Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 14 of 105
Found at i:2750680 original size:19 final size:19
Alignment explanation
Indices: 2750657--2750699 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2750647 TAAAAATATT
2750657 AATTATTATAAT-AAATTAA
1 AATTA-TATAATAAAATTAA
*
2750676 TATTATATAATAAAATTAA
1 AATTATATAATAAAATTAA
2750695 AATTA
1 AATTA
2750700 ATGGTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTATATAATAAAATTAA
Found at i:2752696 original size:40 final size:39
Alignment explanation
Indices: 2752619--2752699 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
2752609 AACTTGGGAG
* *
2752619 ATATAATGAGATTTAGCAACATATTTTCAATCGTTGCAA
1 ATATAATGAGATTTAGCAACATATTTACAATCATTGCAA
* *
2752658 ATATAATGAGATCTTA-CAATGATATTTACAGTCATTGCAA
1 ATATAATGAGAT-TTAGCAA-CATATTTACAATCATTGCAA
2752698 AT
1 AT
2752700 TGTAATTGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (39 bp):
ATATAATGAGATTTAGCAACATATTTACAATCATTGCAA
Found at i:2754310 original size:20 final size:19
Alignment explanation
Indices: 2754287--2754329 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
2754277 TGAAAAACAC
2754287 TATAAAGAAA-TAAAGTATTT
1 TATAAA-AAAGTAAA-TATTT
*
2754307 TATAAAAAAGTTAATATTT
1 TATAAAAAAGTAAATATTT
2754326 TATA
1 TATA
2754330 CATTATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (19 bp):
TATAAAAAAGTAAATATTT
Found at i:2755287 original size:17 final size:18
Alignment explanation
Indices: 2755255--2755296 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2755245 TTTATTTATT
*
2755255 ATATAATAAATATAATTAA
1 ATATATTAAATATAA-TAA
2755274 AT-TATTAAAT-TAATAA
1 ATATATTAAATATAATAA
2755290 ATATATT
1 ATATATT
2755297 CATTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 7 0.33
19 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATATTAAATATAATAA
Found at i:2755303 original size:25 final size:24
Alignment explanation
Indices: 2755240--2755306 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
2755230 AAAACATAGT
* *
2755240 AATAT-TTTATTTATTATATAATA
1 AATATATTAATTTATTAAATAATA
*
2755263 AATATAATTAAATTATTAAATTAATA
1 AATAT-ATTAATTTATTAAA-TAATA
*
2755289 AATATATTCATTTATTAA
1 AATATATTAATTTATTAA
2755307 GTCAACTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 5 0.14
25 21 0.58
26 10 0.28
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
AATATATTAATTTATTAAATAATA
Found at i:2768467 original size:15 final size:16
Alignment explanation
Indices: 2768448--2768493 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
2768438 AATTAAAAAA
2768448 AAAAAAACAAAATAAT
1 AAAAAAACAAAATAAT
*
2768464 AAAAAAACAGAA-AAT
1 AAAAAAACAAAATAAT
**
2768479 AAAACCACAAAATAA
1 AAAAAAACAAAATAA
2768494 AAAGGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.78, C:0.11, G:0.02, T:0.09
Consensus pattern (16 bp):
AAAAAAACAAAATAAT
Found at i:2768469 original size:18 final size:18
Alignment explanation
Indices: 2768446--2768480 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2768436 AAAATTAAAA
2768446 AAAAAAAAACAAAATAAT
1 AAAAAAAAACAAAATAAT
* *
2768464 AAAAAAACAGAAAATAA
1 AAAAAAAAACAAAATAA
2768481 AACCACAAAA
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:0.83, C:0.06, G:0.03, T:0.09
Consensus pattern (18 bp):
AAAAAAAAACAAAATAAT
Found at i:2769837 original size:3 final size:3
Alignment explanation
Indices: 2769829--2769859 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2769819 TATAATTTTG
2769829 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2769860 AAATAAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2774440 original size:2 final size:2
Alignment explanation
Indices: 2774435--2774463 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2774425 TATATTGTTT
2774435 TA TA 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 TA TA T
2774464 GCAAACAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2777471 original size:23 final size:22
Alignment explanation
Indices: 2777445--2777489 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
2777435 ATAAATCTAG
2777445 AAAGTAGTTAAGATTATGGATTA
1 AAAGTAGTTAAGATTAT-GATTA
2777468 AAAGTAGTTAAGATTATGATTA
1 AAAGTAGTTAAGATTATGATTA
2777490 TGGAAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (22 bp):
AAAGTAGTTAAGATTATGATTA
Found at i:2778029 original size:2 final size:2
Alignment explanation
Indices: 2778022--2778049 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2778012 AATCATTTGA
2778022 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
2778050 TTAATGGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2778516 original size:2 final size:2
Alignment explanation
Indices: 2778509--2778543 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2778499 TTTAAGCTTT
2778509 TA TA TA TA TA 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 TA TA TA TA TA T
2778544 TGAAGTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2779951 original size:21 final size:22
Alignment explanation
Indices: 2779918--2779958 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2779908 TTTGAAGTTG
*
2779918 TTAAAATTTAAAATTTTAATTA
1 TTAAAATTTAAAAATTTAATTA
2779940 TTAAAA-TTAAAAATTTAAT
1 TTAAAATTTAAAAATTTAAT
2779959 ACTCTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAATTTAAAAATTTAATTA
Found at i:2781628 original size:16 final size:16
Alignment explanation
Indices: 2781586--2781717 Score: 124
Period size: 16 Copynumber: 8.2 Consensus size: 16
2781576 TAAGTTTCTA
* *
2781586 AAACCCCTAAAAATTCA
1 AAACCCCT-AAAATCCG
2781603 AAATCCCCTAAAATCCG
1 AAA-CCCCTAAAATCCG
*
2781620 AAACCCCTAAAATTC-
1 AAACCCCTAAAATCCG
**
2781635 AAAATCCTAAAATCCG
1 AAACCCCTAAAATCCG
* *
2781651 AAACCCCTAAAATTCA
1 AAACCCCTAAAATCCG
* * *
2781667 AAATCTCTTAAATCC-
1 AAACCCCTAAAATCCG
*
2781682 AAACCCCTAAAATCCT
1 AAACCCCTAAAATCCG
2781698 AAACCCCATAAAATCCG
1 AAACCCC-TAAAATCCG
2781715 AAA
1 AAA
2781718 TTCCAAACCT
Statistics
Matches: 93, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
15 24 0.26
16 41 0.44
17 23 0.25
18 5 0.05
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (16 bp):
AAACCCCTAAAATCCG
Found at i:2781647 original size:31 final size:31
Alignment explanation
Indices: 2781586--2781717 Score: 167
Period size: 31 Copynumber: 4.1 Consensus size: 31
2781576 TAAGTTTCTA
2781586 AAACCCCTAAAAATTCAAAATCCCCTAAAATCCG
1 AAACCCCT-AAAATTCAAAAT--CCTAAAATCCG
2781620 AAACCCCTAAAATTCAAAATCCTAAAATCCG
1 AAACCCCTAAAATTCAAAATCCTAAAATCCG
*
2781651 AAACCCCTAAAATTCAAAATCTCTTAAATCC-
1 AAACCCCTAAAATTCAAAATC-CTAAAATCCG
* **
2781682 AAACCCCTAAAATCCTAAACCCCATAAAATCCG
1 AAACCCCTAAAATTC-AAAATCC-TAAAATCCG
2781715 AAA
1 AAA
2781718 TTCCAAACCT
Statistics
Matches: 89, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
31 47 0.53
32 19 0.21
33 15 0.17
34 8 0.09
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (31 bp):
AAACCCCTAAAATTCAAAATCCTAAAATCCG
Found at i:2781661 original size:47 final size:47
Alignment explanation
Indices: 2781607--2781717 Score: 132
Period size: 47 Copynumber: 2.3 Consensus size: 47
2781597 AATTCAAAAT
* *
2781607 CCCCTAAAATCCGAAACCCCTAAAATTCAAAATCCTAAAATCCGAAA
1 CCCCTAAAATCCGAAACCCCTAAAATCCAAAACCCTAAAATCCGAAA
* * * * * * *
2781654 CCCCTAAAATTCAAAATCTCTTAAATCCAAACCCCTAAAATCCTAAA
1 CCCCTAAAATCCGAAACCCCTAAAATCCAAAACCCTAAAATCCGAAA
2781701 CCCCATAAAATCCGAAA
1 CCCC-TAAAATCCGAAA
2781718 TTCCAAACCT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
47 42 0.81
48 10 0.19
ACGTcount: A:0.46, C:0.32, G:0.03, T:0.19
Consensus pattern (47 bp):
CCCCTAAAATCCGAAACCCCTAAAATCCAAAACCCTAAAATCCGAAA
Found at i:2781696 original size:15 final size:15
Alignment explanation
Indices: 2781586--2781779 Score: 115
Period size: 15 Copynumber: 12.5 Consensus size: 15
2781576 TAAGTTTCTA
*
2781586 AAACCCCTAAAAATTCA
1 AAACCCCT-AAAA-TCC
2781603 AAATCCCCTAAAATCC
1 AAA-CCCCTAAAATCC
*
2781619 GAAACCCCTAAAATTC
1 -AAACCCCTAAAATCC
**
2781635 AAAATCCTAAAATCC
1 AAACCCCTAAAATCC
*
2781650 GAAACCCCTAAAATTCA
1 -AAACCCCTAAAA-TCC
* * *
2781667 AAATCTCTTAAATCC
1 AAACCCCTAAAATCC
2781682 AAACCCCTAAAATCC
1 AAACCCCTAAAATCC
2781697 TAAACCCCATAAAATCC
1 -AAACCCC-TAAAATCC
** * **
2781714 GAAATTCC-AAACCTTT
1 -AAACCCCTAAA-ATCC
* *
2781730 AAA-CTCTTAAATCC
1 AAACCCCTAAAATCC
*
2781744 AAACCCCTAAAATCT
1 AAACCCCTAAAATCC
* *
2781759 AAA-CCCTTAAATCA
1 AAACCCCTAAAATCC
2781773 AAACCCC
1 AAACCCC
2781780 AAACCTCAAA
Statistics
Matches: 135, Mismatches: 32, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
14 17 0.13
15 48 0.36
16 40 0.30
17 25 0.19
18 5 0.04
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.21
Consensus pattern (15 bp):
AAACCCCTAAAATCC
Found at i:2781754 original size:14 final size:14
Alignment explanation
Indices: 2781737--2781779 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2781727 TTTAAACTCT
*
2781737 TAAATCCAAACCCC
1 TAAATCAAAACCCC
* *
2781751 TAAAATCTAAACCCT
1 T-AAATCAAAACCCC
2781766 TAAATCAAAACCCC
1 TAAATCAAAACCCC
2781780 AAACCTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAATCAAAACCCC
Found at i:2781798 original size:22 final size:23
Alignment explanation
Indices: 2781772--2781820 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2781762 CCCTTAAATC
2781772 AAAACCCCAAACCTC-AAATTTT
1 AAAACCCCAAACCTCAAAATTTT
*
2781794 AAAA-CCGAAACCTCAAAATTTT
1 AAAACCCCAAACCTCAAAATTTT
*
2781816 CAAAC
1 AAAAC
2781821 TCTAAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (23 bp):
AAAACCCCAAACCTCAAAATTTT
Found at i:2788890 original size:42 final size:42
Alignment explanation
Indices: 2788823--2788908 Score: 156
Period size: 42 Copynumber: 2.0 Consensus size: 42
2788813 GATTTCAAAA
2788823 GTAAACCTAATTGGATTAATACAGCTATA-TCACACAGACAG
1 GTAAACCTAATTGGATTAATACAGCTATATTCACACAGACAG
2788864 GTAAACCTAATTGGGATTAATACAGCTATATTCACACAGACAG
1 GTAAACCTAATT-GGATTAATACAGCTATATTCACACAGACAG
2788907 GT
1 GT
2788909 CATTTTACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 12 0.28
42 17 0.40
43 14 0.33
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (42 bp):
GTAAACCTAATTGGATTAATACAGCTATATTCACACAGACAG
Found at i:2794310 original size:19 final size:18
Alignment explanation
Indices: 2794269--2794317 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
2794259 TAATTTTCTA
* *
2794269 ATTTTTTTATATTATTAT
1 ATTTTTTTATTTTAGTAT
*
2794287 TTTTTTTTATTTTAAGTAT
1 ATTTTTTTATTTT-AGTAT
*
2794306 ATTTTTATATTT
1 ATTTTTTTATTT
2794318 ATGCATGATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTTATTTTAGTAT
Found at i:2794708 original size:35 final size:34
Alignment explanation
Indices: 2794642--2794713 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 34
2794632 TTCGTGTTTT
** * * * *
2794642 AATTAAACCCCATTCCCTAAAATCCATACCCTTA
1 AATTAAACCCCAAACCCCAAAACCCAAACCCTAA
2794676 AATTAAAACCCCAAACCCCAAAACCCAAACCCTAA
1 AATT-AAACCCCAAACCCCAAAACCCAAACCCTAA
2794711 AAT
1 AAT
2794714 CTCCAAACTC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
34 4 0.13
35 27 0.87
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (34 bp):
AATTAAACCCCAAACCCCAAAACCCAAACCCTAA
Found at i:2794721 original size:16 final size:15
Alignment explanation
Indices: 2794679--2794741 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 15
2794669 ACCCTTAAAT
*
2794679 TAAAACCCCAAACCC
1 TAAAATCCCAAACCC
*
2794694 CAAAA-CCCAAACCC
1 TAAAATCCCAAACCC
*
2794708 TAAAATCTCCAAACTC
1 TAAAATC-CCAAACCC
*
2794724 TAAAAT-CAAAACCC
1 TAAAATCCCAAACCC
2794738 TAAA
1 TAAA
2794742 CCTTCCATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 23 0.56
15 5 0.12
16 13 0.32
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.13
Consensus pattern (15 bp):
TAAAATCCCAAACCC
Found at i:2799905 original size:19 final size:17
Alignment explanation
Indices: 2799865--2799909 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2799855 ATTTAATTTG
2799865 TTATAATTTTTATTAAA
1 TTATAATTTTTATTAAA
*
2799882 ATATAATTTTTAATATAAA
1 TTATAATTTTT-AT-TAAA
2799901 TTAT-ATTTT
1 TTATAATTTT
2799910 AATTTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.42
18 7 0.29
19 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATAATTTTTATTAAA
Found at i:2801707 original size:72 final size:71
Alignment explanation
Indices: 2801443--2801732 Score: 364
Period size: 72 Copynumber: 4.0 Consensus size: 71
2801433 TATACCTTCA
* * * * *
2801443 CAAATTGGGAGTTACTTAAATTTGCCGGTATTGTACCTAAGCAACAACAATTTAGAGGGATACAT
1 CAAATTGGGAGTTGCTTAAATTTG-CGGAATTGGACCTAAGCAACAATAATTTAGAGGGGTACAT
2801508 CCCTCCT
65 CCCTCCT
* * *
2801515 AAAATTGGGAGTTGCTTAAATTTGCAGAGATTGGACCTAAGCAACAATAATTTAGAGGCGTACAT
1 CAAATTGGGAGTTGCTTAAATTTGCGGA-ATTGGACCTAAGCAACAATAATTTAGAGGGGTACAT
*
2801580 CCCTCCG
65 CCCTCCT
** *
2801587 CTTATTGGGAGTTGCTCAAATTTGCAGGAATTGGACCTAAGCAACAATAATTTAGAGGGGTACAT
1 CAAATTGGGAGTTGCTTAAATTTGC-GGAATTGGACCTAAGCAACAATAATTTAGAGGGGTACAT
**
2801652 CCCTTAT
65 CCCTCCT
* * * * * *
2801659 CAAATTGGGAGTTGCTTAAATTTGTCTGCATTGGACCTAAGTAGCAATAATTTAGAGGGGGAGAT
1 CAAATTGGGAGTTGCTTAAATTTG-CGGAATTGGACCTAAGCAACAATAATTTAGAGGGGTACAT
2801724 CCCTCCT
65 CCCTCCT
2801731 CA
1 CA
2801733 GATAGCCAAG
Statistics
Matches: 186, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
71 2 0.01
72 181 0.97
73 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (71 bp):
CAAATTGGGAGTTGCTTAAATTTGCGGAATTGGACCTAAGCAACAATAATTTAGAGGGGTACATC
CCTCCT
Found at i:2803871 original size:3 final size:3
Alignment explanation
Indices: 2803865--2803889 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2803855 TTTTTTTAAC
2803865 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2803890 TATTTAATTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2803921 original size:18 final size:17
Alignment explanation
Indices: 2803897--2803964 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 17
2803887 ATTTATTTAA
2803897 TTTTTTTCTTCTTTTTC
1 TTTTTTTCTTCTTTTTC
* *
2803914 TGTTTTTTATTTTTTTTC
1 T-TTTTTTCTTCTTTTTC
*
2803932 TCTCTTTT-TTCTTTCTTC
1 T-TTTTTTCTTCTTT-TTC
*
2803950 TTTCTTTCCTTCTTT
1 TTT-TTTTCTTCTTT
2803965 CTTTTTCCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
17 7 0.17
18 27 0.68
19 6 0.15
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (17 bp):
TTTTTTTCTTCTTTTTC
Found at i:2803940 original size:14 final size:14
Alignment explanation
Indices: 2803897--2803970 Score: 57
Period size: 15 Copynumber: 5.2 Consensus size: 14
2803887 ATTTATTTAA
2803897 TTTT-TTTCTTC-T
1 TTTTCTTTCTTCTT
2803909 TTTTCTGTT-TT-TT
1 TTTTCT-TTCTTCTT
*
2803922 ATTTTTTTTCTCTCTT
1 -TTTTCTTTCT-TCTT
2803938 TTTTCTTTCTTCTT
1 TTTTCTTTCTTCTT
*
2803952 TCTTTCCTTCTTTCTT
1 T-TTTCTTTC-TTCTT
2803968 TTT
1 TTT
2803971 CCTTATTCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
12 4 0.08
13 6 0.12
14 13 0.26
15 19 0.38
16 8 0.16
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTTCTTTCTTCTT
Found at i:2803946 original size:4 final size:4
Alignment explanation
Indices: 2803928--2803968 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
2803918 TTTTATTTTT
* *
2803928 TTTC TCTC TTT- TTTC TTTC -TTC TTTC TTTC CTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
2803969 TTCCTTATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
3 6 0.19
4 25 0.81
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:2803963 original size:12 final size:11
Alignment explanation
Indices: 2803928--2803968 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2803918 TTTTATTTTT
* *
2803928 TTTCTCTCTTT
1 TTTCTTTCTTC
2803939 TTTCTTTCTTC
1 TTTCTTTCTTC
2803950 TTTCTTTCCTTC
1 TTTCTTT-CTTC
2803962 TTTCTTT
1 TTTCTTT
2803969 TTCCTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTCTTTCTTC
Found at i:2804959 original size:21 final size:23
Alignment explanation
Indices: 2804924--2804970 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
2804914 TTAAAGATTT
* *
2804924 TTTTATATATATTATTTTTGTTA
1 TTTTATATATATTATTATTGATA
2804947 TTTTA-AT-TATTATTATTGATA
1 TTTTATATATATTATTATTGATA
2804968 TTT
1 TTT
2804971 ATGTATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 2 0.09
23 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTTATATATATTATTATTGATA
Found at i:2816433 original size:18 final size:18
Alignment explanation
Indices: 2816412--2816446 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2816402 TAAATTCAAA
2816412 TGCTGTAAAAAA-ATATTT
1 TGCT-TAAAAAATATATTT
2816430 TGCTTAAAAAATATATT
1 TGCTTAAAAAATATATT
2816447 AACTTATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (18 bp):
TGCTTAAAAAATATATTT
Found at i:2817370 original size:55 final size:53
Alignment explanation
Indices: 2817242--2817612 Score: 292
Period size: 55 Copynumber: 7.0 Consensus size: 53
2817232 GATAAAGAGA
* * *
2817242 TTTTTAAAGTTGTTAAGCCTCTGCTGAGAGG-GCCTTTTCCAAGATGAGAGA-TTT
1 TTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAG-CTTTTCCAAGATCA-A-ATTTT
* * *
2817296 TTTTAAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTTTCAAGATCAAATTTT
1 TTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATCAAATTTT
* * * * * * **
2817349 TAATTTTAAAGTTGTTAAGCCTCTGCTAAGAGAAGCTTTTCCAAGATGAGAGATT
1 T--TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATCAAATTTT
* *
2817404 TTTTTAAAGTTGTTGAGCTTCTGTTGAGAGGAGCTTTTCCAAGATCAGATTTT
1 TTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATCAAATTTT
** * * * * **
2817457 TAAAGTTAAAGTTGTTGAGCCTTTGTTGAGAAGAGCTTTTCCAAGATGAGA--GA
1 T--TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATCAAATTTT
** * *
2817510 TTTTTAAAGTTGTTGAGCCTCTGTTGAGAAAAGCTTTTTCAATAT-AAGA----
1 TTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATCAA-ATTTT
* * ** * * *
2817559 ATTTTAAAGTTATTGAGCCTCTACTGAGATGAGCTTTTCCAAGATAAAAATTT
1 TTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATCAAATTTT
2817612 T
1 T
2817613 AAAGCTGTTG
Statistics
Matches: 256, Mismatches: 49, Indels: 25
0.78 0.15 0.08
Matches are distributed among these distances:
49 38 0.15
50 3 0.01
51 39 0.15
52 1 0.00
53 51 0.20
54 39 0.15
55 85 0.33
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (53 bp):
TTTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATCAAATTTT
Found at i:2817466 original size:108 final size:108
Alignment explanation
Indices: 2817245--2817666 Score: 453
Period size: 108 Copynumber: 4.0 Consensus size: 108
2817235 AAAGAGATTT
*
2817245 TTAAAGTTGTTAAGCCTCTGCTGAGAG-GGCCTTTTCCAAGATGAGAGATTTTTTTAAAAGTTGT
1 TTAAAGTTGTTAAGCCTCTGCTGAGAGAAG-CTTTTCCAAGATGAGAGATTTTTTT-AAAGTTGT
* * **
2817309 TGAGCCTCTATTGAGAGGAGCTTTTTCAAGATCAAATTTTTAATT
64 TGAGCCTCTGTTGAGAGGAGCTTTTTCAAGATCAGATTTTTAAAG
*
2817354 TTAAAGTTGTTAAGCCTCTGCTAAGAGAAGCTTTTCCAAGATGAGAGATTTTTTTAAAGTTGTTG
1 TTAAAGTTGTTAAGCCTCTGCTGAGAGAAGCTTTTCCAAGATGAGAGATTTTTTTAAAGTTGTTG
* *
2817419 AGCTTCTGTTGAGAGGAGCTTTTCCAAGATCAGATTTTTAAAG
66 AGCCTCTGTTGAGAGGAGCTTTTTCAAGATCAGATTTTTAAAG
* * *
2817462 TTAAAGTTGTTGAGCCTTTGTTGAGA-AGAGCTTTTCCAAGATGAGAGA--TTTTTAAAGTTGTT
1 TTAAAGTTGTTAAGCCTCTGCTGAGAGA-AGCTTTTCCAAGATGAGAGATTTTTTTAAAGTTGTT
** * * *
2817524 GAGCCTCTGTTGAGAAAAGCTTTTTCAATATAAGAATTTTAAAG
65 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGATCAGATTTTTAAAG
* ** *
2817568 TT--A-TTG---AGCCTCTACTGAGATG-AGCTTTTCCAAGAT-A-A-A-AATTTTAAAGCTGTT
1 TTAAAGTTGTTAAGCCTCTGCTGAGA-GAAGCTTTTCCAAGATGAGAGATTTTTTTAAAGTTGTT
** * * * * *
2817622 GAGCCTAAGCTGAGATGAGCTTTTT-TAGATGAAATTTTTAAAG
65 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGATCAGATTTTTAAAG
2817665 TT
1 TT
2817667 GTTGAGCCTC
Statistics
Matches: 274, Mismatches: 34, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
97 16 0.06
98 33 0.12
99 1 0.00
100 25 0.09
103 3 0.01
104 1 0.00
106 53 0.19
107 1 0.00
108 89 0.32
109 51 0.19
110 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.38
Consensus pattern (108 bp):
TTAAAGTTGTTAAGCCTCTGCTGAGAGAAGCTTTTCCAAGATGAGAGATTTTTTTAAAGTTGTTG
AGCCTCTGTTGAGAGGAGCTTTTTCAAGATCAGATTTTTAAAG
Found at i:2817568 original size:49 final size:49
Alignment explanation
Indices: 2817243--2817832 Score: 403
Period size: 46 Copynumber: 11.8 Consensus size: 49
2817233 ATAAAGAGAT
* * *
2817243 TTTTAAAGTTGTTAAGCCTCTGCTGAGAGG-GCCTTTTCCAAGATGAGAGATTT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTCAAGAT-A-AGA--A
** *
2817296 TTTTAAAAGTTGTTGAGCCTCTATTGAGAGGAGCTTTTTCAAGATCAAATTTTTAA
1 TTTT-AAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT--AA----GAA
* * * * *
2817352 TTTTAAAGTTGTTAAGCCTCTGCTAAGAGAAGCTTTTCCAAGATGAGAGATTT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT-A-AGA--A
* * * * *
2817405 TTTTAAAGTTGTTGAGCTTCTGTTGAGAGGAGCTTTTCCAAGATCAGATTT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGA--A
* * * * *
2817456 TTAAAGTTAAAGTTGTTGAGCCTTTGTTGAGAAGAGCTTTTCCAAGATGAGAGAT
1 TT----TTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT-A-AGAA
* ** *
2817511 TTTTAAAGTTGTTGAGCCTCTGTTGAGAAAAGCTTTTTCAATATAAGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGAA
* * * * *
2817560 TTTTAAAGTTATTGAGCCTCTACTGAGATGAGCTTTTCCAAGATAAAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGAA
* ** * * *
2817609 TTTTAAAGCTGTTGAGCCTAAGCTGAGATGAGCTTTTT-TAGATGAA-AT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGAT-AAGAA
* * * *
2817657 TTTTAAAGTTGTTGAGCCTCTACTTAGATGAGCTTTTTTAA-A-AA-AA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGAA
* * * *
2817703 TTTTAAAGTTGTTGAACCTCTACTGAGAGGAACTTTTTTAAG---AGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGAA
* * *
2817749 TTTTAAAGTTGTTGAGCCTCTACTGAGATGAACTTTTTCAAG---AGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGAA
* * * * *
2817795 TTTCAAAGTTATTGAGCCTCTACTTAGATGAGCTTTTT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTT
2817833 TAAATTTTTA
Statistics
Matches: 452, Mismatches: 65, Indels: 47
0.80 0.12 0.08
Matches are distributed among these distances:
45 1 0.00
46 119 0.26
48 39 0.09
49 79 0.17
50 1 0.00
51 47 0.10
53 43 0.10
54 36 0.08
55 79 0.17
56 4 0.01
57 3 0.01
58 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (49 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATAAGAA
Found at i:2818090 original size:18 final size:17
Alignment explanation
Indices: 2818067--2818145 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 17
2818057 TTTATTTAAT
2818067 TTTTTTCTTCTTTCTCC
1 TTTTTTCTTCTTTCTCC
* *
2818084 ATTTTTTCTCTCTTTTTTC
1 -TTTTTTCT-TCTTTCTCC
*
2818103 TTTTTTCTT-TCTTCTTTC
1 TTTTTTCTTCT-TTC-TCC
*
2818121 TTTCTTTCTTTCTTTTTCC
1 TTT-TTTC-TTCTTTCTCC
2818140 TTTTTT
1 TTTTTT
2818146 TTCCTCCTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.02
17 3 0.06
18 25 0.50
19 16 0.32
20 4 0.08
21 1 0.02
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTCTTTCTCC
Found at i:2818115 original size:4 final size:4
Alignment explanation
Indices: 2818088--2818135 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
2818078 TTCTCCATTT
*
2818088 TTTC TCTC TTT- TTTC TTT- TTTC TTTC -TTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
2818133 TTT
1 TTT
2818136 TTCCTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 9 0.23
4 30 0.77
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:2818129 original size:37 final size:37
Alignment explanation
Indices: 2818066--2818147 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
2818056 ATTTATTTAA
* *
2818066 TTTTTTTCTTCTTTCTCCATTTTTTCTCTCTTTTTTCTT
1 TTTTTTTCTTCTTTCT-C-TTCTTTCTCTCTTTTTCCTT
*
2818105 TTTTCTTTCTTCTTTCT-TTCTTTCTTTCTTTTTCCTT
1 TTTT-TTTCTTCTTTCTCTTCTTTCTCTCTTTTTCCTT
2818142 TTTTTT
1 TTTTTT
2818148 CCTCCTTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
36 2 0.05
37 21 0.54
39 4 0.10
40 12 0.31
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (37 bp):
TTTTTTTCTTCTTTCTCTTCTTTCTCTCTTTTTCCTT
Found at i:2818144 original size:7 final size:7
Alignment explanation
Indices: 2818094--2818145 Score: 68
Period size: 7 Copynumber: 7.1 Consensus size: 7
2818084 ATTTTTTCTC
2818094 TCTTTTT
1 TCTTTTT
2818101 TCTTTTT
1 TCTTTTT
*
2818108 TCTTTCT
1 TCTTTTT
2818115 TCTTTCTT
1 TCTTT-TT
2818123 TCTTTCTT
1 TCTTT-TT
2818131 TCTTTTT
1 TCTTTTT
*
2818138 CCTTTTT
1 TCTTTTT
2818145 T
1 T
2818146 TTCCTCCTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
7 26 0.65
8 14 0.35
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TCTTTTT
Found at i:2818298 original size:23 final size:23
Alignment explanation
Indices: 2818272--2818317 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2818262 TCATGCCAGT
2818272 TGAAAAAATGAGATTTGAATCCC
1 TGAAAAAATGAGATTTGAATCCC
* ** *
2818295 TGAAGATCTGGGATTTGAATCCC
1 TGAAAAAATGAGATTTGAATCCC
2818318 AGCAAGCTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (23 bp):
TGAAAAAATGAGATTTGAATCCC
Found at i:2818410 original size:23 final size:25
Alignment explanation
Indices: 2818380--2818439 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
2818370 AAAAAAAGGC
2818380 AAAAAAAAAAGAG-C-TTTCTGTA-A
1 AAAAAAAAAAGAGCCATTT-TGTAGA
2818403 AAAAAAAAAA-AGCCATTTTGTAGA
1 AAAAAAAAAAGAGCCATTTTGTAGA
2818427 AACAAAAAAAAGA
1 AA-AAAAAAAAGA
2818440 TAGAAACAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 2 0.06
23 15 0.47
24 6 0.19
25 8 0.25
26 1 0.03
ACGTcount: A:0.63, C:0.08, G:0.12, T:0.17
Consensus pattern (25 bp):
AAAAAAAAAAGAGCCATTTTGTAGA
Found at i:2818412 original size:24 final size:25
Alignment explanation
Indices: 2818380--2818439 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
2818370 AAAAAAAGGC
*
2818380 AAAAAAAAAAGAGC-TTTCTGTA-AA
1 AAAAAAAAAAGACCATTT-TGTAGAA
2818404 AAAAAAAAAAG-CCATTTTGTAGAA
1 AAAAAAAAAAGACCATTTTGTAGAA
*
2818428 ACAAAAAAAAGA
1 AAAAAAAAAAGA
2818440 TAGAAACAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.63, C:0.08, G:0.12, T:0.17
Consensus pattern (25 bp):
AAAAAAAAAAGACCATTTTGTAGAA
Found at i:2824453 original size:13 final size:13
Alignment explanation
Indices: 2824435--2824459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2824425 TAAAGTACGG
2824435 TGACTCATCACTA
1 TGACTCATCACTA
2824448 TGACTCATCACT
1 TGACTCATCACT
2824460 TATTTGATAT
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:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (13 bp):
TGACTCATCACTA
Found at i:2824501 original size:18 final size:18
Alignment explanation
Indices: 2824468--2824502 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2824458 CTTATTTGAT
**
2824468 ATAAAGTAAAGGTGACTC
1 ATAAAGTAAACATGACTC
2824486 ATAAAGTAAACATGACT
1 ATAAAGTAAACATGACT
2824503 TGACTTAGAC
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:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (18 bp):
ATAAAGTAAACATGACTC
Found at i:2832888 original size:21 final size:22
Alignment explanation
Indices: 2832855--2832895 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2832845 TTTGAAGTTG
*
2832855 TTAAAATTTAAAATTTTAATTA
1 TTAAAATTTAAAAATTTAATTA
2832877 TTAAAA-TTAAAAATTTAAT
1 TTAAAATTTAAAAATTTAAT
2832896 ACTCTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAATTTAAAAATTTAATTA
Found at i:2833022 original size:15 final size:15
Alignment explanation
Indices: 2832999--2833043 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
2832989 CATTTCAGTA
*
2832999 TAATCTTAATAATTT
1 TAATATTAATAATTT
2833014 TAATATTAATAA---
1 TAATATTAATAATTT
*
2833026 TAATAATAATAATTT
1 TAATATTAATAATTT
2833041 TAA
1 TAA
2833044 AAAGTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 11 0.44
15 14 0.56
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATATTAATAATTT
Found at i:2833187 original size:10 final size:10
Alignment explanation
Indices: 2833171--2833202 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2833161 CGCTCACCAG
2833171 CCTACAGCCA
1 CCTACAGCCA
*
2833181 TCTACAGCCA
1 CCTACAGCCA
2833191 CCTACAGCCA
1 CCTACAGCCA
2833201 CC
1 CC
2833203 CAGATCCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.28, C:0.50, G:0.09, T:0.12
Consensus pattern (10 bp):
CCTACAGCCA
Found at i:2834559 original size:7 final size:7
Alignment explanation
Indices: 2834547--2834621 Score: 51
Period size: 7 Copynumber: 9.9 Consensus size: 7
2834537 AAAACCCCTA
2834547 AAAATCC
1 AAAATCC
2834554 AAAATCCCC
1 AAAAT--CC
2834563 TAAAATCC
1 -AAAATCC
*
2834571 AAAATCTT
1 AAAATC-C
*
2834579 AAAATTC
1 AAAATCC
2834586 AAAATCC
1 AAAATCC
2834593 TAAAATCC
1 -AAAATCC
* *
2834601 GAAACCC
1 AAAATCC
*
2834608 TAAAATTC
1 -AAAATCC
2834616 AAAATC
1 AAAATC
2834622 TCTTAAATCC
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
7 27 0.52
8 18 0.35
9 2 0.04
10 5 0.10
ACGTcount: A:0.52, C:0.25, G:0.01, T:0.21
Consensus pattern (7 bp):
AAAATCC
Found at i:2834567 original size:17 final size:16
Alignment explanation
Indices: 2834537--2834668 Score: 110
Period size: 15 Copynumber: 8.3 Consensus size: 16
2834527 TTAAGTTTCT
*
2834537 AAAACCCCTAAAAATCC
1 AAAATCCCT-AAAATCC
2834554 AAAATCCCCTAAAATCC
1 AAAAT-CCCTAAAATCC
* *
2834571 AAAAT-CTTAAAATTC
1 AAAATCCCTAAAATCC
2834586 AAAAT-CCTAAAATCC
1 AAAATCCCTAAAATCC
* *
2834601 GAAA-CCCTAAAATTC
1 AAAATCCCTAAAATCC
* *
2834616 AAAATCTCTTAAATCC
1 AAAATCCCTAAAATCC
*
2834632 -AAACCCCTAAAATCC
1 AAAATCCCTAAAATCC
**
2834647 TAAACCCCCTAAAATCC
1 -AAAATCCCTAAAATCC
*
2834664 GAAAT
1 AAAAT
2834669 TCCAAACCTT
Statistics
Matches: 92, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
15 48 0.52
16 10 0.11
17 30 0.33
18 4 0.04
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAATCCCTAAAATCC
Found at i:2834692 original size:93 final size:92
Alignment explanation
Indices: 2834537--2834729 Score: 214
Period size: 93 Copynumber: 2.1 Consensus size: 92
2834527 TTAAGTTTCT
* *
2834537 AAAACCCCTAAAAATCCAAAATCCCCTAAAATCCAAAATCTTAAAATTCAAAATCCTAAAATCCG
1 AAAACCCCTAAAAATCCAAAACCCCCTAAAATCCAAAATCTCAAAATTCAAAATCCTAAAATCC-
*
2834602 AAA-CCCTAAAATTCAAAATCTCTTAAATC
65 AAACCCCTAAAA-TCAAAA-CCCTTAAATC
* * * * * * *
2834631 CAAACCCCT-AAAATCCTAAACCCCCTAAAATCCGAAAT-TCCAAACCTTTAAACT-CTTAAATC
1 AAAACCCCTAAAAATCCAAAACCCCCTAAAATCCAAAATCT-CAAA-ATTCAAAATCCTAAAATC
*
2834693 CAAACCCCTAAAATCCAAACCCTTAAATC
64 CAAACCCCTAAAATCAAAACCCTTAAATC
2834722 AAAACCCC
1 AAAACCCC
2834730 AAACCTCAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
91 16 0.19
92 9 0.11
93 45 0.54
94 14 0.17
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.21
Consensus pattern (92 bp):
AAAACCCCTAAAAATCCAAAACCCCCTAAAATCCAAAATCTCAAAATTCAAAATCCTAAAATCCA
AACCCCTAAAATCAAAACCCTTAAATC
Found at i:2834704 original size:14 final size:14
Alignment explanation
Indices: 2834687--2834729 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
2834677 TTTAAACTCT
2834687 TAAATCCAAACCCC
1 TAAATCCAAACCCC
*
2834701 TAAAATCCAAACCCT
1 T-AAATCCAAACCCC
*
2834716 TAAATCAAAACCCC
1 TAAATCCAAACCCC
2834730 AAACCTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (14 bp):
TAAATCCAAACCCC
Found at i:2834708 original size:15 final size:15
Alignment explanation
Indices: 2834688--2834729 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
2834678 TTAAACTCTT
2834688 AAATCCAAACCCCTA
1 AAATCCAAACCCCTA
*
2834703 AAATCCAAA-CCCTT
1 AAATCCAAACCCCTA
*
2834717 AAATCAAAACCCC
1 AAATCCAAACCCC
2834730 AAACCTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (15 bp):
AAATCCAAACCCCTA
Found at i:2834777 original size:30 final size:30
Alignment explanation
Indices: 2834583--2834786 Score: 100
Period size: 30 Copynumber: 6.8 Consensus size: 30
2834573 AATCTTAAAA
* *
2834583 TTCAAAATCCTAAAATCCGAAACCCTAAAA--
1 TTCAAACT-CTAAAAT-CGAAACCCCAAAATC
* *
2834613 TTCAAAATCTCTTAAATCCAAACCCCTAAAATC
1 TTC-AAA-CTCTAAAATCGAAACCCC-AAAATC
* * ** *
2834646 CT-AAACCCCCTAAAATCCGAAATTCC-AAACC
1 TTCAAA--CTCTAAAAT-CGAAACCCCAAAATC
* * *
2834677 TTTAAACTCTTAAATCCAAACCCCTAAAATC
1 TTCAAACTCTAAAATCGAAACCCC-AAAATC
* * *
2834708 --CAAACCCTTAAATCAAAACCCC-AAA-C
1 TTCAAACTCTAAAATCGAAACCCCAAAATC
* * *
2834734 CTCAAATTTTAAAATCGAAACCCCAAAATC
1 TTCAAACTCTAAAATCGAAACCCCAAAATC
*
2834764 TTCAAACTCTAAAATCAAAACCC
1 TTCAAACTCTAAAATCGAAACCC
2834787 TAAACCTTCC
Statistics
Matches: 129, Mismatches: 31, Indels: 28
0.69 0.16 0.15
Matches are distributed among these distances:
26 1 0.01
27 3 0.02
28 17 0.13
29 28 0.22
30 37 0.29
31 25 0.19
32 11 0.09
33 7 0.05
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (30 bp):
TTCAAACTCTAAAATCGAAACCCCAAAATC
Found at i:2834837 original size:58 final size:56
Alignment explanation
Indices: 2834670--2834843 Score: 131
Period size: 58 Copynumber: 3.0 Consensus size: 56
2834660 ATCCGAAATT
* *
2834670 CCAAACCTTTAAACTCTT-AAATCCAAACCCCTAAAA-TC-CAAACCCTTAAATCAAAACC
1 CCAAACC-TCAAAC-CTTAAAATCCAAACCCC-AAAACCCTCAAA--CTTAAATCAAAACC
** * * *
2834728 CCAAACCTCAAATTTTAAAATCGAAACCCCAAAATCTTCAAACTCTAAAATCAAAACC
1 CCAAACCTCAAACCTTAAAATCCAAACCCCAAAACCCTCAAACT-T-AAATCAAAACC
* * * *
2834786 CTAAACCTTCCATACCTTAAAA-CCAAACCCTAAAACCCTCAAAACTTAAATCCAAACC
1 CCAAACC-T-CAAACCTTAAAATCCAAACCCCAAAACCCTC-AAACTTAAATCAAAACC
2834844 TTTAAAATTC
Statistics
Matches: 93, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
56 8 0.09
57 17 0.18
58 38 0.41
59 16 0.17
60 14 0.15
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (56 bp):
CCAAACCTCAAACCTTAAAATCCAAACCCCAAAACCCTCAAACTTAAATCAAAACC
Found at i:2837539 original size:15 final size:14
Alignment explanation
Indices: 2837497--2837529 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2837487 TGTGCTAAAC
*
2837497 AGAAAAAAAAAAAA
1 AGAAAAAGAAAAAA
2837511 AGAAAAAGAAAAAA
1 AGAAAAAGAAAAAA
2837525 AGAAA
1 AGAAA
2837530 GTTGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AGAAAAAGAAAAAA
Found at i:2843127 original size:16 final size:16
Alignment explanation
Indices: 2843082--2843133 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2843072 AACTTATAAA
2843082 TATTTTTATTAAATTT
1 TATTTTTATTAAATTT
** *
2843098 TA-AATTATAAAAATTT
1 TATTTTTAT-TAAATTT
*
2843114 TATTTTTATTAAATTA
1 TATTTTTATTAAATTT
2843130 TATT
1 TATT
2843134 AATCATTATA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 4 0.15
16 19 0.70
17 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTATTAAATTT
Found at i:2848180 original size:144 final size:144
Alignment explanation
Indices: 2848009--2848294 Score: 448
Period size: 144 Copynumber: 2.0 Consensus size: 144
2847999 CTTACTGGCC
* * * * *
2848009 CAATCCCTTCTTCTATTGGTAATTTATCAAAATTGCAGGCGA-TGTCCCTTGGTTCAAATCTTCT
1 CAATCCCTTCTTCTATTGGTAATTTATCAAAACTGAAAGC-ATTGTACCTTGATTCAAATCTTCT
* * * *
2848073 GGAAGGTCCTGTACCAAAAGAAATTGGTAATTTAGAAGCACTCAGGGTCTTGCACCTCTCCCAAA
65 AGAAGGTCCTATACCAAAAGAAATTGGGAATTTAGAAGCACTCAAGGTCTTGCACCTCTCCCAAA
2848138 ACAAATTGAGTGGTT
130 ACAAATTGAGTGGTT
* *
2848153 CAATCCCTTCTTCTATTTGTAATTTATCAAAACTGAAAGCATTGTACCTTGATTCAAATCTTTTA
1 CAATCCCTTCTTCTATTGGTAATTTATCAAAACTGAAAGCATTGTACCTTGATTCAAATCTTCTA
*
2848218 GAAGGTCCTATACCAAAAGAAATTGGGAATTTAGAAGCACTCAAGGTCTTGTACCTCTCCCAAAA
66 GAAGGTCCTATACCAAAAGAAATTGGGAATTTAGAAGCACTCAAGGTCTTGCACCTCTCCCAAAA
2848283 CAAATTGAGTGG
131 CAAATTGAGTGG
2848295 ATCCATACCG
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
143 1 0.01
144 128 0.99
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (144 bp):
CAATCCCTTCTTCTATTGGTAATTTATCAAAACTGAAAGCATTGTACCTTGATTCAAATCTTCTA
GAAGGTCCTATACCAAAAGAAATTGGGAATTTAGAAGCACTCAAGGTCTTGCACCTCTCCCAAAA
CAAATTGAGTGGTT
Found at i:2851088 original size:50 final size:50
Alignment explanation
Indices: 2851027--2851127 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
2851017 AGAAAAGAGA
*
2851027 CTTAGACTCCCGAAATACACGTCTTTAAACTGTTCCACAAAAGACCGAGT
1 CTTAGACTCCCGAAATAAACGTCTTTAAACTGTTCCACAAAAGACCGAGT
* * * *
2851077 CTTAGACTCCCGAAGTAAACGTCTTTAAATTGTTCCACGAGAGACCGAGT
1 CTTAGACTCCCGAAATAAACGTCTTTAAACTGTTCCACAAAAGACCGAGT
2851127 C
1 C
2851128 ATTGGCATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
CTTAGACTCCCGAAATAAACGTCTTTAAACTGTTCCACAAAAGACCGAGT
Found at i:2852415 original size:23 final size:24
Alignment explanation
Indices: 2852385--2852439 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
2852375 ATATGTAAAT
2852385 AAATCATG-TAAATATCT-TAATAA
1 AAATCATGCTAAATAT-TATAATAA
*
2852408 AAATCATGCCTAAATATTATAGTAA
1 AAATCATG-CTAAATATTATAATAA
2852433 AAATCAT
1 AAATCAT
2852440 ACCAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 8 0.29
24 1 0.04
25 19 0.68
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (24 bp):
AAATCATGCTAAATATTATAATAA
Found at i:2852464 original size:13 final size:13
Alignment explanation
Indices: 2852446--2852505 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
2852436 TCATACCAAA
*
2852446 ATCATGCAAGAAT
1 ATCATGCAAAAAT
2852459 ATCATGCAATAAAT
1 ATCATGCAA-AAAT
* **
2852473 ATAAAAC-AAAA-
1 ATCATGCAAAAAT
2852484 ATCATGCAAAAAT
1 ATCATGCAAAAAT
*
2852497 ATTATGCAA
1 ATCATGCAA
2852506 GCAAATCATT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
11 4 0.11
12 7 0.19
13 18 0.50
14 7 0.19
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.23
Consensus pattern (13 bp):
ATCATGCAAAAAT
Found at i:2852668 original size:24 final size:25
Alignment explanation
Indices: 2852612--2852674 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
2852602 CATTCATGAC
*
2852612 AAATATCATAATAAATTCATGCAATT
1 AAATATCATAA-AAATTCATCCAATT
2852638 AAATATCATAAAAA-TCATCC-ATAT
1 AAATATCATAAAAATTCATCCAAT-T
*
2852662 AATTATCATAAAA
1 AAATATCATAAAA
2852675 TAAATCATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 3 0.09
26 11 0.32
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.32
Consensus pattern (25 bp):
AAATATCATAAAAATTCATCCAATT
Found at i:2852806 original size:25 final size:25
Alignment explanation
Indices: 2852772--2852820 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2852762 ATAAAATAGT
2852772 AAAAACAAAAA-ATAAAATAAAAATC
1 AAAAACAAAAAGA-AAAATAAAAATC
* *
2852797 AAAAAGAAAAAGAAAAATGAAAAT
1 AAAAACAAAAAGAAAAATAAAAAT
2852821 TTACTAGTTG
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:0.80, C:0.04, G:0.06, T:0.10
Consensus pattern (25 bp):
AAAAACAAAAAGAAAAATAAAAATC
Found at i:2856195 original size:46 final size:48
Alignment explanation
Indices: 2856133--2856295 Score: 203
Period size: 46 Copynumber: 3.5 Consensus size: 48
2856123 TCTTATCTGG
2856133 AAATCTCATATGAAAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAA
1 AAATCTCATATGAAAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAA
* * *
2856181 AAATCTC-T-TGAAAAAGCTCCTATCAGCAGAGACTCAACAACTTTAA
1 AAATCTCATATGAAAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAA
* * * *
2856227 AATTCTC-T-TGAAAAAGCTCCTCTCAGCAGAAGCTTAACAACTTT-A
1 AAATCTCATATGAAAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAA
* *
2856272 AAATCTCATCTG-AAAATCTCATCT
1 AAATCTCATATGAAAAAGCTCATCT
2856296 GGAAAAGCTC
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
45 7 0.07
46 85 0.83
47 3 0.03
48 7 0.07
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.26
Consensus pattern (48 bp):
AAATCTCATATGAAAAAGCTCATCTCAGCAGAGGCTCAACAACTTTAA
Found at i:2856289 original size:13 final size:14
Alignment explanation
Indices: 2856271--2856301 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2856261 TAACAACTTT
2856271 AAAATCTCATCT-G
1 AAAATCTCATCTGG
2856284 AAAATCTCATCTGG
1 AAAATCTCATCTGG
2856298 AAAA
1 AAAA
2856302 GCTCCTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (14 bp):
AAAATCTCATCTGG
Found at i:2856403 original size:95 final size:94
Alignment explanation
Indices: 2856298--2856721 Score: 586
Period size: 93 Copynumber: 4.5 Consensus size: 94
2856288 TCTCATCTGG
*
2856298 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAATCTCATCTGGAAAAGCTCCTCTTAGC
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAAATCTCATCTGGAAAAGCTCCTCTCAGC
* *
2856363 AGAGACTCAACAACTTTAAAATTCTCTTAA
65 AGAGGCTCAACAACTTTAAAATTCTCTTGA
* * * *
2856393 AAAAGCTCCTCTCAGCAGAAGCTCAACAACTTT-AAAATCTTATATGGAAAAGCTCTTCTCAAG-
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTGGAAAAGCTCCTCTC-AGC
*
2856456 AGAGGCTCAACAACTTTAAAATTCTCTTCTGG
65 AGAGGCTCAACAACTTTAAAATTCTC-T-TGA
* * *
2856488 AAAAGCTTCTCTCAGCAGAAGCTCAACAACTTT-AAAATTTCATCTGGAAAAGCTCCTCTCAGCA
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTGGAAAAGCTCCTCTCAGCA
* *
2856552 GAGGTTCAACAACTTTAAAAATCTCTTGA
66 GAGGCTCAACAACTTTAAAATTCTCTTGA
* * * * * * *
2856581 AAAAGCTCTTCTCAGCAGAGGCTCAACAACTTTAAAAAT-TCTTTTGAAAAAACTTCTCTCAGCT
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTGGAAAAGCTCCTCTCAGCA
2856645 GAGGCTCAACAACTTTAAAAATTCTCTTGA
66 GAGGCTCAACAACTTT-AAAATTCTCTTGA
2856675 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTTCATCT
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATC-TCATCT
2856722 ATTTTCAAAT
Statistics
Matches: 291, Mismatches: 30, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
93 114 0.39
94 61 0.21
95 112 0.38
96 4 0.01
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (94 bp):
AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATCTGGAAAAGCTCCTCTCAGCA
GAGGCTCAACAACTTTAAAATTCTCTTGA
Found at i:2856464 original size:47 final size:48
Alignment explanation
Indices: 2856284--2856721 Score: 506
Period size: 47 Copynumber: 9.2 Consensus size: 48
2856274 ATCTCATCTG
*
2856284 AAAATCTCATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAA
1 AAAATCTTATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-A
* * *
2856333 AAAATCTCATCTGGAAAAGCTCCTCTTAGCAGAGACTCAACAACTTTA
1 AAAATCTTATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
* * ** *
2856381 AAATTC-TCT-TAAAAAAGCTCCTCTCAGCAGAAGCTCAACAACTTT-
1 AAAATCTTATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
* *
2856426 AAAATCTTATATGGAAAAGCTCTTCTCAAG-AGAGGCTCAACAACTTTA
1 AAAATCTTATCTGGAAAAGCTCCTCTC-AGCAGAGGCTCAACAACTTTA
* * *
2856474 AAATTCTCT-TCTGGAAAAGCTTCTCTCAGCAGAAGCTCAACAACTTT-
1 AAAATCT-TATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
*
2856521 AAAAT-TTCATCTGGAAAAGCTCCTCTCAGCAGAGGTTCAACAACTTTA
1 AAAATCTT-ATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
* * *
2856569 AAAATC-TCT-TGAAAAAGCTCTTCTCAGCAGAGGCTCAACAACTTTA
1 AAAATCTTATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
* * * *
2856615 AAAATTCTT-T-TGAAAAAACTTCTCTCAGCTGAGGCTCAACAACTTTA
1 AAAA-TCTTATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
* *
2856662 AAAA--TTCTCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
1 AAAATCTTATC-TGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
2856709 AAAATCTTCATCT
1 AAAATCTT-ATCT
2856722 ATTTTCAAAT
Statistics
Matches: 334, Mismatches: 37, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
44 2 0.01
45 7 0.02
46 72 0.22
47 150 0.45
48 52 0.16
49 49 0.15
50 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (48 bp):
AAAATCTTATCTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA
Found at i:2868547 original size:12 final size:12
Alignment explanation
Indices: 2868530--2868561 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2868520 TTTGTTAGCA
2868530 ATTTTATTAATT
1 ATTTTATTAATT
2868542 ATTTTATTAATT
1 ATTTTATTAATT
*
2868554 TTTTTATT
1 ATTTTATT
2868562 TAAACTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTATTAATT
Found at i:2868968 original size:26 final size:27
Alignment explanation
Indices: 2868938--2868998 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
2868928 TCCTACATTT
2868938 TTTATTATTT-TAGTATTATTATTAAA-
1 TTTATT-TTTATAGTATTATTATTAAAG
* *
2868964 TTTATTTTTATATTATTATTTTTAAAG
1 TTTATTTTTATAGTATTATTATTAAAG
2868991 TTTATTTT
1 TTTATTTT
2868999 AACAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 3 0.10
26 20 0.65
27 8 0.26
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (27 bp):
TTTATTTTTATAGTATTATTATTAAAG
Found at i:2869007 original size:26 final size:26
Alignment explanation
Indices: 2868952--2869007 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
2868942 TTATTTTAGT
* * *
2868952 ATTATTATTAAATTTATTTTTATATT
1 ATTATTATTAAATTTATTTTAACATA
*
2868978 ATTATTTTTAAAGTTTATTTTAACA-A
1 ATTATTATTAAA-TTTATTTTAACATA
2869004 ATTA
1 ATTA
2869008 ACATAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTATTATTAAATTTATTTTAACATA
Found at i:2870632 original size:15 final size:15
Alignment explanation
Indices: 2870601--2870649 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2870591 TTTATTAATT
*
2870601 AAACAAAAATATAAAA
1 AAACAAAAATA-CAAA
*
2870617 AAAGAAAAATACAAA
1 AAACAAAAATACAAA
**
2870632 ACCCAAAAATACAAA
1 AAACAAAAATACAAA
2870647 AAA
1 AAA
2870650 AATAAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.78, C:0.12, G:0.02, T:0.08
Consensus pattern (15 bp):
AAACAAAAATACAAA
Found at i:2878579 original size:72 final size:70
Alignment explanation
Indices: 2878503--2878740 Score: 253
Period size: 72 Copynumber: 3.3 Consensus size: 70
2878493 ATACCTTTAC
* * ** * *
2878503 AAATTGGGAATTGCTTATATTTATCCTATTTGTACCTAAACAACAACAATTTAGAGGGGTACATC
1 AAATTGGGAGTTGCTTAAATTTA-CAGA-TTGGACCTAAGCAACAACAATTTAGAGGGGTACATC
2878568 CCTCCTG
64 CCTCCTG
* * **
2878575 AAATTGGGAGTTGCTTAAATTTGCAGAGATTGGACCTAAGCAACAATAATTTAGAGGCATACATC
1 AAATTGGGAGTTGCTTAAATTT--ACAGATTGGACCTAAGCAACAACAATTTAGAGGGGTACATC
2878640 CCTCC-G
64 CCTCCTG
** * *
2878646 CTCATTGGGAGTTGCTCAAATTTGCAGGGATTGGACCTAAGCAACAACAATTTAGAGGGGTACAT
1 -AAATTGGGAGTTGCTTAAATTTACA--GATTGGACCTAAGCAACAACAATTTAGAGGGGTACAT
** *
2878711 CCCTTATC
63 CCCTCCTG
2878719 AAATTGGGAGTTGCTTAAATTT
1 AAATTGGGAGTTGCTTAAATTT
2878741 GTCTGCATTG
Statistics
Matches: 136, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
70 1 0.01
71 1 0.01
72 132 0.97
73 1 0.01
74 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (70 bp):
AAATTGGGAGTTGCTTAAATTTACAGATTGGACCTAAGCAACAACAATTTAGAGGGGTACATCCC
TCCTG
Found at i:2878741 original size:72 final size:72
Alignment explanation
Indices: 2878536--2878790 Score: 305
Period size: 72 Copynumber: 3.5 Consensus size: 72
2878526 TCCTATTTGT
* *
2878536 ACCTAAACAACAACAATTTAGAGGGGTACATCCCTCCTGAAATTGGGAGTTGCTTAAATTTGCAG
1 ACCTAAGCAACAACAATTTAGAGGGGTACATCCCTCCTCAAATTGGGAGTTGCTTAAATTTGCAG
2878601 AGATTGG
66 AGATTGG
* ** * ** *
2878608 ACCTAAGCAACAATAATTTAGAGGCATACATCCCTCCGCTCATTGGGAGTTGCTCAAATTTGCAG
1 ACCTAAGCAACAACAATTTAGAGGGGTACATCCCTCCTCAAATTGGGAGTTGCTTAAATTTGCAG
*
2878673 GGATTGG
66 AGATTGG
** *
2878680 ACCTAAGCAACAACAATTTAGAGGGGTACATCCCTTATCAAATTGGGAGTTGCTTAAATTTGTCT
1 ACCTAAGCAACAACAATTTAGAGGGGTACATCCCTCCTCAAATTGGGAGTTGCTTAAATTTG-CA
*
2878745 G-CATTGG
65 GAGATTGG
* *** * * *
2878752 ACCAAAGTGGCAATAATTTAGAGGGGGAGATCCCTCCTC
1 ACCTAAGCAACAACAATTTAGAGGGGTACATCCCTCCTC
2878791 TGCTAGCCAA
Statistics
Matches: 152, Mismatches: 30, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
72 150 0.99
73 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (72 bp):
ACCTAAGCAACAACAATTTAGAGGGGTACATCCCTCCTCAAATTGGGAGTTGCTTAAATTTGCAG
AGATTGG
Found at i:2881442 original size:22 final size:22
Alignment explanation
Indices: 2881417--2881459 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2881407 TTATATTTGA
* *
2881417 AATTGTTAAAATTTAAAATTTT
1 AATTATTAAAATTGAAAATTTT
2881439 AATTATTAAAATTGAAAATTT
1 AATTATTAAAATTGAAAATTT
2881460 GATATTCGAT
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:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
AATTATTAAAATTGAAAATTTT
Found at i:2890848 original size:12 final size:13
Alignment explanation
Indices: 2890831--2890864 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2890821 TCAATTTATA
2890831 AAAAATAAATG-T
1 AAAAATAAATGAT
2890843 AAAAATAAATGAT
1 AAAAATAAATGAT
*
2890856 TAAAATAAA
1 AAAAATAAA
2890865 AATGTGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (13 bp):
AAAAATAAATGAT
Found at i:2901413 original size:12 final size:12
Alignment explanation
Indices: 2901396--2901426 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2901386 CTAGAATTGT
2901396 TGAAAATTTAAA
1 TGAAAATTTAAA
2901408 TGAAAATTTAAA
1 TGAAAATTTAAA
*
2901420 TAAAAAT
1 TGAAAAT
2901427 AATTTACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (12 bp):
TGAAAATTTAAA
Found at i:2905537 original size:13 final size:13
Alignment explanation
Indices: 2905519--2905548 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2905509 CAAAAAAATG
2905519 TTTTTTGGTTTTA
1 TTTTTTGGTTTTA
*
2905532 TTTTTTGTTTTTA
1 TTTTTTGGTTTTA
2905545 TTTT
1 TTTT
2905549 CTAAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (13 bp):
TTTTTTGGTTTTA
Found at i:2908636 original size:42 final size:42
Alignment explanation
Indices: 2908589--2908708 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 42
2908579 ACAGATTTAG
2908589 CAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACT
1 CAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACT
** *** *
2908631 CAA-TTTG-T---TT-CC---AG-AG-AGGGACAGATTTA-G
1 CAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACT
2908661 CAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACT
1 CAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACT
2908703 CAATTT
1 CAATTT
2908709 GTTTCCAGAG
Statistics
Matches: 54, Mismatches: 12, Indels: 24
0.60 0.13 0.27
Matches are distributed among these distances:
30 3 0.06
31 12 0.22
32 3 0.06
33 2 0.04
35 2 0.04
36 4 0.07
37 2 0.04
39 2 0.04
40 3 0.06
41 12 0.22
42 9 0.17
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (42 bp):
CAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACT
Found at i:2908753 original size:72 final size:72
Alignment explanation
Indices: 2908503--2908723 Score: 415
Period size: 72 Copynumber: 3.1 Consensus size: 72
2908493 ATTTGAACCA
* * *
2908503 AGGGACAGATATAGCAATTTTGATAAATTACCAATCGAAGAAGGGATTGAACCACTCAATTTGTG
1 AGGGACAGATTTAGCAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTT
2908568 TCCAGAG
66 TCCAGAG
2908575 AGGGACAGATTTAGCAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTT
1 AGGGACAGATTTAGCAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTT
2908640 TCCAGAG
66 TCCAGAG
2908647 AGGGACAGATTTAGCAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTT
1 AGGGACAGATTTAGCAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTT
2908712 TCCAGAG
66 TCCAGAG
2908719 AGGGA
1 AGGGA
2908724 TAATTGAGTT
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 146 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (72 bp):
AGGGACAGATTTAGCAATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTT
TCCAGAG
Found at i:2909034 original size:72 final size:72
Alignment explanation
Indices: 2908958--2909185 Score: 160
Period size: 72 Copynumber: 3.2 Consensus size: 72
2908948 GCAATTTTGA
2908958 TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
1 TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
2909023 GTGCATT
66 GTGCATT
* ******* * * * * * ** * * *** *
2909030 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAAAT-CTTGC
1 TAAATTACCAATAGAAGAAGGGATTGAACC-ACT--CA-ATTTGTTTCCAGAGAGGGATAATTG-
* *
2909094 AATT-TTG-A--
61 AGTTAGTGCATT
2909102 TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
1 TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
2909167 GTGCATT
66 GTGCATT
*
2909174 TAAATTCCCAAT
1 TAAATTACCAAT
2909186 TTCTTTTGGT
Statistics
Matches: 99, Mismatches: 47, Indels: 20
0.60 0.28 0.12
Matches are distributed among these distances:
68 16 0.16
69 6 0.06
70 1 0.01
71 2 0.02
72 49 0.49
73 2 0.02
74 1 0.01
75 6 0.06
76 16 0.16
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (72 bp):
TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
GTGCATT
Found at i:2909901 original size:144 final size:144
Alignment explanation
Indices: 2908400--2909851 Score: 2177
Period size: 144 Copynumber: 10.1 Consensus size: 144
2908390 CGATCTGACG
* * * ** ** **
2908400 AGGGATGGAACCACTCAATTTGTTTTCACAGAGGTCTAATTCTGTTACCGC-TTCTAAATTCCCA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATT-TAAATTCCCA
* * **
2908464 ATTTCTTTTGGTATAAGACCTTCTAAAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAA
65 ATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATAA
*
2908529 ATTACCAATCGAAGA
130 ATTACCAATAGAAGA
* * * * *
2908544 AGGGATTGAACCACTCAATTTGTGTCCAGAGAGGGACAGATTTAGCAATT-TTG-A--TAAATTA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATA-A-TT-G-AGTTAGTGCATTTAAATTC
******* * * * * * *** ** *
2908605 CCAATAGAAGAAGGGATTGAACCACTCAATTTG-TTTCCA-GAGAGGGACAGATTTAGCAATTTT
62 CCAATTTCTTTTGGTATAGGACC-TTCTAGAAGATTTGAAGGA-AGGGACAGATATAGCAATTTT
2908668 GATAAATTACCAATAGAAGA
125 GATAAATTACCAATAGAAGA
2908688 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
*
2908753 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGAACAGATATAGCAATTTTGATAAA
66 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATAAA
2908818 TTACCAATAGAAGA
131 TTACCAATAGAAGA
* ** * *
2908832 AGGGATTGAACCACTCAATTTGTTTTCAGAGAGGTCTAATTCTA-TTACTGC-TTCTAAATTCCC
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATT-GAGTTAGTGCATT-TAAATTCCC
**
2908895 AATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATA
64 AATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATA
2908960 AATTACCAATAGAAGA
129 AATTACCAATAGAAGA
2908976 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
** * * *
2909041 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAAATCTTGCAATTTTGATAAA
66 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATAAA
2909106 TTACCAATAGAAGA
131 TTACCAATAGAAGA
2909120 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
** * * *
2909185 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAAATCTTGCAATTTTGATAAA
66 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATAAA
2909250 TTACCAATAGAAGA
131 TTACCAATAGAAGA
*
2909264 AAGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
* *
2909329 TTTCTTTTGGTATAGGACCTGCTAGAAGATTTGAAGGAAGGGACAGACATAGCAATTTTGATAAA
66 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATAAA
2909394 TTACCAATAGAAGA
131 TTACCAATAGAAGA
2909408 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
* *
2909473 TTTCTTTTGGTATAGGA-CTGCTAGAAGATTTGAAGGAAGGGACAGACATAGCAATTTTGATAAA
66 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATAAA
2909537 TTACCAATAGAAGA
131 TTACCAATAGAAGA
2909551 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
* *
2909616 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATGAAGGGACAGATATTGCAATTTTGATAAA
66 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATAAA
2909681 TTACCAATAGAAGA
131 TTACCAATAGAAGA
*
2909695 AGGGATTGAACCACTCAATTTGTTTCTAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
*
2909760 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGTAGGAAGGGACAGATATAGCAATTTTGATAAA
66 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATAAA
2909825 TTACCAATAGAAGA
131 TTACCAATAGAAGA
2909839 AGGGATTGAACCA
1 AGGGATTGAACCA
2909852 GCAAACAGAT
Statistics
Matches: 1198, Mismatches: 92, Indels: 36
0.90 0.07 0.03
Matches are distributed among these distances:
140 3 0.00
141 3 0.00
142 3 0.00
143 152 0.13
144 1022 0.85
145 10 0.01
146 2 0.00
147 1 0.00
148 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (144 bp):
AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAAGGAAGGGACAGATATAGCAATTTTGATAAA
TTACCAATAGAAGA
Found at i:2922627 original size:72 final size:72
Alignment explanation
Indices: 2922551--2922778 Score: 178
Period size: 72 Copynumber: 3.2 Consensus size: 72
2922541 GCAATTTTGA
2922551 TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
1 TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
2922616 GTGCATT
66 GTGCATT
* ******* * * * * * ** * * **
2922623 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAGAT-ATTGC
1 TAAATTACCAATAGAAGAAGGGATTGAACC-ACT--CA-ATTTGTTTCCAGAGAGGGATAATTG-
* *
2922687 AATT-TTG-A--
61 AGTTAGTGCATT
2922695 TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
1 TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
2922760 GTGCATT
66 GTGCATT
*
2922767 TAAATTCCCAAT
1 TAAATTACCAAT
2922779 TTCTTTTGGT
Statistics
Matches: 103, Mismatches: 43, Indels: 20
0.62 0.26 0.12
Matches are distributed among these distances:
68 17 0.17
69 7 0.07
70 1 0.01
71 2 0.02
72 49 0.48
73 2 0.02
74 1 0.01
75 7 0.07
76 17 0.17
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (72 bp):
TAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTA
GTGCATT
Found at i:2922880 original size:144 final size:144
Alignment explanation
Indices: 2922425--2922869 Score: 766
Period size: 144 Copynumber: 3.1 Consensus size: 144
2922415 CGATCTGATG
* * ** ** *
2922425 AGGGATGGAACCACTCAATTTGTTTTCAGAGAGGTCTAATTCTGTTACTGC-TTCTAAATTCCCA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATT-TAAATTCCCA
* * *
2922489 ATTTCTTTTGGTATAAGACCTTCTAAAAGATTTGAACCAAGGGACAGATATGGCAATTTTGATAA
65 ATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAA
2922554 ATTACCAATAGAAGA
130 ATTACCAATAGAAGA
2922569 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
* *
2922634 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAGATATTGCAATTTTGATAAA
66 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAAA
2922699 TTACCAATAGAAGA
131 TTACCAATAGAAGA
2922713 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
2922778 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAAA
66 TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAAA
2922843 TTACCAATAGAAGA
131 TTACCAATAGAAGA
2922857 AGGGATTGAACCA
1 AGGGATTGAACCA
2922870 ACAAGCTTGT
Statistics
Matches: 287, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
144 285 0.99
145 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (144 bp):
AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATTTAAATTCCCAA
TTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAAA
TTACCAATAGAAGA
Found at i:2923008 original size:288 final size:285
Alignment explanation
Indices: 2922425--2922942 Score: 625
Period size: 288 Copynumber: 1.8 Consensus size: 285
2922415 CGATCTGATG
* * ** *
2922425 AGGGATGGAACCACTCAATTTGTTTTCAGAGAGGTCTAATTCTGTTACTGCTTCTAAATTCCCAA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTCAGTTACTGCTTCTAAATTCCCAA
*
2922490 TTTCTTTTGGTATAAGACCTTCTAAAAGATTTGAACCAAGGGACAGATATGGCAATTTTGATAAA
66 TTTCTTTTGGTATAAGACCTTCTAAAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAAA
* * * * * * * * *
2922555 TTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGC
131 TTACCAATAGAAGAAGGGATTGAACCACACAACTTGTTGCCAGAGA-GAATAAATAAATAAAT-C
** * * * * * *
2922620 ATTTAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAGATATT
194 ATTTAAATTCCCAATTTCTAATGGGATAGGACCATCTAGAAGATTTGAACCAAAGAACAGAGATT
2922685 GCAATTTTGATAAATTACCAATAGAAGA
259 GCAA-TTTGATAAATTACCAATAGAAGA
* *
2922713 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTGAGTTAGTGCATT-TAAATTCCCA
1 AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTCAGTTACTGC-TTCTAAATTCCCA
* *
2922777 ATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAA
65 ATTTCTTTTGGTATAAGACCTTCTAAAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAA
*
2922842 ATTACCAATAGAAGAAGGGATTGAACCA-ACAAGCTTGTTGCCATAGA-AATCCAAATAAATCAA
130 ATTACCAATAGAAGAAGGGATTGAACCACACAA-CTTGTTGCCAGAGAGAAT--AAATAAAT-AA
* *
2922905 AT-TTGTTAGATAT-CCAATTTCTAATGGGAT-GGATCCAT
191 ATCAT-TTAAAT-TCCCAATTTCTAATGGGATAGGA-CCAT
2922943 TAATTTTTTT
Statistics
Matches: 196, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
286 2 0.01
287 7 0.04
288 182 0.93
289 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Consensus pattern (285 bp):
AGGGATTGAACCACTCAATTTGTTTCCAGAGAGGGATAATTCAGTTACTGCTTCTAAATTCCCAA
TTTCTTTTGGTATAAGACCTTCTAAAAGATTTGAACCAAGGGACAGATATAGCAATTTTGATAAA
TTACCAATAGAAGAAGGGATTGAACCACACAACTTGTTGCCAGAGAGAATAAATAAATAAATCAT
TTAAATTCCCAATTTCTAATGGGATAGGACCATCTAGAAGATTTGAACCAAAGAACAGAGATTGC
AATTTGATAAATTACCAATAGAAGA
Found at i:2940407 original size:22 final size:21
Alignment explanation
Indices: 2940371--2940413 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2940361 ATCGAATATC
* *
2940371 AAAATTTCAATTTTAATAATT
1 AAAATTTAAATTTTAACAATT
2940392 AAAATTTTAAATTTTAACAATT
1 AAAA-TTTAAATTTTAACAATT
2940414 TCAAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATTTAAATTTTAACAATT
Found at i:2940488 original size:20 final size:20
Alignment explanation
Indices: 2940465--2940506 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2940455 AAAAAATAAA
*
2940465 TTGTTTCCAAAGAGTTTTTT
1 TTGTTGCCAAAGAGTTTTTT
*
2940485 TTGTTGCCTAAGAGTTTTTT
1 TTGTTGCCAAAGAGTTTTTT
2940505 TT
1 TT
2940507 TTTTTTCGTC
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:0.17, C:0.10, G:0.17, T:0.57
Consensus pattern (20 bp):
TTGTTGCCAAAGAGTTTTTT
Found at i:2943190 original size:72 final size:72
Alignment explanation
Indices: 2943065--2943319 Score: 332
Period size: 72 Copynumber: 3.5 Consensus size: 72
2943055 TTGGCTACCA
* * * * * *
2943065 GAGGAGGGATCTCCCCCTCTAAATTATTGCTACTTAGGTCCAAT-GCAGACAAATTTAAGCAACT
1 GAGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCCAATCCCTG-CAAATTTAAGCAACT
2943129 CCCAATTT
65 CCCAATTT
** *
2943137 GATAAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCCAATCCCTGCAAATTTGAGCAACTC
1 GAGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCCAATCCCTGCAAATTTAAGCAACTC
**
2943202 CCAATGA
66 CCAATTT
* * * *
2943209 GCGGAGGGATGTACGCCTCAAAATTATTGTTGCTTAGGTCCAATCTCTGCAAATTTAAGCAACTC
1 GAGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCCAATCCCTGCAAATTTAAGCAACTC
2943274 CCAATTT
66 CCAATTT
* * *
2943281 CAGGAGGGATGTGCCCCTCTAAATTATTGTTGTTTAGGT
1 GAGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGT
2943320 ACAAATAAGA
Statistics
Matches: 156, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
72 154 0.99
73 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (72 bp):
GAGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCCAATCCCTGCAAATTTAAGCAACTC
CCAATTT
Found at i:2943334 original size:72 final size:71
Alignment explanation
Indices: 2943066--2943352 Score: 299
Period size: 72 Copynumber: 4.0 Consensus size: 71
2943056 TGGCTACCAG
* * * * * *
2943066 AGGAGGGATCTCCCCCTCTAAATTATTGCTACTTAGGTCCAATGCAGACAAATTTAAGCAACTCC
1 AGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCAAATCCAG-CAAATTTAAGCAACTCC
*
2943131 CAATTTG
65 CAATTTC
** * * *
2943138 ATAAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCCAATCCCTGCAAATTTGAGCAACTCC
1 AGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCAAAT-CCAGCAAATTTAAGCAACTCC
**
2943203 CAATGAGC
65 CAAT-TTC
* * * *
2943211 -GGAGGGATGTACGCCTCAAAATTATTGTTGCTTAGGTCCAATCTCTGCAAATTTAAGCAACTCC
1 AGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCAAATC-CAGCAAATTTAAGCAACTCC
2943275 CAATTTC
65 CAATTTC
* * * * *
2943282 AGGAGGGATGTGCCCCTCTAAATTATTGTTGTTTAGGTACAAAT-AAGACAAATATAAGCAATTC
1 AGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGT-CAAATCCAG-CAAATTTAAGCAACTC
2943346 CCAATTT
64 CCAATTT
2943353 GTAAAGGTAT
Statistics
Matches: 181, Mismatches: 28, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
71 3 0.02
72 172 0.95
73 6 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (71 bp):
AGGAGGGATGTACCCCTCTAAATTATTGTTGCTTAGGTCAAATCCAGCAAATTTAAGCAACTCCC
AATTTC
Found at i:2943334 original size:144 final size:143
Alignment explanation
Indices: 2943080--2943350 Score: 348
Period size: 144 Copynumber: 1.9 Consensus size: 143
2943070 GGGATCTCCC
* * *
2943080 CCTCTAAATTATTGCTACTTAGGTCCAATGCAGACAAATTTAAGCAACTCCCAATTTGATAAGGG
1 CCTCAAAATTATTGCTACTTAGGTCCAATGCAGACAAATTTAAGCAACTCCCAATTTCAGAAGGG
* ** * *
2943145 ATGTACCCCTCTAAATTATTGTTGCTTAGGTCCAATCCCTGCAAATTTGAGCAACTCCCAATGAG
66 ATGTACCCCTCTAAATTATTGTTGCTTAGGTCAAAT-CAAGCAAATATAAGCAACTCCCAATGAG
2943210 CGGAGGGATGTACG
130 CGGAGGGATGTACG
* * * * *
2943224 CCTCAAAATTATTGTTGCTTAGGTCCAATCTCTG-CAAATTTAAGCAACTCCCAATTTCAGGAGG
1 CCTCAAAATTATTGCTACTTAGGTCCAAT-GCAGACAAATTTAAGCAACTCCCAATTTCAGAAGG
* * *
2943288 GATGTGCCCCTCTAAATTATTGTTGTTTAGGTACAAAT-AAGACAAATATAAGCAATTCCCAAT
65 GATGTACCCCTCTAAATTATTGTTGCTTAGGT-CAAATCAAG-CAAATATAAGCAACTCCCAAT
2943351 TTGTAAAGGT
Statistics
Matches: 108, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
143 1 0.01
144 101 0.94
145 6 0.06
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (143 bp):
CCTCAAAATTATTGCTACTTAGGTCCAATGCAGACAAATTTAAGCAACTCCCAATTTCAGAAGGG
ATGTACCCCTCTAAATTATTGTTGCTTAGGTCAAATCAAGCAAATATAAGCAACTCCCAATGAGC
GGAGGGATGTACG
Found at i:2950496 original size:14 final size:14
Alignment explanation
Indices: 2950479--2950522 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2950469 TTCCTCTTTT
*
2950479 TGTTTTGTTTATTA
1 TGTTTTTTTTATTA
2950493 TGTTTTTTTTCATT-
1 TGTTTTTTTT-ATTA
2950507 TGTTTTATTTTATTA
1 TGTTTT-TTTTATTA
2950522 T
1 T
2950523 TAGGTTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.75
Consensus pattern (14 bp):
TGTTTTTTTTATTA
Found at i:2955688 original size:26 final size:26
Alignment explanation
Indices: 2955610--2955705 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 26
2955600 GCCTGATTTA
*
2955610 TATTATGATATTTAT--ATGAATGACT
1 TATTATGATATTTTTGCATGAATGA-T
*
2955635 T-TTATGATATTTAATTGTATGAAT--T
1 TATTATGATATTT--TTGCATGAATGAT
*
2955660 TATTATGGTATTTTTGCATGAATGAT
1 TATTATGATATTTTTGCATGAATGAT
* *
2955686 TATAAT-ATATATTTGCATGA
1 TATTATGATATTTTTGCATGA
2955706 TATTTTGTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
24 20 0.34
25 15 0.26
26 17 0.29
28 6 0.10
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (26 bp):
TATTATGATATTTTTGCATGAATGAT
Found at i:2955896 original size:23 final size:25
Alignment explanation
Indices: 2955835--2955897 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
2955825 TCCTTGCATG
*
2955835 ATTTTGGTATGATTTTTACTATAAA
1 ATTTTGGCATGATTTTTACTATAAA
*
2955860 ATTTTGGCATGATTTTTA-T-TAAG
1 ATTTTGGCATGATTTTTACTATAAA
2955883 ATATTT-GCATGATTT
1 AT-TTTGGCATGATTT
2955898 ATTTGTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 14 0.40
24 4 0.11
25 17 0.49
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (25 bp):
ATTTTGGCATGATTTTTACTATAAA
Found at i:2971507 original size:20 final size:20
Alignment explanation
Indices: 2971470--2971508 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2971460 ACATTGATAC
*
2971470 ATACATAAACACATATGAAT
1 ATACATAAACACACATGAAT
* *
2971490 ATACATACATACACATGAA
1 ATACATAAACACACATGAA
2971509 ACACAAGCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.18, G:0.05, T:0.23
Consensus pattern (20 bp):
ATACATAAACACACATGAAT
Found at i:2971590 original size:18 final size:18
Alignment explanation
Indices: 2971569--2971608 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2971559 AAAATGAGGC
2971569 AAAGAAATAAAAAAAAAA
1 AAAGAAATAAAAAAAAAA
* *
2971587 AAAGCAATAAGAAAAAAA
1 AAAGAAATAAAAAAAAAA
2971605 AAAG
1 AAAG
2971609 GAACTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAGAAATAAAAAAAAAA
Found at i:2973760 original size:21 final size:20
Alignment explanation
Indices: 2973727--2973765 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2973717 AGATTCATTT
*
2973727 ATTTTAGTGTAAAGTTAAACA
1 ATTTTAGTATAAA-TTAAACA
*
2973748 ATTTTATTATAAATTAAA
1 ATTTTAGTATAAATTAAA
2973766 AAAATGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (20 bp):
ATTTTAGTATAAATTAAACA
Found at i:2975635 original size:15 final size:15
Alignment explanation
Indices: 2975596--2975642 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
2975586 ATATAATTAT
* *
2975596 TTTTAAAATATTATA
1 TTTTAAAATTTTAAA
2975611 -TTTAATAATTTTAAA
1 TTTTAA-AATTTTAAA
2975626 TTTTAAAA-TTTAAA
1 TTTTAAAATTTTAAA
2975640 TTT
1 TTT
2975643 AATATTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 14 0.50
15 9 0.32
16 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTAAAATTTTAAA
Found at i:2975658 original size:29 final size:30
Alignment explanation
Indices: 2975594--2975658 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
2975584 TTATATAATT
*
2975594 ATTTTTAAAATATTATATTTAATAATTTTA
1 ATTTTTAAAATATTAAATTTAATAATTTTA
*
2975624 AATTTTAAAAT-TTAAATTTAAT-ATTTGTA
1 ATTTTTAAAATATTAAATTTAATAATTT-TA
2975653 ATTTTT
1 ATTTTT
2975659 TTTTATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 17 0.55
30 10 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
ATTTTTAAAATATTAAATTTAATAATTTTA
Found at i:2976687 original size:20 final size:20
Alignment explanation
Indices: 2976664--2976702 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2976654 ATATTTAATA
2976664 TATT-ATTAATATATAAATTT
1 TATTAATTAATA-ATAAATTT
*
2976684 TATTAATTATTAATAAATT
1 TATTAATTAATAATAAATT
2976703 AAATAATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTAATTAATAATAAATTT
Found at i:2976705 original size:25 final size:24
Alignment explanation
Indices: 2976665--2976732 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
2976655 TATTTAATAT
* ** *
2976665 ATTATTAATATATAAATTTTATTA
1 ATTATTAATAAATAAATAATATCA
2976689 ATTATTAATAAATTAAATAATATCA
1 ATTATTAATAAA-TAAATAATATCA
2976714 ATTCATTAATAAATAAATA
1 ATT-ATTAATAAATAAATA
2976733 TCAATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 11 0.29
25 18 0.47
26 9 0.24
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTATTAATAAATAAATAATATCA
Found at i:2976744 original size:18 final size:19
Alignment explanation
Indices: 2976701--2976750 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
2976691 TATTAATAAA
2976701 TTAAAT-AATATCAATTCAT
1 TTAAATAAATATCAATT-AT
2976720 TAATAAATAAATATCAATT-T
1 T--TAAATAAATATCAATTAT
2976740 TTAAAATAAAT
1 TT-AAATAAAT
2976751 GTACAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 1 0.04
19 9 0.33
20 2 0.07
21 5 0.19
22 10 0.37
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAATAAATATCAATTAT
Found at i:2978440 original size:24 final size:27
Alignment explanation
Indices: 2978385--2978441 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2978375 TTTTATAATT
* *
2978385 TATTTATTTGCATGATTTATTTGATGA
1 TATTTATATGCATGAATTATTTGATGA
2978412 TATTTATATGCAT-AATT-TTT-ATGA
1 TATTTATATGCATGAATTATTTGATGA
2978436 TATTTA
1 TATTTA
2978442 ATTGTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 10 0.36
25 3 0.11
26 3 0.11
27 12 0.43
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.56
Consensus pattern (27 bp):
TATTTATATGCATGAATTATTTGATGA
Found at i:2978450 original size:24 final size:26
Alignment explanation
Indices: 2978385--2978466 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
2978375 TTTTATAATT
* *
2978385 TATTTATTTGCAT-GATTTATTTGATGA
1 TATTTATATGCATAAATTTA-TT-ATGA
2978412 TATTTATATGCAT-AATTT-TTATGA
1 TATTTATATGCATAAATTTATTATGA
* *
2978436 TATTTA-ATTGTATAAATTTATTACGA
1 TATTTATA-TGCATAAATTTATTATGA
2978462 TATTT
1 TATTT
2978467 CTCATGAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.02
24 14 0.29
25 7 0.15
26 10 0.21
27 16 0.33
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.55
Consensus pattern (26 bp):
TATTTATATGCATAAATTTATTATGA
Found at i:2987077 original size:39 final size:39
Alignment explanation
Indices: 2987022--2987101 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
2987012 TATTACACAA
* *
2987022 AGTAGCAATTGGAGCATGAAAAATCTATTACAAGTGAGG
1 AGTAGCAATTGAAGCATGAAAAAACTATTACAAGTGAGG
*
2987061 AGTAGCAGTTGAAGCATGAAAAAACTATTACAAGTGAGG
1 AGTAGCAATTGAAGCATGAAAAAACTATTACAAGTGAGG
2987100 AG
1 AG
2987102 ACATGCCACT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.21
Consensus pattern (39 bp):
AGTAGCAATTGAAGCATGAAAAAACTATTACAAGTGAGG
Found at i:2989207 original size:14 final size:16
Alignment explanation
Indices: 2989115--2989209 Score: 63
Period size: 16 Copynumber: 5.8 Consensus size: 16
2989105 TAAATTAAAG
*
2989115 TATTAAATAATAACTT
1 TATTAAATAATAATTT
2989131 TATTAATATAAT-ATTT
1 TATTAA-ATAATAATTT
* *
2989147 AAATATAAATATAGTATTTTT
1 -TAT-TAAATA-A-TA-ATTT
*
2989168 TATTAAATCA-AA--T
1 TATTAAATAATAATTT
2989181 TATTAAATAATAATTT
1 TATTAAATAATAATTT
2989197 TATTAATATAATA
1 TATTAA-ATAATA
2989210 CATATATATA
Statistics
Matches: 61, Mismatches: 7, Indels: 21
0.69 0.08 0.24
Matches are distributed among these distances:
13 10 0.16
14 2 0.03
16 17 0.28
17 16 0.26
18 5 0.08
19 6 0.10
20 2 0.03
21 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (16 bp):
TATTAAATAATAATTT
Found at i:2989219 original size:66 final size:65
Alignment explanation
Indices: 2989082--2989224 Score: 198
Period size: 66 Copynumber: 2.2 Consensus size: 65
2989072 ATATCTTAAT
* **
2989082 TATATATAA-ATAGAATATTTTATTAAATTAAAGTATTAAATAATAACTTTATTAATATAATATT
1 TATATATAATATAGAATATTTTATTAAATCAAAGTATTAAATAATAACTTTATTAATATAATACA
* * * * *
2989146 TAAATATAAATATAGTATTTTTTATTAAATCAAATTATTAAATAATAATTTTATTAATATAATAC
1 TATATAT-AATATAGAATATTTTATTAAATCAAAGTATTAAATAATAACTTTATTAATATAATAC
2989211 A
65 A
2989212 TATATATAATATA
1 TATATATAATATA
2989225 AAATTAAATA
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
64 6 0.09
65 8 0.12
66 54 0.79
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (65 bp):
TATATATAATATAGAATATTTTATTAAATCAAAGTATTAAATAATAACTTTATTAATATAATACA
Found at i:2989420 original size:16 final size:16
Alignment explanation
Indices: 2989400--2989435 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2989390 TAATTATTAT
2989400 TAAAAAAAC-AAAAAA
1 TAAAAAAACAAAAAAA
2989415 TAAAAAAACAAAAAAA
1 TAAAAAAACAAAAAAA
2989431 TAAAA
1 TAAAA
2989436 TAAAATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.86, C:0.06, G:0.00, T:0.08
Consensus pattern (16 bp):
TAAAAAAACAAAAAAA
Found at i:2990837 original size:16 final size:16
Alignment explanation
Indices: 2990818--2990886 Score: 77
Period size: 16 Copynumber: 4.3 Consensus size: 16
2990808 CTAGGTTTCT
2990818 AAAACCTCTAAAATCC
1 AAAACCTCTAAAATCC
*
2990834 AAAATCTCCTAAAATCC
1 AAAACCT-CTAAAATCC
* *
2990851 AAAATCT-TAAAATCT
1 AAAACCTCTAAAATCC
* *
2990866 GAAACCCCTAAAATCC
1 AAAACCTCTAAAATCC
2990882 AAAAC
1 AAAAC
2990887 TCCCAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.25
16 17 0.39
17 16 0.36
ACGTcount: A:0.51, C:0.28, G:0.01, T:0.20
Consensus pattern (16 bp):
AAAACCTCTAAAATCC
Found at i:2990847 original size:17 final size:16
Alignment explanation
Indices: 2990825--2991039 Score: 85
Period size: 15 Copynumber: 13.8 Consensus size: 16
2990815 TCTAAAACCT
2990825 CTAAAATCCAAAATCTC
1 CTAAAATCCAAAA-CTC
2990842 CTAAAATCCAAAA-TC
1 CTAAAATCCAAAACTC
* ** *
2990857 TTAAAATCTGAAACCC
1 CTAAAATCCAAAACTC
2990873 CTAAAATCCAAAACTCC
1 CTAAAATCCAAAACT-C
* **
2990890 CAAAAATCTGAAA-T-
1 CTAAAATCCAAAACTC
* *
2990904 CTCAAA-CCTTTAAACT-
1 CTAAAATCC--AAAACTC
* * *
2990920 TTTAAATCC-AAACCC
1 CTAAAATCCAAAACTC
2990935 CTAAAATCCAAAA-TCC
1 CTAAAATCCAAAACT-C
* * *
2990951 CTTAAAT-CGAAACCC
1 CTAAAATCCAAAACTC
*
2990966 CTAAAATCCAAAACCCC
1 CTAAAATCCAAAA-CTC
*
2990983 CCAAAATCCAAAA-TC
1 CTAAAATCCAAAACTC
* *
2990998 C-CAAATCCTTAAACT-
1 CTAAAATCC-AAAACTC
* *
2991013 CTTAAATCC-AAACCC
1 CTAAAATCCAAAACTC
*
2991028 CTAAAATTCAAA
1 CTAAAATCCAAA
2991040 CCCGTAAATC
Statistics
Matches: 147, Mismatches: 34, Indels: 35
0.68 0.16 0.16
Matches are distributed among these distances:
13 1 0.01
14 18 0.12
15 46 0.31
16 41 0.28
17 41 0.28
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (16 bp):
CTAAAATCCAAAACTC
Found at i:2990877 original size:48 final size:46
Alignment explanation
Indices: 2990819--2991039 Score: 173
Period size: 48 Copynumber: 4.7 Consensus size: 46
2990809 TAGGTTTCTA
* *
2990819 AAACCTCTAAAATCCAAAATCTCCTAAAATCCAAAATCTTAAAATCTG
1 AAACCCCTAAAATCCAAAA-CCCCTAAAATCCAAAATCTT-AAATCTG
* ** * * *
2990867 AAACCCCTAAAATCCAAAACTCCCAAAAATCTGAAATCTCAAACCTTT
1 AAACCCCTAAAATCCAAAAC-CCCTAAAATCCAAAATCTTAAATC-TG
** *
2990915 AAA-CTTTTAAATCC-AAACCCCTAAAATCCAAAATCCCTTAAATC-G
1 AAACCCCTAAAATCCAAAACCCCTAAAATCCAAAAT--CTTAAATCTG
* ** *
2990960 AAACCCCTAAAATCCAAAACCCCCCAAAATCCAAAATCCCAAATCCTT
1 AAACCCCTAAAATCCAAAA-CCCCTAAAATCCAAAATCTTAAAT-CTG
* * *
2991008 AAA-CTCTTAAATCC-AAACCCCTAAAATTCAAA
1 AAACCCCTAAAATCCAAAACCCCTAAAATCCAAA
2991040 CCCGTAAATC
Statistics
Matches: 136, Mismatches: 28, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
45 29 0.21
46 20 0.15
47 32 0.24
48 55 0.40
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (46 bp):
AAACCCCTAAAATCCAAAACCCCTAAAATCCAAAATCTTAAATCTG
Found at i:2990878 original size:31 final size:31
Alignment explanation
Indices: 2990841--2990978 Score: 108
Period size: 31 Copynumber: 4.5 Consensus size: 31
2990831 TCCAAAATCT
2990841 CCTAAAATCCAAAAT-CTTAAAATCTGAAACC
1 CCTAAAATCCAAAATCCTTAAAATC-GAAACC
**
2990872 CCTAAAATCCAAAACTCCCAAAAATCTGAAA--
1 CCTAAAATCCAAAA-TCCTTAAAATC-GAAACC
* * * * * *
2990903 TCTCAAA-CCTTTAAA-CTTTTAAATCCAAACC
1 CCTAAAATCC--AAAATCCTTAAAATCGAAACC
2990934 CCTAAAATCCAAAATCCCTT-AAATCGAAACC
1 CCTAAAATCCAAAAT-CCTTAAAATCGAAACC
2990965 CCTAAAATCCAAAA
1 CCTAAAATCCAAAA
2990979 CCCCCCAAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 18
0.72 0.13 0.16
Matches are distributed among these distances:
29 3 0.04
30 11 0.13
31 48 0.58
32 9 0.11
33 12 0.14
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (31 bp):
CCTAAAATCCAAAATCCTTAAAATCGAAACC
Found at i:2990894 original size:16 final size:16
Alignment explanation
Indices: 2990827--2990894 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
2990817 TAAAACCTCT
*
2990827 AAAATCCAAAATCTCCT
1 AAAATCCAAAA-CTCCC
**
2990844 AAAATCCAAAA-TCTT
1 AAAATCCAAAACTCCC
**
2990859 AAAATCTGAAAC-CCC
1 AAAATCCAAAACTCCC
2990874 TAAAATCCAAAACTCCC
1 -AAAATCCAAAACTCCC
2990891 AAAA
1 AAAA
2990895 ATCTGAAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
15 13 0.32
16 14 0.34
17 14 0.34
ACGTcount: A:0.51, C:0.28, G:0.01, T:0.19
Consensus pattern (16 bp):
AAAATCCAAAACTCCC
Found at i:2990938 original size:93 final size:92
Alignment explanation
Indices: 2990823--2991057 Score: 287
Period size: 93 Copynumber: 2.5 Consensus size: 92
2990813 TTTCTAAAAC
* *
2990823 CTCTAAAATCCAAAATCTCCTAAAATCCAAAAT-CTTAAAATCTGAAACCCCTAAAATCCAAAAC
1 CTCTTAAATCC-AAA-CCCCTAAAATCCAAAATCCTT-AAATC-GAAACCCCTAAAATCCAAAAC
* ** *
2990887 TCCCAAAAATCTGAAATCTCAAA-CCTTTAAA
62 CCCCAAAAATCCAAAATCCCAAATCC-TTAAA
*
2990918 CTTTTAAATCCAAACCCCTAAAATCCAAAATCCCTTAAATCGAAACCCCTAAAATCCAAAACCCC
1 CTCTTAAATCCAAACCCCTAAAATCCAAAAT-CCTTAAATCGAAACCCCTAAAATCCAAAACCCC
*
2990983 CCAAAATCCAAAATCCCAAATCCTTAAA
65 CAAAAATCCAAAATCCCAAATCCTTAAA
* * * *
2991011 CTCTTAAATCCAAACCCCTAAAATTC-AAACCCGTAAATCAAAACCCC
1 CTCTTAAATCCAAACCCCTAAAATCCAAAATCCTTAAATCGAAACCCC
2991058 AAACCTCAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
91 15 0.12
92 3 0.02
93 84 0.68
94 10 0.08
95 12 0.10
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.21
Consensus pattern (92 bp):
CTCTTAAATCCAAACCCCTAAAATCCAAAATCCTTAAATCGAAACCCCTAAAATCCAAAACCCCC
AAAAATCCAAAATCCCAAATCCTTAAA
Found at i:2990957 original size:16 final size:16
Alignment explanation
Indices: 2990923--2991057 Score: 99
Period size: 15 Copynumber: 8.9 Consensus size: 16
2990913 TTAAACTTTT
2990923 AAATCC-AAACCCCTA
1 AAATCCAAAACCCCTA
* *
2990938 AAATCCAAAATCCCTT
1 AAATCCAAAACCCCTA
*
2990954 AAAT-CGAAACCCCTA
1 AAATCCAAAACCCCTA
*
2990969 AAATCCAAAACCCCCCA
1 AAATCCAAAA-CCCCTA
*
2990986 AAATCCAAAATCCC--
1 AAATCCAAAACCCCTA
* * *
2991000 AAATCCTTAAA-CTCTT
1 AAATCC-AAAACCCCTA
2991016 AAATCC-AAACCCCTA
1 AAATCCAAAACCCCTA
* *
2991031 AAATTC-AAACCCGT-
1 AAATCCAAAACCCCTA
2991045 AAAT-CAAAACCCC
1 AAATCCAAAACCCC
2991058 AAACCTCAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
13 1 0.01
14 21 0.22
15 36 0.37
16 24 0.25
17 15 0.15
ACGTcount: A:0.46, C:0.36, G:0.01, T:0.17
Consensus pattern (16 bp):
AAATCCAAAACCCCTA
Found at i:2992908 original size:34 final size:36
Alignment explanation
Indices: 2992868--2992961 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 36
2992858 ATTAAATATA
2992868 AATTAATAAATTATTTTATTTTATTTATT-TAAAAT
1 AATTAATAAATTATTTTATTTTATTTATTATAAAAT
** *
2992903 -ATTAATATTTTATTAATTA-TTT-TTTATTATAACAT
1 AATTAATAAATTATT--TTATTTTATTTATTATAAAAT
*
2992938 CAATTAATAAATAATTTTATTTTA
1 -AATTAATAAATTATTTTATTTTA
2992962 AGATCCTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
34 18 0.39
35 11 0.24
36 6 0.13
37 11 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (36 bp):
AATTAATAAATTATTTTATTTTATTTATTATAAAAT
Found at i:2993308 original size:81 final size:80
Alignment explanation
Indices: 2992993--2993387 Score: 630
Period size: 81 Copynumber: 4.8 Consensus size: 80
2992983 CATCACTTTT
*
2992993 ATGTTTTATGTTTAAAAAAATAAAAAAATAAAAAATAAAGTTAAAGAGTTGTAGTGTGTGACATG
1 ATGTTTTATGTTTAAAAAAAT-----AATAAAAAA-AAAGTTGAAGAGTTGTAGTGTGTGACATG
*
2993058 TGGAAGCTTAGGGAAAGTTTA
60 TGGAAGCTTAAGGAAAGTTTA
*
2993079 ATGTTTTATGTTTAAAAAAATAATAAAAAAAAAGTTGAAGAGTTGTGGTGTGTGACATGTGGAAG
1 ATGTTTTATGTTTAAAAAAATAATAAAAAAAAAGTTGAAGAGTTGTAGTGTGTGACATGTGGAAG
2993144 CTTAAGGAAAGTTTA
66 CTTAAGGAAAGTTTA
* *
2993159 ATGTTTTATGTTTAAAAAAATAATTAAAAAAAAAAGTTGAAGAGTTATAGTGTGTGACACGTGGA
1 ATGTTTTATGTTTAAAAAAATAA-T-AAAAAAAAAGTTGAAGAGTTGTAGTGTGTGACATGTGGA
2993224 AGCTTAAGGAAAGTTTA
64 AGCTTAAGGAAAGTTTA
* *
2993241 ATGTTTTATGTTTAAAAAAATAATTAAAAAAAAAGTTGAAGAGTTATAGTGTGTGACACGTGGAA
1 ATGTTTTATGTTTAAAAAAATAA-TAAAAAAAAAGTTGAAGAGTTGTAGTGTGTGACATGTGGAA
2993306 GCTTAAGGAAAGTTTA
65 GCTTAAGGAAAGTTTA
*
2993322 ATGTTTTATGTTTAAAAAAATAAT-AAAAAAATGTTGAAGAGTTGTAGTGTGTGACATGTGGAAG
1 ATGTTTTATGTTTAAAAAAATAATAAAAAAAAAGTTGAAGAGTTGTAGTGTGTGACATGTGGAAG
2993386 CT
66 CT
2993388 AAAGAAACGT
Statistics
Matches: 298, Mismatches: 9, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
79 39 0.13
80 71 0.24
81 89 0.30
82 78 0.26
86 21 0.07
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (80 bp):
ATGTTTTATGTTTAAAAAAATAATAAAAAAAAAGTTGAAGAGTTGTAGTGTGTGACATGTGGAAG
CTTAAGGAAAGTTTA
Found at i:2998998 original size:25 final size:24
Alignment explanation
Indices: 2998950--2999010 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
2998940 ATATACAAAT
2998950 AAATCATG-CAAATATCTTAATAA
1 AAATCATGCCAAATATCTTAATAA
*
2998973 AAATCATGCCAAGATAT-TATAGTAA
1 AAATCATGCCAA-ATATCT-TAATAA
*
2998998 AAATCATACCAAA
1 AAATCATGCCAAA
2999011 ATCCCGCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 8 0.24
24 5 0.15
25 20 0.61
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATCATGCCAAATATCTTAATAA
Found at i:2999254 original size:27 final size:24
Alignment explanation
Indices: 2999201--2999257 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 24
2999191 TTCATACAAT
* *
2999201 TAAATATCATAAAAATCATGCATA
1 TAAATATCATAAAAATCAGGCAAA
2999225 TAAATATCATAATATAAATCAGGCAAA
1 TAAATATCAT-A-A-AAATCAGGCAAA
2999252 TAAATA
1 TAAATA
2999258 AACTATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 10 0.36
25 1 0.04
26 1 0.04
27 16 0.57
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.28
Consensus pattern (24 bp):
TAAATATCATAAAAATCAGGCAAA
Found at i:3000855 original size:20 final size:20
Alignment explanation
Indices: 3000832--3000870 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3000822 TTAGGATAAA
3000832 GGTTTAGGGTTTAAGTTTAG
1 GGTTTAGGGTTTAAGTTTAG
* *
3000852 GGTTTGGGGTTTAATTTTA
1 GGTTTAGGGTTTAAGTTTA
3000871 AAGTTTAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (20 bp):
GGTTTAGGGTTTAAGTTTAG
Found at i:3000876 original size:20 final size:20
Alignment explanation
Indices: 3000828--3000878 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3000818 AGATTTAGGA
3000828 TAAAGGTTTAGGGTTTAAGTT
1 TAAA-GTTTAGGGTTTAAGTT
** * *
3000849 TAGGGTTTGGGGTTTAATTT
1 TAAAGTTTAGGGTTTAAGTT
3000869 TAAAGTTTAG
1 TAAAGTTTAG
3000879 AGATTGTAGG
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.45
Consensus pattern (20 bp):
TAAAGTTTAGGGTTTAAGTT
Found at i:3000911 original size:15 final size:15
Alignment explanation
Indices: 3000886--3000935 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
3000876 TAGAGATTGT
3000886 AGGGTTTTGGACTTTA
1 AGGGTTTTGGA-TTTA
3000902 AGGG-TTTGGATTTA
1 AGGGTTTTGGATTTA
*
3000916 AGGGATTTTGGATTTT
1 AGGG-TTTTGGATTTA
3000932 AGGG
1 AGGG
3000936 GTTTCAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 8 0.26
15 6 0.19
16 17 0.55
ACGTcount: A:0.20, C:0.02, G:0.36, T:0.42
Consensus pattern (15 bp):
AGGGTTTTGGATTTA
Found at i:3001218 original size:3 final size:3
Alignment explanation
Indices: 3001212--3001262 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3001202 ATAAAAAATA
3001212 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3001260 TAT
1 TAT
3001263 CCTTTTTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.