTTTTTTTTA--AA
179305 TTTTATTATTTTTTTATAA
1 TTTTATT-TTTTTTTA-AA
179324 TTT
1 TTT
179327 ATTAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 12 0.36
18 7 0.21
19 6 0.18
20 8 0.24
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATTTTTTTTTAAA
Found at i:179298 original size:19 final size:18
Alignment explanation
Indices: 179274--179326 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
179264 TGTCAGGTTT
179274 TTTTTTTTTTAAATTTTAA
1 TTTTTTTTTTAAATTTT-A
**
179293 TTTTTTTACT-AATTTTA
1 TTTTTTTTTTAAATTTTA
*
179310 TTATTTTTTTATAATTT
1 TTTTTTTTTTA-AATTT
179327 ATTAAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 8 0.30
18 6 0.22
19 13 0.48
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTTTTAAATTTTA
Found at i:179327 original size:18 final size:18
Alignment explanation
Indices: 179277--179330 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 18
179267 CAGGTTTTTT
*
179277 TTTTTTTA-AATTT-TAA
1 TTTTTTTATAATTTATTA
179293 TTTTTTTACTAATTTTATTA
1 TTTTTTTA-TAA-TTTATTA
179313 TTTTTTTATAATTTATTA
1 TTTTTTTATAATTTATTA
179331 AAATTTGTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.24
18 9 0.27
19 6 0.18
20 10 0.30
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTTTATAATTTATTA
Found at i:179362 original size:18 final size:17
Alignment explanation
Indices: 179296--179381 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
179286 ATTTTAATTT
* *
179296 TTTTACTAATTTTATTAT
1 TTTTA-TAAATTTATTAA
*
179314 TTTTTTATAATTTATTAAA
1 TTTTATA-AATTTATT-AA
* * * *
179333 ATTTGTTAATTTGTTAA
1 TTTTATAAATTTATTAA
*
179350 TTTTATAATATTTATTAT
1 TTTTATAA-ATTTATTAA
179368 TTTTATAAATTTAT
1 TTTTATAAATTTAT
179382 ATCAGTTTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
17 15 0.28
18 33 0.62
19 5 0.09
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTATAAATTTATTAA
Found at i:179382 original size:26 final size:26
Alignment explanation
Indices: 179297--179380 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
179287 TTTTAATTTT
179297 TTTACTAAT-TTTATTATTTTTTTATAA
1 TTTACTAATATTTATTA-TTTTTTA-AA
* * * * *
179324 TTTATTAAAATTTGTTAATTTGTTAAT
1 TTTACTAATATTTATT-ATTTTTTAAA
179351 TTTA-TAATATTTATTATTTTTATAAA
1 TTTACTAATATTTATTATTTTT-TAAA
179377 TTTA
1 TTTA
179381 TATCAGTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
25 5 0.11
26 16 0.36
27 12 0.27
28 11 0.24
29 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTACTAATATTTATTATTTTTTAAA
Found at i:183942 original size:39 final size:39
Alignment explanation
Indices: 183888--183966 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
183878 TTTCTAATGA
183888 AAGCGGCTTTTAATATTGTGACCAAGGGGAATTCGCTTT
1 AAGCGGCTTTTAATATTGTGACCAAGGGGAATTCGCTTT
183927 AAGCGGCTTTTAATATTGTGACCAAGGGGAATTCGCTTT
1 AAGCGGCTTTTAATATTGTGACCAAGGGGAATTCGCTTT
183966 A
1 A
183967 GGTTAGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (39 bp):
AAGCGGCTTTTAATATTGTGACCAAGGGGAATTCGCTTT
Found at i:196994 original size:39 final size:39
Alignment explanation
Indices: 196931--197065 Score: 153
Period size: 39 Copynumber: 3.5 Consensus size: 39
196921 TCGGGTATTA
* *
196931 CACTACCAGTTCAATATATTATTGCAATGTTTAAAGTGT
1 CACTACCAGTTCAATATATCATTGCAATGTTTACAGTGT
* * * * *
196970 CACTGCCAGTTTAATATAGCATTGCATTGTTTACATTGT
1 CACTACCAGTTCAATATATCATTGCAATGTTTACAGTGT
* * * *
197009 CACAACCAGTTCAGTATATCATTGCAGTGTTTACAGTAT
1 CACTACCAGTTCAATATATCATTGCAATGTTTACAGTGT
* *
197048 CACTGCCAGTTCAGTATA
1 CACTACCAGTTCAATATA
197066 CTTCCGATGT
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (39 bp):
CACTACCAGTTCAATATATCATTGCAATGTTTACAGTGT
Found at i:203449 original size:39 final size:39
Alignment explanation
Indices: 203406--203582 Score: 129
Period size: 39 Copynumber: 4.5 Consensus size: 39
203396 TAATAGTCTA
* * *
203406 GTAGTGTTTACAGTGTCACTACTACCTCAGTATAACGTT
1 GTAGTGTTTATAGTGTCACTACCACCTCAGTATAACATT
* * **
203445 GTAGTGTTTATAGTATCACCACCATTTCAGTATAACATT
1 GTAGTGTTTATAGTGTCACTACCACCTCAGTATAACATT
* * ** ** * *
203484 GCAAGTGCTTATAGTGTCACTGTCAATTCATTATATCATT
1 G-TAGTGTTTATAGTGTCACTACCACCTCAGTATAACATT
* * ** * *
203524 GCAGTGTTTATAGTGTCACTATCAGTTTAGTATATCATT
1 GTAGTGTTTATAGTGTCACTACCACCTCAGTATAACATT
** *
203563 GTTCTGTTTACAGTGTCACT
1 GTAGTGTTTATAGTGTCACT
203583 GCTAGTTTAA
Statistics
Matches: 111, Mismatches: 26, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
39 81 0.73
40 30 0.27
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (39 bp):
GTAGTGTTTATAGTGTCACTACCACCTCAGTATAACATT
Found at i:206551 original size:10 final size:9
Alignment explanation
Indices: 206536--206561 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
206526 TCATACTTAT
206536 AAAAAAATC
1 AAAAAAATC
206545 AAAAAAATC
1 AAAAAAATC
206554 AAAAAAAT
1 AAAAAAAT
206562 TAATTAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATC
Found at i:209296 original size:22 final size:22
Alignment explanation
Indices: 209271--209342 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
209261 GCCTTTGTTA
209271 TCAAGTGAGTATTTTTCTTATT
1 TCAAGTGAGTATTTTTCTTATT
* * ** *
209293 TCAATTCTAG-ATTTGCCTTTGTT
1 TCAAGT-GAGTATTTTTC-TTATT
*
209316 ATCAAGTGAGTTTTTTTCTTATT
1 -TCAAGTGAGTATTTTTCTTATT
209339 TCAA
1 TCAA
209343 AATATCACAC
Statistics
Matches: 35, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
22 14 0.40
23 12 0.34
24 9 0.26
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (22 bp):
TCAAGTGAGTATTTTTCTTATT
Found at i:209317 original size:46 final size:46
Alignment explanation
Indices: 209250--209342 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
209240 CCCTTAAAAT
209250 ATTCTAGATTTGCCTTTGTTATCAAGTGAGTATTTTTCTTATTTCA
1 ATTCTAGATTTGCCTTTGTTATCAAGTGAGTATTTTTCTTATTTCA
*
209296 ATTCTAGATTTGCCTTTGTTATCAAGTGAGTTTTTTTCTTATTTCA
1 ATTCTAGATTTGCCTTTGTTATCAAGTGAGTATTTTTCTTATTTCA
209342 A
1 A
209343 AATATCACAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.53
Consensus pattern (46 bp):
ATTCTAGATTTGCCTTTGTTATCAAGTGAGTATTTTTCTTATTTCA
Found at i:209572 original size:31 final size:31
Alignment explanation
Indices: 209537--209600 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
209527 AACTATGAGT
* **
209537 AAGTTTTTATTTTGGTCACTGAACTATTCAA
1 AAGTTTTCATTTAAGTCACTGAACTATTCAA
*
209568 AAGTTTTCATTTAAGTCACTGAATTATTCAA
1 AAGTTTTCATTTAAGTCACTGAACTATTCAA
209599 AA
1 AA
209601 AAAATTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (31 bp):
AAGTTTTCATTTAAGTCACTGAACTATTCAA
Found at i:213323 original size:18 final size:18
Alignment explanation
Indices: 213269--213323 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
213259 ATGGAAGGAC
213269 TTAATTGAAT-AAAATTGA
1 TTAATTGAATGAAAATT-A
* *
213287 TT-ATTG-CTGAAATTGTA
1 TTAATTGAATGAAAAT-TA
213304 TTAATTGAATGAAAATTA
1 TTAATTGAATGAAAATTA
213322 TT
1 TT
213324 TTTAGATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 1 0.03
17 11 0.38
18 11 0.38
19 6 0.21
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.44
Consensus pattern (18 bp):
TTAATTGAATGAAAATTA
Found at i:213909 original size:38 final size:38
Alignment explanation
Indices: 213823--214014 Score: 147
Period size: 38 Copynumber: 5.0 Consensus size: 38
213813 ATGTAAATTC
* * *
213823 CCGGTGTTTGTAGGGCTTAGTGCCTAGCAGGCTTCGTG
1 CCGGTGTTTATCGGGCTTAGTGACTAGCAGGCTTCGTG
* * * *
213861 CCGATTTTTATTC-GCCTTAGTGACTAGCAGGCTTCATG
1 CCGGTGTTTA-TCGGGCTTAGTGACTAGCAGGCTTCGTG
* *
213899 GCGGTGTTTATCGGGCTTAGT-ACTTAGCAAGCTTCGTG
1 CCGGTGTTTATCGGGCTTAGTGAC-TAGCAGGCTTCGTG
** * * * *
213937 TTGGTGTTTATCGGGCTTAATGCCTAGCAGGCTTAGTT
1 CCGGTGTTTATCGGGCTTAGTGACTAGCAGGCTTCGTG
* * * *
213975 CCGATGTATTTATCAGGCTTTGT-ACCTAGTAGGCTTCGTG
1 CCG--GTGTTTATCGGGCTTAGTGA-CTAGCAGGCTTCGTG
214015 TCAGTGTATA
Statistics
Matches: 117, Mismatches: 30, Indels: 12
0.74 0.19 0.08
Matches are distributed among these distances:
37 4 0.03
38 85 0.73
39 2 0.02
40 26 0.22
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.36
Consensus pattern (38 bp):
CCGGTGTTTATCGGGCTTAGTGACTAGCAGGCTTCGTG
Found at i:215314 original size:21 final size:21
Alignment explanation
Indices: 215290--215341 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
215280 TGAGACAATA
215290 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* * *
215311 CTACGGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
*
215332 TTACCGATAC
1 CTACCGATAC
215342 TAAAAATTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Done.