Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 3 of 143
Found at i:834192 original size:18 final size:18
Alignment explanation
Indices: 834169--834205 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
834159 TAACTTGGGT
*
834169 TTTTTTTTTTTCTTTTTC
1 TTTTTTTTTTTCGTTTTC
834187 TTTTTTTTTTTCGTTTTC
1 TTTTTTTTTTTCGTTTTC
834205 T
1 T
834206 CTCCTCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTTTCGTTTTC
Found at i:842750 original size:3 final size:3
Alignment explanation
Indices: 842742--842789 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
842732 TGTTTATACA
* *
842742 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GTG GAG GAG GAG GTG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
842790 ATTGATCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.29, C:0.00, G:0.67, T:0.04
Consensus pattern (3 bp):
GAG
Found at i:850957 original size:6 final size:6
Alignment explanation
Indices: 850946--850985 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
850936 ATATATACAT
*
850946 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAG ACAT
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACAT
850986 TTACTGTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.50, C:0.30, G:0.03, T:0.17
Consensus pattern (6 bp):
ACATAC
Found at i:852687 original size:31 final size:30
Alignment explanation
Indices: 852652--852729 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
852642 TTCAAACTTA
* *
852652 AAAAAGTATAGGGACTAAAATTGATCAATTT
1 AAAAAGTACAGAGACTAAAATTGATCAA-TT
* *
852683 AAAAAGTACATAGACTAAAATTGATTAATT
1 AAAAAGTACAGAGACTAAAATTGATCAATT
*
852713 -AAAA-TACAGAGATTAAA
1 AAAAAGTACAGAGACTAAA
852730 TCCACAATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 11 0.27
29 4 0.10
30 2 0.05
31 24 0.59
ACGTcount: A:0.54, C:0.06, G:0.13, T:0.27
Consensus pattern (30 bp):
AAAAAGTACAGAGACTAAAATTGATCAATT
Found at i:858752 original size:32 final size:32
Alignment explanation
Indices: 858705--858766 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
858695 AATTATTAGA
* * *
858705 AATTAATTTAAAACAATAAAATTTATAAAAGT
1 AATTAATTAAAAACAAAAAAATTTAAAAAAGT
*
858737 AATTTATTAAAAACAAAAAAATTTAAAAAA
1 AATTAATTAAAAACAAAAAAATTTAAAAAA
858767 TCATTTCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (32 bp):
AATTAATTAAAAACAAAAAAATTTAAAAAAGT
Found at i:861271 original size:27 final size:26
Alignment explanation
Indices: 861241--861294 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
861231 ACAAGTCTCT
* *
861241 CAATTATTTAGAGATTTTCAAGACTTG
1 CAATTATATAGAGA-ATTCAAGACTTG
*
861268 CAATTATATAGAGAATTCGAGACTTG
1 CAATTATATAGAGAATTCAAGACTTG
861294 C
1 C
861295 TAACATAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (26 bp):
CAATTATATAGAGAATTCAAGACTTG
Found at i:869710 original size:21 final size:21
Alignment explanation
Indices: 869668--869711 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
869658 AATTTAATAT
* *
869668 TTAATAATTTTTTATTATTTA
1 TTAATAATTTTATATTAATTA
869689 TTAA-AATTTTATATATAATTA
1 TTAATAATTTTATAT-TAATTA
869710 TT
1 TT
869712 TTTAATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAATAATTTTATATTAATTA
Found at i:878185 original size:13 final size:14
Alignment explanation
Indices: 878166--878203 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
878156 TTTTTAAATA
878166 CATATTTATATTTT
1 CATATTTATATTTT
878180 -ATATTTATAATTTT
1 CATATTTAT-ATTTT
*
878194 CATACTTATA
1 CATATTTATA
878204 CGAGTATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 8 0.38
14 6 0.29
15 7 0.33
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (14 bp):
CATATTTATATTTT
Found at i:878393 original size:28 final size:28
Alignment explanation
Indices: 878353--878409 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
878343 CAACTTTCAA
878353 AATTTCTGTGAATGTATGTTAGTGGCTT
1 AATTTCTGTGAATGTATGTTAGTGGCTT
878381 AATTTCTGTGAATGTATGTTAGTGGCTT
1 AATTTCTGTGAATGTATGTTAGTGGCTT
878409 A
1 A
878410 GTTGACAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.07, G:0.25, T:0.46
Consensus pattern (28 bp):
AATTTCTGTGAATGTATGTTAGTGGCTT
Found at i:888163 original size:22 final size:22
Alignment explanation
Indices: 888138--888185 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
888128 AACAATTGTA
*
888138 TCATTTTCTAGTAGTTTTAATT
1 TCATTTTCTAATAGTTTTAATT
888160 TCATTTTCTAATAGTTTTAATT
1 TCATTTTCTAATAGTTTTAATT
888182 TCAT
1 TCAT
888186 CTTGAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.58
Consensus pattern (22 bp):
TCATTTTCTAATAGTTTTAATT
Found at i:890465 original size:18 final size:18
Alignment explanation
Indices: 890442--890480 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
890432 TAGATTAATT
* *
890442 TATGATTTTTTAAAAAAA
1 TATGATATTTGAAAAAAA
890460 TATGATATTTGAAAAAAA
1 TATGATATTTGAAAAAAA
890478 TAT
1 TAT
890481 AAATTTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (18 bp):
TATGATATTTGAAAAAAA
Found at i:895748 original size:16 final size:17
Alignment explanation
Indices: 895727--895762 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
895717 TTTTGATCCC
895727 AAAATTTG-AAAATATA
1 AAAATTTGAAAAATATA
895743 AAAATTTGATAAAATATA
1 AAAATTTGA-AAAATATA
895761 AA
1 AA
895763 TTTTATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAATTTGAAAAATATA
Found at i:897602 original size:29 final size:30
Alignment explanation
Indices: 897570--897651 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
897560 TAAAATAACA
897570 AAAATATATATATAAAT-TAAAAAATTA-TG
1 AAAATATATATA-AAATATAAAAAATTATTG
*
897599 AAAA-ATACT-TAAAACTATAAAAAATTATTT
1 AAAATATA-TATAAAA-TATAAAAAATTATTG
*
897629 AAAATAT-TATAAAATATAGAAAA
1 AAAATATATATAAAATATAAAAAA
897652 GTGCAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
27 3 0.07
28 6 0.13
29 24 0.53
30 10 0.22
31 2 0.04
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAATATATATAAAATATAAAAAATTATTG
Found at i:897643 original size:20 final size:20
Alignment explanation
Indices: 897586--897643 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
897576 TATATATAAA
* *
897586 TTAAAAAATTATGAAAAATAC
1 TTAAAATATTAT-AAAATTAC
* *
897607 TTAAAACTA-TAAAAAATTAT
1 TTAAAA-TATTATAAAATTAC
897627 TTAAAATATTATAAAAT
1 TTAAAATATTATAAAAT
897644 ATAGAAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.07
20 19 0.63
21 8 0.27
22 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAAATATTATAAAATTAC
Found at i:904835 original size:61 final size:61
Alignment explanation
Indices: 904751--904926 Score: 212
Period size: 61 Copynumber: 2.9 Consensus size: 61
904741 TTGGCCATGC
*
904751 ATGGTCGACA-CCCCCTTTTCTCGAGAAAAAAATTCAAAGTTTTTTAGTGTTAGCCATCAA
1 ATGGTCGACACCCCCCTTTTCTCGAGAAAAAAATTCAAATTTTTTTAGTGTTAGCCATCAA
* * * * *
904811 ATGGTAGACACCCCCCTTTTCTCGAGAAAAAAATTC-AATTTTTTTTGTGTTGGTCGTCAA
1 ATGGTCGACACCCCCCTTTTCTCGAGAAAAAAATTCAAATTTTTTTAGTGTTAGCCATCAA
** * * * * *
904871 ATGACCGACACCCTCCTTTTTTTTGAGAAAAAAATTAAAATTTTTTTGGTGTTAGC
1 ATGGTCGACACCC-CCCTTTTCTCGAGAAAAAAATTCAAATTTTTTTAGTGTTAGC
904927 TATTGCATGA
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
60 38 0.39
61 44 0.45
62 15 0.15
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (61 bp):
ATGGTCGACACCCCCCTTTTCTCGAGAAAAAAATTCAAATTTTTTTAGTGTTAGCCATCAA
Found at i:905284 original size:36 final size:36
Alignment explanation
Indices: 905244--905313 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 36
905234 CCGACATCAA
905244 AAAATTTGAATTTTTTTTCT-GAAGAAAAAGGGGTGT
1 AAAATTTGAATTTTTTTTCTCG-AGAAAAAGGGGTGT
905280 AAAATTTGAATTTTTTTTCTCGAGAAAAAGGGGT
1 AAAATTTGAATTTTTTTTCTCGAGAAAAAGGGGT
905314 TGTCGGCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (36 bp):
AAAATTTGAATTTTTTTTCTCGAGAAAAAGGGGTGT
Found at i:905406 original size:107 final size:107
Alignment explanation
Indices: 905290--905491 Score: 280
Period size: 106 Copynumber: 1.9 Consensus size: 107
905280 AAAATTTGAA
* * * *** * * ** *
905290 TTTTTTTTCTCGAGAAAAAGGGGTTGTCGGCCATTTGATGGCTAACACCAAAAAAATTTGAATTT
1 TTTTTTTTCTCGAG-AAAAGGGGGTATCGACCATGCAATGGCCAACACAAAAAAAATTAAAAATT
905355 TTTTCTCGA-GAAAAAAGGGGTGTCGACCATGCAATGGCCAAT
65 TTTTCTCGAGGAAAAAAGGGGTGTCGACCATGCAATGGCCAAT
905397 TTTTTTTTCTCGAGAAAAGGGGGTATCGACCATGCAATGGCCAACACAAAAAAAATTAAAAATTT
1 TTTTTTTTCTCGAGAAAAGGGGGTATCGACCATGCAATGGCCAACACAAAAAAAATTAAAAATTT
*
905462 TTTCTCGAGGAAAAAGGGGGTGTCGACCAT
66 TTTCTCGAGGAAAAAAGGGGTGTCGACCAT
905492 TTGATGGCCA
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
106 48 0.59
107 34 0.41
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (107 bp):
TTTTTTTTCTCGAGAAAAGGGGGTATCGACCATGCAATGGCCAACACAAAAAAAATTAAAAATTT
TTTCTCGAGGAAAAAAGGGGTGTCGACCATGCAATGGCCAAT
Found at i:905420 original size:45 final size:46
Alignment explanation
Indices: 905352--905440 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 46
905342 AAAATTTGAA
*
905352 TTTTTTTCTCGAGAAAAAAGGGGTGTCGACCATGCAATGGCCAATT
1 TTTTTTTCTCGAGAAAAAAGGGGTATCGACCATGCAATGGCCAATT
*
905398 TTTTTTTCTCGAG-AAAAGGGGGTATCGACCATGCAATGGCCAA
1 TTTTTTTCTCGAGAAAAAAGGGGTATCGACCATGCAATGGCCAA
905441 CACAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 28 0.68
46 13 0.32
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (46 bp):
TTTTTTTCTCGAGAAAAAAGGGGTATCGACCATGCAATGGCCAATT
Found at i:905543 original size:59 final size:58
Alignment explanation
Indices: 905399--905608 Score: 271
Period size: 59 Copynumber: 3.5 Consensus size: 58
905389 TGGCCAATTT
* *
905399 TTTTTTCTCGAGAAAAGGGGGTATCGACCATGCAATGGCCAACACAAAAAAAATTAAAAA
1 TTTTTTCTCGAGAAAAGGGGGTGTCGACCATGCAATGGCCAACACAAAAAAAATT--GAA
***
905459 TTTTTTCTCGAGGAAAAAGGGGGTGTCGACCATTTGATGGCCAACACAAAAAAAAATTGAA
1 TTTTTTCTCGA-G-AAAAGGGGGTGTCGACCATGCAATGGCCAACAC-AAAAAAAATTGAA
* * *
905520 TTTTTT-TCGAGAAAAAGGGGGTGTCGGCCATGCAATGGCCTACACCAAAAAAATTTGAA
1 TTTTTTCTCGAG-AAAAGGGGGTGTCGACCATGCAATGGCCAACA-CAAAAAAAATTGAA
905579 TTTTTTCTCGAGAAAA-GGGGTGTCGACCAT
1 TTTTTTCTCGAGAAAAGGGGGTGTCGACCAT
905609 TTGATGGCCA
Statistics
Matches: 133, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
58 13 0.10
59 51 0.38
60 21 0.16
61 9 0.07
62 29 0.22
63 10 0.08
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (58 bp):
TTTTTTCTCGAGAAAAGGGGGTGTCGACCATGCAATGGCCAACACAAAAAAAATTGAA
Found at i:907678 original size:21 final size:21
Alignment explanation
Indices: 907653--907692 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
907643 TACTTACTAG
907653 TACTAACAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
* *
907674 TACTAACAAACTTAAATTA
1 TACTAACAAAATAAAATTA
907693 AAGTAAATTG
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:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
TACTAACAAAATAAAATTACT
Found at i:908032 original size:13 final size:13
Alignment explanation
Indices: 908013--908055 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
908003 TCTCTTATTC
908013 TTCTTTCTTCCTT
1 TTCTTTCTTCCTT
* *
908026 TTTTTTCTTTCTT
1 TTCTTTCTTCCTT
908039 TTCTTTCTT--TT
1 TTCTTTCTTCCTT
908050 TTCTTT
1 TTCTTT
908056 GTTCTGCCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 8 0.30
13 19 0.70
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTCTTCCTT
Found at i:910684 original size:21 final size:21
Alignment explanation
Indices: 910659--910706 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
910649 CTTTTCCTAT
910659 TATTGTATTGAAGCTTTTACA
1 TATTGTATTGAAGCTTTTACA
**
910680 TATTGTATTTTAGCTTTTACA
1 TATTGTATTGAAGCTTTTACA
*
910701 TGTTGT
1 TATTGT
910707 GATGCATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (21 bp):
TATTGTATTGAAGCTTTTACA
Found at i:912739 original size:56 final size:57
Alignment explanation
Indices: 912588--912741 Score: 195
Period size: 56 Copynumber: 2.7 Consensus size: 57
912578 TATATTATGA
* *
912588 TTTTTATT-AATTCATAATTTAATAATAATTATATTAAGAATGTTATTAAATTATATACT
1 TTTTTATTAAATT-AT-ATTTAATAATAATTATATTAA-AATATGATTAAATTATATACT
* * * *
912647 ATTTTATTAAATTATATTTAATAATAATCATGTTAAAATATGATTAAATTATTTA-T
1 TTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATACT
* *
912703 TTTTTATTAAATTATTTTTAATAATAATTTTATTAAAAT
1 TTTTTATTAAATTATATTTAATAATAATTATATTAAAAT
912742 TTAACAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
56 35 0.42
57 16 0.19
58 19 0.23
59 9 0.11
60 4 0.05
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.53
Consensus pattern (57 bp):
TTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATACT
Found at i:925911 original size:31 final size:31
Alignment explanation
Indices: 925876--925970 Score: 167
Period size: 31 Copynumber: 3.1 Consensus size: 31
925866 GGAAGTTATG
925876 AAAATGGAACCCAATAATTGGCTTTAGTAGA
1 AAAATGGAACCCAATAATTGGCTTTAGTAGA
925907 AAAATGGAACCCAATAATTGGCTTTAGTAGA
1 AAAATGGAACCCAATAATTGGCTTTAGTAGA
*
925938 AAAATGGAACCCAATAATT-GATTTAGTA-A
1 AAAATGGAACCCAATAATTGGCTTTAGTAGA
925967 AAAA
1 AAAA
925971 GAGGATATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 5 0.08
30 8 0.13
31 50 0.79
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (31 bp):
AAAATGGAACCCAATAATTGGCTTTAGTAGA
Found at i:927288 original size:15 final size:17
Alignment explanation
Indices: 927265--927304 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
927255 ATAAAAGAAA
927265 AATAAAAAAACAAA-TT
1 AATAAAAAAACAAAGTT
*
927281 AA-AAAAAATCAAAGTT
1 AATAAAAAAACAAAGTT
927297 AATAAAAA
1 AATAAAAA
927305 TTAGTATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 10 0.48
16 6 0.29
17 5 0.24
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (17 bp):
AATAAAAAAACAAAGTT
Found at i:927298 original size:16 final size:15
Alignment explanation
Indices: 927268--927305 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
927258 AAAGAAAAAT
927268 AAAAAAA-CAAATTA
1 AAAAAAATCAAATTA
927282 AAAAAAATCAAAGTTA
1 AAAAAAATCAAA-TTA
*
927298 ATAAAAAT
1 AAAAAAAT
927306 TAGTATAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAAAAATCAAATTA
Found at i:927367 original size:21 final size:20
Alignment explanation
Indices: 927343--927392 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
927333 CATGTTTCTT
*
927343 TTTTTTAATTTCTTTTTTATA
1 TTTTTTAATTT-TCTTTTATA
927364 TTTTATGT-ATTTTCTTTTATA
1 TTTT-T-TAATTTTCTTTTATA
927385 TTTTTTAA
1 TTTTTTAA
927393 CCTTTTCTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.04
20 2 0.08
21 16 0.64
22 5 0.20
23 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTTAATTTTCTTTTATA
Found at i:933203 original size:21 final size:20
Alignment explanation
Indices: 933178--933217 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
933168 TTTATATTTG
*
933178 AACTCAAATTCGAATTTAATA
1 AACTC-AATTCGAAGTTAATA
*
933199 AACTCATTTCGAAGTTAAT
1 AACTCAATTCGAAGTTAAT
933218 TGATAACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (20 bp):
AACTCAATTCGAAGTTAATA
Found at i:939056 original size:9 final size:9
Alignment explanation
Indices: 939042--939068 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
939032 CTTACAGCAC
939042 ATAAAGGAT
1 ATAAAGGAT
939051 ATAAAGGAT
1 ATAAAGGAT
939060 ATAAAGGAT
1 ATAAAGGAT
939069 TCAACTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
ATAAAGGAT
Found at i:948775 original size:17 final size:18
Alignment explanation
Indices: 948755--948789 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
948745 ACGAACTCCG
948755 AACATAAA-TTATAAAAC
1 AACATAAAGTTATAAAAC
948772 AACATAAAGTTTATAAAA
1 AACATAAAG-TTATAAAA
948790 AAAAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.63, C:0.09, G:0.03, T:0.26
Consensus pattern (18 bp):
AACATAAAGTTATAAAAC
Found at i:951525 original size:29 final size:29
Alignment explanation
Indices: 951468--951525 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
951458 TTAGGTTTCT
* * *
951468 TTTTTTCTTTTTTTTCTTTTTAGATTAGA
1 TTTTCTCTTCTTTTTCTTTTTAGAATAGA
951497 TTTTCTCTTCTTTTTCTTTTTAGAATAGA
1 TTTTCTCTTCTTTTTCTTTTTAGAATAGA
951526 CTTTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.10, G:0.07, T:0.67
Consensus pattern (29 bp):
TTTTCTCTTCTTTTTCTTTTTAGAATAGA
Found at i:960375 original size:76 final size:76
Alignment explanation
Indices: 960249--960407 Score: 300
Period size: 76 Copynumber: 2.1 Consensus size: 76
960239 AGAATATCTC
960249 CCTCTTAAAAAAGAAATAAATAAAAACCCATTTTTCTCTATACTTTTCCTTACAAATCTATGTAT
1 CCTCTTAAAAAAGAAATAAATAAAAACCCATTTTTCTCTATACTTTTCCTTACAAATCTATGTAT
*
960314 GTTATATGAGA
66 GCTATATGAGA
960325 CCTCTTAAAAAAGAAATAAATAAAAACCCATTTTTCTCTATACTTTTCCTTACAAATCTATGTAT
1 CCTCTTAAAAAAGAAATAAATAAAAACCCATTTTTCTCTATACTTTTCCTTACAAATCTATGTAT
960390 GCTATATGAGA
66 GCTATATGAGA
*
960401 TCTCTTA
1 CCTCTTA
960408 TTGTATTAAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 81 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.37
Consensus pattern (76 bp):
CCTCTTAAAAAAGAAATAAATAAAAACCCATTTTTCTCTATACTTTTCCTTACAAATCTATGTAT
GCTATATGAGA
Found at i:966170 original size:64 final size:63
Alignment explanation
Indices: 966049--966171 Score: 142
Period size: 64 Copynumber: 1.9 Consensus size: 63
966039 AATACCCATA
* * * * **
966049 AAAATAATAATATTATAAATTAATCTTTGATAAAATTATATTTAACCATTCTATTTAATATTTT
1 AAAATAATAAAATTATAAATTAATCTAT-ATAAAATTATATTGAAACACCCTATTTAATATTTT
966113 AAAATAATAAAATTATAAATTAATAC-ATATTAAAATTATA-TGAAACACCCTACTTTAAT
1 AAAATAATAAAATTATAAATTAAT-CTATA-TAAAATTATATTGAAACACCCTA-TTTAAT
966172 GTATTCTCCC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
63 9 0.18
64 40 0.80
65 1 0.02
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.41
Consensus pattern (63 bp):
AAAATAATAAAATTATAAATTAATCTATATAAAATTATATTGAAACACCCTATTTAATATTTT
Found at i:966313 original size:19 final size:19
Alignment explanation
Indices: 966289--966329 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
966279 ATAATTATTT
966289 ATATTTTATAATTAATAAA
1 ATATTTTATAATTAATAAA
966308 ATATTTTATAATTAATAAA
1 ATATTTTATAATTAATAAA
966327 ATA
1 ATA
966330 ATATATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATTTTATAATTAATAAA
Found at i:966329 original size:24 final size:24
Alignment explanation
Indices: 966268--966340 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 24
966258 ATCATTTAAG
*
966268 AATTAATAAAA-ATAAT-TATTTAT
1 AATTAATAAAATAAAATAT-TTTAT
* *
966291 ATTTTATAATTAATAAAATATTTTAT
1 AATTAATAA--AATAAAATATTTTAT
*
966317 AATTAATAAAATAATATATTTTAT
1 AATTAATAAAATAAAATATTTTAT
966341 TATAAAATTG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
23 7 0.17
24 14 0.35
25 2 0.05
26 16 0.40
27 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTAATAAAATAAAATATTTTAT
Found at i:966816 original size:21 final size:22
Alignment explanation
Indices: 966792--966834 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
966782 AAATGTTCTC
*
966792 AAAATAAAAAGTTCA-AAAAAT
1 AAAATAAAAAATTCATAAAAAT
966813 AAAATAAAAAATTCATAAAAAT
1 AAAATAAAAAATTCATAAAAAT
966835 TCAAATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATAAAAAATTCATAAAAAT
Found at i:973193 original size:20 final size:18
Alignment explanation
Indices: 973143--973194 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
973133 TATCAAGAGA
973143 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
973160 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
973180 AATATTAAATTAATA
1 AATATTAAATTAATA
973195 AAATACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:981112 original size:21 final size:20
Alignment explanation
Indices: 981088--981135 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
981078 TAATAGTTAC
981088 ATAAAATTTAAAATTTAAAAA
1 ATAAAA-TTAAAATTTAAAAA
* *
981109 ATAAAGATTAAATTTTTAAAA
1 ATAAA-ATTAAAATTTAAAAA
981130 ATAAAA
1 ATAAAA
981136 ATATAGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATAAAATTAAAATTTAAAAA
Found at i:981126 original size:29 final size:29
Alignment explanation
Indices: 981094--981153 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
981084 TTACATAAAA
*
981094 TTTAAAATTTAAAAA-ATAAAGATTAAATT
1 TTTAAAA-ATAAAAATATAAAGATTAAATT
*
981123 TTTAAAAATAAAAATATAGAGATTAAATT
1 TTTAAAAATAAAAATATAAAGATTAAATT
981152 TT
1 TT
981154 AATTTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (29 bp):
TTTAAAAATAAAAATATAAAGATTAAATT
Found at i:981444 original size:18 final size:18
Alignment explanation
Indices: 981421--981459 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
981411 AAAATCGAGT
*
981421 AATTAACTGAA-TTAATCA
1 AATTAACCGAACTTAAT-A
981439 AATTAACCGAACTTAATA
1 AATTAACCGAACTTAATA
981457 AAT
1 AAT
981460 AATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (18 bp):
AATTAACCGAACTTAATA
Found at i:981661 original size:27 final size:28
Alignment explanation
Indices: 981631--981700 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
981621 AAATATTTCG
* *
981631 ATTCGATTAATTTTTTAAAAAAATT-CA
1 ATTCGATTAATTTTTAAAAAAAATTAAA
**
981658 ATTCGATTAATGGTTAAAAAAAATTAAAAA
1 ATTCGATTAATTTTTAAAAAAAATT--AAA
981688 ATTCGATTAATTT
1 ATTCGATTAATTT
981701 AATTAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 22 0.65
30 12 0.35
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (28 bp):
ATTCGATTAATTTTTAAAAAAAATTAAA
Found at i:982976 original size:164 final size:163
Alignment explanation
Indices: 982702--983190 Score: 879
Period size: 164 Copynumber: 3.0 Consensus size: 163
982692 ATGAAAGCCT
**
982702 TCACAACACTTATGGTAGTAAATAAACAGATGAACATGTATCTGCAGCCTGCATTTTCCCTTCTT
1 TCACAACACTTATGGTAGTCGATAAACAGATGAACATGTATCTGCAGCCTGCATTTTCCCTTCTT
*
982767 TTTCACATATCAATGGTAAAATCATTTCATTATGTAGTGGACTTTACTTTGTGTATCCCTTTCCA
66 TTTCACATATCAATGGTATAATCATTTCATTATGTAGTGGACTTTACTTTGTGTATCCCTTTCCA
982832 TGTAGTAATAGGATGTTCATGTAGTGCAGACCC
131 TGTAGTAATAGGATGTTCATGTAGTGCAGACCC
982865 TCACAACACTTATGGTAGTCGATAAACAGATGAACATGTATCTGCAGCCTGCATTTTTCCCTTCT
1 TCACAACACTTATGGTAGTCGATAAACAGATGAACATGTATCTGCAGCCTGCA-TTTTCCCTTCT
*
982930 TTTTCACATATCAATGGCATAATCATTTCATTATGTAGTGGACTTTACTTTGTGTATCCCTTTCC
65 TTTTCACATATCAATGGTATAATCATTTCATTATGTAGTGGACTTTACTTTGTGTATCCCTTTCC
982995 ATGTAGTAATAGGATGTTCATGTAGTGCAGACCC
130 ATGTAGTAATAGGATGTTCATGTAGTGCAGACCC
983029 TCACAACACTTATGGTAGTCGATAAACAGATGAACATGTATCTGCAGCCTGCATTTTCCCTTCTT
1 TCACAACACTTATGGTAGTCGATAAACAGATGAACATGTATCTGCAGCCTGCATTTTCCCTTCTT
* * * * *
983094 TTCCACATATCAATGGTATAATCATTTCATTATGCAGTGGGCTCTGCTTTGTGTATCCCTTTCCA
66 TTTCACATATCAATGGTATAATCATTTCATTATGTAGTGGACTTTACTTTGTGTATCCCTTTCCA
*
983159 TGTAGTAATAGGATGTTCATGTAGTTCAGACC
131 TGTAGTAATAGGATGTTCATGTAGTGCAGACC
983191 ACTTGCTTAG
Statistics
Matches: 314, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
163 153 0.49
164 161 0.51
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (163 bp):
TCACAACACTTATGGTAGTCGATAAACAGATGAACATGTATCTGCAGCCTGCATTTTCCCTTCTT
TTTCACATATCAATGGTATAATCATTTCATTATGTAGTGGACTTTACTTTGTGTATCCCTTTCCA
TGTAGTAATAGGATGTTCATGTAGTGCAGACCC
Found at i:985310 original size:13 final size:14
Alignment explanation
Indices: 985292--985361 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
985282 GCATTATATG
985292 AAATATA-AAAATC
1 AAATATATAAAATC
*
985305 AAATATATAAATTC
1 AAATATATAAAATC
* *
985319 AAAAATTATAATATATT
1 AAATA-TATAA-A-ATC
* *
985336 AATTATATAAAATA
1 AAATATATAAAATC
*
985350 AAATTTATAAAA
1 AAATATATAAAA
985362 GATCACATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
13 7 0.16
14 21 0.48
15 6 0.14
16 6 0.14
17 4 0.09
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATATATAAAATC
Found at i:985331 original size:22 final size:21
Alignment explanation
Indices: 985298--985339 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
985288 TATGAAATAT
985298 AAAAATCAAATATATAAATTC
1 AAAAATCAAATATATAAATTC
* *
985319 AAAAATTATAATATATTAATT
1 AAAAATCA-AATATATAAATT
985340 ATATAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATCAAATATATAAATTC
Found at i:988528 original size:29 final size:31
Alignment explanation
Indices: 988491--988551 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
988481 AATCTTTGAG
*
988491 ATAATTTTTTAATT-ATTTAAATAA-TAAAAA
1 ATAA-TTTTTAATTAAATTAAATAATTAAAAA
*
988521 ATAA-TTTTATTTAAATTAAATAATTAAAAA
1 ATAATTTTTAATTAAATTAAATAATTAAAAA
988551 A
1 A
988552 ATTGTCCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.26
29 9 0.33
30 11 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATTTTTAATTAAATTAAATAATTAAAAA
Found at i:989786 original size:27 final size:24
Alignment explanation
Indices: 989738--989783 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
989728 ATATAAGCAA
*
989738 CAATAATGATGATGATATAAAAGT
1 CAATAATGATGATCATATAAAAGT
989762 CAATAATGATGATCATATAAAA
1 CAATAATGATGATCATATAAAA
989784 AAAATTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (24 bp):
CAATAATGATGATCATATAAAAGT
Found at i:993157 original size:18 final size:19
Alignment explanation
Indices: 993131--993179 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
993121 AAAATATCAC
993131 AAAAA-TAAATTTAATAA-
1 AAAAATTAAATTTAATAAT
*
993148 AAAAATTAAAGTTAATAAT
1 AAAAATTAAATTTAATAAT
*
993167 TAAAATTAAATTT
1 AAAAATTAAATTT
993180 TAAAATCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 5 0.19
18 11 0.41
19 11 0.41
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTAAATTTAATAAT
Found at i:1002481 original size:22 final size:23
Alignment explanation
Indices: 1002455--1002504 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
1002445 TAATTTATAA
*
1002455 TTTAAATAATTTTTTTA-AATAT
1 TTTAAATAATTATTTTATAATAT
*
1002477 TTT-AATAATTATTTTATAATTT
1 TTTAAATAATTATTTTATAATAT
1002499 TTTAAA
1 TTTAAA
1002505 ACTAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 10 0.42
23 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAAATAATTATTTTATAATAT
Found at i:1002500 original size:21 final size:21
Alignment explanation
Indices: 1002448--1002500 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1002438 ACTTTAATAA
* *
1002448 TTTATAA-TTTAAATAATTTT
1 TTTATAATTTTTAATAATTAT
1002468 TTTA-AATATTTTAATAATTAT
1 TTTATAAT-TTTTAATAATTAT
1002489 TTTATAATTTTT
1 TTTATAATTTTT
1002501 TAAAACTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 4 0.14
21 19 0.68
22 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATAATTTTTAATAATTAT
Found at i:1016468 original size:17 final size:18
Alignment explanation
Indices: 1016443--1016486 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1016433 AATAATAATA
*
1016443 ATAATTAAAT-ATATATTT
1 ATAAATAAATAATAT-TTT
1016461 A-AAATAAATAATATTTT
1 ATAAATAAATAATATTTT
1016478 ATAAATAAA
1 ATAAATAAA
1016487 AAGTTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAATAAATAATATTTT
Found at i:1016483 original size:18 final size:18
Alignment explanation
Indices: 1016443--1016486 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
1016433 AATAATAATA
*
1016443 ATAATTAAATATATATTT
1 ATAAATAAATATATATTT
1016461 A-AAATAAATA-ATATTTT
1 ATAAATAAATATATA-TTT
1016478 ATAAATAAA
1 ATAAATAAA
1016487 AAGTTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 12 0.52
18 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAATAAATATATATTT
Found at i:1022411 original size:27 final size:28
Alignment explanation
Indices: 1022371--1022441 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
1022361 AAATCATCGA
**
1022371 TTTAATTAACTTAATAT-TTAATATATT
1 TTTAATTATTTTAATATATTAATATATT
* *
1022398 TTTAATTATTTTAAATATATTCATATTTT
1 TTTAATTATTTT-AATATATTAATATATT
1022427 TATTAATTATTTTAA
1 T-TTAATTATTTTAA
1022442 ATAAATCGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 10 0.27
28 5 0.14
29 11 0.30
30 11 0.30
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTAATTATTTTAATATATTAATATATT
Found at i:1032677 original size:3 final size:3
Alignment explanation
Indices: 1032669--1032719 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
1032659 GATATCTACT
* *
1032669 TTC TTC TTC TTC TTC TTC TCC TTC TCC TTC TTC TTC TTC TTC TTCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C
1032715 TTC TT
1 TTC TT
1032720 GCTTGGATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:1033954 original size:21 final size:21
Alignment explanation
Indices: 1033915--1033954 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1033905 CGTGAAAATG
***
1033915 GGTTTAGGGTTTTTCAATTAA
1 GGTTTAGGGTTTAAAAATTAA
1033936 GGTTTAGGGTTTAAAAATT
1 GGTTTAGGGTTTAAAAATT
1033955 TTAATTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.45
Consensus pattern (21 bp):
GGTTTAGGGTTTAAAAATTAA
Found at i:1038890 original size:15 final size:16
Alignment explanation
Indices: 1038863--1038892 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1038853 AAATAAAAAA
1038863 TTAAAACATATATATC
1 TTAAAACATATATATC
1038879 TTAAAA-ATATATAT
1 TTAAAACATATATAT
1038893 ATAAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAACATATATATC
Found at i:1047939 original size:2 final size:2
Alignment explanation
Indices: 1047932--1047956 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1047922 ATTTACCTTC
1047932 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
1047957 AGAGAGAGAA
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:1049519 original size:29 final size:29
Alignment explanation
Indices: 1049474--1049536 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1049464 ATATGAACCG
* * *
1049474 CAAATCAAATTTTATATAT-ATATTTATAT
1 CAAATCAAAATTCATATATCA-AATTATAT
*
1049503 CAAATCAAAATTCATATTTCAAATTATAT
1 CAAATCAAAATTCATATATCAAATTATAT
1049532 CAAAT
1 CAAAT
1049537 TATATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (29 bp):
CAAATCAAAATTCATATATCAAATTATAT
Found at i:1050601 original size:31 final size:32
Alignment explanation
Indices: 1050540--1050608 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
1050530 GTTTGGGTAT
1050540 CAAATTGAACATTATAAAGTCAAACTTAAGTAC
1 CAAATTGAACA-TATAAAGTCAAACTTAAGTAC
*
1050573 CAAATTGAACA-ATGAAA-TCAAA-TATAAGTAT
1 CAAATTGAACATAT-AAAGTCAAACT-TAAGTAC
1050604 CAAAT
1 CAAAT
1050609 GATATATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 1 0.03
31 18 0.55
32 3 0.09
33 11 0.33
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (32 bp):
CAAATTGAACATATAAAGTCAAACTTAAGTAC
Found at i:1051610 original size:20 final size:20
Alignment explanation
Indices: 1051574--1051620 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1051564 ATATCAAGTC
*
1051574 AATTAATTCGATTAAAT-TA
1 AATTAATTCGATCAAATATA
1051593 AATTAATATCGATCAAATATA
1 AATTAAT-TCGATCAAATATA
1051614 AA-TAATT
1 AATTAATT
1051621 AAGTAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 8 0.32
20 13 0.52
21 4 0.16
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (20 bp):
AATTAATTCGATCAAATATA
Found at i:1057391 original size:4 final size:4
Alignment explanation
Indices: 1057367--1057480 Score: 120
Period size: 4 Copynumber: 28.0 Consensus size: 4
1057357 TCAAAAATAT
* * * *
1057367 TTTA TTTA GTTA GTTA GTTA TTTA TTTTA TTTA TTTA GTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
1057416 TTTA TTTA TTTA TTTA GTTA TTTTA TTTG TTTA CTTA ATTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
1057465 CTTA TTAA TTTA TTTA
1 TTTA TTTA TTTA TTTA
1057481 CATTGTAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
4 86 0.92
5 7 0.08
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:1060652 original size:25 final size:24
Alignment explanation
Indices: 1060615--1060763 Score: 148
Period size: 23 Copynumber: 6.4 Consensus size: 24
1060605 ACACTAGCGC
1060615 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTCT-GT
*
1060638 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTCTGT
* *
1060663 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
1060686 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * *
1060709 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
1060732 ACTCTCTGT-TTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
1060755 GCTCTCTGT
1 GCTCTCTGT
1060764 TGCCCAGCAC
Statistics
Matches: 115, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
23 94 0.82
24 1 0.01
25 17 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTCTGT
Found at i:1060715 original size:46 final size:46
Alignment explanation
Indices: 1060636--1060762 Score: 200
Period size: 46 Copynumber: 2.7 Consensus size: 46
1060626 AGCACGTCTC
1060636 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
* *
1060684 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
* *
1060730 GTACTCTCTGTTTAGCACTGTGTGTGCTCTCTG
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTG
1060763 TTGCCCAGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
46 64 0.86
48 10 0.14
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
Found at i:1060754 original size:69 final size:68
Alignment explanation
Indices: 1060615--1060805 Score: 208
Period size: 69 Copynumber: 2.7 Consensus size: 68
1060605 ACACTAGCGC
* * * * * *
1060615 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
1 GCTCTCTGTTCAGCACTTAT-GTGCTCTCTG--ATTAGTACTTTGTGTACTCTCTGATTAGCACT
*
1060680 TTGTGT
63 GTGTGT
* *
1060686 GCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTG
1 GCTCTCTG-TTCAGCAC-TTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGATTAGCACTG
1060750 TGTGT
64 TGTGT
1060755 GCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG-TTAGTACTTTG-GTACTCT
1 GCTCTCTGTT---CAGCACTTATGTGCTCTCTGATTAGTACTTTGTGTACTCT
1060806 TTGCTTGTTC
Statistics
Matches: 106, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
68 2 0.02
69 48 0.45
70 11 0.10
71 36 0.34
72 9 0.08
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (68 bp):
GCTCTCTGTTCAGCACTTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGATTAGCACTGTG
TGT
Found at i:1067803 original size:25 final size:24
Alignment explanation
Indices: 1067766--1067914 Score: 148
Period size: 23 Copynumber: 6.4 Consensus size: 24
1067756 ACACTAGCGC
1067766 GCTCTCTGT-TTAGCAC-GTCTCGT
1 GCTCTCTGTATTAGCACTGTCT-GT
*
1067789 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-TATTAGCACTGTCTGT
* *
1067814 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
1067837 GCTCTCTG-ATTAGCACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* * *
1067860 GCTCTCTG-ATTAGTACTTTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
* *
1067883 ACTCTCTGT-TTAGCACTGTGTGT
1 GCTCTCTGTATTAGCACTGTCTGT
1067906 GCTCTCTGT
1 GCTCTCTGT
1067915 TGCCCAGCAC
Statistics
Matches: 115, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
23 94 0.82
24 1 0.01
25 17 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (24 bp):
GCTCTCTGTATTAGCACTGTCTGT
Found at i:1067866 original size:46 final size:46
Alignment explanation
Indices: 1067787--1067913 Score: 200
Period size: 46 Copynumber: 2.7 Consensus size: 46
1067777 AGCACGTCTC
1067787 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
* *
1067835 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
* *
1067881 GTACTCTCTGTTTAGCACTGTGTGTGCTCTCTG
1 GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTG
1067914 TTGCCCAGCA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
46 64 0.86
48 10 0.14
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
Found at i:1067905 original size:69 final size:68
Alignment explanation
Indices: 1067766--1067956 Score: 208
Period size: 69 Copynumber: 2.7 Consensus size: 68
1067756 ACACTAGCGC
* * * * * *
1067766 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
1 GCTCTCTGTTCAGCACTTAT-GTGCTCTCTG--ATTAGTACTTTGTGTACTCTCTGATTAGCACT
*
1067831 TTGTGT
63 GTGTGT
* *
1067837 GCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTG
1 GCTCTCTG-TTCAGCAC-TTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGATTAGCACTG
1067901 TGTGT
64 TGTGT
1067906 GCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG-TTAGTACTTTG-GTACTCT
1 GCTCTCTGTT---CAGCACTTATGTGCTCTCTGATTAGTACTTTGTGTACTCT
1067957 TTGCTTGTTC
Statistics
Matches: 106, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
68 2 0.02
69 48 0.45
70 11 0.10
71 36 0.34
72 9 0.08
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (68 bp):
GCTCTCTGTTCAGCACTTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGATTAGCACTGTG
TGT
Found at i:1069041 original size:16 final size:16
Alignment explanation
Indices: 1069020--1069057 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1069010 TTAATAAAAA
1069020 TAAATTTAAC-AATATT
1 TAAATTTAACGAA-ATT
1069036 TAAA-TTAACGAAATT
1 TAAATTTAACGAAATT
1069051 TAAATTT
1 TAAATTT
1069058 TTGTATTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTAACGAAATT
Found at i:1070966 original size:2 final size:2
Alignment explanation
Indices: 1070959--1071022 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1070949 TTAAAAGATA
1070959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1071001 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1071023 TTATTATAAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1073478 original size:24 final size:23
Alignment explanation
Indices: 1073451--1073535 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 23
1073441 TTCAACTTAA
1073451 AAAATGAAAAAATA-AAAAAAATTT
1 AAAAT-AAAAAATATAAAAAAA-TT
* *
1073475 AAAATCTAAAAATATATAAAAATT
1 AAAAT-AAAAAATATAAAAAAATT
* *
1073499 AAAACTAAAAAATTTACAAAAA--
1 AAAA-TAAAAAATATAAAAAAATT
1073521 AAAATAAAAAA-ATAA
1 AAAATAAAAAATATAA
1073536 TGAAAACTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.04
21 7 0.14
22 4 0.08
24 31 0.61
25 7 0.14
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (23 bp):
AAAATAAAAAATATAAAAAAATT
Found at i:1073521 original size:25 final size:25
Alignment explanation
Indices: 1073458--1073509 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1073448 TAAAAAATGA
1073458 AAAAATA-AAAAAAATTTAAAATCT
1 AAAAATATAAAAAAATTTAAAATCT
*
1073482 AAAAATATATAAAAA-TTAAAA-CT
1 AAAAATATAAAAAAATTTAAAATCT
1073505 AAAAA
1 AAAAA
1073510 ATTTACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.27
24 13 0.50
25 6 0.23
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAAATATAAAAAAATTTAAAATCT
Found at i:1074729 original size:28 final size:27
Alignment explanation
Indices: 1074651--1074729 Score: 65
Period size: 28 Copynumber: 2.9 Consensus size: 27
1074641 TTTAGTCCTT
* *
1074651 TTAATATGTTTAAATTTGAGATTTAATTC
1 TTAATATGCTTAAATTTGA-ATTT-AGTC
* *
1074680 TT-ATA--CTTTAATTTCAATTTTAGTC
1 TTAATATGCTTAAATTTGAA-TTTAGTC
1074705 TTAATATGCTTAAATTTGATATTTA
1 TTAATATGCTTAAATTTGA-ATTTA
1074730 ATCCTTATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
25 6 0.15
26 14 0.36
28 16 0.41
29 3 0.08
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (27 bp):
TTAATATGCTTAAATTTGAATTTAGTC
Found at i:1075108 original size:60 final size:60
Alignment explanation
Indices: 1075034--1075224 Score: 222
Period size: 59 Copynumber: 3.2 Consensus size: 60
1075024 AATATATAAT
* * * *
1075034 ATTTGGCACTTGAACTTGACATTTTTTCTTAATTTGATACCTAAATTTTTTTTTGACTCA
1 ATTTGGTACCTGAACTTGACATTTTTTCTTAATTTGGTACCTAAATTTTTTTTAGACTCA
* * * * *
1075094 ATTTGGTACCTGAACTTGACATTTTTTTTTAATTTGGTACCTAAA-CTTTTTTGGACCCG
1 ATTTGGTACCTGAACTTGACATTTTTTCTTAATTTGGTACCTAAATTTTTTTTAGACTCA
* ** * * *
1075153 ATTTGGTATCTGAACTTGGTATTTTTTCCTAATTTGGTACCTAAGCTTTTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGACATTTTTTCTTAATTTGGTACCTAA-ATTTTTTTTAGACTCA
*
1075214 AATTGGTACCT
1 ATTTGGTACCT
1075225 AAATTTATTA
Statistics
Matches: 108, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
59 49 0.45
60 41 0.38
61 18 0.17
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACATTTTTTCTTAATTTGGTACCTAAATTTTTTTTAGACTCA
Found at i:1075131 original size:31 final size:31
Alignment explanation
Indices: 1075034--1075141 Score: 91
Period size: 31 Copynumber: 3.5 Consensus size: 31
1075024 AATATATAAT
* * *
1075034 ATTTGGCACTTGAACTTGACATTTTTTCTTA
1 ATTTGGTACCTGAACTTGACATTTTTTTTTA
* * *
1075065 ATTTGATACCT-AAATT----TTTTTTTGACTCA
1 ATTTGGTACCTGAACTTGACATTTTTTT---TTA
1075094 ATTTGGTACCTGAACTTGACATTTTTTTTTA
1 ATTTGGTACCTGAACTTGACATTTTTTTTTA
*
1075125 ATTTGGTACCTAAACTT
1 ATTTGGTACCTGAACTT
1075142 TTTTGGACCC
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
26 6 0.10
29 12 0.20
30 8 0.14
31 26 0.44
34 7 0.12
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (31 bp):
ATTTGGTACCTGAACTTGACATTTTTTTTTA
Found at i:1076064 original size:16 final size:15
Alignment explanation
Indices: 1076022--1076065 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1076012 TTAAAATAGT
1076022 AAATTTTTAATTTAA
1 AAATTTTTAATTTAA
**
1076037 ACCTTTTATAATTTATA
1 AAATTTT-TAATTTA-A
1076054 AAATTTTTAATT
1 AAATTTTTAATT
1076066 AGTAGTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.22
16 12 0.52
17 6 0.26
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTTTTAATTTAA
Found at i:1077057 original size:8 final size:8
Alignment explanation
Indices: 1077044--1077071 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1077034 TAACCGAAAG
1077044 AAAAAAAT
1 AAAAAAAT
1077052 AAAAAAAT
1 AAAAAAAT
1077060 AAAAAAAT
1 AAAAAAAT
1077068 AAAA
1 AAAA
1077072 CCTCCCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1077269 original size:22 final size:25
Alignment explanation
Indices: 1077244--1077294 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
1077234 TATTTTGGGT
*
1077244 TTAT-TTTCAAAATT-TATTAA-AA
1 TTATATTTCAAAATTATATCAATAA
*
1077266 TTATATTTCACAATTATATCAATAA
1 TTATATTTCAAAATTATATCAATAA
1077291 TTAT
1 TTAT
1077295 CATATGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.17
23 9 0.38
24 5 0.21
25 6 0.25
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (25 bp):
TTATATTTCAAAATTATATCAATAA
Found at i:1078584 original size:18 final size:17
Alignment explanation
Indices: 1078558--1078596 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1078548 AAAGTTTATA
1078558 ATATATTATATAATTTTT
1 ATATATTATATAA-TTTT
* *
1078576 ATATGTTATGTAATTTT
1 ATATATTATATAATTTT
1078593 ATAT
1 ATAT
1078597 TACATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
ATATATTATATAATTTT
Found at i:1079632 original size:54 final size:56
Alignment explanation
Indices: 1079546--1079664 Score: 188
Period size: 54 Copynumber: 2.1 Consensus size: 56
1079536 TATAAATCGG
*
1079546 TTAATTTTCAACTTTAGTCCTTTTAATATGCTTAAATTTGAGATTTAATTCTTATACT
1 TTAATTTTCAACTTTAGTCC--TTAATATGCTTAAATTTGAGATTTAATCCTTATACT
*
1079604 TTAATTTT-AATTTTAGTCC-TAATATGCTTAAATTTGAGATTTAATCCTTATACT
1 TTAATTTTCAACTTTAGTCCTTAATATGCTTAAATTTGAGATTTAATCCTTATACT
1079658 TTAATTT
1 TTAATTT
1079665 CTAACATCAT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
54 41 0.69
57 10 0.17
58 8 0.14
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (56 bp):
TTAATTTTCAACTTTAGTCCTTAATATGCTTAAATTTGAGATTTAATCCTTATACT
Found at i:1079646 original size:28 final size:28
Alignment explanation
Indices: 1079569--1079651 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 28
1079559 TTAGTCCTTT
*
1079569 TAATATGCTTAAATTTGAGATTTAATTC
1 TAATATGCTTAAATTTGAGATTTAATCC
* * * *
1079597 T--TATACTTTAATTTTA-ATTTTAGTCC
1 TAATATGCTTAAATTTGAGA-TTTAATCC
1079623 TAATATGCTTAAATTTGAGATTTAATCC
1 TAATATGCTTAAATTTGAGATTTAATCC
1079651 T
1 T
1079652 TATACTTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
25 1 0.02
26 19 0.45
28 21 0.50
29 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (28 bp):
TAATATGCTTAAATTTGAGATTTAATCC
Found at i:1081486 original size:25 final size:24
Alignment explanation
Indices: 1081458--1081514 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
1081448 AAAGGGAGAT
*
1081458 TTAAATTT-TTTAAAAAGATTAATAA
1 TTAAATTTATTTAAAAA-A-TAAGAA
1081483 TTAAATTTAATTTAAAAAATAAGAA
1 TTAAATTT-ATTTAAAAAATAAGAA
1081508 TTAAATT
1 TTAAATT
1081515 GACAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 20 0.69
26 1 0.03
27 8 0.28
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
TTAAATTTATTTAAAAAATAAGAA
Found at i:1088270 original size:63 final size:63
Alignment explanation
Indices: 1088164--1088289 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 63
1088154 TAACACTCCC
* * * *
1088164 AATTCTCCAATTCAACAACCCTAATTTGAGCCGATTGAATCTTAATTTGATTAATATGAGTAT
1 AATTCTCCAATTCAACAACCCTAATTTGAACCGATCGAATCTTAACTCGATTAATATGAGTAT
* * * *
1088227 AATTCTCCAATTCAACAACCTTAATTTGAACCGATCGAGTCTTAGCTCGATTACTATGAGTAT
1 AATTCTCCAATTCAACAACCCTAATTTGAACCGATCGAATCTTAACTCGATTAATATGAGTAT
1088290 TGCTGTTAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (63 bp):
AATTCTCCAATTCAACAACCCTAATTTGAACCGATCGAATCTTAACTCGATTAATATGAGTAT
Found at i:1089623 original size:25 final size:24
Alignment explanation
Indices: 1089586--1089633 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1089576 AGTAAAAAAA
*
1089586 TATAAATTTAAATATAGTTGAATT
1 TATAAATTAAAATATAGTTGAATT
* *
1089610 TATAAATTCAAAATCTTGTTGAAT
1 TATAAATT-AAAATATAGTTGAAT
1089634 AGTTTATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (24 bp):
TATAAATTAAAATATAGTTGAATT
Found at i:1092183 original size:2 final size:2
Alignment explanation
Indices: 1092176--1092204 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1092166 AATATTATGG
1092176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1092205 TGAATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1098849 original size:19 final size:19
Alignment explanation
Indices: 1098810--1098847 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1098800 AATATAATTA
1098810 TATTTACTTTTTATTTATT
1 TATTTACTTTTTATTTATT
1098829 TATTTA-TTTTCT-TTTATT
1 TATTTACTTTT-TATTTATT
1098847 T
1 T
1098848 TAAATTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTACTTTTTATTTATT
Found at i:1103207 original size:24 final size:26
Alignment explanation
Indices: 1103157--1103209 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
1103147 TTTTTGGGGA
*
1103157 ATTTTTATGAACTTTTTATATTTTTT
1 ATTTTTATGAACTTTTTATATTATTT
1103183 ATTTTTAT-AA-TTTTTGA-ATTATTT
1 ATTTTTATGAACTTTTT-ATATTATTT
1103207 ATT
1 ATT
1103210 GATATGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 14 0.56
25 3 0.12
26 8 0.32
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (26 bp):
ATTTTTATGAACTTTTTATATTATTT
Found at i:1103982 original size:17 final size:17
Alignment explanation
Indices: 1103951--1103984 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1103941 TTTAATTAAC
**
1103951 TTAATTTAATTTAATAA
1 TTAATTTAACATAATAA
1103968 TTAATTTAACATAATAA
1 TTAATTTAACATAATAA
1103985 ATTTCTTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTTAACATAATAA
Found at i:1113291 original size:31 final size:31
Alignment explanation
Indices: 1113253--1113318 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1113243 TATTTTATTT
*
1113253 TCTCTTAAAATTTTTAAAAATTT-AATTAAAC
1 TCTCTTAAAA-TTTTAAAAATTTCAACTAAAC
*
1113284 TCTCTTAAAATTTTAAAATTTTCAACTAAAC
1 TCTCTTAAAATTTTAAAAATTTCAACTAAAC
1113315 TCTC
1 TCTC
1113319 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (31 bp):
TCTCTTAAAATTTTAAAAATTTCAACTAAAC
Found at i:1113326 original size:29 final size:29
Alignment explanation
Indices: 1113260--1113326 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
1113250 TTTTCTCTTA
*
1113260 AAATTTTTAAAAATTTAATTAAACTCTCTT
1 AAATTTTTAAAAATTTAACTAAACTCTC-T
* *
1113290 AAAATTTTAAAATTTTCAACTAAACTCTC-
1 AAATTTTTAAAAATTT-AACTAAACTCTCT
*
1113319 AATTTTTT
1 AAATTTTT
1113327 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 6 0.19
30 14 0.45
31 11 0.35
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (29 bp):
AAATTTTTAAAAATTTAACTAAACTCTCT
Found at i:1116395 original size:16 final size:18
Alignment explanation
Indices: 1116369--1116402 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1116359 AATTTTAAAA
1116369 TTATGTAAAAATT-ATAT
1 TTATGTAAAAATTCATAT
1116386 TTAT-TAAAAATTCATAT
1 TTATGTAAAAATTCATAT
1116403 AAAAATCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TTATGTAAAAATTCATAT
Found at i:1117065 original size:28 final size:28
Alignment explanation
Indices: 1117029--1117082 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1117019 AATAACAATT
* *
1117029 TAAATTCAAAATAATCTGAATTCGAACG
1 TAAACTCAAAATAATCTAAATTCGAACG
*
1117057 TAAACTCAAAATAATTTAAATTCGAA
1 TAAACTCAAAATAATCTAAATTCGAA
1117083 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (28 bp):
TAAACTCAAAATAATCTAAATTCGAACG
Found at i:1117100 original size:16 final size:16
Alignment explanation
Indices: 1117057--1117100 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1117047 AATTCGAACG
1117057 TAAACTCAAAATAATT
1 TAAACTCAAAATAATT
* *
1117073 TAAATTCGAAATAATT
1 TAAACTCAAAATAATT
*
1117089 TAAACCCAAAAT
1 TAAACTCAAAAT
1117101 TAATCGAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (16 bp):
TAAACTCAAAATAATT
Found at i:1117992 original size:15 final size:16
Alignment explanation
Indices: 1117967--1117997 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1117957 AGGGAGTTAG
1117967 TGAAGTTAAATTAATT
1 TGAAGTTAAATTAATT
1117983 TGAA-TTAAATTAATT
1 TGAAGTTAAATTAATT
1117998 GTATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (16 bp):
TGAAGTTAAATTAATT
Found at i:1119313 original size:16 final size:17
Alignment explanation
Indices: 1119265--1119313 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
1119255 CCAAACAATA
*
1119265 ATTATTTTTC-AAATTA
1 ATTATTTTTCAAAATTT
**
1119281 ATTATTTTT-AATTTTT
1 ATTATTTTTCAAAATTT
1119297 A-TATTTTTCAAAATTT
1 ATTATTTTTCAAAATTT
1119313 A
1 A
1119314 AAATTTCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTTTTCAAAATTT
Found at i:1124815 original size:22 final size:22
Alignment explanation
Indices: 1124790--1124841 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1124780 ATCAAAATCC
1124790 ATTTTGAAAAATTGGATTCACT
1 ATTTTGAAAAATTGGATTCACT
1124812 ATTTTGAAAAATTGGATTCACT
1 ATTTTGAAAAATTGGATTCACT
1124834 ATTTTGAA
1 ATTTTGAA
1124842 CATAGATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (22 bp):
ATTTTGAAAAATTGGATTCACT
Found at i:1131165 original size:149 final size:149
Alignment explanation
Indices: 1130895--1131698 Score: 1137
Period size: 149 Copynumber: 5.4 Consensus size: 149
1130885 ACGGTCATCA
*
1130895 GGGTCCATAGCTCAGTGGCAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
1130960 GGGCCCTTTCTTTAGTTTTTTTTTGCCAAGTCCGTCCTGCTATAGTTATATATGTAGCAACCAAA
66 GGGCCCTTTCTTTAGTTTTTTTTTGCCAAGTCCGTCCTGCTATAGTTATATATGTAGCAACCAAA
1131025 GTAAACTTGTATCACAATT
131 GTAAACTTGTATCACAATT
1131044 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
1131109 GGG-CCTTTCCTTTAGTTTTTTTTTGCCAAGTCCGTCCTGCTATAGTTATATATGTAGCAACCAA
66 GGGCCCTTT-CTTTAGTTTTTTTTTGCCAAGTCCGTCCTGCTATAGTTATATATGTAGCAACCAA
1131173 AGTAAACTTGTATCACAATT
130 AGTAAACTTGTATCACAATT
1131193 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
* * *
1131258 GGGCCCTCCCTTTTAACTTA-TTTATTTTTTGCCAAGTCCGTCCT-TTCATAGTTTATACATGTA
66 GGGCCCT---TTCT---TTAGTTT-TTTTTTGCCAAGTCCGTCCTGCT-ATAG-TTATATATGTA
* *
1131321 GCAACCAAAGTAATAAC--ATATCACAACT
122 GCAACCAAAGT-A-AACTTGTATCACAATT
1131349 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
* * * *
1131414 GGGCCCTTTCTTTAGTTTTTTTTTTGCGAAGTCCGTCCTTCCATAGTTATATATGTAGCAACCAC
66 GGGCCCTTTCTTTAG-TTTTTTTTTGCCAAGTCCGTCCTGCTATAGTTATATATGTAGCAACCAA
* *
1131479 AGTAAACTTGCATCACAAAT
130 AGTAAACTTGTATCACAATT
*
1131499 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
* * * * ** * * *
1131564 GGGCCCTTTTTTTAATTTTTTTTTTCCAAGTCCGTCCTTCCGTTGTTTATAGATGTAGGAACCAA
66 GGGCCCTTTCTTTAGTTTTTTTTTGCCAAGTCCGTCCTGCTATAG-TTATATATGTAGCAACCAA
* *
1131629 TG-ACAAC----ATCCCACA--
130 AGTA-AACTTGTATCACA-ATT
* *
1131644 GGGTCCACAGCTCATTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCTGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACC-GGTT
1131699 GGGCCCTTTG
Statistics
Matches: 604, Mismatches: 29, Indels: 47
0.89 0.04 0.07
Matches are distributed among these distances:
145 48 0.08
146 9 0.01
147 1 0.00
148 8 0.01
149 238 0.39
150 131 0.22
151 23 0.04
152 4 0.01
153 5 0.01
154 4 0.01
155 27 0.04
156 102 0.17
157 1 0.00
158 3 0.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (149 bp):
GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
GGGCCCTTTCTTTAGTTTTTTTTTGCCAAGTCCGTCCTGCTATAGTTATATATGTAGCAACCAAA
GTAAACTTGTATCACAATT
Found at i:1131548 original size:306 final size:297
Alignment explanation
Indices: 1130895--1131698 Score: 1176
Period size: 306 Copynumber: 2.7 Consensus size: 297
1130885 ACGGTCATCA
*
1130895 GGGTCCATAGCTCAGTGGCAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
* * * *
1130960 GGGCCCTTTCT--TTAGTTTTTTTTTGCCAAGTCCGTCCTGCTATAG-TTATATATGTAGCAACC
66 GGGCCCTTTTTAATTA-TTTTTTTTTGCCAAGTCCGTCCTTCCATAGTTTATACATGTAGCAACC
*
1131022 AAAGTAAACTTGTATCACAATTGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGA
130 AAAGTAAAC---TATCACAACTGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGA
*
1131087 GGTCACCGGTTCGAACCTGGTTGGGCCTTTCCTTTAGTTTTTTTTTGCCAAGTCCGTCCTGCTAT
192 GGTCACCGGTTCGAACCTGGTTGGGCCTTTCCTTTAGTTTTTTTTTGCCAAGTCCGTCCTGCCAT
* *
1131152 AGTTATATATGTAGCAACCAAAGTAAACTTGTATCACAATT
257 AGTTATATATGTAGCAACCAAAGTAAACTTGCATCACAAAT
1131193 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
*
1131258 GGGCCCTCCCTTTTAACTTATTTATTTTTTGCCAAGTCCGTCCTTTCATAGTTTATACATGTAGC
66 GGGCCCT---TTTTAA-TTATTT-TTTTTTGCCAAGTCCGTCCTTCCATAGTTTATACATGTAGC
1131323 AACCAAAGTAATAACATATCACAACTGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATC
126 AACCAAAGT-A-AAC-TATCACAACTGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATC
*
1131388 AAGAGGTCACCGGTTCGAACCTGGTTGGGCCCTTT-CTTTAGTTTTTTTTTTGCGAAGTCCGTCC
188 AAGAGGTCACCGGTTCGAACCTGGTTGGG-CCTTTCCTTTAG-TTTTTTTTTGCCAAGTCCGTCC
* *
1131452 TTCCATAGTTATATATGTAGCAACCACAGTAAACTTGCATCACAAAT
251 TGCCATAGTTATATATGTAGCAACCAAAGTAAACTTGCATCACAAAT
*
1131499 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
* * * * *
1131564 GGGCCCTTTTT--TTAATTTTTTTTTTCCAAGTCCGTCCTTCCGTTGTTTATAGATGTAGGAACC
66 GGGCCCTTTTTAATT-ATTTTTTTTTGCCAAGTCCGTCCTTCCATAGTTTATACATGTAGCAACC
* * * * *
1131627 AATG-ACAAC-ATC-CCACAGGGTCCACAGCTCATTGGTAGAGCATTTGACTGCAGATCAAGAGG
130 AAAGTA-AACTATCACAACTGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGG
1131689 TCACCTGGTT
194 TCACC-GGTT
1131699 GGGCCCTTTG
Statistics
Matches: 465, Mismatches: 27, Indels: 30
0.89 0.05 0.06
Matches are distributed among these distances:
295 51 0.11
296 7 0.02
298 75 0.16
300 44 0.09
301 7 0.02
303 7 0.02
304 27 0.06
305 104 0.22
306 140 0.30
307 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (297 bp):
GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCTGGTT
GGGCCCTTTTTAATTATTTTTTTTTGCCAAGTCCGTCCTTCCATAGTTTATACATGTAGCAACCA
AAGTAAACTATCACAACTGGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTC
ACCGGTTCGAACCTGGTTGGGCCTTTCCTTTAGTTTTTTTTTGCCAAGTCCGTCCTGCCATAGTT
ATATATGTAGCAACCAAAGTAAACTTGCATCACAAAT
Found at i:1138387 original size:22 final size:22
Alignment explanation
Indices: 1138341--1138388 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1138331 TTTATAATTT
* *
1138341 ATAAAATTTTAAATTATCAATA
1 ATAAAATTATAAATTATCAAAA
1138363 ATAAAATTATAAATT-TCTAAAA
1 ATAAAATTATAAATTATC-AAAA
1138385 ATAA
1 ATAA
1138389 TAAAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAATTATAAATTATCAAAA
Found at i:1141101 original size:27 final size:26
Alignment explanation
Indices: 1141062--1141112 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1141052 CCAAAAAACC
* *
1141062 AAGTTTAGATACCAATTTGAATTAAGA
1 AAGTTCAGATACCAAATT-AATTAAGA
*
1141089 AAGTTCAGGTACCAAATTAATTAA
1 AAGTTCAGATACCAAATTAATTAA
1141113 ACCTTTAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (26 bp):
AAGTTCAGATACCAAATTAATTAAGA
Found at i:1161712 original size:216 final size:216
Alignment explanation
Indices: 1161338--1161766 Score: 646
Period size: 216 Copynumber: 2.0 Consensus size: 216
1161328 TATATTACAA
* * * * * *
1161338 AACTTGAGTTCCTCGAAGCAGCTAAATAACGGAAGCTAAAATCGATCATCATATACGCATCTCTT
1 AACTTGAATTCCTCAAAGCAGCTAAATAACAGAAGCTAAAATCAATCATCACAAACGCATCTCTT
*
1161403 AGATATTTTATCAGTAACGACAACTTTCCTTAAGACCTTTAAATTCCTTACAGCTCCAAAATAAT
66 AGATATTTTATCAGTAACGACAACTTTCCTTAAGACATTTAAATTCCTTACAGCTCCAAAATAAT
* * * ** *
1161468 GGAATCTAACACTAATCACAATAACCACGTATCTGAGGCATGTGATCAA-AATACATTCAAATTT
131 GCAATCTAAAACTAATCACAAGAACCACGTATCCAAGGCATGTGAT-AATAATACATTCAAATCT
*
1161532 CTTCAAAGTTCCGACATAACAG
195 CTTCAAAGTTCCAACATAACAG
*
1161554 AACTTGAATTCCTCAAAGCTA-CTAAATAACAGAAGCTAAAATCAATCATCACAAATGCATCTCT
1 AACTTGAATTCCTCAAAGC-AGCTAAATAACAGAAGCTAAAATCAATCATCACAAACGCATCTCT
* * * *
1161618 TAGATATTTTATCGGTAAGGACAACTTTCCTTAAGACATTTAAGTTCCTTGCAGCTCCAAAATAA
65 TAGATATTTTATCAGTAACGACAACTTTCCTTAAGACATTTAAATTCCTTACAGCTCCAAAATAA
*
1161683 TGCAATCTAAAACTAATCACCAGAACCACGTATCCAAGGCATGTGATAATAATACATTCAAATCT
130 TGCAATCTAAAACTAATCACAAGAACCACGTATCCAAGGCATGTGATAATAATACATTCAAATCT
1161748 CTTCAAAGTTCCAACATAA
195 CTTCAAAGTTCCAACATAA
1161767 GGGAACCAAA
Statistics
Matches: 191, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
215 2 0.01
216 188 0.98
217 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (216 bp):
AACTTGAATTCCTCAAAGCAGCTAAATAACAGAAGCTAAAATCAATCATCACAAACGCATCTCTT
AGATATTTTATCAGTAACGACAACTTTCCTTAAGACATTTAAATTCCTTACAGCTCCAAAATAAT
GCAATCTAAAACTAATCACAAGAACCACGTATCCAAGGCATGTGATAATAATACATTCAAATCTC
TTCAAAGTTCCAACATAACAG
Found at i:1171992 original size:36 final size:36
Alignment explanation
Indices: 1171952--1172025 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
1171942 CCTGAGCTTT
1171952 AGTTTAATTAGTATGAACATTATTGTTAATATAAGA
1 AGTTTAATTAGTATGAACATTATTGTTAATATAAGA
*
1171988 AGTTTAATTAGTATGAGCATTATTGTTAATATAAGA
1 AGTTTAATTAGTATGAACATTATTGTTAATATAAGA
1172024 AG
1 AG
1172026 ATGTAAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.41
Consensus pattern (36 bp):
AGTTTAATTAGTATGAACATTATTGTTAATATAAGA
Found at i:1173938 original size:17 final size:17
Alignment explanation
Indices: 1173913--1173951 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1173903 GTAAAATATT
1173913 TTTAT-TATTTTAATAA
1 TTTATATATTTTAATAA
* *
1173929 TTTATATATTTTTATTA
1 TTTATATATTTTAATAA
1173946 TTTATA
1 TTTATA
1173952 AAATTTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATATTTTAATAA
Found at i:1173939 original size:26 final size:26
Alignment explanation
Indices: 1173908--1173959 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1173898 TGATAGTAAA
1173908 ATATTTTTATTATTT-TAATAATTTAT
1 ATATTTTTATTATTTATAA-AATTTAT
1173934 ATATTTTTATTATTTATAAAATTTAT
1 ATATTTTTATTATTTATAAAATTTAT
1173960 CACATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATTTTTATTATTTATAAAATTTAT
Found at i:1174063 original size:17 final size:19
Alignment explanation
Indices: 1174041--1174075 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1174031 CATATTTATA
1174041 AATT-AAAT-TTTTTATTC
1 AATTAAAATATTTTTATTC
1174058 AATTAAAATATTTTTATT
1 AATTAAAATATTTTTATT
1174076 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTAAAATATTTTTATTC
Found at i:1174083 original size:19 final size:18
Alignment explanation
Indices: 1174040--1174084 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1174030 TCATATTTAT
* *
1174040 AAATTAAATTTTTTATTC
1 AAATAAAATTTTTTATTA
*
1174058 AATTAAAATATTTTTATTA
1 AAATAAAAT-TTTTTATTA
1174077 AAATAAAA
1 AAATAAAA
1174085 AGAAAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAAAATTTTTTATTA
Found at i:1174334 original size:15 final size:16
Alignment explanation
Indices: 1174314--1174343 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1174304 AGGTTAATTT
1174314 TTTATATTTA-ATTAC
1 TTTATATTTACATTAC
1174329 TTTATATTTACATTA
1 TTTATATTTACATTA
1174344 TTATTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATATTTACATTAC
Found at i:1174369 original size:2 final size:2
Alignment explanation
Indices: 1174362--1174407 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1174352 CATTAACCCA
1174362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1174404 AT AT
1 AT AT
1174408 TGCTCTAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1175261 original size:6 final size:6
Alignment explanation
Indices: 1175243--1175336 Score: 99
Period size: 6 Copynumber: 16.0 Consensus size: 6
1175233 TTAAATTGAT
**
1175243 TTTAAA TTT--A TTTAAA TTTAAA TTTATC TTTAAA TTTAAA TTTAAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
*
1175290 --TAAA TTTAAA TTTAATTA TTTAAA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1175337 ATAAAATTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
4 5 0.07
5 7 0.09
6 55 0.74
7 1 0.01
8 6 0.08
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:1175295 original size:17 final size:16
Alignment explanation
Indices: 1175243--1175347 Score: 79
Period size: 17 Copynumber: 6.4 Consensus size: 16
1175233 TTAAATTGAT
**
1175243 TTTAAATTTATTTAAA
1 TTTAAATTTAAATAAA
**
1175259 TTTAAATTTATCTTTAAA
1 TTTAAATTTA--AATAAA
1175277 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
*
1175294 TTTAAATTT-AAT-TA
1 TTTAAATTTAAATAAA
**
1175308 TTTAAATTTACTTTAAA
1 TTTAAATTTA-AATAAA
1175325 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
*
1175342 ATTAAA
1 TTTAAA
1175348 AACATTAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.14
15 2 0.03
16 12 0.16
17 32 0.44
18 17 0.23
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:1175314 original size:31 final size:31
Alignment explanation
Indices: 1175276--1175335 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1175266 TTATCTTTAA
1175276 ATTTAAATTTAAGATAAATTTAAATTTAATT
1 ATTTAAATTTAAGATAAATTTAAATTTAATT
***
1175307 ATTTAAATTTACTTTAAATTTAAATTTAA
1 ATTTAAATTTAAGATAAATTTAAATTTAA
1175336 AATAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (31 bp):
ATTTAAATTTAAGATAAATTTAAATTTAATT
Found at i:1175727 original size:27 final size:27
Alignment explanation
Indices: 1175697--1175766 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 27
1175687 CCCGACATTC
*
1175697 AAAATCAATATACAAAACCCTGATCTG
1 AAAATCAATAAACAAAACCCTGATCTG
** * * *
1175724 AAAATCAATACGCAGAGACCTTGATTTG
1 AAAATCAATAAACA-AAACCCTGATCTG
1175752 AAAATCAATAAACAA
1 AAAATCAATAAACAA
1175767 CCTTCCTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
27 13 0.37
28 22 0.63
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (27 bp):
AAAATCAATAAACAAAACCCTGATCTG
Found at i:1176122 original size:3 final size:3
Alignment explanation
Indices: 1176114--1176161 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
1176104 ATTAATTATG
* * *
1176114 ATA ATA ATA ATA ATA GTA AGTA ATA ATA CTA ATA ATA TTA ATTA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA A-TA ATA
1176161 A
1 A
1176162 ATCTTTTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1176146 original size:22 final size:22
Alignment explanation
Indices: 1176114--1176161 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1176104 ATTAATTATG
1176114 ATAATAATAATAATAGTAAGTA
1 ATAATAATAATAATAGTAAGTA
* * *
1176136 ATAATACTAATAATATTAATTA
1 ATAATAATAATAATAGTAAGTA
1176158 ATAA
1 ATAA
1176162 ATCTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
ATAATAATAATAATAGTAAGTA
Found at i:1177212 original size:161 final size:163
Alignment explanation
Indices: 1177008--1177353 Score: 486
Period size: 164 Copynumber: 2.1 Consensus size: 163
1176998 ATTTTATTAG
** * * *
1177008 TTTTCAATTTAATCCTTTGA-TGTTTGACTGGACCAGAGGCTGCCACGTGTC-CTTTTTTGCTTA
1 TTTTCAAACTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTCTGGCTTA
*
1177071 TTTCTACATTTAGTCCCTGACA-TTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTATT
66 TTTATACATTTAGTCCCTGACATTTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTATT
* *
1177135 TAATTACAAAATTGGCCCAATAATTTTTCAAGG
131 TAATTACAAAATTGGCCCAAAAATTTTTCAAGA
* *
1177168 TTTAT-AAATTAGTCCTTTGACTGTTTGACTGCACCA-AGGGCTGCCACGTGTCACTTTCTGGCT
1 TTT-TCAAACTAATCCTTTGACTGTTTGACTGCACCAGA-GGCTGCCACGTGTCACTTTCTGGCT
* * * * *
1177231 TATTTATGCATTTAGTCCCTGACATTTTTTTTATTTATTTTAATTTAGTCCTTAAATTAACTTTT
64 TATTTATACATTTAGTCCCTGACA-TTTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTT
*
1177296 ATTTAATTACAAAATTGGTCCAAAAATTTTTCAAGA
128 ATTTAATTACAAAATTGGCCCAAAAATTTTTCAAGA
1177332 TTTTCAAACTAATCCTTTGACT
1 TTTTCAAACTAATCCTTTGACT
1177354 TCTGGATGCC
Statistics
Matches: 163, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
160 17 0.10
161 29 0.18
162 30 0.18
163 1 0.01
164 86 0.53
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.45
Consensus pattern (163 bp):
TTTTCAAACTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTCTGGCTTA
TTTATACATTTAGTCCCTGACATTTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTATT
TAATTACAAAATTGGCCCAAAAATTTTTCAAGA
Found at i:1177460 original size:30 final size:30
Alignment explanation
Indices: 1177421--1177632 Score: 198
Period size: 30 Copynumber: 7.0 Consensus size: 30
1177411 CTCTAAATTG
*
1177421 TCCAGAAATTACATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
* *
1177452 CCCAAAATTATATTTTGACCCCAAAA-TTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
1177481 TCTAGAAATTACATTTTGACCCCTAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
1177512 TCCAAAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
1177542 TCCAAAATCATATTTTGACCCCAAAA-TTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * * * *
1177571 ACAAAAAAAAATTGCATTTTTACCCCGAAAC-TT
1 TC----CAAAATTACATTTTGACCCCAAAACTTT
* *
1177604 TCAAAAATTACCATTTT-ACCCCCAAACTT
1 TCCAAAATTA-CATTTTGACCCCAAAACTT
1177633 CCCTAAATCC
Statistics
Matches: 149, Mismatches: 23, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
29 25 0.17
30 94 0.63
31 9 0.06
33 21 0.14
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:1177670 original size:58 final size:58
Alignment explanation
Indices: 1177607--1177743 Score: 220
Period size: 58 Copynumber: 2.3 Consensus size: 58
1177597 GAAACTTTCA
*
1177607 AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCAATTTCACT
1 AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCAATTTCACC
* * *
1177665 AAAATTACCATTTTACCCTCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCAATTTCACC
*
1177723 AAAATCTACCATTTTGCCCCC
1 AAAAT-TACCATTTTACCCCC
1177744 GGGTATCCAA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
58 59 0.82
59 13 0.18
ACGTcount: A:0.32, C:0.35, G:0.01, T:0.31
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCAATTTCACC
Found at i:1179883 original size:1 final size:1
Alignment explanation
Indices: 1179879--1179908 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1179869 AACGACATAA
1179879 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1179909 AAAACCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1184515 original size:29 final size:32
Alignment explanation
Indices: 1184481--1184546 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 32
1184471 TTGAAGTTAT
* *
1184481 ATTTTTATAATTTTTAAAT-GATT-AAAT-TA
1 ATTTTTATAATGTTAAAATAGATTAAAATATA
*
1184510 ATTTTTATCATGTTAAAATAGATTAAAATATA
1 ATTTTTATAATGTTAAAATAGATTAAAATATA
1184542 ATTTT
1 ATTTT
1184547 ATTTTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 16 0.52
30 4 0.13
31 4 0.13
32 7 0.23
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (32 bp):
ATTTTTATAATGTTAAAATAGATTAAAATATA
Found at i:1184578 original size:17 final size:18
Alignment explanation
Indices: 1184556--1184589 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1184546 TATTTTTATT
1184556 AATTTAAAAT-TCTAAAA
1 AATTTAAAATGTCTAAAA
1184573 AATTTAAAATGTCTAAA
1 AATTTAAAATGTCTAAA
1184590 CTAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTTAAAATGTCTAAAA
Found at i:1184656 original size:6 final size:6
Alignment explanation
Indices: 1184645--1184678 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1184635 TTAATAAAGC
1184645 CCCTAA CCCTAA CCCTAA CCCTAA CCCTAA CCCT
1 CCCTAA CCCTAA CCCTAA CCCTAA CCCTAA CCCT
1184679 GTCAAAATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (6 bp):
CCCTAA
Found at i:1202412 original size:31 final size:33
Alignment explanation
Indices: 1202367--1202428 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1202357 ATAAAAAATG
*
1202367 TATAAATTTATT-AAATATT-AAAATAATATAA
1 TATAAATTTATTAAAAAATTAAAAATAATATAA
1202398 TATAAATATT-TTAAAAAATTAAAAATAATAT
1 TATAAAT-TTATTAAAAAATTAAAAATAATAT
1202429 GGGCAGGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 9 0.33
32 8 0.30
33 10 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
TATAAATTTATTAAAAAATTAAAAATAATATAA
Done.