Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_pilon, 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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 39
Found at i:406006 original size:24 final size:24
Alignment explanation
Indices: 405955--406006 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
405945 AAATCTATGT
* * *
405955 GGCACTTCGGTGCATATTCTACGT
1 GGCACTTCGGTGCAAATTCTAAGC
*
405979 GGCACTTCGGTGCAAATTTTAAGC
1 GGCACTTCGGTGCAAATTCTAAGC
406003 GGCA
1 GGCA
406007 ATTTCAACTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (24 bp):
GGCACTTCGGTGCAAATTCTAAGC
Found at i:410427 original size:6 final size:6
Alignment explanation
Indices: 410416--410462 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
410406 ATAAGTGCTT
410416 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
410463 TTTCACAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.15, C:0.34, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTTCA
Found at i:414950 original size:40 final size:40
Alignment explanation
Indices: 414895--414980 Score: 172
Period size: 40 Copynumber: 2.1 Consensus size: 40
414885 TCTCAGCAAT
414895 ATTCCAGATTGTGACGTTGGACCTAAAATAAGGCTATTGG
1 ATTCCAGATTGTGACGTTGGACCTAAAATAAGGCTATTGG
414935 ATTCCAGATTGTGACGTTGGACCTAAAATAAGGCTATTGG
1 ATTCCAGATTGTGACGTTGGACCTAAAATAAGGCTATTGG
414975 ATTCCA
1 ATTCCA
414981 ATGAAACTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (40 bp):
ATTCCAGATTGTGACGTTGGACCTAAAATAAGGCTATTGG
Found at i:418899 original size:13 final size:13
Alignment explanation
Indices: 418881--418906 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
418871 TTCACACAAA
418881 GGGCAAGCAACAT
1 GGGCAAGCAACAT
418894 GGGCAAGCAACAT
1 GGGCAAGCAACAT
418907 CAACAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.31, T:0.08
Consensus pattern (13 bp):
GGGCAAGCAACAT
Found at i:424668 original size:14 final size:16
Alignment explanation
Indices: 424649--424684 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
424639 TCATATAAAG
424649 AAAAAAGG-T-AGAAT
1 AAAAAAGGCTGAGAAT
424663 AAAAAAGGCTGAGAAT
1 AAAAAAGGCTGAGAAT
424679 AAAAAA
1 AAAAAA
424685 AGAAGGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 11 0.55
ACGTcount: A:0.67, C:0.03, G:0.19, T:0.11
Consensus pattern (16 bp):
AAAAAAGGCTGAGAAT
Found at i:434554 original size:46 final size:46
Alignment explanation
Indices: 434504--434857 Score: 299
Period size: 46 Copynumber: 8.0 Consensus size: 46
434494 TAGGGTCACT
* ***
434504 TTTCATGCATTAATAG-ATCCGTTCATACATTTTAACCATGGCATCC
1 TTTCATGCATTAAT-GCATCCTTTCATACATTTTAGTTATGGCATCC
* * * *
434550 TTTCATGCCA-TAATGTATCCTTTCATGCATTTTAGTTATGACATCT
1 TTTCATG-CATTAATGCATCCTTTCATACATTTTAGTTATGGCATCC
* * * *
434596 TTTCATACTTTAATGCAT-ATGTTCATCCATTTTAGTTATGGCATCC
1 TTTCATGCATTAATGCATCCT-TTCATACATTTTAGTTATGGCATCC
* * * * *
434642 TTTCATGCCTTACTGCATCCTTTTATGCATTTTAGTTATGGTATCC
1 TTTCATGCATTAATGCATCCTTTCATACATTTTAGTTATGGCATCC
* * * *
434688 TTTCATGCCTTAATGCATCATTTCATACATTTTAATTATGACATCC
1 TTTCATGCATTAATGCATCCTTTCATACATTTTAGTTATGGCATCC
* *
434734 -TT--T-C----ATG---CC-TTCATGCATTTTAGTTATGCCATCC
1 TTTCATGCATTAATGCATCCTTTCATACATTTTAGTTATGGCATCC
* * * *
434768 TTTCATGGC-TTAATGCATCATTTCATGCATTTTAATTATGACATCC
1 TTTCAT-GCATTAATGCATCCTTTCATACATTTTAGTTATGGCATCC
* *
434814 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCAT
1 TTTCATGCATTAATGCATCCTTTCATACATTTTAGTTATGGCAT
434858 TCATGCATTT
Statistics
Matches: 252, Mismatches: 38, Indels: 36
0.77 0.12 0.11
Matches are distributed among these distances:
34 22 0.09
35 3 0.01
37 1 0.00
38 3 0.01
39 1 0.00
42 4 0.02
43 1 0.00
45 8 0.03
46 206 0.82
47 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.44
Consensus pattern (46 bp):
TTTCATGCATTAATGCATCCTTTCATACATTTTAGTTATGGCATCC
Found at i:434753 original size:34 final size:34
Alignment explanation
Indices: 434709--434785 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 34
434699 AATGCATCAT
*
434709 TTCATACATTTTAATTATGACATCCTTTCATGCC
1 TTCATGCATTTTAATTATGACATCCTTTCATGCC
* * *
434743 TTCATGCATTTTAGTTATGCCATCCTTTCATGGC
1 TTCATGCATTTTAATTATGACATCCTTTCATGCC
*
434777 TTAATGCAT
1 TTCATGCAT
434786 CATTTCATGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.44
Consensus pattern (34 bp):
TTCATGCATTTTAATTATGACATCCTTTCATGCC
Found at i:434785 original size:126 final size:126
Alignment explanation
Indices: 434617--434853 Score: 366
Period size: 126 Copynumber: 1.9 Consensus size: 126
434607 AATGCATATG
* * * * *
434617 TTCATCCATTTTAGTTATGGCATCCTTTCATGCCTTACTGCATCCTTTTATGCATTTTAGTTATG
1 TTCATCCATTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATG
**
434682 GTATCCTTTCATGCCTTAATGCATCATTTCATACATTTTAATTATGACATCCTTTCATGCC
66 ACATCCTTTCATGCCTTAATGCATCATTTCATACATTTTAATTATGACATCCTTTCATGCC
* *
434743 TTCATGCATTTTAGTTATGCCATCCTTTCATGGCTTAATGCATCATTTCATGCATTTTAATTATG
1 TTCATCCATTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATG
* * *
434808 ACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
66 ACATCCTTTCATGCCTTAATGCATCATTTCATACATTTTAATTATG
434854 GCATTCATGC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
126 99 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (126 bp):
TTCATCCATTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATG
ACATCCTTTCATGCCTTAATGCATCATTTCATACATTTTAATTATGACATCCTTTCATGCC
Found at i:434799 original size:80 final size:80
Alignment explanation
Indices: 434666--434831 Score: 287
Period size: 80 Copynumber: 2.1 Consensus size: 80
434656 GCATCCTTTT
**
434666 ATGCATTTTAGTTATGGTATCCTTTCATGCCTTAATGCATCATTTCATACATTTTAATTATGACA
1 ATGCATTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCATTTCATACATTTTAATTATGACA
*
434731 TCCTTTCATGCCTTC
66 TCCTTTCATGCCTTA
* *
434746 ATGCATTTTAGTTATGCCATCCTTTCATGGCTTAATGCATCATTTCATGCATTTTAATTATGACA
1 ATGCATTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCATTTCATACATTTTAATTATGACA
434811 TCCTTTCATGCCTTA
66 TCCTTTCATGCCTTA
434826 ATGCAT
1 ATGCAT
434832 CCTTTCATGC
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (80 bp):
ATGCATTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCATTTCATACATTTTAATTATGACA
TCCTTTCATGCCTTA
Found at i:434819 original size:26 final size:25
Alignment explanation
Indices: 434743--434875 Score: 89
Period size: 20 Copynumber: 5.8 Consensus size: 25
434733 CTTTCATGCC
*
434743 TTCATGCATTTTAGTTATGCCATCCT
1 TTCATGCATTTTAATTATG-CATCCT
*
434769 TTCATGGC---TT-A--ATGCATCAT
1 TTCAT-GCATTTTAATTATGCATCCT
434789 TTCATGCATTTTAATTATGACATCCT
1 TTCATGCATTTTAATTATG-CATCCT
*
434815 TTCATGC--CTT-A--ATGCATCCT
1 TTCATGCATTTTAATTATGCATCCT
*
434835 TTCATGCATTTTAGTTATGGCA----
1 TTCATGCATTTTAATTAT-GCATCCT
434857 TTCATGCATTTTAATTATG
1 TTCATGCATTTTAATTATG
434876 GATTCGATTT
Statistics
Matches: 86, Mismatches: 7, Indels: 33
0.68 0.06 0.26
Matches are distributed among these distances:
19 2 0.02
20 23 0.27
21 7 0.08
22 21 0.24
23 2 0.02
24 4 0.05
25 5 0.06
26 20 0.23
27 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (25 bp):
TTCATGCATTTTAATTATGCATCCT
Found at i:434863 original size:22 final size:21
Alignment explanation
Indices: 434835--434880 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
434825 AATGCATCCT
*
434835 TTCATGCATTTTAGTTATGGCA
1 TTCATGCATTTTAATTATGG-A
434857 TTCATGCATTTTAATTATGGA
1 TTCATGCATTTTAATTATGGA
434878 TTC
1 TTC
434881 GATTTAGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCATGCATTTTAATTATGGA
Found at i:435454 original size:94 final size:94
Alignment explanation
Indices: 435290--435461 Score: 240
Period size: 94 Copynumber: 1.8 Consensus size: 94
435280 CCTAGTACCG
* * * * *
435290 ATACTTCTATACTATAGTACTGATACCCCTTTCAGTATCGATACCATTTATATATTATGTGTTGT
1 ATACTACTATACTATAGTACTGATACCCCTTTCAGTATCGATACCATTTAGACATTATGTGATCT
*
435355 CTGGTATCGATACCCTTCTCTCAGTATCA
66 ATGGTATCGATACCCTTCTCTCAGTATCA
* *
435384 ATACTACTATACTATGGTA-TCGATACTCCCTTTCAGTATCGATACCATTTAGACATTTTG-GAT
1 ATACTACTATACTATAGTACT-GATAC-CCCTTTCAGTATCGATACCATTTAGACATTATGTGAT
435447 CTATGGTATCGATAC
64 CTATGGTATCGATAC
435462 TTCCCTTTGT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
93 1 0.01
94 37 0.54
95 30 0.44
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (94 bp):
ATACTACTATACTATAGTACTGATACCCCTTTCAGTATCGATACCATTTAGACATTATGTGATCT
ATGGTATCGATACCCTTCTCTCAGTATCA
Found at i:441140 original size:30 final size:30
Alignment explanation
Indices: 441104--441175 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
441094 CCCGCAGGAC
*
441104 CTATCCAGAGGTCATAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAAATCCTCGGCAA
*
441134 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAAATCCTCGGCAA
* *
441164 CTGTCCATAGGT
1 CTATCCAGAGGT
441176 TCCGAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAAATCCTCGGCAA
Found at i:441222 original size:31 final size:30
Alignment explanation
Indices: 441162--441286 Score: 119
Period size: 31 Copynumber: 4.0 Consensus size: 30
441152 GATCCTCGGC
* * *
441162 AACTGTCCATAGGTTCCGAAAAACCTAGGT
1 AACTGTCCATATGTTCCGTAAAACATAGGT
* *
441192 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATATGTTCCGTAAAACATAGGT
*
441223 ATACTGTCCATATG-T-CTTGAAAGACATAGGT
1 A-ACTGTCCATATGTTCCGT-AAA-ACATAGGT
*
441254 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGTAAAACATAGGT
441286 A
1 A
441287 CCCTCGACTC
Statistics
Matches: 79, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
29 3 0.04
30 5 0.06
31 46 0.58
32 20 0.25
33 3 0.04
34 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (30 bp):
AACTGTCCATATGTTCCGTAAAACATAGGT
Found at i:446916 original size:21 final size:21
Alignment explanation
Indices: 446890--446948 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
446880 TCGAGGGTTC
*
446890 TACGAGGTCTTTCGGGACATA
1 TACGAGGTCCTTCGGGACATA
**
446911 TACGAGGTCCTTCTAGACATA
1 TACGAGGTCCTTCGGGACATA
*
446932 TATGAGGTCCTTCGGGA
1 TACGAGGTCCTTCGGGA
446949 TAATTTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (21 bp):
TACGAGGTCCTTCGGGACATA
Found at i:451262 original size:16 final size:16
Alignment explanation
Indices: 451241--451272 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
451231 GACGATGGAT
451241 TTTATGATGGGGTTAC
1 TTTATGATGGGGTTAC
451257 TTTATGATGGGGTTAC
1 TTTATGATGGGGTTAC
451273 CCTTAGCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (16 bp):
TTTATGATGGGGTTAC
Found at i:453584 original size:18 final size:18
Alignment explanation
Indices: 453557--453602 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
453547 GCATGGCTAG
453557 TGCA-TCGATGCATCAAA
1 TGCATTCGATGCATCAAA
453574 TGCATTCGATGCATCAAA
1 TGCATTCGATGCATCAAA
453592 TGCATTCGATG
1 TGCATTCGATG
453603 TTTTCATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (18 bp):
TGCATTCGATGCATCAAA
Found at i:453627 original size:83 final size:82
Alignment explanation
Indices: 453499--453667 Score: 236
Period size: 83 Copynumber: 2.0 Consensus size: 82
453489 AGAGTGCATA
* * *
453499 GATGCATCAAGTGCATTCGATGTTTCAAAATAGCTAGAGTGCATCGATGCATGGCT-AGTGCATC
1 GATGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTGCATCGATGCATGG-TAAGTGCATC
453563 GATGCATCAAATGCATTC
65 GATGCATCAAATGCATTC
*
453581 GATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCT-CAGTGCATCGGTGCATGGTAAGTGCA
1 GATGCATCAAATGCATTCGATG-TTTCA-AAATA-CCTACAGTGCATCGATGCATGGTAAGTGCA
*
453644 TCGATGCATGAAATGCATTC
63 TCGATGCATCAAATGCATTC
453664 GATG
1 GATG
453668 TTCAATTTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
82 22 0.28
83 51 0.65
84 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (82 bp):
GATGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTGCATCGATGCATGGTAAGTGCATCG
ATGCATCAAATGCATTC
Found at i:453731 original size:20 final size:20
Alignment explanation
Indices: 453682--453737 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
453672 ATTTAATTCA
*
453682 TGGTGCATCAATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
453702 TGGTTCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
453722 TGGTGCATCGTTGCAT
1 TGGTGCATCGATGCAT
453738 CACTCTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:463883 original size:21 final size:21
Alignment explanation
Indices: 463857--463936 Score: 142
Period size: 21 Copynumber: 3.8 Consensus size: 21
463847 TCGAGGGTTC
463857 TACGAGGTCCTTCGGGACATA
1 TACGAGGTCCTTCGGGACATA
463878 TACGAGGTCCTTCGGGACATA
1 TACGAGGTCCTTCGGGACATA
463899 TACGAGGTCCTTCGGGACATA
1 TACGAGGTCCTTCGGGACATA
* *
463920 TATGAGGTCTTTCGGGA
1 TACGAGGTCCTTCGGGA
463937 TAATTTTATA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (21 bp):
TACGAGGTCCTTCGGGACATA
Found at i:465215 original size:48 final size:48
Alignment explanation
Indices: 465163--465255 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
465153 GATGCCTTAA
465163 TTCTATTT-TTTTTCAGCTATGCTTATTTTTTTAATAACATACAATTAG
1 TTCTATTTGTTTTTCAGCTATGCTTA-TTTTTTAATAACATACAATTAG
* * * *
465211 TTCTATTTGTTTTTTAGTTATGTTTATTTTTTAATAATATACAAT
1 TTCTATTTGTTTTTCAGCTATGCTTATTTTTTAATAACATACAAT
465256 AAAAATGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 26 0.65
49 14 0.35
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (48 bp):
TTCTATTTGTTTTTCAGCTATGCTTATTTTTTAATAACATACAATTAG
Found at i:465985 original size:20 final size:20
Alignment explanation
Indices: 465960--466016 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
465950 CTTCCATATT
465960 TTTCATACTCTTCCATAAGG-
1 TTTCATACTCTTCCA-AAGGA
*
465980 TTTCATACATC-TCCAGAGGA
1 TTTCATAC-TCTTCCAAAGGA
*
466000 TTTCACACTCTTCCAAA
1 TTTCATACTCTTCCAAA
466017 AGCTTCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.16
20 24 0.77
21 2 0.06
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (20 bp):
TTTCATACTCTTCCAAAGGA
Found at i:466074 original size:20 final size:19
Alignment explanation
Indices: 466051--466107 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
466041 TCTAGAGTTC
466051 TCTAGAATGTTCTAGAAA-A
1 TCTAGAAT-TTCTAGAAACA
* *
466070 TTCTACACTTCTCTAGAAACA
1 -TCTAGAATT-TCTAGAAACA
466091 TCTAGAATTTTCTAGAA
1 TCTAGAA-TTTCTAGAA
466108 CCTCTCCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.03
20 26 0.87
21 3 0.10
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (19 bp):
TCTAGAATTTCTAGAAACA
Found at i:468367 original size:21 final size:20
Alignment explanation
Indices: 468327--468367 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
468317 TTCGAACTCT
468327 TTCTTCAATAGTTATATTCA
1 TTCTTCAATAGTTATATTCA
468347 TTCTCTCATATAGTT-TATTCA
1 TTCT-TCA-ATAGTTATATTCA
468368 ATTATGGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (20 bp):
TTCTTCAATAGTTATATTCA
Found at i:470738 original size:40 final size:40
Alignment explanation
Indices: 470654--470741 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
470644 TTCCACAAGC
* * *** *
470654 TTCTAGAGAGTTCTAAACTTCTCAAGAGTTCTCTGGAATG
1 TTCTAGAAAATTCTAAACTTCTCAAGAAAGCTCTAGAATG
* *
470694 TTCTAGAAAATTCTAAACTTCTCCAGAAAGCTCTAGAATT
1 TTCTAGAAAATTCTAAACTTCTCAAGAAAGCTCTAGAATG
470734 TTCTAGAA
1 TTCTAGAA
470742 TCTCTCTAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (40 bp):
TTCTAGAAAATTCTAAACTTCTCAAGAAAGCTCTAGAATG
Found at i:471530 original size:30 final size:31
Alignment explanation
Indices: 471484--471543 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
471474 GGAAATGGTC
* *
471484 CCTAATGTTATAGATCCATTTGAT-TTAGTA
1 CCTAATATTATAGATCCATTCGATGTTAGTA
*
471514 CCTAATATTATCGATCCATTCGATGTTAGT
1 CCTAATATTATAGATCCATTCGATGTTAGT
471544 CCCTCAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (31 bp):
CCTAATATTATAGATCCATTCGATGTTAGTA
Found at i:473172 original size:13 final size:13
Alignment explanation
Indices: 473151--473190 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
473141 AACAACTATC
*
473151 CCTAGTTTTCTCT
1 CCTAATTTTCTCT
473164 CCTAATTTTCTCT
1 CCTAATTTTCTCT
*
473177 TCTAATTTTCTCT
1 CCTAATTTTCTCT
473190 C
1 C
473191 ATTGATAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.12, C:0.30, G:0.03, T:0.55
Consensus pattern (13 bp):
CCTAATTTTCTCT
Found at i:474090 original size:3 final size:3
Alignment explanation
Indices: 474084--474111 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
474074 AATTATTATC
474084 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
474112 AATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:474934 original size:17 final size:17
Alignment explanation
Indices: 474914--474952 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
474904 CTATTTAAAG
474914 AAAACCCTAATTTAGAC
1 AAAACCCTAATTTAGAC
*
474931 AAAACTCTAATTTAGAC
1 AAAACCCTAATTTAGAC
474948 AAAAC
1 AAAAC
474953 AAACCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.23
Consensus pattern (17 bp):
AAAACCCTAATTTAGAC
Found at i:481806 original size:3 final size:3
Alignment explanation
Indices: 481794--481838 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
481784 AATAGCTCAC
481794 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
481839 ATTTTGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:493220 original size:24 final size:22
Alignment explanation
Indices: 493192--493263 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 22
493182 TCAAAATTAT
493192 TAATATAAAAGTAATTTAAAATAA
1 TAATATAAAA-T-ATTTAAAATAA
* * *
493216 TAATAAAATAATATTTATAATAT
1 TAATATAA-AATATTTAAAATAA
*
493239 TAAATTTAAAATTATTTAAAATAA
1 T-AATATAAAA-TATTTAAAATAA
493263 T
1 T
493264 TATTATCATT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
23 12 0.32
24 24 0.63
25 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (22 bp):
TAATATAAAATATTTAAAATAA
Found at i:493235 original size:36 final size:36
Alignment explanation
Indices: 493195--493263 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
493185 AAATTATTAA
493195 TATAAAAGT-AATTTAAAATAATAATAAAATAATATT
1 TATAAAAGTAAATTTAAAATAAT-ATAAAATAATATT
* * * *
493231 TATAATATTAAATTTAAAATTATTTAAAATAAT
1 TATAAAAGTAAATTTAAAATAATATAAAATAAT
493264 TATTATCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 16 0.57
37 12 0.43
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (36 bp):
TATAAAAGTAAATTTAAAATAATATAAAATAATATT
Found at i:498161 original size:41 final size:41
Alignment explanation
Indices: 498104--498181 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
498094 TATTTATGTT
* *
498104 TTTATATATTTTTACTTAATTCGTATCATAATTAAATAGTC
1 TTTATATATTATTACTTAATTCGAATCATAATTAAATAGTC
* *
498145 TTTATATATTATTACTTAATTTGAATCGTAATTAAAT
1 TTTATATATTATTACTTAATTCGAATCATAATTAAAT
498182 TTAAGGTGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (41 bp):
TTTATATATTATTACTTAATTCGAATCATAATTAAATAGTC
Found at i:498366 original size:43 final size:43
Alignment explanation
Indices: 498319--498485 Score: 208
Period size: 43 Copynumber: 3.9 Consensus size: 43
498309 GCGGGTTTAA
* * *
498319 AAAAACGTTGCTAAATAACAAACTTGTTGTGGCGTTTGTGCCT
1 AAAAACGCTGCTAAATAACAAACATGTTGCGGCGTTTGTGCCT
* * *
498362 AAAAACACTGCTAAATAACAAACATGTTGTGGAGTTTGTGCCT
1 AAAAACGCTGCTAAATAACAAACATGTTGCGGCGTTTGTGCCT
* * * *
498405 AAAAACGCAGCTAGATAACAAACATGTTGCAGCGTTTATGCCT
1 AAAAACGCTGCTAAATAACAAACATGTTGCGGCGTTTGTGCCT
** * *
498448 AAAAACGCCACTAAATAACAAACCTATTGCGGCGTTTG
1 AAAAACGCTGCTAAATAACAAACATGTTGCGGCGTTTG
498486 AAAATACAAA
Statistics
Matches: 106, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 106 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (43 bp):
AAAAACGCTGCTAAATAACAAACATGTTGCGGCGTTTGTGCCT
Found at i:503140 original size:22 final size:22
Alignment explanation
Indices: 503115--503177 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 22
503105 GCAACGCGAT
503115 TTTGAAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
503137 TTTGAAAAACGTGTTGTTGCGATAG
1 TTTGAAAAA--TG-TGTTGCGAGAG
503162 --TGAAAAA-GTGTTGCGA
1 TTTGAAAAATGTGTTGCGA
503178 TAGTGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 8 0.22
20 1 0.03
22 9 0.24
23 7 0.19
24 2 0.05
25 10 0.27
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:503175 original size:19 final size:19
Alignment explanation
Indices: 503151--503187 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
503141 AAAAACGTGT
503151 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
503170 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
503188 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:503547 original size:19 final size:20
Alignment explanation
Indices: 503509--503549 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
503499 TTCTTAAGAA
503509 ATCGCAACGTGAACTTGGACT
1 ATCGCAACG-GAACTTGGACT
*
503530 ATCGCAAC-GAATTTGGACT
1 ATCGCAACGGAACTTGGACT
503549 A
1 A
503550 ACGTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAACGGAACTTGGACT
Found at i:503655 original size:20 final size:19
Alignment explanation
Indices: 503632--503669 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
503622 GGAAATTGAT
503632 TTGCGATACTAGAGATCGCG
1 TTGCGAT-CTAGAGATCGCG
*
503652 TTGCGATTTAGAGATCGC
1 TTGCGATCTAGAGATCGC
503670 ATTGTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCG
Found at i:503665 original size:19 final size:19
Alignment explanation
Indices: 503641--503679 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
503631 TTTGCGATAC
*
503641 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCGATT
*
503660 TAGAGATCGCATTGTGATT
1 TAGAGATCGCATTGCGATT
503679 T
1 T
503680 TGTTGGTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (19 bp):
TAGAGATCGCATTGCGATT
Found at i:504181 original size:15 final size:15
Alignment explanation
Indices: 504161--504190 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
504151 TCATTTTGAA
504161 TTTGTTAACTAAATT
1 TTTGTTAACTAAATT
*
504176 TTTGTTTACTAAATT
1 TTTGTTAACTAAATT
504191 AAAGAATCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTGTTAACTAAATT
Found at i:506798 original size:20 final size:19
Alignment explanation
Indices: 506775--506821 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
506765 CGATATAACA
*
506775 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
506795 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
506815 GGTAAAA
1 GGTAAAA
506822 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:509152 original size:33 final size:33
Alignment explanation
Indices: 509110--509175 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
509100 AAATAGATGG
*
509110 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
509143 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
509176 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:511029 original size:19 final size:19
Alignment explanation
Indices: 510966--511028 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
510956 AATGTCGAGT
*
510966 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
510985 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
511004 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
511023 T-ATTTT
1 TAATTTT
511029 TTTATGTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.12
19 38 0.88
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:511925 original size:197 final size:199
Alignment explanation
Indices: 511111--512521 Score: 2490
Period size: 199 Copynumber: 7.1 Consensus size: 199
511101 TTAAGGGTCA
* * ***
511111 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
511175 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
511240 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
511305 TAATG
195 TAATG
511310 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
511375 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
511440 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
511505 AATG
196 AATG
*
511509 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
*
511573 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
511638 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
511703 TAATG
195 TAATG
* ***
511708 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
511772 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
511837 TAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
511901 AATG
196 AATG
*
511905 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
*
511970 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
512035 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
512100 TAATG
195 TAATG
***
512105 TGTCGACA-T-A-ATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
512165 AATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
512228 TAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
512292 AATG
196 AATG
*
512296 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
*
512361 CATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
512424 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
512489 AATG
196 AATG
*
512493 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
512522 CTAATTTAAA
Statistics
Matches: 1164, Mismatches: 36, Indels: 26
0.95 0.03 0.02
Matches are distributed among these distances:
191 65 0.06
192 54 0.05
193 5 0.00
194 23 0.02
195 38 0.03
196 95 0.08
197 212 0.18
198 153 0.13
199 390 0.34
200 129 0.11
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:511936 original size:397 final size:397
Alignment explanation
Indices: 511111--512521 Score: 2583
Period size: 397 Copynumber: 3.6 Consensus size: 397
511101 TTAAGGGTCA
* * *** *
511111 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
511175 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
511240 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
* ***
511305 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGT
511370 GCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
260 GCATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
511435 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
325 TAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
511500 TAAATAATG
389 TAAATAATG
511509 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
511573 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
511638 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
511703 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
511768 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
511833 AATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
326 AATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
511898 AATAATG
391 AATAATG
511905 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
511970 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
512035 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
512100 TAATGTGTCGACA-T-A-ATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
512161 CATCAATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
512224 AATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
326 AATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
512289 AATAATG
391 AATAATG
512296 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
512361 CATAAAGTGTCGATCC--ATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
512423 GTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAA
131 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
*
512488 TAATGTGTCGACACTAATATATTTTGTGTCGATA
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
512522 CTAATTTAAA
Statistics
Matches: 992, Mismatches: 16, Indels: 17
0.97 0.02 0.02
Matches are distributed among these distances:
388 117 0.12
389 5 0.01
390 1 0.00
391 211 0.21
393 50 0.05
394 16 0.02
395 1 0.00
396 76 0.08
397 307 0.31
398 208 0.21
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (397 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
AATAATG
Found at i:514014 original size:3 final size:3
Alignment explanation
Indices: 513995--514044 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
513985 TGAAGCTGAC
* * *
513995 GAT GA- GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
514042 GAT
1 GAT
514045 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:516027 original size:183 final size:184
Alignment explanation
Indices: 515405--516082 Score: 1232
Period size: 184 Copynumber: 3.7 Consensus size: 184
515395 CTTTCAACAT
**
515405 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
515470 GGTCTACAACCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTG
66 GG--T-----CTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTG
515535 GAAGAAAATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
124 GAAGAAAATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
515596 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
515661 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
515726 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
515780 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
515845 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA-TGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
515909 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
515963 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
516028 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
516083 CCATTTAAAA
Statistics
Matches: 481, Mismatches: 6, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
183 179 0.37
184 236 0.49
189 1 0.00
191 65 0.14
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
ATTGTGTCGATATAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:518599 original size:23 final size:23
Alignment explanation
Indices: 518572--518629 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
518562 ATTACATAAG
518572 ATGTAATAGGTAGCCCTTATATA
1 ATGTAATAGGTAGCCCTTATATA
* **
518595 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCCCTTATATA
518618 ATGTAATAGGTA
1 ATGTAATAGGTA
518630 ATGGTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCCCTTATATA
Found at i:518637 original size:23 final size:23
Alignment explanation
Indices: 518572--518639 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
518562 ATTACATAAG
* **
518572 ATGTAATAGGTAGCCCTTATATA
1 ATGTAATAGGTATCGGTTATATA
*
518595 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTATCGGTTATATA
518618 ATGTAATAGGTAAT-GGTTATAT
1 ATGTAATAGGT-ATCGGTTATAT
518640 TGTAAAGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 38 0.95
24 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
ATGTAATAGGTATCGGTTATATA
Found at i:519026 original size:23 final size:23
Alignment explanation
Indices: 518995--519057 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
518985 ATAGGTAAAC
*
518995 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
519018 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
519041 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
519058 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:519065 original size:23 final size:23
Alignment explanation
Indices: 518995--519067 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
518985 ATAGGTAAAC
* * **
518995 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
519018 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
519041 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
519064 ATAT
1 ATAT
519068 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:519840 original size:12 final size:12
Alignment explanation
Indices: 519823--519847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
519813 GTAAACGAGG
519823 AGAGATATTATA
1 AGAGATATTATA
519835 AGAGATATTATA
1 AGAGATATTATA
519847 A
1 A
519848 TTTAAAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
AGAGATATTATA
Found at i:519890 original size:40 final size:40
Alignment explanation
Indices: 519835--519911 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
519825 AGATATTATA
* * *
519835 AGAGATATTATAATTTAAAGTTGAAAAATAATAATTTAGG
1 AGAGATAGTATAATTTAAAGTTAAAAAACAATAATTTAGG
519875 AGAGATAGTATAATTTAAAGTTAAAAAACAATAATTT
1 AGAGATAGTATAATTTAAAGTTAAAAAACAATAATTT
519912 TAGAACGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.52, C:0.01, G:0.13, T:0.34
Consensus pattern (40 bp):
AGAGATAGTATAATTTAAAGTTAAAAAACAATAATTTAGG
Found at i:520249 original size:13 final size:13
Alignment explanation
Indices: 520227--520256 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
520217 AATCATCAAT
*
520227 TTCAGTTAAAAGA
1 TTCAGGTAAAAGA
520240 TTCAGGTAAAAGA
1 TTCAGGTAAAAGA
520253 TTCA
1 TTCA
520257 AAACTAGATT
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:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (13 bp):
TTCAGGTAAAAGA
Found at i:522194 original size:21 final size:20
Alignment explanation
Indices: 522140--522200 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
522130 TATTTAAGGT
522140 ATATTTTATT-ATATT-TTTA
1 ATATTTTATTAAT-TTATTTA
522159 ATATTTTGTATTTAATTTATTTA
1 ATA-TTT-TA-TTAATTTATTTA
522182 ATATTTTACTTAA-TTATTT
1 ATATTTTA-TTAATTTATTT
522201 TTTTTGCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 3 0.08
20 9 0.25
21 8 0.22
22 7 0.19
23 9 0.25
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
ATATTTTATTAATTTATTTA
Found at i:524672 original size:20 final size:21
Alignment explanation
Indices: 524635--524674 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
524625 AAATTAAGTT
524635 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
524656 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
524675 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:524960 original size:65 final size:63
Alignment explanation
Indices: 524844--525050 Score: 220
Period size: 65 Copynumber: 3.2 Consensus size: 63
524834 ATTTGAGGTG
* * * * *
524844 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
524908 C
63 C
* *
524909 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * * **
524974 ATGCATCAATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATC-A-CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
525038 ATGCATCGATGCA
1 ATGCACCGATGCA
525051 CACTTGGTGC
Statistics
Matches: 122, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 36 0.30
65 83 0.68
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:532396 original size:21 final size:21
Alignment explanation
Indices: 532354--532397 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
532344 ACCCCGGGAG
*
532354 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
532375 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
532396 CT
1 CT
532398 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:533171 original size:20 final size:21
Alignment explanation
Indices: 533134--533173 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
533124 AAATTAAGTT
533134 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
533155 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
533174 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:533477 original size:65 final size:60
Alignment explanation
Indices: 533390--533541 Score: 159
Period size: 57 Copynumber: 2.5 Consensus size: 60
533380 GAATTAATTG
* * * *
533390 AAACATCGAATGTATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTC
1 AAACATCGAATGCATTTCATGCA-CGATGCA---GCCATGCATCGATGCACTCAGAATATTTTC
* **
533454 AAAACATCGAATGCATTTGATGCAC-A---AGCCATGCATCGATGCACTCAGGCTATTTTC
1 -AAACATCGAATGCATTTCATGCACGATGCAGCCATGCATCGATGCACTCAGAATATTTTC
533511 AAACATCGAATGCATTTCATGCATCGATGCA
1 AAACATCGAATGCATTTCATGCA-CGATGCA
533542 CACTTGGTGC
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
56 22 0.30
57 27 0.36
58 1 0.01
60 1 0.01
61 1 0.01
63 1 0.01
64 1 0.01
65 20 0.27
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (60 bp):
AAACATCGAATGCATTTCATGCACGATGCAGCCATGCATCGATGCACTCAGAATATTTTC
Found at i:533522 original size:56 final size:57
Alignment explanation
Indices: 533425--533533 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
533415 GATGCATTCT
* *
533425 CCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTGATGCACAAG
1 CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCACAAG
**
533482 CCATGCATCGATGCACTCAGGCTATTTTC-AAACATCGAATGCATTTCATGCA
1 CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCA
533534 TCGATGCACA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
56 22 0.46
57 26 0.54
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (57 bp):
CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCACAAG
Found at i:536980 original size:182 final size:183
Alignment explanation
Indices: 536687--537166 Score: 770
Period size: 182 Copynumber: 2.6 Consensus size: 183
536677 CGATCCAAAT
* *
536687 TAAAAATGTATCGATCCA-TATCAATATAACAAGTAAAAATATGACAAAACCGGTCA-CGAAAA-
1 TAAAAATGTATCGATCCACAAT-GATATAACAAGTAAAAATATGACAAAACCGGT-ATC-AAAAT
*
536749 GATAATACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
63 GATAAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
*
536814 TTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAAGTGTCGATACTTT-A
128 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAAGTGTCGATACTTTAA
* *
536869 TAAAAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAATCGGTATCAAAATGAT
1 TAAAAATGTATCGATCCACAATGATATAACAAGTAAAAATATGACAAAACCGGTATCAAAATGAT
536934 AAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
66 AAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* *
536999 TGTGAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAAGTGTCGATACTTTAA
* * * * *
537052 AAAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCAGTATCGAAATGAT
1 TAAAAATGTATCGATCCACAATGATATAACAAGTAAAAATATGACAAAACCGGTATCAAAATGAT
* *
537117 AAAACCAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
66 AAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATA
537167 AGTACGTGTA
Statistics
Matches: 278, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
181 5 0.02
182 163 0.59
183 110 0.40
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (183 bp):
TAAAAATGTATCGATCCACAATGATATAACAAGTAAAAATATGACAAAACCGGTATCAAAATGAT
AAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAAGTGTCGATACTTTAA
Found at i:538649 original size:199 final size:195
Alignment explanation
Indices: 538186--538802 Score: 602
Period size: 200 Copynumber: 3.1 Consensus size: 195
538176 GGATAGTGAA
** * *
538186 AAATATACTAGTTTTATGAGAGAATATGTCTACAA-CATGTATCGACACTTTTTAATATTGTGTC
1 AAATATACCGGTTTTATGAGAAAATA-GTCTACAATAATGTATCGACACTTTTTAAT-TTGTGTC
* ** * * * * *
538250 GATACTTTTTGTCCAGAATGGATGCCAAA-AAGGGTGAACGCACAAAGTGTTGATACATTT-TAA
64 GATAC-TTTTGTCCATAATTAATGCCAAACGA-GGTGCACGCATAAAATGTCGATACATTTAT-A
* * *
538313 AAACGTGTCGATCCAAAAAACATCGAAATCCATAATTATAATATAATAGGTAAATTTACAATGTA
126 AAA-GTATCGATCCAAAAAACATCGAAA-CCAAAATTATAATGTAATAGGTAAATTTACAATGT-
538378 ACCGGTAT
188 ACCGGTAT
* * * * * *
538386 AAATATATCGGGTTTATGAAAAAATAGGT-GAGC-ATAAAGTATCGACACTTGTTAAATTTGTGT
1 AAATATACCGGTTTTATGAGAAAATA-GTCTA-CAATAATGTATCGACACTT-TTTAATTTGTGT
* * *
538449 CGATACATTTTGTCCATAATTAATGCCAAACGAGGTGCACGCATAGATTGTCAATACATTTATTA
63 CGATAC-TTTTGTCCATAATTAATGCCAAACGAGGTGCACGCATAAAATGTCGATACATTTA-TA
* * * *
538514 AAAGTATCGATCCCAAAAACATCGAAACGAAAATTACAATGTGATAGGTAAATTTACAATGTACC
126 AAAGTATCGATCCAAAAAACATCGAAACCAAAATTATAATGTAATAGGTAAATTTACAATGTA-C
538579 CGGTAT
190 CGGTAT
* * *
538585 AAATATACCGGTTTTATGAGAAAATAGATCTA-AATAATGTAGCTACACCTTTTTAGTTTGTGTC
1 AAATATACCGGTTTTATGAGAAAATAG-TCTACAATAATGTATCGACA-CTTTTTAATTTGTGTC
* *
538649 GATACTTTT-TCCAGAATGAAATATGAATGCCCAACGAGGTGCAAGCATAAAATGTCGATACATT
64 GATACTTTTGTCC---AT--AAT-T-AATGCCAAACGAGGTGCACGCATAAAATGTCGATACATT
* * * *
538713 TA-AAATTGTATCGATCTAAAAAACATCGAAACCAATAATAATAATGTAATAGATAAATTTACAA
122 TATAAA-AGTATCGATCCAAAAAACATCGAAACCAA-AATTATAATGTAATAGGTAAATTTACAA
*
538777 TGTTACCAGTAT
185 TG-TACCGGTAT
538789 AAATATACCGGTTT
1 AAATATACCGGTTT
538803 ACTTCGAAAA
Statistics
Matches: 344, Mismatches: 52, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
197 3 0.01
198 6 0.02
199 90 0.26
200 118 0.34
201 10 0.03
202 7 0.02
203 26 0.08
204 82 0.24
205 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (195 bp):
AAATATACCGGTTTTATGAGAAAATAGTCTACAATAATGTATCGACACTTTTTAATTTGTGTCGA
TACTTTTGTCCATAATTAATGCCAAACGAGGTGCACGCATAAAATGTCGATACATTTATAAAAGT
ATCGATCCAAAAAACATCGAAACCAAAATTATAATGTAATAGGTAAATTTACAATGTACCGGTAT
Found at i:538791 original size:204 final size:198
Alignment explanation
Indices: 538228--538802 Score: 576
Period size: 199 Copynumber: 2.9 Consensus size: 198
538218 CAACATGTAT
* * * ** *
538228 CGACACTT-TTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAA-AAGGGTG-AACG
1 CGACACTTGTTAAAT-TTGTGTCGATACATTTTGTCCATAATTAATGCCAAACGA-GGTGCAA-G
* * * *
538290 CACAAAGTGTTGATACATTTTAAAAACGTGTCGATCCAAAAAACATCGAAATCC-ATAATTATAA
63 CATAAAATGTCGATACA-TTTAAAAA-GTATCGATCCAAAAAACATCGAAA-CCAATAATTATAA
* * * * * *
538354 TATAATAGGTAAATTTACAATGTAACCGGTATAAATATATCGGGTTTATGAAAAAATAGGTGAGC
125 TGTAATAGGTAAATTTACAATGTTACCGGTATAAATATACCGGTTTTATGAAAAAATAGATGAGA
*
538419 ATAAAGTAT
190 ATAAAGTAG
*
538428 CGACACTTGTTAAATTTGTGTCGATACATTTTGTCCATAATTAATGCCAAACGAGGTGCACGCAT
1 CGACACTTGTTAAATTTGTGTCGATACATTTTGTCCATAATTAATGCCAAACGAGGTGCAAGCAT
* * * * * * *
538493 AGATTGTCAATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACGAA-AATTACAATGTG
66 AAAATGTCGATACATTTA--AAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTA
* *
538557 ATAGGTAAATTTACAATG-TACCCGGTATAAATATACCGGTTTTATGAGAAAATAGATCTA-AAT
129 ATAGGTAAATTTACAATGTTA-CCGGTATAAATATACCGGTTTTATGAAAAAATAGAT-GAGAAT
*
538620 AATGTAG
192 AAAGTAG
* * * *
538627 CTACACCTT-TTTAGTTTGTGTCGATAC-TTTT-TCCAGAATGAAATATGAATGCCCAACGAGGT
1 CGACA-CTTGTTAAATTTGTGTCGATACATTTTGTCC---AT--AAT-T-AATGCCAAACGAGGT
* * *
538689 GCAAGCATAAAATGTCGATACATTTAAAATTGTATCGATCTAAAAAACATCGAAACCAATAATAA
58 GCAAGCATAAAATGTCGATACATTTAAAA-AGTATCGATCCAAAAAACATCGAAACCAATAATTA
* *
538754 TAATGTAATAGATAAATTTACAATGTTACCAGTATAAATATACCGGTTT
122 TAATGTAATAGGTAAATTTACAATGTTACCGGTATAAATATACCGGTTT
538803 ACTTCGAAAA
Statistics
Matches: 312, Mismatches: 44, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
197 3 0.01
198 5 0.02
199 91 0.29
200 86 0.28
201 11 0.04
202 6 0.02
203 26 0.08
204 82 0.26
205 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (198 bp):
CGACACTTGTTAAATTTGTGTCGATACATTTTGTCCATAATTAATGCCAAACGAGGTGCAAGCAT
AAAATGTCGATACATTTAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAAT
AGGTAAATTTACAATGTTACCGGTATAAATATACCGGTTTTATGAAAAAATAGATGAGAATAAAG
TAG
Found at i:538956 original size:26 final size:23
Alignment explanation
Indices: 538896--538945 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
538886 CGGTTAAATG
538896 CCTATTTTATTATATAAGCGCTA
1 CCTATTTTATTATATAAGCGCTA
**
538919 CCTATTACATTATATAAGCGCTA
1 CCTATTTTATTATATAAGCGCTA
538942 CCTA
1 CCTA
538946 ATATGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (23 bp):
CCTATTTTATTATATAAGCGCTA
Found at i:540222 original size:50 final size:48
Alignment explanation
Indices: 540166--540265 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 48
540156 TATAAAATAA
*
540166 ATTTTAAATTAGTAATATTTTA-AATTGTTTACTATATATATATATATATTT
1 ATTTAAAATTA-TAAT-TTTTATAA-T-TTTACTATATATATATATATATTT
*
540217 ATTTAAAAAATTATAATTTTTATAATTTTATTATATATATATATATATT
1 ATTT--AAAATTATAATTTTTATAATTTTACTATATATATATATATATT
540266 CACATTATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
50 22 0.50
51 10 0.23
52 6 0.14
53 6 0.14
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (48 bp):
ATTTAAAATTATAATTTTTATAATTTTACTATATATATATATATATTT
Found at i:544381 original size:19 final size:20
Alignment explanation
Indices: 544359--544399 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
544349 AAATTTATGC
*
544359 ATGATATAT-AATTTTTTAT
1 ATGATATATAAATTATTTAT
*
544378 ATGATGTATAAATTATTTAT
1 ATGATATATAAATTATTTAT
544398 AT
1 AT
544400 TTTATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
ATGATATATAAATTATTTAT
Found at i:544724 original size:3 final size:3
Alignment explanation
Indices: 544706--544755 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
544696 TCTACAAAAA
* *
544706 TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TA- TAA TAT TAT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
544751 TAT TA
1 TAT TA
544756 ATTTATATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 6 0.15
3 35 0.85
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:544736 original size:20 final size:20
Alignment explanation
Indices: 544706--544755 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
544696 TCTACAAAAA
*
544706 TATTA-TATTATATTATTAT
1 TATTATTATTATAATATTAT
544725 TATTATTATTATAATATTAT
1 TATTATTATTATAATATTAT
*
544745 TATTTTTATTA
1 TATTATTATTA
544756 ATTTATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTATTATTATAATATTAT
Found at i:544761 original size:17 final size:17
Alignment explanation
Indices: 544704--544767 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
544694 GGTCTACAAA
544704 AATATTA-TATTA-TATT
1 AATATTATTATTATTA-T
*
544720 ATTATTATTATTATTAT
1 AATATTATTATTATTAT
*
544737 AATATTATTATTTTTATT
1 AATATTATTATTATTA-T
544755 AAT-TTATATATTA
1 AATATTAT-TATTA
544768 CAATTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
16 6 0.15
17 24 0.60
18 10 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATATTATTATTATTAT
Found at i:547577 original size:18 final size:18
Alignment explanation
Indices: 547522--547585 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
547512 CGAAACCGAT
547522 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
* *
547540 ATTTTT---TAACAGTTCGGG
1 -TTTTTCGGT-TCGGTTC-GG
547558 TTTTTCGGTTCGGTTCGG
1 TTTTTCGGTTCGGTTCGG
*
547576 TTTTTTGGTT
1 TTTTTCGGTT
547586 TTTCAATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
16 1 0.03
17 10 0.29
18 13 0.37
19 10 0.29
20 1 0.03
ACGTcount: A:0.06, C:0.12, G:0.28, T:0.53
Consensus pattern (18 bp):
TTTTTCGGTTCGGTTCGG
Found at i:553082 original size:69 final size:69
Alignment explanation
Indices: 552964--553139 Score: 235
Period size: 69 Copynumber: 2.6 Consensus size: 69
552954 AACTTACACA
* * * * * *
552964 AGATTGGATTTCAACTTCATAACGAAGGATATCCAACTCAAATCCAATTTGGCGAAGCAATACAA
1 AGATTGGATTTCAACTTCACAACGAAGGACATCCAACTAAAAACCAATTTAGCAAAGCAATACAA
553029 CTCG
66 CTCG
* * *
553033 AGATTGGATTTCAACTTCACAACGTAGGACATCCAACTAAAAACTAATTTAGTAAAGCAATACAA
1 AGATTGGATTTCAACTTCACAACGAAGGACATCCAACTAAAAACCAATTTAGCAAAGCAATACAA
553098 CTCG
66 CTCG
* * * *
553102 AGATTGGATTTTAACTTCACAATGAAGTATATCCAACT
1 AGATTGGATTTCAACTTCACAACGAAGGACATCCAACT
553140 CAAAGCTCAA
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 93 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (69 bp):
AGATTGGATTTCAACTTCACAACGAAGGACATCCAACTAAAAACCAATTTAGCAAAGCAATACAA
CTCG
Found at i:553402 original size:2 final size:2
Alignment explanation
Indices: 553390--553517 Score: 123
Period size: 2 Copynumber: 73.5 Consensus size: 2
553380 TACAAAACAG
553390 TA TA T- TA TA TA TA TA T- TA TA T- TA TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
553426 TA TA T- TA TA TA TA T- TA T- TA TA TA TA T- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
553463 T- TA TA T- TA TA TA TA TA TA T- TA TA T- TA TA T- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
553499 TA TA TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
553518 TATTATTATT
Statistics
Matches: 107, Mismatches: 0, Indels: 38
0.74 0.00 0.26
Matches are distributed among these distances:
1 19 0.18
2 88 0.82
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:553409 original size:5 final size:5
Alignment explanation
Indices: 553390--553565 Score: 204
Period size: 5 Copynumber: 34.4 Consensus size: 5
553380 TACAAAACAG
553390 TATAT TATAT ATATAT TATAT TATAT TATAT TATAT TATAT TATA- TATAT
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
553440 TATTAT ATATAT TATATT ATATAT TATAT TATA- TATA- TATAT TATAT
1 TA-TAT -TATAT TATA-T -TATAT TATAT TATAT TATAT TATAT TATAT
553487 TATAT TATAT TATAT ATATAT TATAT TATA- T-TAT TATTAT TATTAT
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TA-TAT TA-TAT
553533 TATAT TATTAT TATTAT TATTAT TA-A- TATAT TA
1 TATAT TA-TAT TA-TAT TA-TAT TATAT TATAT TA
553566 CAATTATTTT
Statistics
Matches: 157, Mismatches: 0, Indels: 28
0.85 0.00 0.15
Matches are distributed among these distances:
3 4 0.03
4 16 0.10
5 85 0.54
6 46 0.29
7 6 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:553443 original size:12 final size:12
Alignment explanation
Indices: 553392--553565 Score: 168
Period size: 12 Copynumber: 14.2 Consensus size: 12
553382 CAAAACAGTA
553392 TATTATATATA-
1 TATTATATATAT
553403 TATTATAT-TA-
1 TATTATATATAT
553413 TATTATATTATATT
1 TATTATA-TATA-T
553427 ATATTATATATAT
1 -TATTATATATAT
553440 TATTATATATAT
1 TATTATATATAT
553452 TA-TATTATATATT
1 TATTA-TATATA-T
553465 ATATTATATATAT
1 -TATTATATATAT
553478 ATATTATATTATAT
1 -TATTATA-TATAT
553492 TA-TATTATATAT
1 TATTA-TATATAT
553504 ATATTATATTATAT
1 -TATTATA-TATAT
553518 TATTAT-TATTAT
1 TATTATATA-TAT
553530 TATTATAT-TAT
1 TATTATATATAT
553541 TATTAT-TATTAT
1 TATTATATA-TAT
553553 TATTA-ATATAT
1 TATTATATATAT
553564 TA
1 TA
553566 CAATTATTTT
Statistics
Matches: 144, Mismatches: 0, Indels: 38
0.79 0.00 0.21
Matches are distributed among these distances:
10 10 0.07
11 27 0.19
12 48 0.33
13 26 0.18
14 24 0.17
15 9 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATATATAT
Found at i:553450 original size:26 final size:26
Alignment explanation
Indices: 553395--553565 Score: 196
Period size: 26 Copynumber: 6.5 Consensus size: 26
553385 AACAGTATAT
553395 TATATA-TATATTATAT-TA-TATTA
1 TATATATTATATTATATATATTATTA
553418 TATTATATTATATTATATATATTATTA
1 TA-TATATTATATTATATATATTATTA
553445 TATATATTATATTATATATTATATTATATA
1 TATATATTATA-T-TATA-TATATTAT-TA
553475 TATATATTATATTATATTATATTA-TA
1 TATATATTATATTATA-TATATTATTA
553501 TATATATTATATTATAT-TATTATTA
1 TATATATTATATTATATATATTATTA
553526 T-TATTATTATATTAT-TATTATTATTA
1 TATA-TATTATATTATATA-TATTATTA
*
553552 T-TATTAATATATTA
1 TATA-TATTATATTA
553566 CAATTATTTT
Statistics
Matches: 135, Mismatches: 1, Indels: 21
0.86 0.01 0.13
Matches are distributed among these distances:
23 2 0.01
24 12 0.09
25 25 0.19
26 50 0.37
27 8 0.06
28 16 0.12
29 9 0.07
30 13 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TATATATTATATTATATATATTATTA
Found at i:553572 original size:20 final size:23
Alignment explanation
Indices: 553404--553557 Score: 75
Period size: 21 Copynumber: 6.9 Consensus size: 23
553394 TTATATATAT
*
553404 ATTA-TATTATATTA-TATTA-T
1 ATTATTATTATATTATTATTACA
*
553424 ATTA-TATTATATATATTATTA-T
1 ATTATTATTATAT-TATTATTACA
*
553446 A-TA-TATTATATTATATATTA-T
1 ATTATTATTATATTAT-TATTACA
*
553467 ATTATATATATATATTA-TATTA-T
1 ATTAT-TAT-TATATTATTATTACA
*
553490 ATTA-TATTATA-TATATATTA-T
1 ATTATTATTATATTAT-TATTACA
*
553511 ATTA-TATTATTATTATTATTATTA
1 ATTATTATTA-TATTATTATTA-CA
553535 TATTATTATTATTATTATTATTA
1 -ATTATTATTA-TATTATTATTA
553558 ATATATTACA
Statistics
Matches: 118, Mismatches: 1, Indels: 24
0.83 0.01 0.17
Matches are distributed among these distances:
19 2 0.02
20 19 0.16
21 37 0.31
22 16 0.14
23 13 0.11
24 3 0.03
25 11 0.09
26 17 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTATTATTATATTATTATTACA
Found at i:566521 original size:11 final size:11
Alignment explanation
Indices: 566505--566532 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
566495 AGAAAAAAGA
566505 AAAAAAGGAAC
1 AAAAAAGGAAC
566516 AAAAAAGGAAC
1 AAAAAAGGAAC
566527 AAAAAA
1 AAAAAA
566533 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAGGAAC
Found at i:566541 original size:11 final size:11
Alignment explanation
Indices: 566483--566551 Score: 50
Period size: 11 Copynumber: 6.1 Consensus size: 11
566473 CCTGAAGATG
*
566483 AAAAAATGAAA
1 AAAAAAAGAAA
*
566494 AAGAAAAA-AGA
1 AA-AAAAAGAAA
* *
566505 AAAAAAGGAAC
1 AAAAAAAGAAA
*
566516 AAAAAAGGAACAA
1 AAAAAAAG-A-AA
*
566529 AAAAAAATAAA
1 AAAAAAAGAAA
566540 AAAAAAAGAAA
1 AAAAAAAGAAA
566551 A
1 A
566552 TGAGAGTTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
10 4 0.09
11 28 0.62
12 6 0.13
13 7 0.16
ACGTcount: A:0.83, C:0.03, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:568017 original size:54 final size:53
Alignment explanation
Indices: 567827--568843 Score: 939
Period size: 54 Copynumber: 19.8 Consensus size: 53
567817 TAGTGAAGCG
* * *
567827 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTT
* * * *
567881 ---GAAGATGTCCAAGTTCCATACTCCCTAGAGAAAGA-GGAGTGAACCCGTGT
1 GAAGAAGATGTCCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTT
** * *
567931 GAAG-TTAT-T-AGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTT
567982 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTT
* * *
568036 ---GAAGATGTCTGAGTT-TCATACTCCCTAGAGAAAGAGGGAGC-AAACCG--C
1 GAAGAAGATGTCCGAGTTCT-ATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTT
** * *
568084 G-A-ATTAT-T-GGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTT
*
568134 GAAGAAGATGTCCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTT
* *
568188 GAAGAAGATGTTCGAGTTCCATACTCCCTGAGGAAAGAGGGAGCGAACCCG--T
1 GAAGAAGATGTCCGAGTTCTATACTCCCTGA-GAAAGAGGGAGCGAACCCGTTT
*
568240 -------ATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCC-ATT
1 GAAGAAGATGTCCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTT
* *
568286 ---GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
1 GAAGAAGATGTCCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTT
** * * *
568337 GAAG-TTAT-T-GGAGTTCTATACTTCCTGAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTGAGAAAGAGGGAGCGAACCCGTTT
*
568387 GAAGAAGATGTCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTT
* *
568441 ---GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
1 GAAGAAGATGTCCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTTT
** * *
568492 GAAG-TTAT-T-GGAGTTCTATACTTCCTGAAGAAAGA--GAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTT
* *
568541 GAAGAAGATGTCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACTCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTT
* *
568595 GAAGAAGATGTTCGAGTTCCATACT-CCT-AG-AAG-GGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTGAGAAAGAGGGAGCGAACCCGTTT
* * * *
568644 GAAGAAGATGTCTGAATTCCATACTCCCT-AGAAAGAGGGAGCGAA-CCG-AT
1 GAAGAAGATGTCCGAGTTCTATACTCCCTGAGAAAGAGGGAGCGAACCCGTTT
* * * **
568694 GAAAAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAGGG-GCGAACCCGTAA
1 GAAGAAGATGTCCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTT
* * ** * * * **
568747 GAAGACGATTTTTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGAGAACTCGTAA
1 GAAGAAGA--TGTCCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTTT
* * * *
568803 GAAGAAGATGTTCGAG-TCTCATACTCTCTGAAAAATAGGGA
1 GAAGAAGATGTCCGAGTTCT-ATACTCCCTGAGAAAGAGGGA
568844 ACACACGATA
Statistics
Matches: 815, Mismatches: 91, Indels: 115
0.80 0.09 0.11
Matches are distributed among these distances:
45 38 0.05
46 4 0.00
47 26 0.03
48 7 0.01
49 58 0.07
50 142 0.17
51 190 0.23
52 58 0.07
53 45 0.06
54 198 0.24
55 32 0.04
56 17 0.02
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (53 bp):
GAAGAAGATGTCCGAGTTCTATACTCCCTGAGAAAGAGGGAGCGAACCCGTTT
Found at i:568141 original size:155 final size:153
Alignment explanation
Indices: 567827--568744 Score: 967
Period size: 155 Copynumber: 6.0 Consensus size: 153
567817 TAGTGAAGCG
* * ***
567827 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTCCA
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTGG
* * ** *
567892 AGTTCCATACTCCCTAGAGAAAGA-GGAGTGAACCCGTGTGAAGTTATTAGAGTTCTATACTTCC
66 AGTTCCATACTCCCT-GAGAAAGAGGGAG-CAAACCGT-TGAAAATATTCGAGTTCTATACTTCC
567956 TGAAGAAAGAGGGAGCGAACCCGTTT
128 TGAAGAAAGAGGGAGCGAACCCGTTT
*
567982 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCT-
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGT-TG
* * * *
568046 GAGTTTCATACTCCCTAGAGAAAGAGGGAGCAAACCG-CG-AATTATTGGAGTTCTATACTTCCT
65 GAGTTCCATACTCCCT-GAGAAAGAGGGAGCAAACCGTTGAAAATATTCGAGTTCTATACTTCCT
568109 GAAGAAAGAGGGAGCGAACCCGTTT
129 GAAGAAAGAGGGAGCGAACCCGTTT
* *
568134 GAAGAAGATGTCCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATG
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAGATG
* * * *
568198 TTCGAGTTCCATACTCCCTGAGGAAAGAGGGAGCGAACCCG-T----ATGTCCGAGTTCTATACT
62 TTGGAGTTCCATACTCCCTGA-GAAAGAGGGAGC-AAACCGTTGAAAATATTCGAGTTCTATACT
* *
568258 CCCT-AGAGAAAGAGGGAGCGAACCC-ATT
125 TCCTGA-AGAAAGAGGGAGCGAACCCGTTT
* * *
568286 ---GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGG
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTGG
* * * *
568348 AGTTCTATACTTCCTGAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTCTGAGTTCTATACTC
66 AGTTCCATACTCCCTGAGAAAGAGGGAGCAAA-CCG-TTGAA-AATAT-TC-GAGTTCTATACTT
568413 CCT-AGAGAAAGAGGGAGCGAACCCGTTT
126 CCTGA-AGAAAGAGGGAGCGAACCCGTTT
* * *
568441 ---GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGG
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTGG
* * * *
568503 AGTTCTATACTTCCTGAAGAAAGA--GAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACT
66 AGTTCCATACTCCCTG-AGAAAGAGGGAGC-AAACCG-TTGAA-AATAT-T-CGAGTTCTATACT
*
568566 TCCTGAAGAAAGAGGGAGCGAACTCGTTT
125 TCCTGAAGAAAGAGGGAGCGAACCCGTTT
*
568595 GAAGAAGATGTTCGAGTTCCATACT-CCT--AG-AAG-GGGAGCGAACCCGTTTGAAGAAGATGT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT---GAAGATGT
* * * *
568655 CT-GAATTCCATACTCCCT-AGAAAGAGGGAGCGAACCGATGAAAAAGATGTTCGAGTTCTATAC
63 -TGGAGTTCCATACTCCCTGAGAAAGAGGGAGCAAACCGTTG--AAA-ATATTCGAGTTCTATAC
568718 TTCCTGAAGAAAGAGGG-GCGAACCCGT
124 TTCCTGAAGAAAGAGGGAGCGAACCCGT
568745 AAGAAGACGA
Statistics
Matches: 675, Mismatches: 50, Indels: 79
0.84 0.06 0.10
Matches are distributed among these distances:
144 2 0.00
145 15 0.02
146 23 0.03
147 1 0.00
149 46 0.07
150 1 0.00
151 1 0.00
152 127 0.19
153 79 0.12
154 106 0.16
155 233 0.35
156 20 0.03
157 21 0.03
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.22
Consensus pattern (153 bp):
GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTGG
AGTTCCATACTCCCTGAGAAAGAGGGAGCAAACCGTTGAAAATATTCGAGTTCTATACTTCCTGA
AGAAAGAGGGAGCGAACCCGTTT
Found at i:568185 original size:206 final size:206
Alignment explanation
Indices: 567830--568843 Score: 1080
Period size: 206 Copynumber: 4.9 Consensus size: 206
567820 TGAAGCGGAA
* * * * * * *
567830 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTCCAAGT
1 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAAC-CG--CGAAGTTATTCGAGT
* * * * ** *
567895 TCCATACTCCCT-AGAGAAAGA-GGAGTGAACCCGTGTGAAG-TTAT-T-AGAGTTCTATACTTC
63 TCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTC
* *
567955 CTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGA
127 CTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCT-GAGAAAGA
568020 GGGAGCGAACCCGTTT
191 GGGAGCGAACCCGTTT
* * *
568036 GAAGATGTCTGAGTTTCATACTCCCTAGAGAAAGAGGGAGCAAACCGCGAA-TTATTGGAGTTCT
1 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCGCGAAGTTATTCGAGTTCT
*
568100 ATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTGA
66 ATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCCTGA
*
568165 AGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTGAGGAAAGAGGGA
131 AGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGA-GAAAGAGGGA
568230 GCGAACCCG--T
195 GCGAACCCGTTT
* * * * *
568240 ----ATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACC-CATTGAAGATGTCCGAGT
1 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCGC---GAAGTTATTCGAGT
* * * ** *
568300 TCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTGTGAAG-TTAT-T-GGAGTTCTATACTTC
63 TCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTC
568361 CTG-AGAAAGAGGGAGCAAACCCGTTTGAAGAAGATG-TCTGAGTTCTATACTCCCTAGAGAAAG
127 CTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTC-GAGTTCTATACTCCCT-GAGAAAG
568424 AGGGAGCGAACCCGTTT
190 AGGGAGCGAACCCGTTT
* * *
568441 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGT
1 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGC-AAACC--GCGAAGTTATTCGAGT
568506 TCTATACTTCCTGAAGAAAGA--GAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCC
63 TCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCC
* * *
568569 TGAAGAAAGAGGGAGCGAACTCGTTTGAAGAAGATGTTCGAGTTCCATACT-CCT-AG-AAG-GG
128 TGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGAGAAAGAGG
568630 GAGCGAACCCGTTT
193 GAGCGAACCCGTTT
* * * * * *
568644 GAAGAAGATGTCTGAATTCCATACTCCCT--AGAAAGAGGGAGCGAACCGATGAAAAAGATGTTC
1 ---GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCG-CG---AAGTTATTC
** * * **
568707 GAGTTCTATACTTCCTGAAGAAAGAGGG-GCGAACCCGTAAGAAGACGATTTTTTTGAGTTCTAT
59 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA--TGTCCGAGTTCTAT
* ** *
568771 ACTTCCTGAAGAAAGAGGGAG-AGAACTCGTAAGAAGAAGATGTTCGAG-TCTCATACTCTCTGA
122 ACTTCCTGAAGAAAGAGGGAGCA-AACCCGTTTGAAGAAGATGTTCGAGTTCT-ATACTCCCTGA
* *
568834 AAAATAGGGA
185 GAAAGAGGGA
568844 ACACACGATA
Statistics
Matches: 688, Mismatches: 74, Indels: 86
0.81 0.09 0.10
Matches are distributed among these distances:
198 2 0.00
199 68 0.10
200 56 0.08
201 3 0.00
202 30 0.04
203 82 0.12
204 36 0.05
205 76 0.11
206 198 0.29
207 24 0.03
208 102 0.15
209 4 0.01
210 1 0.00
211 2 0.00
212 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (206 bp):
GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCGCGAAGTTATTCGAGTTCT
ATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCCTGA
AGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGAGAAAGAGGGAG
CGAACCCGTTT
Found at i:568484 original size:456 final size:451
Alignment explanation
Indices: 567830--568690 Score: 1154
Period size: 456 Copynumber: 1.9 Consensus size: 451
567820 TGAAGCGGAA
* * * *
567830 GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTCCAAGT
1 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCAAGT
** ** *
567895 TCCATACTCCCTAGAGAAAGAGGAGTGAACCCGTGTGAAGTTATTAGAGTTCTATACTTCCTGAA
66 TCCATACTCCCTAGAGAAAGAGGAGCAAACCCGTGTGAAGAGATTAGAGTTCTATACTCCCTGAA
*
567960 GAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAG
131 GAAAGAGGGAGCGAACCCGTTT--AGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAG
* *
568025 CGAACCCGTTTGAAGATGTCT-GAGTT-TCATACTCCCT-AGAGAAAGAGGGAGC-AAACCG-CG
194 CGAACCCGTGTGAAGATAT-TGGAGTTCT-ATACTCCCTGA-AGAAAGA--GAGCGAAACCGTCG
** *
568085 -A-ATTAT-T-GGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
254 AAGAAGATGTCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
* *
568146 CGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGT-TCGAGTTCCAT
319 CGAGTTCCATACT-CCT--AG-AAG-GGGAGCAAACCCGTTTGAAGAAGATGTCT-GAATTCCAT
568210 ACTCCCTGAGGAAAGAGGGAGCGAACCCGTATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGA
378 ACTCCCT-A-GAAAGAGGGAGCGAACCCGTATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGA
568275 GCGAACCCATT
441 GCGAACCCATT
* ***
568286 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGT
1 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCAAGT
* * * *
568351 TCTATACTTCCT-GAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATGTCTGAGTTCTATACTCCC
66 TCCATACTCCCTAGAGAAAGA-GGAGCAAACCCGTGTGAAG-AGAT-T-AGAGTTCTATACTCCC
568415 T-AGAGAAAGAGGGAGCGAACCCGTTT-GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGG
127 TGA-AGAAAGAGGGAGCGAACCCGTTTAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGG
* * * *
568478 GAGCGAACCCGTGTGAAGTTATTGGAGTTCTATACTTCCTGAAGAAAGAGAGCGAACCCGTTTGA
191 GAGCGAACCCGTGTGAAGATATTGGAGTTCTATACTCCCTGAAGAAAGAGAGCGAAACCG-TCGA
* *
568543 AGAAGATGTCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACTCGTTTGAAGAAGATGTTC
255 AGAAGATGTCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCC
*
568608 GAGTTCCATACTCCTAGAAGGGGAGCGAACCCGTTTGAAGAAGATGTCTGAATTCCATACTCCCT
320 GAGTTCCATACTCCTAGAAGGGGAGCAAACCCGTTTGAAGAAGATGTCTGAATTCCATACTCCCT
568673 AGAAAGAGGGAGCGAACC
385 AGAAAGAGGGAGCGAACC
568691 GATGAAAAAG
Statistics
Matches: 357, Mismatches: 32, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
454 21 0.06
455 15 0.04
456 199 0.56
457 9 0.03
458 5 0.01
459 41 0.11
460 4 0.01
461 63 0.18
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (451 bp):
GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATCCAAGT
TCCATACTCCCTAGAGAAAGAGGAGCAAACCCGTGTGAAGAGATTAGAGTTCTATACTCCCTGAA
GAAAGAGGGAGCGAACCCGTTTAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCG
AACCCGTGTGAAGATATTGGAGTTCTATACTCCCTGAAGAAAGAGAGCGAAACCGTCGAAGAAGA
TGTCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTC
CATACTCCTAGAAGGGGAGCAAACCCGTTTGAAGAAGATGTCTGAATTCCATACTCCCTAGAAAG
AGGGAGCGAACCCGTATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATT
Found at i:568949 original size:55 final size:55
Alignment explanation
Indices: 568806--569166 Score: 512
Period size: 55 Copynumber: 6.7 Consensus size: 55
568796 CTCGTAAGAA
568806 GAAGA-TGTTCGAGTCTCATACTCTCTGAAA-AATAGGGAAC--ACACGA-TATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
*
568856 GAAGATTGTTCGAGTCTCATACTCTCT-AAAGAATAGGGAACAGACACAATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
*
568910 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAAACACGATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
* *
568965 GAAGATTGTTCGAGTTCTCATACTCTCTGAAGGAATA-GGAACAGACACAATTATT
1 GAAGATTGTTCGAG-TCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
* * *
569020 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAAACACTATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
* *
569075 GAAGATTG-TCGAGTCTTATACTCTCT-AAAGAAATAGGGAGCAGACACGA-TATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAG-AATAGGGAACAGACACGATTATT
* *
569128 GAAGATTGTTCGAAGTCTCGTA--CTCTGAATGAATAGGGA
1 GAAGATTGTTCG-AGTCTCATACTCTCTGAAAGAATAGGGA
569167 GTGAACATGT
Statistics
Matches: 283, Mismatches: 16, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
50 8 0.03
51 31 0.11
53 33 0.12
54 91 0.32
55 99 0.35
56 21 0.07
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAACAGACACGATTATT
Found at i:574379 original size:24 final size:27
Alignment explanation
Indices: 574337--574386 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
574327 TCTATTTACC
*
574337 TTAAAATAAAATGACAAGAATCAAATA
1 TTAAAATAAAATGACAAGAATAAAATA
574364 TTAAAA-AAAA-GA-AAGAATAAAAT
1 TTAAAATAAAATGACAAGAATAAAAT
574387 CAAATTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 2 0.09
26 4 0.18
27 6 0.27
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (27 bp):
TTAAAATAAAATGACAAGAATAAAATA
Found at i:576588 original size:13 final size:15
Alignment explanation
Indices: 576570--576625 Score: 53
Period size: 17 Copynumber: 3.7 Consensus size: 15
576560 CCTAGTTTTA
576570 ATAAAT-TAATA-AT
1 ATAAATATAATATAT
576583 ATAAATATAATATAT
1 ATAAATATAATATAT
*
576598 ATATAATAAAATAATACT
1 ATA-AATATAAT-ATA-T
*
576616 TTAAATATAA
1 ATAAATATAA
576626 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 6 0.17
14 5 0.14
15 5 0.14
16 7 0.20
17 9 0.26
18 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAATATAATATAT
Found at i:576592 original size:11 final size:11
Alignment explanation
Indices: 576578--576625 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
576568 TAATAAATTA
576578 ATAATATAAAT
1 ATAATATAAAT
*
576589 ATAATATATAT
1 ATAATATAAAT
576600 ATAATA-AAAT
1 ATAATATAAAT
* *
576610 AATACTTTAAAT
1 -ATAATATAAAT
576622 ATAA
1 ATAA
576626 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
10 3 0.10
11 23 0.77
12 4 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:576593 original size:22 final size:21
Alignment explanation
Indices: 576568--576610 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
576558 ATCCTAGTTT
576568 TAATAAAT-TAATAATATAAATA
1 TAATAAATAT-ATAATA-AAATA
*
576590 TAATATATATATAATAAAATA
1 TAATAAATATATAATAAAATA
576611 ATACTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 13 0.68
23 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAAATATATAATAAAATA
Found at i:576625 original size:19 final size:18
Alignment explanation
Indices: 576580--576627 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
576570 ATAAATTAAT
576580 AATATAAATATAATATATA
1 AATATAAA-ATAATATATA
* *
576599 TATAATAAAATAATACTTTA
1 AAT-ATAAAATAATA-TATA
576619 AATATAAAA
1 AATATAAAA
576628 AATTAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAAAATAATATATA
Found at i:577902 original size:3 final size:3
Alignment explanation
Indices: 577887--577972 Score: 131
Period size: 3 Copynumber: 28.7 Consensus size: 3
577877 TTGAGCATGC
*
577887 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
577935 AAT AA- AAT ATAT AAAT AAT AAT AAT AAT AA- AAT AAT AA
1 AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AA
577973 AGCAGCTGAG
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
2 4 0.05
3 68 0.88
4 4 0.05
5 1 0.01
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:580207 original size:24 final size:25
Alignment explanation
Indices: 580178--580235 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 25
580168 CACAAAAAAT
580178 TATTTTAGATATCTA-AATAA-TAAA
1 TATTTTA-ATATCTACAATAACTAAA
*
580202 TATTTTAAGTATCTACTATAACTAAA
1 TATTTTAA-TATCTACAATAACTAAA
580228 TATTTTAA
1 TATTTTAA
580236 ATATAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 1 0.03
24 13 0.43
25 4 0.13
26 12 0.40
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (25 bp):
TATTTTAATATCTACAATAACTAAA
Found at i:580232 original size:26 final size:25
Alignment explanation
Indices: 580178--580239 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
580168 CACAAAAAAT
580178 TATTTT-AGATATCTAAATAATAAA
1 TATTTTAAGATATCTAAATAATAAA
*
580202 TATTTTAAG-TATCTACTATAACTAAA
1 TATTTTAAGATATCTA-AATAA-TAAA
580228 TATTTTAA-ATAT
1 TATTTTAAGATAT
580240 AAAATTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 12 0.36
25 6 0.18
26 15 0.45
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (25 bp):
TATTTTAAGATATCTAAATAATAAA
Found at i:581837 original size:2 final size:2
Alignment explanation
Indices: 581830--581854 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
581820 AGTAATATTA
581830 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
581855 ACACTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:583552 original size:15 final size:15
Alignment explanation
Indices: 583524--583590 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
583514 GATGAAGACT
583524 CAAATCGAAAATAATC
1 CAAATCG-AAATAATC
* *
583540 TAAATTGAAATAATC
1 CAAATCGAAATAATC
583555 CAAATCGAAAGTAA-C
1 CAAATCGAAA-TAATC
* *
583570 TCAAACCGAAAGAATC
1 -CAAATCGAAATAATC
583586 CAAAT
1 CAAAT
583591 TTTATTTATC
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
15 23 0.56
16 18 0.44
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (15 bp):
CAAATCGAAATAATC
Found at i:583559 original size:31 final size:31
Alignment explanation
Indices: 583524--583590 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
583514 GATGAAGACT
** *
583524 CAAATCGAAAATAA-TCTAAATTGAAATAATC
1 CAAATCGAAAATAACTC-AAACCGAAAGAATC
*
583555 CAAATCGAAAGTAACTCAAACCGAAAGAATC
1 CAAATCGAAAATAACTCAAACCGAAAGAATC
583586 CAAAT
1 CAAAT
583591 TTTATTTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (31 bp):
CAAATCGAAAATAACTCAAACCGAAAGAATC
Found at i:588731 original size:22 final size:21
Alignment explanation
Indices: 588703--588748 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
588693 CCAGAAATGT
*
588703 TAAAAAATATTAATGTTTCAGG
1 TAAAAAA-AATAATGTTTCAGG
*
588725 TAAAAAAAATAATGTTTTAGG
1 TAAAAAAAATAATGTTTCAGG
588746 TAA
1 TAA
588749 TTTTTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (21 bp):
TAAAAAAAATAATGTTTCAGG
Found at i:599209 original size:21 final size:21
Alignment explanation
Indices: 599177--599216 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
599167 AACTGCCCAA
599177 TATAGAGGGTATCGGTACTCC
1 TATAGAGGGTATCGGTACTCC
599198 TATAG-GGAGTATCGGTACT
1 TATAGAGG-GTATCGGTACT
599217 ACCTTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (21 bp):
TATAGAGGGTATCGGTACTCC
Found at i:601149 original size:2 final size:2
Alignment explanation
Indices: 601132--601171 Score: 62
Period size: 2 Copynumber: 19.0 Consensus size: 2
601122 TCTAAACTTG
601132 AT AT GAT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
601172 CAACAACAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 32 0.89
3 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:605869 original size:21 final size:21
Alignment explanation
Indices: 605845--605903 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
605835 AAATATCAAA
*
605845 TATTAGAAAAAC-AATATTACT
1 TATTACAAAAACTAATATTA-T
605866 TATTACAAAAACTTAATATTAT
1 TATTACAAAAAC-TAATATTAT
605888 TATTTA-AAAAA-TAATA
1 TA-TTACAAAAACTAATA
605904 ATTTAGGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 5 0.15
21 11 0.32
22 8 0.24
23 10 0.29
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
TATTACAAAAACTAATATTAT
Found at i:606083 original size:30 final size:30
Alignment explanation
Indices: 606021--606112 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
606011 ATTAATCATG
** *
606021 TTAATTCTTTATTAATATAATAATAGTATA
1 TTAATTCTTTATTAATATAAGGATATTATA
*
606051 TTAATTCTTTATTAATATAAGGATATTGTA
1 TTAATTCTTTATTAATATAAGGATATTATA
* *
606081 TTATATTATATTATTAAAATAATGGATATTAT
1 TTA-ATTCT-TTATTAATATAA-GGATATTAT
606113 TTATTAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 29 0.56
31 4 0.08
32 11 0.21
33 8 0.15
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (30 bp):
TTAATTCTTTATTAATATAAGGATATTATA
Found at i:606118 original size:35 final size:32
Alignment explanation
Indices: 606059--606135 Score: 84
Period size: 35 Copynumber: 2.3 Consensus size: 32
606049 TATTAATTCT
* *
606059 TTATTAATATAAGGATATTGTATTATATTATA
1 TTATTAAAATAAGGATATTGTATTAAATTATA
*
606091 TTATTAAAATAATGGATATTATTTATTAAATTATA
1 TTATTAAAATAA-GGATA-T-TGTATTAAATTATA
606126 TT-TTGAAAAT
1 TTATT-AAAAT
606136 TATTAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 11 0.29
33 5 0.13
34 3 0.08
35 19 0.50
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (32 bp):
TTATTAAAATAAGGATATTGTATTAAATTATA
Found at i:607094 original size:9 final size:9
Alignment explanation
Indices: 607066--607099 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
607056 ATATTATTCT
607066 TTAATTAAA
1 TTAATTAAA
*
607075 TT-ATAAAA
1 TTAATTAAA
607083 TTAATTAAA
1 TTAATTAAA
607092 TTAATTAA
1 TTAATTAA
607100 CATAAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:608600 original size:16 final size:16
Alignment explanation
Indices: 608553--608592 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
608543 TTCGGACGAG
608553 TTCTTCTTCAGATGAA
1 TTCTTCTTCAGATGAA
608569 TTCTTCTTCAGATGAA
1 TTCTTCTTCAGATGAA
608585 TTCTTCTT
1 TTCTTCTT
608593 ATTATGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.50
Consensus pattern (16 bp):
TTCTTCTTCAGATGAA
Found at i:609236 original size:122 final size:121
Alignment explanation
Indices: 608946--609358 Score: 494
Period size: 122 Copynumber: 3.5 Consensus size: 121
608936 GTTGAACAAG
* * * * *
608946 TTCTTCTCCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTGGAAATGTTAAGGCTGATC
1 TTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT-TCCTGGAAATGTTGATGCTGATC
*
609011 TATCTCTTTCTGTGATAGAATCAAGCGAAAGGTTGAACAGTTCTTCTTATTATGAAC
65 TATCTCTTTATGTGATAGAATCAAGCGAAAGGTTGAACAGTTCTTCTTATTATGAAC
*
609068 TTATTCTT-TCTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCCTGGAAATGTTGATGCTGAT
1 TTCTTCTTCT-TCTTCAGATGAGTTCTTCTCATTATGAACTT-TCCTGGAAATGTTGATGCTGAT
*
609132 CTATCTCTTTATGTGATAGAATCAAGCGAAAGGTTGAACAGTTCTTCTCATTATGAAC
64 CTATCTCTTTATGTGATAGAATCAAGCGAAAGGTTGAACAGTTCTTCTTATTATGAAC
*
609190 TTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTGGCAA--TT--T--TGATC
1 TTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCCTGGAAATGTTGATGCTGATC
* * ** ** * *
609249 CA--TC--GA-GTGAT-GAATTTGAGTAAAAGCTTGAACAAATTCTTCTTATTATGAAC
65 TATCTCTTTATGTGATAGAA-TCAAGCGAAAGGTTGAAC-AGTTCTTCTTATTATGAAC
* *
609302 TTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-TTTTCTGGAAATGTTGAT
1 TTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCTGGAAATGTTGAT
609359 CCATTGAGTG
Statistics
Matches: 259, Mismatches: 22, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
110 3 0.01
111 26 0.10
112 26 0.10
113 32 0.12
114 2 0.01
115 1 0.00
116 6 0.02
118 1 0.00
120 2 0.01
122 158 0.61
123 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (121 bp):
TTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCTGGAAATGTTGATGCTGATCT
ATCTCTTTATGTGATAGAATCAAGCGAAAGGTTGAACAGTTCTTCTTATTATGAAC
Found at i:609378 original size:111 final size:111
Alignment explanation
Indices: 609160--609378 Score: 325
Period size: 111 Copynumber: 2.0 Consensus size: 111
609150 GAATCAAGCG
* * *
609160 AAAGGTTGAACAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAAGCTTGAACAATTCTTCTCATTATGAACTTCTTATTCTTCTTCAGATGAGTTCTTCTCATTAT
* *
609225 GAACTCTTCCTGGCAATTTTGATCCATCGAGTGATGAATTTGAGTA
66 GAACTCTTCCTGGAAATGTTGATCCATCGAGTGATGAATTTGAGTA
*
609271 AAAGCTTGAACAAATTCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGCTTGAAC-AATTCTTCTCATTATGAACTTCTTATT-CTTCTTCAGATGAGTTCTTCTCATT
* * *
609336 ATGAA-T-TTTCTGGAAATGTTGATCCATTGAGTGATGGATTTGA
64 ATGAACTCTTCCTGGAAATGTTGATCCATCGAGTGATGAATTTGA
609379 ATCTTTGCTA
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
111 42 0.43
112 25 0.26
113 30 0.31
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.42
Consensus pattern (111 bp):
AAAGCTTGAACAATTCTTCTCATTATGAACTTCTTATTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTTCCTGGAAATGTTGATCCATCGAGTGATGAATTTGAGTA
Found at i:609767 original size:22 final size:22
Alignment explanation
Indices: 609733--609791 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
609723 GAATCTAATA
* *
609733 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
*
609755 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
*
609777 AATATATCATCTTTG
1 AATCTATCATCTTTG
609792 TAGATGTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:610446 original size:22 final size:21
Alignment explanation
Indices: 610418--610468 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
610408 TGTTTATATG
*
610418 AATGAATAAATTGAATTTCGAA
1 AATGAATAAATTAAATTTC-AA
610440 AATGAATAAATTAAATTTCAA
1 AATGAATAAATTAAATTTCAA
*
610461 AAAGAATA
1 AATGAATA
610469 CTTGGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (21 bp):
AATGAATAAATTAAATTTCAA
Found at i:610833 original size:7 final size:7
Alignment explanation
Indices: 610821--610873 Score: 81
Period size: 7 Copynumber: 7.6 Consensus size: 7
610811 TTCTATATAT
610821 TTTTTCA
1 TTTTTCA
610828 TTTTTCA
1 TTTTTCA
*
610835 TTTTCCTA
1 TTTTTC-A
610843 TTTTTCA
1 TTTTTCA
610850 TTTTTCA
1 TTTTTCA
610857 TTTTTCA
1 TTTTTCA
610864 TTTTTC-
1 TTTTTCA
610870 TTTT
1 TTTT
610874 CTTTTTTTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
6 4 0.09
7 33 0.77
8 6 0.14
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:610849 original size:22 final size:21
Alignment explanation
Indices: 610821--610873 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
610811 TTCTATATAT
610821 TTTTTCATTTTTCATTTTCCTA
1 TTTTTCATTTTTCATTTTCC-A
*
610843 TTTTTCATTTTTCATTTTTCA
1 TTTTTCATTTTTCATTTTCCA
610864 TTTTTC-TTTT
1 TTTTTCATTTT
610874 CTTTTTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 4 0.13
21 7 0.23
22 19 0.63
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTCATTTTTCATTTTCCA
Found at i:610880 original size:7 final size:7
Alignment explanation
Indices: 610820--610903 Score: 59
Period size: 7 Copynumber: 12.3 Consensus size: 7
610810 TTTCTATATA
610820 TTTTTTC
1 TTTTTTC
*
610827 ATTTTTC
1 TTTTTTC
* *
610834 ATTTTCC
1 TTTTTTC
610841 TATTTTTC
1 T-TTTTTC
*
610849 ATTTTTC
1 TTTTTTC
*
610856 ATTTTTC
1 TTTTTTC
*
610863 ATTTTTC
1 TTTTTTC
610870 --TTTTC
1 TTTTTTC
610875 TTTTTT-
1 TTTTTTC
*
610881 TCTTTTC
1 TTTTTTC
610888 TTTTTAT-
1 TTTTT-TC
610895 TTTTTTC
1 TTTTTTC
610902 TT
1 TT
610904 CTTCAAGCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
5 5 0.08
6 6 0.09
7 47 0.73
8 6 0.09
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:610880 original size:13 final size:13
Alignment explanation
Indices: 610864--610903 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
610854 TCATTTTTCA
610864 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
610877 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
*
610890 TTTATTTTTTTCTT
1 TTT-TTCTTTTCTT
610904 CTTCAAGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:610898 original size:19 final size:18
Alignment explanation
Indices: 610865--610903 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
610855 CATTTTTCAT
*
610865 TTTTCTTTTCTTTTTTTC
1 TTTTCTTTTATTTTTTTC
610883 TTTTCTTTTTATTTTTTTC
1 TTTTC-TTTTATTTTTTTC
610902 TT
1 TT
610904 CTTCAAGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTCTTTTATTTTTTTC
Found at i:616960 original size:21 final size:21
Alignment explanation
Indices: 616934--616973 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
616924 CAGAACCCCA
*
616934 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
616955 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
616974 TCAAATGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:620861 original size:22 final size:21
Alignment explanation
Indices: 620819--620858 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
620809 GAGTTTGTTT
*
620819 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
620840 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
620859 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:624114 original size:7 final size:8
Alignment explanation
Indices: 624090--624120 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
624080 AGAAATAATG
624090 AATGTAAA
1 AATGTAAA
624098 AATGTAAA
1 AATGTAAA
624106 AATGT-AA
1 AATGTAAA
624113 AATGTAAA
1 AATGTAAA
624121 GAATAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (8 bp):
AATGTAAA
Found at i:624114 original size:15 final size:16
Alignment explanation
Indices: 624090--624120 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
624080 AGAAATAATG
624090 AATGTAAAAATGTAAA
1 AATGTAAAAATGTAAA
624106 AATGT-AAAATGTAAA
1 AATGTAAAAATGTAAA
624121 GAATAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (16 bp):
AATGTAAAAATGTAAA
Found at i:628608 original size:12 final size:12
Alignment explanation
Indices: 628593--628617 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
628583 TGAGGAATAA
628593 GAGGAGGATTTG
1 GAGGAGGATTTG
628605 GAGGAGGATTTG
1 GAGGAGGATTTG
628617 G
1 G
628618 TTGACGACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.52, T:0.24
Consensus pattern (12 bp):
GAGGAGGATTTG
Found at i:637475 original size:15 final size:15
Alignment explanation
Indices: 637455--637484 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
637445 ACTTATGAGT
637455 AATGTATGAAAAATG
1 AATGTATGAAAAATG
*
637470 AATGTATGCAAAATG
1 AATGTATGAAAAATG
637485 GTGTTGATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.27
Consensus pattern (15 bp):
AATGTATGAAAAATG
Found at i:641054 original size:9 final size:9
Alignment explanation
Indices: 641026--641059 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
641016 ATATTATTCT
641026 TTAATTAAA
1 TTAATTAAA
*
641035 TT-ATAAAA
1 TTAATTAAA
641043 TTAATTAAA
1 TTAATTAAA
641052 TTAATTAA
1 TTAATTAA
641060 CATAAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:642364 original size:27 final size:27
Alignment explanation
Indices: 642279--642367 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
642269 GTTGGTGGAA
* *
642279 GCTGTTGGAATTTGTTGTGGTAGAGGG
1 GCTGCTGGAATTTGTTGTGGTGGAGGG
* ** **
642306 GCTGCT-GAGTTACTTGAAACGTGGAGGG
1 GCTGCTGGAATTTGTTG--TGGTGGAGGG
642334 GCTGCTGGAATTTGTTGTGGTGGAGGG
1 GCTGCTGGAATTTGTTGTGGTGGAGGG
642361 GCTGCTG
1 GCTGCTG
642368 CAGGTGCTAA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
26 7 0.15
27 20 0.43
28 13 0.28
29 7 0.15
ACGTcount: A:0.15, C:0.10, G:0.44, T:0.31
Consensus pattern (27 bp):
GCTGCTGGAATTTGTTGTGGTGGAGGG
Done.