Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 43 of 216
Found at i:12250679 original size:28 final size:28
Alignment explanation
Indices: 12250647--12250725 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
12250637 GAATCATTGC
* * *
12250647 AATATAGCACACATTAAATGTTGAGTCA
1 AATATAACACACATTAAACGTTGAATCA
*
12250675 AATATAACACACATTAACCGTTGAATCA
1 AATATAACACACATTAAACGTTGAATCA
** *
12250703 AATATAACATGCATTAAGCGTTG
1 AATATAACACACATTAAACGTTG
12250726 GATCTCCCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (28 bp):
AATATAACACACATTAAACGTTGAATCA
Found at i:12251925 original size:5 final size:5
Alignment explanation
Indices: 12251915--12251943 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12251905 ACAACCGATC
12251915 TAATT TAATT TAATT TAATT TAATT TAAT
1 TAATT TAATT TAATT TAATT TAATT TAAT
12251944 AATTCAACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:12252612 original size:21 final size:19
Alignment explanation
Indices: 12252548--12252642 Score: 136
Period size: 19 Copynumber: 4.8 Consensus size: 19
12252538 ATCTTCAAGA
*
12252548 ATATGTAATCTTAGATATG
1 ATATGCAATCTTAGATATG
12252567 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
*
12252586 ATATGCACTCTTAGATATG
1 ATATGCAATCTTAGATATG
12252605 ATATATGCAATCTTAGATATG
1 --ATATGCAATCTTAGATATG
12252626 ATTTATGCAATCTTAGA
1 A--TATGCAATCTTAGA
12252643 AGATATGATT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
19 37 0.54
21 32 0.46
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (19 bp):
ATATGCAATCTTAGATATG
Found at i:12252664 original size:23 final size:24
Alignment explanation
Indices: 12252598--12252665 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 24
12252588 ATGCACTCTT
*
12252598 AGATATGATATATGCAATCTT---
1 AGATATGATTTATGCAATCTTAGA
12252619 AGATATGATTTATGCAATCTTAGA
1 AGATATGATTTATGCAATCTTAGA
12252643 AGATATGATTT-T-CTAATCTTAGA
1 AGATATGATTTATGC-AATCTTAGA
12252666 GATTTAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
21 20 0.48
22 1 0.02
23 10 0.24
24 11 0.26
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (24 bp):
AGATATGATTTATGCAATCTTAGA
Found at i:12253178 original size:17 final size:17
Alignment explanation
Indices: 12253147--12253190 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
12253137 CATAACTTTT
*
12253147 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
12253163 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
12253180 ATATACATTTT
1 ATATACATTTT
12253191 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:12253380 original size:24 final size:26
Alignment explanation
Indices: 12253318--12253369 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
12253308 TTCTAAATTA
*
12253318 ATTAATTTTA-ATATATGTAATTATT
1 ATTATTTTTATATATATGTAATTATT
12253343 ATTATTAGTTTATATATATGTAATTAT
1 ATTATT--TTTATATATATGTAATTAT
12253370 CTTTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
27 4 0.17
28 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (26 bp):
ATTATTTTTATATATATGTAATTATT
Found at i:12253391 original size:31 final size:31
Alignment explanation
Indices: 12253353--12253411 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12253343 ATTATTAGTT
*
12253353 TATATATATGTA-ATTATCTTTTTTTATAATC
1 TATATATATGTATATAAT-TTTTTTTATAATC
12253384 TATATATATGTATATAATTTTTTTTATA
1 TATATATATGTATATAATTTTTTTTATA
12253412 TATGTACATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
TATATATATGTATATAATTTTTTTTATAATC
Found at i:12253572 original size:4 final size:4
Alignment explanation
Indices: 12253563--12253608 Score: 65
Period size: 4 Copynumber: 11.2 Consensus size: 4
12253553 GTTATTGATT
* *
12253563 TTTA TTTA TTTA TTTA TTTA TTTA TTTG TTTG TTTA TATTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA T
12253609 ATGCCATTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
4 35 0.90
5 4 0.10
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:12257012 original size:19 final size:19
Alignment explanation
Indices: 12256966--12257012 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
12256956 CATATTGCCC
*
12256966 AAAAAAATAGATGGCGCAA
1 AAAAAAAAAGATGGCGCAA
*
12256985 ACAAAAAAAGATGGCGCAA
1 AAAAAAAAAGATGGCGCAA
12257004 AAAAAAAAA
1 AAAAAAAAA
12257013 CTCTACCTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.66, C:0.11, G:0.17, T:0.06
Consensus pattern (19 bp):
AAAAAAAAAGATGGCGCAA
Found at i:12258724 original size:88 final size:88
Alignment explanation
Indices: 12258565--12258966 Score: 579
Period size: 88 Copynumber: 4.6 Consensus size: 88
12258555 GTGAAGATAA
* * * *
12258565 CAGATTTTGCCTTCCTACACCGACAGCGAAGCAGATTGAAGACACCAACCTTGTCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
*
12258630 GTAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * *
12258653 CAAATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGATACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
12258718 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
12258741 CAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
* **
12258806 GTAGCAAAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
12258829 CAGATCTTGCCTTCCTGCACCGACAGCGAAGAATATCGAAGACACCAACCTTGCTTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
*
12258894 ACAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
12258917 CAGATCTTACCTTCCTGCACCGACAACGAAGCAGATCGATGACCCCAACC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACC
12258967 CTATCTCCCT
Statistics
Matches: 279, Mismatches: 35, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 279 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:12258750 original size:44 final size:44
Alignment explanation
Indices: 12258614--12258845 Score: 130
Period size: 44 Copynumber: 5.3 Consensus size: 44
12258604 AGACACCAAC
* * * *
12258614 CTTGTCTCCCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAAAT
1 CTTGCCTCCCTGGGTTGCAGCGAAGCAGGTTAAAAATAGCAGAT
* **** * * ** * *
12258658 CTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGATA-CTAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGAAGCAGGTTAAAAATAGC-AGAT
*
12258702 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGAAGCAGGTTAAAAATAGCAGAT
* ***** * * * * *
12258746 CTTGCCTTCCTACACCGACAGCGAAGCAGATTGAAGACA-CTAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGAAGCAGGTTAAAAATAGC-AGAT
* *
12258790 CTTGCCTCCCTGGGTTGTAGCAAAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGAAGCAGGTTAAAAATAGCAGAT
*
12258834 CTTGCCTTCCTG
1 CTTGCCTCCCTG
12258846 CACCGACAGC
Statistics
Matches: 127, Mismatches: 53, Indels: 16
0.65 0.27 0.08
Matches are distributed among these distances:
43 34 0.27
44 60 0.47
45 33 0.26
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGAAGCAGGTTAAAAATAGCAGAT
Found at i:12259504 original size:44 final size:44
Alignment explanation
Indices: 12259407--12259528 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
12259397 AAAGATGGTG
* *
12259407 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAT
* *
12259451 AATCCTATCTTCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA-
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACCA-AT
* * * *
12259495 GATCTTATC-TCTCTGACGTTGCAGTAGAGTAGAT
1 AATCTTATCTTC-CTGAAGTTGCAGTGGAGCAGAT
12259529 CACATCGAGT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
43 2 0.03
44 63 0.95
45 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAT
Found at i:12260010 original size:21 final size:21
Alignment explanation
Indices: 12259970--12260041 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 21
12259960 AAGGATACGT
12259970 AATCTTAGATATGA--TATGC
1 AATCTTAGATATGATTTATGC
12259989 AATCTTAGATATGATTTATGC
1 AATCTTAGATATGATTTATGC
*
12260010 AATCTTAGAAGATATGATTT-TGT
1 AATCTT---AGATATGATTTATGC
12260033 AATCTTAGA
1 AATCTTAGA
12260042 GATTTAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
19 14 0.30
20 3 0.06
21 11 0.23
23 8 0.17
24 11 0.23
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (21 bp):
AATCTTAGATATGATTTATGC
Found at i:12260040 original size:23 final size:24
Alignment explanation
Indices: 12259976--12260041 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 24
12259966 ACGTAATCTT
12259976 AGATATGA--TATGCAATCTT---
1 AGATATGATTTATGCAATCTTAGA
12259995 AGATATGATTTATGCAATCTTAGA
1 AGATATGATTTATGCAATCTTAGA
*
12260019 AGATATGATTT-TGTAATCTTAGA
1 AGATATGATTTATGCAATCTTAGA
12260042 GATTTAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
19 8 0.20
21 11 0.27
23 11 0.27
24 11 0.27
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (24 bp):
AGATATGATTTATGCAATCTTAGA
Found at i:12260371 original size:20 final size:20
Alignment explanation
Indices: 12260315--12260374 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
12260305 CTTTTTTTAT
* *
12260315 TTATTATTTATTTTTATTAAAT
1 TTATTA-TTATTGTTATT-AAG
*
12260337 TTGATT-TTCTTGTTATTAAG
1 TT-ATTATTATTGTTATTAAG
12260357 TTATTATTATTGTTATTA
1 TTATTATTATTGTTATTA
12260375 TTACCAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.09
20 15 0.47
21 9 0.28
22 2 0.06
23 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.65
Consensus pattern (20 bp):
TTATTATTATTGTTATTAAG
Found at i:12260554 original size:17 final size:17
Alignment explanation
Indices: 12260523--12260566 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
12260513 CATAACTTTT
*
12260523 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
12260539 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
12260556 ATATACATTTT
1 ATATACATTTT
12260567 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:12260671 original size:24 final size:24
Alignment explanation
Indices: 12260644--12260690 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12260634 ATACGTATGT
12260644 TTTTTTATAT-TATTCTTCATAAAA
1 TTTTTTATATATATTCTTC-TAAAA
*
12260668 TTTTTTATATATATTTTTCTAAA
1 TTTTTTATATATATTCTTCTAAA
12260691 TTAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTTTATATATATTCTTCTAAAA
Found at i:12260763 original size:30 final size:30
Alignment explanation
Indices: 12260727--12260783 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
12260717 TTATTATTTA
*
12260727 TATATATATGTA-ATTATCTTTTTTATAATC
1 TATATATATGTATATAAT-TTTTTTATAATC
12260757 TATATATATGTATATAATTTTTTTATA
1 TATATATATGTATATAATTTTTTTATA
12260784 TATGTGCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (30 bp):
TATATATATGTATATAATTTTTTTATAATC
Found at i:12262359 original size:17 final size:16
Alignment explanation
Indices: 12262318--12262359 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
12262308 AAATATATCA
12262318 TTTAAAA-ATAATTTT
1 TTTAAAATATAATTTT
**
12262333 TTTATGATATGAATTTT
1 TTTAAAATAT-AATTTT
12262350 TTTAAAATAT
1 TTTAAAATAT
12262360 TACACAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 5 0.24
16 2 0.10
17 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TTTAAAATATAATTTT
Found at i:12273150 original size:6 final size:6
Alignment explanation
Indices: 12273139--12273164 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12273129 TTTATCATTT
12273139 TAATCA TAATCA TAATCA TAATCA TA
1 TAATCA TAATCA TAATCA TAATCA TA
12273165 TTTTATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TAATCA
Found at i:12277437 original size:26 final size:26
Alignment explanation
Indices: 12277374--12277457 Score: 98
Period size: 26 Copynumber: 3.2 Consensus size: 26
12277364 ATATTGAAAT
*
12277374 AATTTTCTCAAAATTTTATCGAGGGTA
1 AATTTT-TCAAAATTTTATCGGGGGTA
* **
12277401 AAATTGCCAAAATTTTATCGGGGGTA
1 AATTTTTCAAAATTTTATCGGGGGTA
*
12277427 AATTTTTCAAAAATTTTA-CTGGGGTA
1 AATTTTTC-AAAATTTTATCGGGGGTA
12277453 AATTT
1 AATTT
12277458 GCGATAAGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
26 35 0.73
27 13 0.27
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (26 bp):
AATTTTTCAAAATTTTATCGGGGGTA
Found at i:12310088 original size:18 final size:18
Alignment explanation
Indices: 12310065--12310099 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12310055 TGTCTCTTCT
*
12310065 ACCTTTTCCCCTTCCTCG
1 ACCTTTGCCCCTTCCTCG
*
12310083 ACCTTTGCCTCTTCCTC
1 ACCTTTGCCCCTTCCTC
12310100 TGAAAGAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.06, T:0.40
Consensus pattern (18 bp):
ACCTTTGCCCCTTCCTCG
Found at i:12314347 original size:50 final size:54
Alignment explanation
Indices: 12314258--12314397 Score: 153
Period size: 50 Copynumber: 2.6 Consensus size: 54
12314248 TGATCATAAC
* ***
12314258 ATGCCAAAGCCATGTCCTAGACATGGTCTTACGGGGGACCT-C-TCATCTC-GG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATAGGACCTCCATCATCTCAGG
* * *
12314309 -TGCCAACGCTATGTCCCAGACATGGTCTTACATAGGACCTCGCATGATCTCAAGG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATAGGACCTC-CATCATCTC-AGG
* *
12314364 ATGCCAATGCCATGTCCCAAACATGGTCTTACAT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAT
12314398 GAGATCTCTT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
50 34 0.47
52 1 0.01
53 6 0.08
55 2 0.03
56 30 0.41
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.24
Consensus pattern (54 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATAGGACCTCCATCATCTCAGG
Found at i:12320083 original size:66 final size:66
Alignment explanation
Indices: 12319977--12320108 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
12319967 TCTTAGGAAG
12319977 TTATCATGAGTTTCTTTATTTCTTCCTGTTATACTGTCTATTGGATTTTTTATATTCAAGCATTA
1 TTATCATGAGTTTCTTTATTTCTTCCTGTTATACTGTCTATTGGATTTTTTATATTCAAGCATTA
12320042 A
66 A
12320043 TTATCATGAGTTTCTTTATTTCTTCCTGTTATACTGTCTATTGGATTTTTTATATTCAAGCATTA
1 TTATCATGAGTTTCTTTATTTCTTCCTGTTATACTGTCTATTGGATTTTTTATATTCAAGCATTA
12320108 A
66 A
12320109 CTAATTTTCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.53
Consensus pattern (66 bp):
TTATCATGAGTTTCTTTATTTCTTCCTGTTATACTGTCTATTGGATTTTTTATATTCAAGCATTA
A
Found at i:12333185 original size:51 final size:53
Alignment explanation
Indices: 12333108--12333214 Score: 148
Period size: 51 Copynumber: 2.1 Consensus size: 53
12333098 GTCATTCTCA
*
12333108 TTTAGGAGAAAACCACATTCATTTCCAAATGA-TT-CCACTTCTCCATTTTTAT
1 TTTAGGAGAAAACCACAATCATTTCCAAAT-ATTTCCCACTTCTCCATTTTTAT
* * *
12333160 TTTA-GAGAAAACCATAATCATTTCCAAATATTTCCCATTTCTTCATTTTTAT
1 TTTAGGAGAAAACCACAATCATTTCCAAATATTTCCCACTTCTCCATTTTTAT
12333212 TTT
1 TTT
12333215 CATTTTCGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
50 1 0.02
51 25 0.51
52 23 0.47
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.43
Consensus pattern (53 bp):
TTTAGGAGAAAACCACAATCATTTCCAAATATTTCCCACTTCTCCATTTTTAT
Found at i:12336524 original size:23 final size:22
Alignment explanation
Indices: 12336483--12336529 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
12336473 TTGTGTTTAT
*
12336483 ATGTTTTTAATTGAAATATATAA
1 ATGTTTTGAATTGAAATATA-AA
**
12336506 ATGTTTTGAATTGTTATATAAA
1 ATGTTTTGAATTGAAATATAAA
12336528 AT
1 AT
12336530 TTCCTAGTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATGTTTTGAATTGAAATATAAA
Found at i:12336748 original size:25 final size:25
Alignment explanation
Indices: 12336672--12336753 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
12336662 CAGCTCATGA
*
12336672 GAGCATATCGATTTATAGCTCGTGA-
1 GAGCATATCGATTCATAGCTCGT-AT
**
12336697 GAGCATATCGA-TCA-ACGACTCAAAT
1 GAGCATATCGATTCATA-G-CTCGTAT
12336722 GAGCATATCGATTCATAGCTCGTAT
1 GAGCATATCGATTCATAGCTCGTAT
12336747 GAGCATA
1 GAGCATA
12336754 CTCGTATATG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
23 1 0.02
24 4 0.09
25 37 0.79
26 4 0.09
27 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (25 bp):
GAGCATATCGATTCATAGCTCGTAT
Found at i:12342686 original size:25 final size:25
Alignment explanation
Indices: 12342631--12342724 Score: 97
Period size: 25 Copynumber: 3.8 Consensus size: 25
12342621 CGAATACTCC
* *
12342631 ACAGCTCGTGA-GAGCATACCAATTT
1 ACAGCTCATGATGAGCATACCGA-TT
*
12342656 ATAGCTCATGA-GAGCATACCGATCT
1 ACAGCTCATGATGAGCATACCGAT-T
*
12342681 ACAGCTCA-AATGAGCATACCGATT
1 ACAGCTCATGATGAGCATACCGATT
12342705 CACAGCTCAT-ATGAGCATAC
1 -ACAGCTCATGATGAGCATAC
12342725 TTGTACATGA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.05
25 57 0.95
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (25 bp):
ACAGCTCATGATGAGCATACCGATT
Found at i:12353279 original size:2 final size:2
Alignment explanation
Indices: 12353272--12353318 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
12353262 CAATAATAAA
12353272 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
12353314 AC AC A
1 AC AC A
12353319 TATATATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12356640 original size:2 final size:2
Alignment explanation
Indices: 12356633--12356657 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12356623 ATCAACATCA
12356633 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
12356658 TATATAATCA
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:12360437 original size:19 final size:21
Alignment explanation
Indices: 12360410--12360448 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12360400 AATTAATTTA
12360410 ATTTAATTTAAT-TAAAAATT
1 ATTTAATTTAATCTAAAAATT
*
12360430 ATTT-ATTTTATCTAAAAAT
1 ATTTAATTTAATCTAAAAAT
12360449 ACAAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTAATTTAATCTAAAAATT
Found at i:12369640 original size:64 final size:64
Alignment explanation
Indices: 12369518--12369693 Score: 167
Period size: 64 Copynumber: 2.8 Consensus size: 64
12369508 GTGCAGGGTT
* * * * * *
12369518 CACACGGGTAAGACACACGGGCATGTG-CCAGGCCGTGTAACTCTCTGTGTTAGGATTTGTAGC
1 CACACGGGCAAAACACACGGGCGTGTGTCCAGGCCGTGTAACTCTCTGAGTTAGGATTTGGAGA
* * * * *
12369581 CATATGGGCAAAACACACGGGCGTGTGTCCAGGCTGTGTAACTCAT-TGAGTTCGTATTTGGAGA
1 CACACGGGCAAAACACACGGGCGTGTGTCCAGGCCGTGTAACTC-TCTGAGTTAGGATTTGGAGA
* * * * * * *
12369645 CACACGGGCAAGAGACAAGGGCGTGTGTTCAAGCCATGTAACTCACTGA
1 CACACGGGCAAAACACACGGGCGTGTGTCCAGGCCGTGTAACTCTCTGA
12369694 CTTCAGATTT
Statistics
Matches: 89, Mismatches: 21, Indels: 5
0.77 0.18 0.04
Matches are distributed among these distances:
63 22 0.25
64 66 0.74
65 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.23
Consensus pattern (64 bp):
CACACGGGCAAAACACACGGGCGTGTGTCCAGGCCGTGTAACTCTCTGAGTTAGGATTTGGAGA
Found at i:12370336 original size:60 final size:60
Alignment explanation
Indices: 12370215--12370337 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
12370205 TCTGTATCTA
* * *
12370215 TACCGTATGACATATACATCTGATCGTATTTCTGTTATATGTGCATTTATACTAATATGC
1 TACCATATGACATATACATCTGATCGTATTTCTGTTATACGTGCATCTATACTAATATGC
* * * * * *
12370275 TACCATATGACATGTGCATCTGATCGTATTTGTGTTATACGTGCATCTGTATTAATCTGC
1 TACCATATGACATATACATCTGATCGTATTTCTGTTATACGTGCATCTATACTAATATGC
12370335 TAC
1 TAC
12370338 GTATAAGGAC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (60 bp):
TACCATATGACATATACATCTGATCGTATTTCTGTTATACGTGCATCTATACTAATATGC
Found at i:12377924 original size:21 final size:21
Alignment explanation
Indices: 12377898--12377939 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12377888 CAATGAATTA
*
12377898 ACTTTTCTTGTTTTGATTTTG
1 ACTTTTCTTGTTTCGATTTTG
12377919 ACTTTTCTTGTTTCGATTTTG
1 ACTTTTCTTGTTTCGATTTTG
12377940 TTGATCACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (21 bp):
ACTTTTCTTGTTTCGATTTTG
Found at i:12378174 original size:15 final size:15
Alignment explanation
Indices: 12378154--12378187 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
12378144 TCAAATTAAA
12378154 AATTGATCCAAAAAC
1 AATTGATCCAAAAAC
12378169 AATTGATCCAAAAAC
1 AATTGATCCAAAAAC
12378184 AATT
1 AATT
12378188 TTTTGAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.24
Consensus pattern (15 bp):
AATTGATCCAAAAAC
Found at i:12380793 original size:44 final size:44
Alignment explanation
Indices: 12380730--12380819 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
12380720 TAAAATCATA
*
12380730 AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGCAAAG
1 AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGAAAAG
*
12380774 AGATATGCTTGTTATATGTGATGAATTTCAGTGTAATAGAAAAG
1 AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGAAAAG
12380818 AG
1 AG
12380820 CATACTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.36
Consensus pattern (44 bp):
AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGAAAAG
Found at i:12386960 original size:21 final size:21
Alignment explanation
Indices: 12386934--12386985 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12386924 TCATATAGTT
12386934 GAAGAAGCTACCTG-GAAACAA
1 GAAGAAGCTACCTGAG-AACAA
*
12386955 GAAGAAGCTACCTGAGAACCA
1 GAAGAAGCTACCTGAGAACAA
12386976 GAAGAAGCTA
1 GAAGAAGCTA
12386986 TGAAAGTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.10
Consensus pattern (21 bp):
GAAGAAGCTACCTGAGAACAA
Found at i:12388439 original size:38 final size:38
Alignment explanation
Indices: 12388190--12388438 Score: 275
Period size: 38 Copynumber: 6.4 Consensus size: 38
12388180 TTCAAATTGG
12388190 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCGGT-
1 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAATG-C--TA
* * *
12388230 GTATTGATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCA
1 GTGTT-ATTCAGGCTTTGTGCCTAGCAGGCTTAATGCTA
* * *
12388269 GTGTATTGATTCAGGCTTTGTGCCTAGGAGACTTAGTGCTA
1 GTG--TT-ATTCAGGCTTTGTGCCTAGCAGGCTTAATGCTA
* *
12388310 GTGTTATTCAGGCTTAGTGCCTAGCAGGCTTAATGCCA
1 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAATGCTA
* * * * *
12388348 GCGTTACTCAGGCTTTGTGCCTAGGAGACTTAGTGCTA
1 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAATGCTA
* *
12388386 GTGTTATTTAGGCTTAGTGCCTAGCAGGCTTAATGCTA
1 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAATGCTA
* *
12388424 GCGTTACTCAGGCTT
1 GTGTTATTCAGGCTT
12388439 AAAGCCTAGT
Statistics
Matches: 176, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
38 102 0.58
39 4 0.02
40 5 0.03
41 65 0.37
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (38 bp):
GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAATGCTA
Found at i:12388447 original size:76 final size:76
Alignment explanation
Indices: 12388192--12388438 Score: 325
Period size: 76 Copynumber: 3.2 Consensus size: 76
12388182 CAAATTGGGT
* * * * * *
12388192 GTTATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCGGT-GTATTGATTCAGGCTTTGTGCCTAGC
1 GTTACTCAGGCTTTGTGCCTAGGAGACTT-A-GT-GCTAGTGTT-ATTCAGGCTTAGTGCCTAGC
* *
12388256 AGGCTTAGTGCCAGT
62 AGGCTTAATGCCAGC
*
12388271 GTATTGATTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTCAGGCTTAGTGCCTAGCA
1 G--TT-ACTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTCAGGCTTAGTGCCTAGCA
12388336 GGCTTAATGCCAGC
63 GGCTTAATGCCAGC
*
12388350 GTTACTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTTAGGCTTAGTGCCTAGCAGGC
1 GTTACTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTCAGGCTTAGTGCCTAGCAGGC
*
12388415 TTAATGCTAGC
66 TTAATGCCAGC
12388426 GTTACTCAGGCTT
1 GTTACTCAGGCTT
12388439 AAAGCCTAGT
Statistics
Matches: 154, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
76 83 0.54
77 2 0.01
79 36 0.23
80 6 0.04
81 3 0.02
82 24 0.16
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (76 bp):
GTTACTCAGGCTTTGTGCCTAGGAGACTTAGTGCTAGTGTTATTCAGGCTTAGTGCCTAGCAGGC
TTAATGCCAGC
Found at i:12394222 original size:114 final size:114
Alignment explanation
Indices: 12393782--12394222 Score: 512
Period size: 114 Copynumber: 3.8 Consensus size: 114
12393772 AAAATAAGCA
* *
12393782 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGT-CGTTTCCCGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGAC-TCCGTTTTCTGAGCT
* * * *
12393845 TTCGGGGATTTAGCGGCGTTTCTAAGAAAGCACCGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCTGCTAATGCTCAGGGCT
* * *
12393895 TTAGCGGCGTTTTCAGGAAGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCAAACGACGCC
1 TTA-----G----C--G--GCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACTCC
* * * * *
12393960 GTTTTCTAATCTTTCGGGGGTTTAGCGGCGTTTTTAAGGAAGCG-TCGCTAATGCTCAAGGAT
53 GTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCT-GCTAATGCTCAGGGCT
* * * *
12394022 TTAGCGGCGTTTTTGATAAAGCGCTGCAAAAAAACCTAAGCCTAACGA-TGCCATTTTCTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACT-CCGTTTTCTGAGCT
*
12394086 TTCGGGGATTTAGCGGCATTTTTAAGGAAGCGCTGCTAATGCTCAGGGCT
65 TTCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCTGCTAATGCTCAGGGCT
* *
12394136 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACTTAAGCCCAACGACTCCGTTTTTTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACTCCGTTTTCTGAGCTT
*
12394201 TCGGGGATTTAGCGGTGTTTTT
66 TCGGGGATTTAGCGGCGTTTTT
12394223 GGAAAAGCGC
Statistics
Matches: 275, Mismatches: 34, Indels: 37
0.79 0.10 0.11
Matches are distributed among these distances:
113 3 0.01
114 170 0.62
115 2 0.01
116 1 0.00
118 2 0.01
122 2 0.01
124 1 0.00
126 20 0.07
127 74 0.27
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACTCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGGAAGCGCTGCTAATGCTCAGGGCT
Found at i:12394504 original size:15 final size:15
Alignment explanation
Indices: 12394486--12394516 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12394476 TACATTTTAA
12394486 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
12394501 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
12394516 G
1 G
12394517 ATTAGGGGTT
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:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:12394542 original size:28 final size:27
Alignment explanation
Indices: 12394489--12394564 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 27
12394479 ATTTTAAGGT
*
12394489 TTAGGGAGTATGGGTTTAGGGATTATGGA
1 TTAGGG-GT-TGGGTTTAAGGATTATGGA
* *
12394518 TTAGGGGTTGGGATTTAAGGTTTATGGG
1 TTAGGGGTTGGG-TTTAAGGATTATGGA
12394546 TTAGAGGGTTAAGGGTTTA
1 TTAG-GGGTT--GGGTTTA
12394565 GGAATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 4 0.10
28 18 0.45
29 11 0.28
30 4 0.10
31 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (27 bp):
TTAGGGGTTGGGTTTAAGGATTATGGA
Found at i:12394774 original size:15 final size:15
Alignment explanation
Indices: 12394754--12394800 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
12394744 TATTTTCAGG
*
12394754 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
12394769 TTTAGGGATTAT-GA
1 TTTAGGGATTATGGA
*
12394783 ATTAGGGATTATGG-
1 TTTAGGGATTATGGA
12394797 TTTA
1 TTTA
12394801 AGGGTTGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:12395685 original size:131 final size:134
Alignment explanation
Indices: 12395538--12395948 Score: 603
Period size: 131 Copynumber: 3.0 Consensus size: 134
12395528 TTTTATGAAA
12395538 AGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTT
1 AGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTT
12395603 ATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG-AAAAAATTT
66 ATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTT
12395667 TGTG
131 TGTG
**
12395671 -GCG-CTTTAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTT
1 AGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTT
* *
12395734 ATAAAAAATAAATTAATTTTTAGAATAGGAAAACAGCGTCGTTTTGTTCAAAATGAAAAAGAAAT
66 ATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATG-AAAA-AAA-
*
12395799 TTGCGGCGTTTTATG
128 --------TTTTGTG
*
12395814 AAAAGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAATGCCGCAAAAAATAAATCAA
1 ---AGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAA
* *
12395879 TTTATAAAAAATAAATTAATTTTTAAAATAGCAAAACGGCGTTGTTTTGTTCAAAATGAAAAAAA
63 TTTATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAA
12395944 TTTTG
128 TTTTG
12395949 CGACACTTTA
Statistics
Matches: 248, Mismatches: 13, Indels: 30
0.85 0.04 0.10
Matches are distributed among these distances:
131 111 0.45
132 3 0.01
133 3 0.01
134 3 0.01
137 4 0.02
143 6 0.02
146 3 0.01
147 7 0.03
148 108 0.44
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (134 bp):
AGCGCCGCTAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTT
ATAAAAAATAAATTAATTTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAATTT
TGTG
Found at i:12395841 original size:148 final size:147
Alignment explanation
Indices: 12395677--12395975 Score: 508
Period size: 148 Copynumber: 2.0 Consensus size: 147
12395667 TGTGGCGCTT
12395677 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
1 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
* * * *
12395742 TAAATTAATTTTTAGAATAGGAAAACAGCGTCGTTTTGTTCAAAATGAAAAAGAAATTTGCGGCG
66 TAAATTAATTTTTAAAATAGCAAAACAGCGTCGTTTTGTTCAAAATGAAAAA-AAATTTGCGACA
*
12395807 TTTTATGAAAAGCGCCGC
130 CTTTATGAAAAGCGCCGC
*
12395825 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAATGCCGCAAAAAATAAATCAATTTATAAAAAA
1 TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
* * *
12395890 TAAATTAATTTTTAAAATAGCAAAACGGCGTTGTTTTGTTCAAAATGAAAAAAATTTTGCGACAC
66 TAAATTAATTTTTAAAATAGCAAAACAGCGTCGTTTTGTTCAAAATGAAAAAAAATTTGCGACAC
12395955 TTTATGAAAAGCGCCGC
131 TTTATGAAAAGCGCCGC
12395972 TAAA
1 TAAA
12395976 AGCAAAAACG
Statistics
Matches: 142, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
147 30 0.21
148 112 0.79
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (147 bp):
TAAAGGTAGGCAATAGCGGCGTTTGTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAA
TAAATTAATTTTTAAAATAGCAAAACAGCGTCGTTTTGTTCAAAATGAAAAAAAATTTGCGACAC
TTTATGAAAAGCGCCGC
Found at i:12395889 original size:19 final size:19
Alignment explanation
Indices: 12395865--12395906 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
12395855 AAAATGCCGC
12395865 AAAAAATAAATCAATTTAT
1 AAAAAATAAATCAATTTAT
* *
12395884 AAAAAATAAATTAATTTTT
1 AAAAAATAAATCAATTTAT
12395903 AAAA
1 AAAA
12395907 TAGCAAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAAATAAATCAATTTAT
Found at i:12400766 original size:20 final size:19
Alignment explanation
Indices: 12400722--12400768 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
12400712 AAAAATAAAA
12400722 TAAAATAAAATATTTATCAT
1 TAAAATAAAATATTTA-CAT
*
12400742 AAAAATAAATATTATTTA-AT
1 TAAAATAAA-A-TATTTACAT
12400762 TAAAATA
1 TAAAATA
12400769 TATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 16 0.70
21 1 0.04
22 6 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATAAAATATTTACAT
Found at i:12400898 original size:43 final size:43
Alignment explanation
Indices: 12400850--12401123 Score: 266
Period size: 43 Copynumber: 6.4 Consensus size: 43
12400840 CATTTGTGAT
* * * * *
12400850 AAAAGCGCCGCTAAAGTTCATGTTTTTTAGCGGCGTTTATAGA
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTATTGG
* * *
12400893 AAAAGCGCCGCTAAAGGTCATGGTTTTTAGCGGCGTTT-GTGTG
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTATTG-G
* * * * *
12400936 AAAAGCGCCGCTAAAGGTCAGGGTCTATAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTATTGG
* * * * * * *
12400979 AGAAGTGCCGCTAAATGTCAGGATCTATAGCGACGTTTTTTGG
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTATTGG
* * *
12401022 ATAAGCGCCACTAAAGGTCATGATCTTTAGCGGCGTTTCTT-G
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTATTGG
* * *
12401064 AAATGCGCCGCTAAAGATCATGATCTTTAGCGGCGTTTATTTCTG
1 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTA-TT-GG
12401109 AAAA-CGCCGCTAAAG
1 AAAAGCGCCGCTAAAG
12401124 TTAGCGACGC
Statistics
Matches: 195, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
42 36 0.18
43 143 0.73
44 12 0.06
45 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTATTGG
Found at i:12402946 original size:55 final size:58
Alignment explanation
Indices: 12402840--12402970 Score: 178
Period size: 55 Copynumber: 2.3 Consensus size: 58
12402830 TTAATATGAA
* * * *
12402840 AATAATTATATTGAGAATGTTATTAAATTATATATTATTTTTATTAAATTATATTTAAT
1 AATAATTATATT-AAAATATGATTAAATTATATATTATTATTATTAAATTATATTTAAT
12402899 AATAATTATATTAAAATATGATTAAA-T-TAT-TTATTATTATTAAATTATATTTAAT
1 AATAATTATATTAAAATATGATTAAATTATATATTATTATTATTAAATTATATTTAAT
**
12402954 AATAATCCTATTAAAAT
1 AATAATTATATTAAAAT
12402971 TTAATAACAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
55 39 0.59
56 3 0.05
57 1 0.02
58 11 0.17
59 12 0.18
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.50
Consensus pattern (58 bp):
AATAATTATATTAAAATATGATTAAATTATATATTATTATTATTAAATTATATTTAAT
Found at i:12404720 original size:39 final size:38
Alignment explanation
Indices: 12404677--12404757 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 38
12404667 GCCCGGCCCG
12404677 AATATATAAT-AAAT-ATTTTTTTATTTTTTTTAATTTTAA
1 AATAT-TAATAAAATAATTTTTTTA--TTTTTTAATTTTAA
** *
12404716 AATATTTTTAAAATAATTTTTTTATTTTTTATTTTTAA
1 AATATTAATAAAATAATTTTTTTATTTTTTAATTTTAA
12404754 AATA
1 AATA
12404758 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 19 0.51
39 9 0.24
40 9 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (38 bp):
AATATTAATAAAATAATTTTTTTATTTTTTAATTTTAA
Found at i:12404772 original size:26 final size:27
Alignment explanation
Indices: 12404718--12404774 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
12404708 AATTTTAAAA
* * *
12404718 TATTTTTAAAATAATTTTTTTATTTTT
1 TATTTTTAAAATAATATTTTTAGTGTT
*
12404745 TATTTTTAAAATAA-ATTTTTGGTGTT
1 TATTTTTAAAATAATATTTTTAGTGTT
12404771 TATT
1 TATT
12404775 AAAAAATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTTTTAAAATAATATTTTTAGTGTT
Found at i:12405592 original size:20 final size:21
Alignment explanation
Indices: 12405567--12405608 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12405557 TTGTAAATTA
12405567 ATTTAATT-TTT-TGATTTATT
1 ATTTAATTGTTTATGA-TTATT
12405587 ATTTAATTGTTTATGATTATT
1 ATTTAATTGTTTATGATTATT
12405608 A
1 A
12405609 ATTGAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 9 0.45
22 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATTTAATTGTTTATGATTATT
Found at i:12413799 original size:13 final size:13
Alignment explanation
Indices: 12413781--12413819 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
12413771 AGATAAATTG
12413781 AACATCTTTTTGT
1 AACATCTTTTTGT
*
12413794 AACATC-TTTAGTT
1 AACATCTTTTTG-T
12413807 AACATCTTTTTGT
1 AACATCTTTTTGT
12413820 TGATATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (13 bp):
AACATCTTTTTGT
Found at i:12416918 original size:21 final size:21
Alignment explanation
Indices: 12416894--12416934 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12416884 TGGCTTAAAA
*
12416894 GCATGGTCGTG-AGGCTACTTT
1 GCATGCTCGTGTA-GCTACTTT
12416915 GCATGCTCGTGTAGCTACTT
1 GCATGCTCGTGTAGCTACTT
12416935 CACACACCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.34
Consensus pattern (21 bp):
GCATGCTCGTGTAGCTACTTT
Found at i:12421273 original size:12 final size:12
Alignment explanation
Indices: 12421253--12421285 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12421243 TTTACACTAC
12421253 ATTTATTTTGAT
1 ATTTATTTTGAT
*
12421265 ATTTGTTTTGAT
1 ATTTATTTTGAT
12421277 -TTTATTTTG
1 ATTTATTTTG
12421286 CAACTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (12 bp):
ATTTATTTTGAT
Found at i:12426438 original size:41 final size:41
Alignment explanation
Indices: 12426365--12426682 Score: 213
Period size: 41 Copynumber: 7.8 Consensus size: 41
12426355 ATTTTTAAAC
* * *
12426365 CTTTAGCGGCGTTTTTA-CTTTAGCACCGCTAATTCTCCGAT
1 CTTTAGCGGCGTTTTTATC-TAAGCGCCGCTAATTCTCTGAT
* * * **
12426406 CTTTAGCGGCATTTTTATCTGAGCGCCACTAATGT-TCTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT-TCTCTGAT
* *
12426447 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC-GTAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATTCTCTG-AT
* * * * * * * * *
12426488 CATTAGTGGCGTTATTGTCTGAGTGCCACTAATTCTTTGTT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATTCTCTGAT
* * *
12426529 CTTTAGCGGCGTTTTTTTCTAAACGCCGCTAAAGTTC-GTG-T
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCT-AA-TTCTCTGAT
* * * * * **
12426570 TTTTAGTGGCGTTTTTATCTGAGCGCCACTAATACTCTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATTCTCTGAT
* * *
12426611 CTTTAGCGGCGTTTTATATGTAAGCGCCGCTAA-T-GCT-AC
1 CTTTAGCGGCGTTTT-TATCTAAGCGCCGCTAATTCTCTGAT
*
12426650 CTTTAGCGGCGTTTTT-TCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTAT-CTAAGCGCCGCTAAT
12426683 AGTAACAAAA
Statistics
Matches: 214, Mismatches: 51, Indels: 26
0.74 0.18 0.09
Matches are distributed among these distances:
37 1 0.00
38 13 0.06
39 18 0.08
40 7 0.03
41 151 0.71
42 21 0.10
43 3 0.01
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATTCTCTGAT
Found at i:12426509 original size:82 final size:80
Alignment explanation
Indices: 12426364--12426647 Score: 300
Period size: 82 Copynumber: 3.5 Consensus size: 80
12426354 GATTTTTAAA
* * * * * *
12426364 CCTTTAGCGGCGTTTTTACTTTAGCACCGCTAATTCTCCG-ATCTTTAGCGGCATTTTTATCTGA
1 CCTTTAGCGGCGTTTTTTC-TAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGA
12426428 GCGCCACTAATGTTCTGG
64 GCGCCACTAAT-TTCTGG
* * *
12426446 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTATTGTCTGAG
1 CCTTTAGCGGCGTTTTT-TCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
* * *
12426511 TGCCACTAATTCTTTGT
65 CGCCACTAATT-TCTGG
* * * * * *
12426528 TCTTTAGCGGCGTTTTTTTCTAAACGCCGCTAAAGTTCGTGTTTTTAGTGGCGTTTTTATCTGAG
1 CCTTTAGCGGCG-TTTTTTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
*
12426593 CGCCACTAATACTCTGG
65 CGCCACTAAT-TTCTGG
*
12426610 CCTTTAGCGGCGTTTTATATGTAAGCGCCGCTAATGCT
1 CCTTTAGCGGCGTTTT-T-TCTAAGCGCCGCTAATGCT
12426648 ACCTTTAGCG
Statistics
Matches: 165, Mismatches: 30, Indels: 13
0.79 0.14 0.06
Matches are distributed among these distances:
81 7 0.04
82 137 0.83
83 21 0.13
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (80 bp):
CCTTTAGCGGCGTTTTTTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAGC
GCCACTAATTTCTGG
Found at i:12427218 original size:15 final size:15
Alignment explanation
Indices: 12427197--12427234 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12427187 TTTAAGGTTA
12427197 ATTTAGGGGTTGGAG
1 ATTTAGGGGTTGGAG
* *
12427212 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTGGAG
12427227 ATTTAGGG
1 ATTTAGGG
12427235 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTGGAG
Found at i:12427237 original size:14 final size:14
Alignment explanation
Indices: 12427170--12427237 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
12427160 GACTGGGTAT
*
12427170 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
12427184 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
12427196 A-ATTTAGGGGTTGG
1 AGATTTA-GGGTTTG
*
12427210 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
12427225 AGATTTAGGGTTT
1 AGATTTAGGGTTT
12427238 CAACGGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:12428985 original size:8 final size:10
Alignment explanation
Indices: 12428963--12428999 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
12428953 TATTTTTACT
12428963 TATATATGGA
1 TATATATGGA
*
12428973 TATATATGAA
1 TATATATGGA
12428983 TATATATGGA
1 TATATATGGA
12428993 TATATAT
1 TATATAT
12429000 ATAGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (10 bp):
TATATATGGA
Found at i:12431527 original size:13 final size:13
Alignment explanation
Indices: 12431509--12431533 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12431499 AGACATAATA
12431509 CATAACTTACATT
1 CATAACTTACATT
12431522 CATAACTTACAT
1 CATAACTTACAT
12431534 AAACTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAACTTACATT
Found at i:12431641 original size:34 final size:34
Alignment explanation
Indices: 12431598--12431757 Score: 129
Period size: 34 Copynumber: 4.7 Consensus size: 34
12431588 GGGTGATGTG
*
12431598 ATATTATACATAAATTACATAACTTAATTAATTA
1 ATATTATACATAACTTACATAACTTAATTAATTA
12431632 ATATTATACATAACTTACATTAA--T-ATT-A-TA
1 ATATTATACATAACTTACA-TAACTTAATTAATTA
* *
12431662 CATA-AATTACATAACTTA-ATTAA-TTAATATTATACATAA
1 -ATATTA-TACATAACTTACA-TAACTT-A-A-T-TA-ATTA
* * *
12431701 ATATTATAAATAAATTACATAACTTAGTTAATTA
1 ATATTATACATAACTTACATAACTTAATTAATTA
12431735 ATATTATACATAACTTACATAAC
1 ATATTATACATAACTTACATAAC
12431758 ATTTTAACAA
Statistics
Matches: 101, Mismatches: 10, Indels: 30
0.72 0.07 0.21
Matches are distributed among these distances:
30 8 0.08
31 16 0.16
32 3 0.03
33 1 0.01
34 43 0.43
35 6 0.06
36 2 0.02
38 17 0.17
39 5 0.05
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (34 bp):
ATATTATACATAACTTACATAACTTAATTAATTA
Found at i:12431656 original size:22 final size:22
Alignment explanation
Indices: 12431623--12431673 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
12431613 TACATAACTT
12431623 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
*
12431644 ACTTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
12431666 AATTACAT
1 AATTACAT
12431674 AACTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:12431660 original size:56 final size:55
Alignment explanation
Indices: 12431598--12431756 Score: 235
Period size: 56 Copynumber: 3.0 Consensus size: 55
12431588 GGGTGATGTG
12431598 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACA-TA
12431654 ATATTATACATAAATTACATAACTTAATTAATTAATATTATAC---A--T--A-A
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATA
* *
12431701 ATATTATAAATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACATA
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATA
12431756 A
1 A
12431757 CATTTTAACA
Statistics
Matches: 93, Mismatches: 2, Indels: 17
0.83 0.02 0.15
Matches are distributed among these distances:
47 42 0.45
49 1 0.01
50 1 0.01
51 1 0.01
52 1 0.01
53 1 0.01
54 1 0.01
55 2 0.02
56 43 0.46
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (55 bp):
ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATA
Found at i:12431698 original size:47 final size:47
Alignment explanation
Indices: 12431647--12431747 Score: 175
Period size: 47 Copynumber: 2.1 Consensus size: 47
12431637 ATACATAACT
* *
12431647 TACATTAATATTATACATAAATTACATAACTTAATTAATTAATATTA
1 TACATAAATATTATAAATAAATTACATAACTTAATTAATTAATATTA
*
12431694 TACATAAATATTATAAATAAATTACATAACTTAGTTAATTAATATTA
1 TACATAAATATTATAAATAAATTACATAACTTAATTAATTAATATTA
12431741 TACATAA
1 TACATAA
12431748 CTTACATAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (47 bp):
TACATAAATATTATAAATAAATTACATAACTTAATTAATTAATATTA
Found at i:12431719 original size:22 final size:22
Alignment explanation
Indices: 12431623--12431722 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
12431613 TACATAACTT
* *
12431623 AATTA-ATTAATATTATACATA
1 AATTACATAAATATTATAAATA
* * *
12431644 ACTTACATTAATATTATACATA
1 AATTACATAAATATTATAAATA
* *
12431666 AATTACATAACTTAATTAATTAAT-
1 AATTACATAA-AT-ATT-ATAAATA
*
12431690 ATTATACATAAATATTATAAATA
1 AAT-TACATAAATATTATAAATA
12431713 AATTACATAA
1 AATTACATAA
12431723 CTTAGTTAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
21 4 0.06
22 36 0.57
23 6 0.10
24 6 0.10
25 11 0.17
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTACATAAATATTATAAATA
Found at i:12431794 original size:9 final size:9
Alignment explanation
Indices: 12431780--12431910 Score: 70
Period size: 9 Copynumber: 15.9 Consensus size: 9
12431770 TGCATAATAA
12431780 ATAACTTAC
1 ATAACTTAC
12431789 ATAACTTAC
1 ATAACTTAC
12431798 ATAA--TAC
1 ATAACTTAC
*
12431805 ATAACTTAT
1 ATAACTTAC
* *
12431814 ATGACTTAT
1 ATAACTTAC
12431823 ATAACTTAC
1 ATAACTTAC
*
12431832 AT-A---GC
1 ATAACTTAC
* *
12431837 ATAATTTTC
1 ATAACTTAC
12431846 ATAA--TAC
1 ATAACTTAC
*
12431853 ACAACTTAC
1 ATAACTTAC
** *
12431862 ATAGTTTTC
1 ATAACTTAC
*
12431871 ATAA--TAA
1 ATAACTTAC
12431878 ATAACTTAC
1 ATAACTTAC
12431887 ATAA--TAC
1 ATAACTTAC
12431894 ATAACTTAC
1 ATAACTTAC
*
12431903 ATAGCTTA
1 ATAACTTA
12431911 ATTATACTTA
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 24 0.26
8 1 0.01
9 64 0.69
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:12431801 original size:25 final size:25
Alignment explanation
Indices: 12431772--12431897 Score: 91
Period size: 25 Copynumber: 5.2 Consensus size: 25
12431762 TAACAATTTG
12431772 CATAATAAATAACTTACATAACTTA
1 CATAATAAATAACTTACATAACTTA
* * *
12431797 CATAATACATAACTTATATGACTT-
1 CATAATAAATAACTTACATAACTTA
* * * * *
12431821 -AT-ATAACTTACATAGCATAATTTT
1 CATAATAAATAACTTA-CATAACTTA
* * ** *
12431845 CATAATACACAACTTACATAGTTTT
1 CATAATAAATAACTTACATAACTTA
12431870 CATAATAAATAACTTACATAA--TA
1 CATAATAAATAACTTACATAACTTA
12431893 CATAA
1 CATAA
12431898 CTTACATAGC
Statistics
Matches: 77, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
22 8 0.10
23 13 0.17
25 49 0.64
26 7 0.09
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (25 bp):
CATAATAAATAACTTACATAACTTA
Found at i:12431805 original size:16 final size:16
Alignment explanation
Indices: 12431786--12431905 Score: 78
Period size: 16 Copynumber: 7.9 Consensus size: 16
12431776 ATAAATAACT
12431786 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
12431802 TACATAACTTATATGACT
1 TACATAACTTACAT-A-A
*
12431820 TATATAACTTACAT-A
1 TACATAACTTACATAA
* * *
12431835 -GCATAATTTTCATAA
1 TACATAACTTACATAA
* *
12431850 TACACAACTTACATAG
1 TACATAACTTACATAA
12431866 T---T---TT-CATAA
1 TACATAACTTACATAA
*
12431875 TAAATAACTTACATAA
1 TACATAACTTACATAA
12431891 TACATAACTTACATA
1 TACATAACTTACATA
12431906 GCTTAATTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
12 1 0.01
14 9 0.12
15 3 0.04
16 43 0.57
17 1 0.01
18 12 0.16
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:12437446 original size:66 final size:65
Alignment explanation
Indices: 12437326--12437489 Score: 204
Period size: 66 Copynumber: 2.5 Consensus size: 65
12437316 GAGCAAATTA
* *
12437326 CACAACTTAAAGCAGATGCAACATCGAGAGAAGCTGAGGCTCAAAAAATATATGAAGAACTCCAG
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGCTCAAAAAATATATGAAGAACTCCAG
* * * *
12437391 CTACAACTGAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAA-GTATGAAGAACTCC
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGCTCAA-AAAATATATGAAGAACTCC
12437455 AG
64 AG
* * * *
12437457 CAGCAGCTTAAAGTAGATGCGGCAGCAAGAGAA
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAA
12437490 ACAGAGGCGG
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 80 0.94
67 3 0.04
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGCTCAAAAAATATATGAAGAACTCCAG
Found at i:12437518 original size:21 final size:21
Alignment explanation
Indices: 12437475--12437524 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
12437465 TAAAGTAGAT
*
12437475 GCGGCAGCAAGAGAAACAGAG
1 GCGGCAGCAAGAGAAACACAG
* **
12437496 GCGGCAGCTAGAGAAGTACAG
1 GCGGCAGCAAGAGAAACACAG
*
12437517 GCTGCAGC
1 GCGGCAGC
12437525 GAGGGAAGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.22, G:0.38, T:0.06
Consensus pattern (21 bp):
GCGGCAGCAAGAGAAACACAG
Found at i:12437532 original size:21 final size:21
Alignment explanation
Indices: 12437491--12437579 Score: 115
Period size: 21 Copynumber: 4.2 Consensus size: 21
12437481 GCAAGAGAAA
* * *
12437491 CAGAGGCGGCAGCTAGAGAAG
1 CAGAGGCTGCAGCGAGGGAAG
* *
12437512 TACAGGCTGCAGCGAGGGAAG
1 CAGAGGCTGCAGCGAGGGAAG
**
12437533 CAGAGGCTAAAGCGAGGGAAG
1 CAGAGGCTGCAGCGAGGGAAG
12437554 CAGAGGCTGCAGCGAGGGAAG
1 CAGAGGCTGCAGCGAGGGAAG
12437575 CAGAG
1 CAGAG
12437580 CAGCGTCAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.33, C:0.18, G:0.44, T:0.06
Consensus pattern (21 bp):
CAGAGGCTGCAGCGAGGGAAG
Found at i:12437970 original size:43 final size:43
Alignment explanation
Indices: 12437923--12438183 Score: 256
Period size: 43 Copynumber: 6.0 Consensus size: 43
12437913 AGGTGTTGGC
* * *
12437923 CTTTAGTGGCATTTTTGGTCAAAGCGTCGCTAAAGATAAGGGT
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * ** * *
12437966 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * * ** * *
12438009 CTTTAGCGACATTTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *
12438052 CTTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGTGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * *
12438096 CTATT-GTGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *
12438139 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAA-ATCAAGGT
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTA-AAGATCAGGGT
12438182 CT
1 CT
12438184 ATTGCGACGT
Statistics
Matches: 173, Mismatches: 41, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
42 2 0.01
43 133 0.77
44 36 0.21
45 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:12438116 original size:87 final size:86
Alignment explanation
Indices: 12437943--12438191 Score: 329
Period size: 87 Copynumber: 2.9 Consensus size: 86
12437933 ATTTTTGGTC
* * * * ** * * *
12437943 AAAGCGTCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAAGG
*
12438008 TCT-TTAGCGACATTTTTGGGG
66 TCTATT-GCGACATTTTAGGGG
* *
12438029 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTCAAAGCGCCGCTATAGATCAAG
* * *
12438094 GTCTATTGTGGCGTTTTAGGGG
65 GTCTATTGCGACATTTTAGGGG
*
12438116 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAAATCAAGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAAGG
12438181 TCTATTGCGAC
66 TCTATTGCGAC
12438192 GTTTGAGAAA
Statistics
Matches: 142, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
86 67 0.47
87 73 0.51
88 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAAGG
TCTATTGCGACATTTTAGGGG
Found at i:12438217 original size:86 final size:86
Alignment explanation
Indices: 12437943--12438195 Score: 330
Period size: 86 Copynumber: 2.9 Consensus size: 86
12437933 ATTTTTGGTC
* * * * ** * *
12437943 AAAGCGTCGCTAAAGATAAGGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCACTA-AAGATCATG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAA-ATCAAG
* *
12438007 GTCT-TTAGCGACATTTTTGGGG
65 GTCTATT-GCGACGTTTTAGGGG
* * *
12438029 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTCAAAGCGCCGCTATAAATCAAG
* *
12438094 GTCTATTGTGGCGTTTTAGGGG
65 GTCTATTGCGACGTTTTAGGGG
12438116 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAAATCAAGG
1 AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAAATCAAGG
12438181 TCTATTGCGACGTTT
66 TCTATTGCGACGTTT
12438196 GAGAAAAAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
86 71 0.49
87 71 0.49
88 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (86 bp):
AAAGCGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAAATCAAGG
TCTATTGCGACGTTTTAGGGG
Found at i:12438228 original size:86 final size:87
Alignment explanation
Indices: 12438033--12438230 Score: 218
Period size: 86 Copynumber: 2.3 Consensus size: 87
12438023 TTGGGGAAAG
** * * * *
12438033 CGCCGCTAAAGATTAGGTTCTTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGTCT
1 CGCCGCTAAAGACCAGGATCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAAATCAAGGTCT
* * * *** *
12438098 ATTGTGGCGTTTTAGGGGAAAG
66 ATTGCGACGTTTGAGAAAAAAA
** *
12438120 CGCCGCTAAAGATTAGGTTCTTTAGTGGCG-TTTGTGGTCAAAGCGCCGCTATAAATCAAGGTCT
1 CGCCGCTAAAGACCAGGATCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAAATCAAGGTCT
12438184 ATTGCGACGTTTGAGAAAAAAA
66 ATTGCGACGTTTGAGAAAAAAA
* **
12438206 TGCCGCTAAAGACCCTGATCTTTAG
1 CGCCGCTAAAGACCAGGATCTTTAG
12438231 CGATGCTTCT
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
86 65 0.68
87 30 0.32
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (87 bp):
CGCCGCTAAAGACCAGGATCTTTAGTGGCGTTTTGTGGTCAAAGCGCCGCTATAAATCAAGGTCT
ATTGCGACGTTTGAGAAAAAAA
Found at i:12438488 original size:22 final size:22
Alignment explanation
Indices: 12438460--12438502 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12438450 CTGCGGCGCT
* *
12438460 AAAAAGCGCCGCTAAATGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
12438482 AAAAAGCACCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
12438503 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.16, T:0.12
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:12438698 original size:25 final size:25
Alignment explanation
Indices: 12438670--12438720 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12438660 TACCAGTGAT
12438670 AATCGTGTGAGGAAACAAGAACAAA
1 AATCGTGTGAGGAAACAAGAACAAA
12438695 AATCGTGTGAGGAAACAAGAACAAA
1 AATCGTGTGAGGAAACAAGAACAAA
12438720 A
1 A
12438721 TCCTGGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.12, G:0.24, T:0.12
Consensus pattern (25 bp):
AATCGTGTGAGGAAACAAGAACAAA
Found at i:12445852 original size:19 final size:19
Alignment explanation
Indices: 12445808--12445852 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
12445798 TATATATTCA
12445808 ATTATTTGATTTATTTCTT
1 ATTATTTGATTTATTTCTT
12445827 -TTCATTT-ATTTACTTTCTT
1 ATT-ATTTGATTTA-TTTCTT
12445846 ATTATTT
1 ATTATTT
12445853 TATAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 7 0.30
19 14 0.61
20 2 0.09
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (19 bp):
ATTATTTGATTTATTTCTT
Found at i:12447657 original size:3 final size:3
Alignment explanation
Indices: 12447651--12447703 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
12447641 TTTTTTTAAT
* * * *
12447651 TTA TTA TTA TTA TTG TTA TTA CTA TTA TTA TTA TTG TTA -TA GGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
12447696 TTA TTA TT
1 TTA TTA TT
12447704 GTATTAGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:12447678 original size:21 final size:21
Alignment explanation
Indices: 12447625--12447703 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
12447615 AAAATTGTCC
*
12447625 TTGTTTTTACTATTATT-TT-
1 TTGTTATTACTATTATTATTA
12447644 TT-TTAATT--TATTATTATTA
1 TTGTT-ATTACTATTATTATTA
12447663 TTGTTATTACTATTATTATTA
1 TTGTTATTACTATTATTATTA
*
12447684 TTGTTA-TAGGTATTATTATT
1 TTGTTATTA-CTATTATTATT
12447704 GTATTAGTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
17 7 0.14
18 4 0.08
19 9 0.18
20 4 0.08
21 27 0.53
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.66
Consensus pattern (21 bp):
TTGTTATTACTATTATTATTA
Found at i:12447862 original size:15 final size:16
Alignment explanation
Indices: 12447844--12447873 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12447834 TTATATGAAG
12447844 ATTTTATATA-ATATT
1 ATTTTATATACATATT
12447859 ATTTTATATACATAT
1 ATTTTATATACATAT
12447874 ATGATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTATATACATATT
Found at i:12448056 original size:2 final size:2
Alignment explanation
Indices: 12448049--12448073 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12448039 TTTCAACATT
12448049 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12448074 TATTTGTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12450872 original size:38 final size:38
Alignment explanation
Indices: 12450821--12450898 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
12450811 ATTTGTTAGC
12450821 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
1 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
12450859 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
1 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
12450897 AT
1 AT
12450899 GATCTCAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (38 bp):
ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
Found at i:12459714 original size:30 final size:30
Alignment explanation
Indices: 12459637--12459714 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
12459627 TTAACATTAG
*
12459637 CATCGACTACTACACGGGCATCTACATCAA
1 CATCGACTACTACATGGGCATCTACATCAA
* * *
12459667 CATCGACTGCTGCATGGGCATCTACATCGA
1 CATCGACTACTACATGGGCATCTACATCAA
* *
12459697 CATCGATTACTATATGGG
1 CATCGACTACTACATGGG
12459715 AAGCTACACC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (30 bp):
CATCGACTACTACATGGGCATCTACATCAA
Found at i:12461514 original size:15 final size:15
Alignment explanation
Indices: 12461496--12461526 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12461486 TAATTAAATT
*
12461496 TAACATAATTTAAAA
1 TAACAAAATTTAAAA
12461511 TAACAAAATTTAAAA
1 TAACAAAATTTAAAA
12461526 T
1 T
12461527 TTCGTCTTAC
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:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (15 bp):
TAACAAAATTTAAAA
Found at i:12463223 original size:19 final size:18
Alignment explanation
Indices: 12463196--12463234 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12463186 CTTTTTTATA
*
12463196 TATTCTTTATATTGTTTTT
1 TATTCTTTATAAT-TTTTT
*
12463215 TATTTTTTATAATTTTTT
1 TATTCTTTATAATTTTTT
12463233 TA
1 TA
12463235 AAAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TATTCTTTATAATTTTTT
Found at i:12463261 original size:18 final size:16
Alignment explanation
Indices: 12463240--12463283 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 16
12463230 TTTTAAAAAA
12463240 TATAAATTTTGAAATTTT
1 TATAAATTTTG-AA-TTT
12463258 TATAAATATTTTGAATTT
1 TAT-AA-ATTTTGAATTT
12463276 TATAAATT
1 TATAAATT
12463284 ATTTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.12
17 2 0.08
18 9 0.38
19 4 0.17
20 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TATAAATTTTGAATTT
Found at i:12463270 original size:20 final size:20
Alignment explanation
Indices: 12463245--12463290 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
12463235 AAAAATATAA
12463245 ATTTTGAAATTTTTATAAA-T
1 ATTTTGAAA-TTTTATAAATT
12463265 ATTTTG-AATTTTATAAATT
1 ATTTTGAAATTTTATAAATT
12463284 ATTTTGA
1 ATTTTGA
12463291 TTTTTTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.38
19 9 0.38
20 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
ATTTTGAAATTTTATAAATT
Found at i:12463276 original size:19 final size:20
Alignment explanation
Indices: 12463245--12463295 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
12463235 AAAAATATAA
12463245 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AATTTTTATAAATT
12463265 ATTTTGAA-TTTTATAAATT
1 ATTTTGAATTTTTATAAATT
12463284 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
12463296 TTGTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.34
19 13 0.45
20 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:12471842 original size:39 final size:39
Alignment explanation
Indices: 12471783--12471948 Score: 215
Period size: 39 Copynumber: 4.2 Consensus size: 39
12471773 AATAAAAATA
*
12471783 TGGTGATTATTCGGGCTATGTGGCTAGCAGGCTGTGTGC
1 TGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
* * *
12471822 TGGTAATTATTTGGGCTATGTGCCTAGCAAGCTGTGTGC
1 TGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
** * * * * *
12471861 CAGTGATTATCCAGGTTATGTGTCTAGTAGGCTGTGTGC
1 TGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
*
12471900 CGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
1 TGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
12471939 TGGTGTATTA
1 TGGTG-ATTA
12471949 AAAATTTGCA
Statistics
Matches: 105, Mismatches: 21, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
39 101 0.96
40 4 0.04
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.35
Consensus pattern (39 bp):
TGGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGC
Found at i:12474207 original size:70 final size:71
Alignment explanation
Indices: 12473984--12474371 Score: 373
Period size: 70 Copynumber: 5.6 Consensus size: 71
12473974 TAATTAGAAA
* * * * * ** * * *
12473984 AGTTAAAAGCTCTCAACTGTCATTCTAAGGCTCGCAGGTCTAATCT-ATG-GCCACCAAACAGTT
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCGCAGGTTTAATATCGCGAGCCTCTAAATAGTT
12474047 AGCGAG
66 AGCGAG
* * * * *
12474053 AGTTAGAAGCTCCCAACTATCATTTTAAGGCTTGCAAGTTTAATA-CTGCGA-CCTCTATAA-A-
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCGCAGGTTTAATATC-GCGAGCCTCTA-AATAG
*
12474114 TTAGTGAG
64 TTAGCGAG
* *
12474122 AGTTAAAAGCTCCCAGCTATCATTCTAAGGTTCGCAGGTTCAATATCGCGA-CCTCTAAATAGTT
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCGCAGGTTTAATATCGCGAGCCTCTAAATAGTT
**
12474186 AGTTAG
66 AGCGAG
* * *
12474192 AGTTAAAAGCTCCCAGCTTTCATTTTAAGGCTCGCAGGTTTAATACCGC-AGCCTCTAAATAGTT
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCGCAGGTTTAATATCGCGAGCCTCTAAATAGTT
*
12474256 AGCGAT
66 AGCGAG
* * * * * *
12474262 AGTTAAAAGCTCCCAGCTGTCATTGTAAGGGTCACAGGTTTAATATCG-TAGCCT-TCAAACAGT
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCGCAGGTTTAATATCGCGAGCCTCT-AAATAGT
*
12474325 TAGCAAG
65 TAGCGAG
* * *
12474332 AGTTAAAAGCTCTCAACTATCATTCTAAGGCTCGTAGGTT
1 AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCGCAGGTT
12474372 CGATACCATA
Statistics
Matches: 265, Mismatches: 44, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
68 2 0.01
69 95 0.36
70 166 0.63
71 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (71 bp):
AGTTAAAAGCTCCCAGCTATCATTCTAAGGCTCGCAGGTTTAATATCGCGAGCCTCTAAATAGTT
AGCGAG
Found at i:12474378 original size:140 final size:138
Alignment explanation
Indices: 12473984--12474371 Score: 424
Period size: 140 Copynumber: 2.8 Consensus size: 138
12473974 TAATTAGAAA
* * * * * * *
12473984 AGTTAAAAGCTCTCAACTGTCATTCTAAGGCTCGCAGGTCTAATCT-ATGGCCACCAAACAGTTA
1 AGTTAAAAGCTCCCAGCTGTCATTCTAAGGCTCGCAGGTTTAATATCGTAGCC-TCAAACAGTTA
* * * * *
12474048 GCGAGAGTTAGAAGCTCCCAACTATCATTTTAAGGCTTGCAAGTTTAATACTGCGACCTCTATAA
65 GCAAGAGTTAAAAGCTCCCAACTATCATTTTAAGGCTCGCAGGTTTAATACCGCGACCTCTATAA
*
12474113 ATTAGTGAG
130 ATTAGCGAG
* * * * *
12474122 AGTTAAAAGCTCCCAGCTATCATTCTAAGGTTCGCAGGTTCAATATCG-CGACCTCTAAATAGTT
1 AGTTAAAAGCTCCCAGCTGTCATTCTAAGGCTCGCAGGTTTAATATCGTAG-CCTC-AAACAGTT
** * *
12474186 AGTTAGAGTTAAAAGCTCCCAGCTTTCATTTTAAGGCTCGCAGGTTTAATACCGC-AGCCTCTA-
64 AGCAAGAGTTAAAAGCTCCCAACTATCATTTTAAGGCTCGCAGGTTTAATACCGCGA-CCTCTAT
*
12474249 AATAGTTAGCGAT
128 AA-A-TTAGCGAG
* * *
12474262 AGTTAAAAGCTCCCAGCTGTCATTGTAAGGGTCACAGGTTTAATATCGTAGCCTTCAAACAGTTA
1 AGTTAAAAGCTCCCAGCTGTCATTCTAAGGCTCGCAGGTTTAATATCGTAGCC-TCAAACAGTTA
* * *
12474327 GCAAGAGTTAAAAGCTCTCAACTATCATTCTAAGGCTCGTAGGTT
65 GCAAGAGTTAAAAGCTCCCAACTATCATTTTAAGGCTCGCAGGTT
12474372 CGATACCATA
Statistics
Matches: 207, Mismatches: 35, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
138 44 0.21
139 63 0.30
140 97 0.47
141 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (138 bp):
AGTTAAAAGCTCCCAGCTGTCATTCTAAGGCTCGCAGGTTTAATATCGTAGCCTCAAACAGTTAG
CAAGAGTTAAAAGCTCCCAACTATCATTTTAAGGCTCGCAGGTTTAATACCGCGACCTCTATAAA
TTAGCGAG
Found at i:12474384 original size:70 final size:70
Alignment explanation
Indices: 12473939--12474409 Score: 327
Period size: 70 Copynumber: 6.8 Consensus size: 70
12473929 TTTATTAAAA
* * * * * * * * * * *
12473939 CTAAGGCTTGCAAGTTTAACACCATAACCTTCAAATAATTAG-AAAAGTTAAAAGCTCTCAACTG
1 CTAAGGCTCGCAGGTTCAATACCATAGCCTTCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTA
12474003 TCATT
66 TCATT
* * ** *
12474008 CTAAGGCTCGCAGG-TCTAAT-CTATGGCCACCAAACAGTTAGCGAGAGTTAGAAGCTCCCAACT
1 CTAAGGCTCGCAGGTTC-AATACCATAGCCTTCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACT
12474071 ATCATT
65 ATCATT
* * * * * *
12474077 TTAAGGCTTGCAAGTTTAATA-C-T-GCGACCTCTATAA-A-TTAGTGAGAGTTAAAAGCTCCCA
1 CTAAGGCTCGCAGGTTCAATACCATAGC--CTTC-A-AACAGTTAGCGAGAGTTAAAAGCTCCCA
*
12474137 GCTATCATT
62 ACTATCATT
* * * ** *
12474146 CTAAGGTTCGCAGGTTCAATATCGC-GA-CC-TCTAAATAGTTAGTTAGAGTTAAAAGCTCCCAG
1 CTAAGGCTCGCAGGTTCAATA-C-CATAGCCTTC-AAACAGTTAGCGAGAGTTAAAAGCTCCCAA
*
12474208 CTTTCATT
63 CTATCATT
* * ** * * *
12474216 TTAAGGCTCGCAGGTTTAATACCGCAGCC-TCTAAATAGTTAGCGATAGTTAAAAGCTCCCAGCT
1 CTAAGGCTCGCAGGTTCAATACCATAGCCTTC-AAACAGTTAGCGAGAGTTAAAAGCTCCCAACT
*
12474280 GTCATT
65 ATCATT
* * * * * * * *
12474286 GTAAGGGTCACAGGTTTAATATCGTAGCCTTCAAACAGTTAGCAAGAGTTAAAAGCTCTCAACTA
1 CTAAGGCTCGCAGGTTCAATACCATAGCCTTCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTA
12474351 TCATT
66 TCATT
* * *
12474356 CTAAGGCTCGTAGGTTCGATACCATAGCCTTCAAACAGTTAGCGCGAGCTTAAA
1 CTAAGGCTCGCAGGTTCAATACCATAGCCTTCAAACAGTTAGCGAGAG-TTAAA
12474410 CTCCCGACTG
Statistics
Matches: 321, Mismatches: 63, Indels: 34
0.77 0.15 0.08
Matches are distributed among these distances:
67 2 0.01
68 19 0.06
69 104 0.32
70 185 0.58
71 9 0.03
72 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (70 bp):
CTAAGGCTCGCAGGTTCAATACCATAGCCTTCAAACAGTTAGCGAGAGTTAAAAGCTCCCAACTA
TCATT
Found at i:12474621 original size:18 final size:18
Alignment explanation
Indices: 12474578--12474624 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
12474568 CTTATGTCTA
* *
12474578 AAATTTTGCTTGAGTTTG
1 AAATTTTACTTGAGTTTC
* *
12474596 AAAGTTTACTTTAGTTTC
1 AAATTTTACTTGAGTTTC
12474614 AAATTTTACTT
1 AAATTTTACTT
12474625 AAGTCAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.51
Consensus pattern (18 bp):
AAATTTTACTTGAGTTTC
Found at i:12477633 original size:20 final size:20
Alignment explanation
Indices: 12477608--12477650 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12477598 TCATAAGAAT
12477608 AGTGGGGTCAAGTCATGAAC
1 AGTGGGGTCAAGTCATGAAC
* * *
12477628 AGTGGGGTTATGTCGTGAAC
1 AGTGGGGTCAAGTCATGAAC
12477648 AGT
1 AGT
12477651 AATAGTATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.37, T:0.26
Consensus pattern (20 bp):
AGTGGGGTCAAGTCATGAAC
Found at i:12477887 original size:11 final size:11
Alignment explanation
Indices: 12477871--12477898 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12477861 TAATGAATGG
12477871 GAAAAAGAAAA
1 GAAAAAGAAAA
12477882 GAAAAAGAAAA
1 GAAAAAGAAAA
12477893 GAAAAA
1 GAAAAA
12477899 CGCTACGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:12478914 original size:16 final size:16
Alignment explanation
Indices: 12478893--12478924 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12478883 CATACCTTAT
12478893 ATCCAAGTTGATCTAA
1 ATCCAAGTTGATCTAA
12478909 ATCCAAGTTGATCTAA
1 ATCCAAGTTGATCTAA
12478925 CAGTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
ATCCAAGTTGATCTAA
Found at i:12485679 original size:40 final size:41
Alignment explanation
Indices: 12485527--12485683 Score: 226
Period size: 41 Copynumber: 3.9 Consensus size: 41
12485517 TTTCTACCTT
12485527 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * *
12485568 TCAGATCTTTCGCAGCGTTTTTAAAAAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
** *
12485609 TCAGATCTTTAGCGGCGTTTTCCAAGAAGCGCCGCTAATGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
** *
12485650 TC-GGGCTTTAGCGGCATTTTTGAAAAAGCGCCGC
1 TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
12485684 AAAAACATTT
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 26 0.25
41 76 0.75
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (41 bp):
TCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:12485795 original size:26 final size:27
Alignment explanation
Indices: 12485750--12485801 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
12485740 AAAATGGATA
** *
12485750 AATTTGAAATAATGACACATA-AAAAT
1 AATTTGAAATAAAAAAACATAGAAAAT
12485776 AATTTGAAATAAAAAAACATAGAAAA
1 AATTTGAAATAAAAAAACATAGAAAA
12485802 ATATTTGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.23
Consensus pattern (27 bp):
AATTTGAAATAAAAAAACATAGAAAAT
Found at i:12486120 original size:21 final size:22
Alignment explanation
Indices: 12486096--12486140 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
12486086 GGGATTCTGA
* *
12486096 TTTAAGGGTTGTGA-TTTAAGG
1 TTTAAGGGTTATGAGTTAAAGG
*
12486117 TTTATGGGTTATGAGTTAAAGG
1 TTTAAGGGTTATGAGTTAAAGG
12486139 TT
1 TT
12486141 AGAGGTTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.44
Consensus pattern (22 bp):
TTTAAGGGTTATGAGTTAAAGG
Found at i:12486334 original size:22 final size:22
Alignment explanation
Indices: 12486309--12486360 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
12486299 TATTAAAAAA
* *
12486309 GGTTTAGAGGTTAGTGGTTTGG
1 GGTTTAGAGGTTAGTGATTTAG
*
12486331 GGTTAAGA-GTTAGTGATTTAG
1 GGTTTAGAGGTTAGTGATTTAG
12486352 GGTTTAGAG
1 GGTTTAGAG
12486361 ATTCAGGGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.38
Consensus pattern (22 bp):
GGTTTAGAGGTTAGTGATTTAG
Found at i:12487197 original size:103 final size:105
Alignment explanation
Indices: 12487076--12487286 Score: 347
Period size: 105 Copynumber: 2.0 Consensus size: 105
12487066 TAGCGGCGTT
*
12487076 TTTTATAAAAACAGCGCAAAAGGTAAGCAATAGCGGCGTTTTAAT-AAAAAACG-CAAAAAAAAT
1 TTTTATAAAAACAGCGCAAAAGGTAAGCAATAGCGCCGTTTTAATAAAAAAACGCCAAAAAAAAT
* *
12487139 AATTTTACTTTAAAAAATAGTCATTTTATATAGCAAAATA
66 AATTTTACTTTAAAAAATAGCCATTTTATATAGCAAAACA
* *
12487179 TTTTATAAAAAC-GCCGCAAAAGGTAAGCAATAGCGCCGTTTTTATAAAAAAACGCCACAAAAAA
1 TTTTATAAAAACAG-CGCAAAAGGTAAGCAATAGCGCCGTTTTAATAAAAAAACGCCAAAAAAAA
12487243 TAATTTTACTTTAAAAAATAGCCATTTTATATAGCAAAACA
65 TAATTTTACTTTAAAAAATAGCCATTTTATATAGCAAAACA
12487284 TTT
1 TTT
12487287 AGTGGCGTTT
Statistics
Matches: 100, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
102 1 0.01
103 41 0.41
104 8 0.08
105 50 0.50
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.28
Consensus pattern (105 bp):
TTTTATAAAAACAGCGCAAAAGGTAAGCAATAGCGCCGTTTTAATAAAAAAACGCCAAAAAAAAT
AATTTTACTTTAAAAAATAGCCATTTTATATAGCAAAACA
Found at i:12487296 original size:77 final size:77
Alignment explanation
Indices: 12487209--12487435 Score: 418
Period size: 77 Copynumber: 2.9 Consensus size: 77
12487199 AGGTAAGCAA
* *
12487209 TAGCGCCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGCCATTTTATA
1 TAGCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
12487274 TAGCAAAACATT
66 TAGCAAAACATT
*
12487286 TAGTGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
1 TAGCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
*
12487351 TAGAAAAACATT
66 TAGCAAAACATT
12487363 TAGCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
1 TAGCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
12487428 TAGCAAAA
66 TAGCAAAA
12487436 TATTATAAAA
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 144 1.00
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (77 bp):
TAGCGGCGTTTTTATAAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAATAGTCATTTTATA
TAGCAAAACATT
Found at i:12487552 original size:74 final size:74
Alignment explanation
Indices: 12487466--12487605 Score: 178
Period size: 74 Copynumber: 1.9 Consensus size: 74
12487456 AGGTAAGCAA
* * *
12487466 TAGCGGCGTTTTTGTAAAAAACGCCAC--AAAATATAATTTTACTTTAAAAAATA-GCCATTTTA
1 TAGCGGCATTTTTATAAAAAACGCCACAGAAAAT-TAATTTTA--TAAAAAAATACGCCATTTTA
12487528 TAACAAAACATT
63 TAACAAAACATT
* *
12487540 TAGCGGCATTTTTATGAAAAATGCCACAGAAAATTAATTTTATAAAAAAATAGCGCCATTTTATA
1 TAGCGGCATTTTTATAAAAAACGCCACAGAAAATTAATTTTATAAAAAAATA-CGCCATTTTATA
12487605 A
65 A
12487606 AATCTCCTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
73 9 0.16
74 23 0.40
75 20 0.35
76 5 0.09
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (74 bp):
TAGCGGCATTTTTATAAAAAACGCCACAGAAAATTAATTTTATAAAAAAATACGCCATTTTATAA
CAAAACATT
Found at i:12490059 original size:42 final size:43
Alignment explanation
Indices: 12489938--12490206 Score: 355
Period size: 43 Copynumber: 6.3 Consensus size: 43
12489928 AGGTTATGTT
* * * * *
12489938 TTTAGTGGCGTTTCTGTGCAAAGCGCCGCTAAAGGTCAT-GGTC
1 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTC-TCGGCC
* *
12489981 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTCGGCC
1 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTCGGCC
* *
12490024 TTTAGCGGCTTTTTTGGG-AAAGCGCCGCTGAAGGTCTCGGCC
1 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTCGGCC
* *
12490066 TTTAGCAGCGTTTTTGGG-AAAGCGCCGCTGAAGGTCTCGGCC
1 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTCGGCC
* *
12490108 TTTAGCGGCGTTTTTGGGAAAAGCACCGCTGAAGGTCTCGGCC
1 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTCGGCC
* * * *
12490151 TTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTCGGCC
12490194 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
12490207 GTGGTAAAGA
Statistics
Matches: 204, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 80 0.39
43 124 0.61
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTCGGCC
Found at i:12490069 original size:85 final size:86
Alignment explanation
Indices: 12489938--12490206 Score: 366
Period size: 85 Copynumber: 3.2 Consensus size: 86
12489928 AGGTTATGTT
* * * * * *
12489938 TTTAGTGGCGTTTCTGTGCAAAGCGCCGCTAAAGGTCAT-GGTCTTTAGCGGCGTTTGTGGGAAA
1 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTGAAGGTC-TCGGCCTTTAGCGGCGTTTGTGGGAAA
12490002 AGCACCGCTAAAGGTCTCGGCC
65 AGCACCGCTAAAGGTCTCGGCC
* * *
12490024 TTTAGCGGCTTTTTTGGG-AAAGCGCCGCTGAAGGTCTCGGCCTTTAGCAGCGTTTTTGGG-AAA
1 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTGAAGGTCTCGGCCTTTAGCGGCGTTTGTGGGAAAA
* *
12490087 GCGCCGCTGAAGGTCTCGGCC
66 GCACCGCTAAAGGTCTCGGCC
*
12490108 TTTAGCGGCGTTTTTGGGAAAAGCACCGCTGAAGGTCTCGGCCTTTAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTGAAGGTCTCGGCCTTTAGCGGCGTTTGTGGGAAAA
* *
12490173 GCGA-CGCTAAAGGTCTTGGTC
66 GC-ACCGCTAAAGGTCTCGGCC
12490194 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
12490207 GTGGTAAAGA
Statistics
Matches: 161, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
84 40 0.25
85 75 0.47
86 46 0.29
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.28
Consensus pattern (86 bp):
TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTGAAGGTCTCGGCCTTTAGCGGCGTTTGTGGGAAAA
GCACCGCTAAAGGTCTCGGCC
Found at i:12490421 original size:43 final size:43
Alignment explanation
Indices: 12490368--12490615 Score: 338
Period size: 43 Copynumber: 5.8 Consensus size: 43
12490358 AGATAAAAAT
** *
12490368 GCCGCTAAAGACCGTGACCTTTAGCGGCGCTTTTCTCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
*
12490411 GCCGCTAAAGACCAAGACCTTTAGCGGCGCATTTCCCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
*
12490454 GCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
* ** * *
12490497 GCTGCTAAAGACCAAGACCTTTAGCGATGATTTTCCTACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
*** *
12490540 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTATAACAATC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
*
12490583 GCCGCTATAGACCATA-A-CTTTAGCGGCGCTTTT
1 GCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTT
12490616 ATTAAAAACT
Statistics
Matches: 185, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
42 16 0.09
43 168 0.91
44 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:12495758 original size:41 final size:41
Alignment explanation
Indices: 12495669--12495823 Score: 229
Period size: 41 Copynumber: 3.8 Consensus size: 41
12495659 TTCTTTGCGA
* *
12495669 CGCTTCTTTAAAAACGCCGCATAAAAGCCCGAGAATTAGCGG
1 CGCTTCTTTAAAAACGCCGC-TAAAGGCCCGAGCATTAGCGG
*
12495711 CGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCATTAGTGG
1 CGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
* * *
12495752 CACTTCTTTAAAAACACCGCTAAAGGCCCAAGCATTAGCGG
1 CGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
* *
12495793 CGCTTCTTAAAAAACGCCGCTAAAGCCCCGA
1 CGCTTCTTTAAAAACGCCGCTAAAGGCCCGA
12495824 AAACTCAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
41 81 0.80
42 20 0.20
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (41 bp):
CGCTTCTTTAAAAACGCCGCTAAAGGCCCGAGCATTAGCGG
Found at i:12495923 original size:39 final size:39
Alignment explanation
Indices: 12495875--12495990 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 39
12495865 GCACTTTTTG
*
12495875 GAAAACGCCGCTAATGCTCATTTTTAGCGGCGTTTTCCT
1 GAAAGCGCCGCTAATGCTCATTTTTAGCGGCGTTTTCCT
* * * *
12495914 GAAAGCGCCGCTAATACTCGATCTTTAGTGGCGTTTTCTT
1 GAAAGCGCCGCTAATGCTC-ATTTTTAGCGGCGTTTTCCT
* * * * *
12495954 AAAAGCGCCGGTAATGTTTAATTTTTAGCGGCATTTT
1 GAAAGCGCCGCTAATG-CTCATTTTTAGCGGCGTTTT
12495991 TTATCCAAAC
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
39 17 0.27
40 44 0.71
41 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (39 bp):
GAAAGCGCCGCTAATGCTCATTTTTAGCGGCGTTTTCCT
Found at i:12497654 original size:13 final size:13
Alignment explanation
Indices: 12497636--12497661 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12497626 CGCAAACGAT
12497636 AAAAATTTTCACA
1 AAAAATTTTCACA
12497649 AAAAATTTTCACA
1 AAAAATTTTCACA
12497662 CATATAAATT
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTTTCACA
Found at i:12498421 original size:124 final size:125
Alignment explanation
Indices: 12498124--12498515 Score: 520
Period size: 126 Copynumber: 3.1 Consensus size: 125
12498114 GTCAAGCAAA
*
12498124 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAACTTTTTTCAGTAATTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* ** * *
12498189 TGTTTGAAGTGTTTTTTACACTATTTTTTTAAAACCGTCTTC-TAAAATTTATTTTTTCAAG
66 TGCTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTTAAAA-TTA-TTTTTCAAG
* * * * *
12498250 AACTACTGCAGAAAAAGAGGGTCCACGTGGGAGCTTTTTTCAATAATTCTGTTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * *
12498315 TGCTTGAAG-AATTTTGAAACTATTTTTTTAGAATCGTCTTCTTAAAATTATTTTTCAAG
66 TGCTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTTAAAATTATTTTTCAAG
* * * * * *
12498374 AACTACTATAGAAAAGGAGTGTCCACATGGGAGCTTTTTTTAGTAATTTTGCTAACAGTGCATCC
1 AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * *
12498439 TGCTTGAAGCATTTTTGACATTATTTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCTAA-
66 TGCTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTTAAAATT-ATTTTTC-AAG
12498500 AACTACTGTAGAAAAA
1 AACTACTGTAGAAAAA
12498516 AACAAAATCC
Statistics
Matches: 231, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
124 73 0.32
125 63 0.27
126 93 0.40
127 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (125 bp):
AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCC
TGCTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTTAAAATTATTTTTCAAG
Found at i:12498617 original size:34 final size:33
Alignment explanation
Indices: 12498576--12498690 Score: 140
Period size: 34 Copynumber: 3.4 Consensus size: 33
12498566 CACAAATTTA
12498576 TTTTTAAAAAAACTAAACCCTAATTTAATTAAT
1 TTTTTAAAAAAACTAAACCCTAATTTAATTAAT
*** *
12498609 TTTCTTAAAAACTTTAAACCCTAATTTAATTTAT
1 TTT-TTAAAAAAACTAAACCCTAATTTAATTAAT
*** *
12498643 TTATTTAAAACCCCTAAAACCTAATTTAATTAAT
1 TT-TTTAAAAAAACTAAACCCTAATTTAATTAAT
12498677 TTTTTAAAAAAACT
1 TTTTTAAAAAAACT
12498691 TTAAACCTTG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 12 0.18
34 55 0.81
35 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (33 bp):
TTTTTAAAAAAACTAAACCCTAATTTAATTAAT
Found at i:12498632 original size:68 final size:68
Alignment explanation
Indices: 12498567--12498697 Score: 160
Period size: 68 Copynumber: 1.9 Consensus size: 68
12498557 TAACCTAAAC
*
12498567 ACAAATTTA-TT-TTTAAAAAAACTAAACCCTAATTTAATTAATTTTCTT-AAAAACTTTAAACC
1 ACAAATTTATTTATTTAAAAAAACTAAAACCTAATTTAATTAATTTT-TTAAAAAACTTTAAACC
12498629 CTAA
65 CTAA
*** ***
12498633 TTTAATTTATTTATTTAAAACCCCTAAAACCTAATTTAATTAATTTTTTAAAAAAACTTTAAACC
1 ACAAATTTATTTATTTAAAAAAACTAAAACCTAATTTAATTAATTTTTT-AAAAAACTTTAAACC
12498698 TTGATTTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
66 6 0.11
67 4 0.07
68 30 0.56
69 14 0.26
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (68 bp):
ACAAATTTATTTATTTAAAAAAACTAAAACCTAATTTAATTAATTTTTTAAAAAACTTTAAACCC
TAA
Found at i:12498698 original size:34 final size:34
Alignment explanation
Indices: 12498570--12498697 Score: 138
Period size: 34 Copynumber: 3.8 Consensus size: 34
12498560 CCTAAACACA
* *
12498570 AATTTATTTTTAAAAAAAC--TAAACCCTAATTT
1 AATTAATTTTTTAAAAAACTTTAAACCCTAATTT
12498602 AATTAATTTTCTT-AAAAACTTTAAACCCTAATTT
1 AATTAATTTT-TTAAAAAACTTTAAACCCTAATTT
* * ** *
12498636 AATTTATTTATTT-AAAACCCCTAAAACCTAATTT
1 AATTAATTT-TTTAAAAAACTTTAAACCCTAATTT
12498670 AATTAATTTTTTAAAAAAACTTTAAACC
1 AATTAATTTTTT-AAAAAACTTTAAACC
12498698 TTGATTTATT
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
32 15 0.19
33 4 0.05
34 48 0.62
35 11 0.14
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (34 bp):
AATTAATTTTTTAAAAAACTTTAAACCCTAATTT
Found at i:12500524 original size:21 final size:21
Alignment explanation
Indices: 12500486--12500525 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12500476 GTCAAGGATG
* *
12500486 CTCAATTTCATGATACCTAGT
1 CTCAATGTCATGACACCTAGT
*
12500507 CTCAATGTCGTGACACCTA
1 CTCAATGTCATGACACCTA
12500526 CATCAAATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (21 bp):
CTCAATGTCATGACACCTAGT
Found at i:12513507 original size:21 final size:21
Alignment explanation
Indices: 12513482--12513523 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12513472 ATTATCAGTG
12513482 CAAAAGCAACCAA-AACACCAA
1 CAAAAGCAACCAAGAA-ACCAA
*
12513503 CAAAAGCACCCAAGAAACCAA
1 CAAAAGCAACCAAGAAACCAA
12513524 ATACCAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.60, C:0.33, G:0.07, T:0.00
Consensus pattern (21 bp):
CAAAAGCAACCAAGAAACCAA
Found at i:12514187 original size:3 final size:3
Alignment explanation
Indices: 12514179--12514211 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
12514169 AAAGGGGGAT
12514179 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
12514212 AAGGTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12515937 original size:22 final size:22
Alignment explanation
Indices: 12515909--12515954 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
12515899 TACACTACTA
*
12515909 AGAGTTTAAGTGGGAAAAAAAT
1 AGAGTTTAACTGGGAAAAAAAT
* *
12515931 AGAGTTTAACTGGGAGAAGAAT
1 AGAGTTTAACTGGGAAAAAAAT
12515953 AG
1 AG
12515955 CTAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (22 bp):
AGAGTTTAACTGGGAAAAAAAT
Found at i:12518403 original size:21 final size:20
Alignment explanation
Indices: 12518377--12518426 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
12518367 TAAATGTGTA
*
12518377 TTTATTTTTTTCCTAGTTTT
1 TTTATTTTTTTCCTAATTTT
**
12518397 TCTTATTTATTTTTTTAATTTT
1 T-TTATTT-TTTTCCTAATTTT
12518419 TTTATTTT
1 TTTATTTT
12518427 AATAGTAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 2 0.08
21 12 0.48
22 11 0.44
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTATTTTTTTCCTAATTTT
Done.