Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000398.1 Hibiscus syriacus cultivar Beakdansim tig00000731_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: 357049
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:360 original size:130 final size:131
Alignment explanation
Indices: 201--490 Score: 406
Period size: 131 Copynumber: 2.2 Consensus size: 131
191 AAATTTTGAT
* * *
201 TCAAATTTCAACTTCACGACGAAATATATCAG-CTCGAGTCATCTAAGATTAACTTAACCCGTAA
1 TCAAATTTCAACTTCATGACGAAAGATATCAGTCTCGAGTCATCCAAGATTAACTTAACCCGTAA
*
265 TAGAGGAGTCATCTACAACATAGCTTAACTCAACA-AATGAGGAGCTATTTTCTAACAGATTCT-
66 TAGAAGAGTCATCTACAACATAGCTTAACTC--CATAATGAGGAGCTATTTTCTAACAGATTCTC
328 GAG
129 GAG
* * * **
331 TCAGATTTCAACTTCATGATGAAGGATATCAGTCTCGAGTCATCCAAGATTAACTTAACTTGTAA
1 TCAAATTTCAACTTCATGACGAAAGATATCAGTCTCGAGTCATCCAAGATTAACTTAACCCGTAA
* * * *
396 TGGAAGAGTCATCTACAACATAGCTTAACTCCATAGTGATGAGCTATTTTCTAACAGATTTTCGA
66 TAGAAGAGTCATCTACAACATAGCTTAACTCCATAATGAGGAGCTATTTTCTAACAGATTCTCGA
461 G
131 G
* *
462 TCAAATTTCAACTTCATGGCGAATGATAT
1 TCAAATTTCAACTTCATGACGAAAGATAT
491 TTGGGTTCGA
Statistics
Matches: 140, Mismatches: 17, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
129 2 0.01
130 52 0.37
131 86 0.61
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (131 bp):
TCAAATTTCAACTTCATGACGAAAGATATCAGTCTCGAGTCATCCAAGATTAACTTAACCCGTAA
TAGAAGAGTCATCTACAACATAGCTTAACTCCATAATGAGGAGCTATTTTCTAACAGATTCTCGA
G
Found at i:2684 original size:5 final size:5
Alignment explanation
Indices: 2674--2993 Score: 300
Period size: 5 Copynumber: 64.6 Consensus size: 5
2664 TTCTAATTCT
2674 TATTA TATTA TATTA -ATTA TATTA TA-T- TATTA TATTA TA-TA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
2720 TATTA TATTA TATTATA TATTA TATTA TATTA TATTA TATTA TATTA -ATTA
1 TATTA TATTA TA-T-TA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
2771 TATTATA TATTA TATTA TA-T- TATTA TATTA TA-TA TATTATA TATTA
1 TA-T-TA TATTA TATTA TATTA TATTA TATTA TATTA TA-T-TA TATTA
*
2817 TATTA TATTA TATTA TATTA TA-TA TATTA TA-TA TA-CA TATT- TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* *
2863 T-TGA TA-TA TA-TA TATTA TATTA TATATA TATAA T-TTA TA-TA TATTATA
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TATTA TATTA TATTA TA-T-TA
* *
2911 TATTA TATATA TATATA TATATA TATAA CA-TA TATTA TATATA TATATA
1 TATTA TAT-TA TAT-TA TAT-TA TATTA TATTA TATTA TAT-TA TAT-TA
* *
2960 TATATA TATATA TATAA TATTA T-TTT TATTA TAT
1 TAT-TA TAT-TA TATTA TATTA TATTA TATTA TAT
2994 ATGTAAATAT
Statistics
Matches: 273, Mismatches: 14, Indels: 56
0.80 0.04 0.16
Matches are distributed among these distances:
3 4 0.01
4 57 0.21
5 145 0.53
6 51 0.19
7 16 0.06
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:2716 original size:2 final size:2
Alignment explanation
Indices: 2691--3032 Score: 264
Period size: 2 Copynumber: 191.5 Consensus size: 2
2681 TTATATTAAT
2691 TA TA T- TA TA T- TA T- TA TA T- TA TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2727 T- TA TA T- TA TA TA T- 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
2762 TA T- TA -A T- TA TA T- TA TA TA T- TA TA T- TA TA T- 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
2796 TA T- TA TA TA TA T- 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
* *
2832 TA T- TA TA TA TA T- TA TA TA TA CA TA TT TA T- TA T- TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
*
2871 TA TA TA T- TA TA T- TA TA TA TA TA TA -A TT TA TA 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
*
2909 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA -A CA 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
* *
2948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TT TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
2988 T- TA TA TA TG TA AA TA TT TT TA TT TT TA TA T- TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3028 TA TA T
1 TA TA T
3033 CTTACATATT
Statistics
Matches: 278, Mismatches: 19, Indels: 86
0.73 0.05 0.22
Matches are distributed among these distances:
1 42 0.15
2 235 0.85
3 1 0.00
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (2 bp):
TA
Found at i:13507 original size:41 final size:43
Alignment explanation
Indices: 13414--13512 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 43
13404 GTCCTTCGGG
* * * *
13414 CCATTAATAAGCCTTTTGAGCATGATGATTAAATCCTTCAGGT
1 CCATTTATAAGCCTTTCGAGCAAGATGATTAAATCATTCAGGT
* * *
13457 -CATCTATAAGTCTTTCGAGCAAGATGA-TAAGTCATTCA-GT
1 CCATTTATAAGCCTTTCGAGCAAGATGATTAAATCATTCAGGT
13497 CCATTTATAAGACCTT
1 CCATTTATAAG-CCTT
13513 CGTGTAGGAT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
40 2 0.04
41 18 0.40
42 25 0.56
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (43 bp):
CCATTTATAAGCCTTTCGAGCAAGATGATTAAATCATTCAGGT
Found at i:13688 original size:36 final size:36
Alignment explanation
Indices: 13633--13924 Score: 239
Period size: 36 Copynumber: 7.7 Consensus size: 36
13623 TTCACTCAAG
* * *
13633 ATTTTATCTCACTTAAGATTATTTTCCTTAAAACAT
1 ATTTTATCTCACTTGAGATTTTTTTCCTTAAAACAA
* ** * *
13669 ATTTTATCTCAATTGAGATTTTTTTAAATAAAATAAATAA
1 ATTTTATCTCACTTGAGATTTTTTT-CCT--TA-AAACAA
* * *
13709 ATTTTGTCTCACTTGAGATTGTTTTTTTTTTCTAAAAAAACAA
1 ATTTTATCTCACTTGAGA-----TTTTTTTCCT--TAAAACAA
* *
13752 ATTTCATCTCACTCGAGATTGTTTCTTCCTTAAAACAA
1 ATTTTATCTCACTTGAGATT-TTT-TTCCTTAAAACAA
*
13790 ATTTTATCTCACTTGAGATTGTTCTTT--TTAAAACAG
1 ATTTTATCTCACTTGAGATT-TT-TTTCCTTAAAACAA
*
13826 ATTTGATCTCACTTGAGATTGTTTTT-CTTAAAACAA
1 ATTTTATCTCACTTGAGATT-TTTTTCCTTAAAACAA
* * *
13862 ATTTTATCTCACTTGAGATTGTTTTTACTTTAAACAT
1 ATTTTATCTCACTTGAGATT-TTTTTCCTTAAAACAA
*
13899 ATTTTATCTCACTTGAGATTGTTTTC
1 ATTTTATCTCACTTGAGATTTTTTTC
13925 ATTGAAACCA
Statistics
Matches: 214, Mismatches: 28, Indels: 28
0.79 0.10 0.10
Matches are distributed among these distances:
35 3 0.01
36 89 0.42
37 29 0.14
38 32 0.15
39 5 0.02
40 24 0.11
43 20 0.09
44 5 0.02
45 7 0.03
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (36 bp):
ATTTTATCTCACTTGAGATTTTTTTCCTTAAAACAA
Found at i:13875 original size:72 final size:73
Alignment explanation
Indices: 13633--13923 Score: 264
Period size: 72 Copynumber: 3.8 Consensus size: 73
13623 TTCACTCAAG
* * ** * * * **
13633 ATTTTATCTCACTTAAGATTATTTTCCTTAAAACATATTTTATCTCAATTGAGATT-TTTTTAAA
1 ATTTTATCTCACTTGAGATTGTTTTTATTAAAACAAATTTCATCTCACTTGAGATTGTTTTT-CC
* *
13697 TAAAATAAATAA
65 T--TA-AAACAA
* * *
13709 ATTTTGTCTCACTTGAGATTGTTTTTTTTTTCTAAAAAAACAAATTTCATCTCACTCGAGATTGT
1 ATTTTATCTCACTTGAGATTG---TTTTTAT-T---AAAACAAATTTCATCTCACTTGAGATTGT
13774 TTCTTCCTTAAAACAA
59 TT-TTCCTTAAAACAA
* *
13790 ATTTTATCTCACTTGAGATTGTTCTTT-TTAAAACAGATTTGATCTCACTTGAGATTGTTTTT-C
1 ATTTTATCTCACTTGAGATTGTT-TTTATTAAAACAAATTTCATCTCACTTGAGATTGTTTTTCC
13853 TTAAAACAA
65 TTAAAACAA
* * *
13862 ATTTTATCTCACTTGAGATTGTTTTTACTTTAAACATATTTTATCTCACTTGAGATTGTTTT
1 ATTTTATCTCACTTGAGATTGTTTTTA-TTAAAACAAATTTCATCTCACTTGAGATTGTTTT
13924 CATTGAAACC
Statistics
Matches: 183, Mismatches: 20, Indels: 27
0.80 0.09 0.12
Matches are distributed among these distances:
71 3 0.02
72 33 0.18
73 33 0.18
74 28 0.15
76 18 0.10
77 1 0.01
78 3 0.02
79 8 0.04
80 1 0.01
81 25 0.14
82 1 0.01
83 23 0.13
84 4 0.02
85 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (73 bp):
ATTTTATCTCACTTGAGATTGTTTTTATTAAAACAAATTTCATCTCACTTGAGATTGTTTTTCCT
TAAAACAA
Found at i:14395 original size:22 final size:22
Alignment explanation
Indices: 14363--14406 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
14353 AAATTAATCC
*
14363 AGATGGCATTAAGAGCATTTGG
1 AGATGGCATTAAGAACATTTGG
* *
14385 AGATGGTATTAGGAACATTTGG
1 AGATGGCATTAAGAACATTTGG
14407 GGCCGTATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.07, G:0.32, T:0.30
Consensus pattern (22 bp):
AGATGGCATTAAGAACATTTGG
Found at i:14634 original size:53 final size:52
Alignment explanation
Indices: 14573--14677 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 52
14563 ATCAAAATAA
*
14573 ACATATTCCAAAACCCAAATTAGAAACAGTCCACATGAAATTCACATACATAG
1 ACATATTCCAAAACCCAAATTAGAAACAGTCCACA-CAAATTCACATACATAG
*
14626 ACATATTCCATAACCCAAATTAGAAACAGTCCACACAAATTCACATACATAG
1 ACATATTCCAAAACCCAAATTAGAAACAGTCCACACAAATTCACATACATAG
14678 TCCAAAGGTC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 16 0.32
53 34 0.68
ACGTcount: A:0.47, C:0.26, G:0.07, T:0.21
Consensus pattern (52 bp):
ACATATTCCAAAACCCAAATTAGAAACAGTCCACACAAATTCACATACATAG
Found at i:19521 original size:37 final size:37
Alignment explanation
Indices: 19448--19521 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
19438 CAAAAGCTAC
* * ***
19448 ATTGATTTCAGTATATTCAGCATTGGTTTTTGTATGT
1 ATTGATTTCAGTATATTCAACATTGATTTCAATATGT
* *
19485 ATTGATTTTAGTATGTTCAACATTGATTTCAATATGT
1 ATTGATTTCAGTATATTCAACATTGATTTCAATATGT
19522 TGAACATTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (37 bp):
ATTGATTTCAGTATATTCAACATTGATTTCAATATGT
Found at i:19536 original size:21 final size:21
Alignment explanation
Indices: 19485--19529 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19475 TTTTGTATGT
* *
19485 ATTGATTTTAGTATGTTCAAC
1 ATTGATTTCAATATGTTCAAC
*
19506 ATTGATTTCAATATGTTGAAC
1 ATTGATTTCAATATGTTCAAC
19527 ATT
1 ATT
19530 TGTTTCAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47
Consensus pattern (21 bp):
ATTGATTTCAATATGTTCAAC
Found at i:19627 original size:28 final size:28
Alignment explanation
Indices: 19578--19633 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
19568 TTTTCAGAAT
*
19578 TTCTTGGATATAAACATGAACATACTTA
1 TTCTTGGATAAAAACATGAACATACTTA
*
19606 TTCTTGGATAAAGAACCT-AACATACTTA
1 TTCTTGGATAAA-AACATGAACATACTTA
19634 ACATATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (28 bp):
TTCTTGGATAAAAACATGAACATACTTA
Found at i:20060 original size:151 final size:152
Alignment explanation
Indices: 19764--20068 Score: 531
Period size: 151 Copynumber: 2.0 Consensus size: 152
19754 TAAACAGTTA
* * *
19764 ACAAACACATTTAAATTTGGTGGATTGTTTATTTAAATATAATTTTATTCCTTAAATTTAATGGT
1 ACAAACACATTTAAATTTAGTGAATTGTTTATTTAAATATAATTTTATTCCTTAAATCTAATGGT
*
19829 CCACCAACACACACTGTCCAATACAAATCAAGTGGTCCCCTTCACTAACAATCACTAATAATGTA
66 CCACCAACACACACTGTCCAATACAAATCAAGTGATCCCCTTCACTAACAATCACTAATAATGTA
19894 TGTACATGTGATTCTCACTAAC
131 TGTACATGTGATTCTCACTAAC
*
19916 ACAAACATATTTAAATTTAGTGAATTGTTTATTTAAATATAATTTTATTCCTTAAATCTAATGGT
1 ACAAACACATTTAAATTTAGTGAATTGTTTATTTAAATATAATTTTATTCCTTAAATCTAATGGT
* * *
19981 CCACCAACA-ACACTGTCCAATACAAATCAAGTGATCCCCTTGACTAACAGTCACTAATAGTGTA
66 CCACCAACACACACTGTCCAATACAAATCAAGTGATCCCCTTCACTAACAATCACTAATAATGTA
20045 TGTACATGTGATTCTCACTAAC
131 TGTACATGTGATTCTCACTAAC
20067 AC
1 AC
20069 GATATTTTTG
Statistics
Matches: 145, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
151 75 0.52
152 70 0.48
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (152 bp):
ACAAACACATTTAAATTTAGTGAATTGTTTATTTAAATATAATTTTATTCCTTAAATCTAATGGT
CCACCAACACACACTGTCCAATACAAATCAAGTGATCCCCTTCACTAACAATCACTAATAATGTA
TGTACATGTGATTCTCACTAAC
Found at i:20145 original size:54 final size:53
Alignment explanation
Indices: 20053--20157 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 53
20043 TATGTACATG
* * *
20053 TGATTCTCACTAACACGATATTTTTGCATTATTTCCTAAATAAAATATACACAA
1 TGATCCTCACTAACACAATATTTTTG-ATTATTCCCTAAATAAAATATACACAA
20107 TGATCCTCACTAACACAATAATTTTTTG-TTATTCCCTAAATAAAATATACA
1 TGATCCTCACTAACACAAT-A-TTTTTGATTATTCCCTAAATAAAATATACA
20158 TATGTGGTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
54 39 0.85
55 1 0.02
56 6 0.13
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (53 bp):
TGATCCTCACTAACACAATATTTTTGATTATTCCCTAAATAAAATATACACAA
Found at i:20772 original size:25 final size:27
Alignment explanation
Indices: 20714--20773 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
20704 CTAATTCACA
20714 AACCCTAAATTGATTTGTCACTAACCC
1 AACCCTAAATTGATTTGTCACTAACCC
* *
20741 TACCCTAAATTGATTT-TGA-TAACCC
1 AACCCTAAATTGATTTGTCACTAACCC
*
20766 AATCCTAA
1 AACCCTAA
20774 TCCCCTAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 12 0.41
26 2 0.07
27 15 0.52
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.32
Consensus pattern (27 bp):
AACCCTAAATTGATTTGTCACTAACCC
Found at i:23281 original size:18 final size:16
Alignment explanation
Indices: 23258--23292 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
23248 ACTTAAGCTG
23258 CAAATCCAGAATTATTAA
1 CAAATCCA-AATT-TTAA
23276 CAAATCCAAATTTTAA
1 CAAATCCAAATTTTAA
23292 C
1 C
23293 TGAAGTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 4 0.24
18 8 0.47
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.29
Consensus pattern (16 bp):
CAAATCCAAATTTTAA
Found at i:24351 original size:6 final size:6
Alignment explanation
Indices: 24340--24371 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
24330 AGTTGCGAAT
24340 ATTAAA ATTAAA ATTAAA ATTAAA ATTTAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA A-TTAAA A
24372 ATTTGATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTAAA
Found at i:24459 original size:11 final size:11
Alignment explanation
Indices: 24425--24464 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
24415 AAAAAGTCAA
*
24425 AAATATTATAAA
1 AAATATTA-AAT
24437 AATATATTAAAT
1 AA-ATATTAAAT
24449 AAATATTAAAT
1 AAATATTAAAT
24460 AAATA
1 AAATA
24465 AGAAACGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 14 0.54
12 6 0.23
13 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATATTAAAT
Found at i:26208 original size:35 final size:36
Alignment explanation
Indices: 26154--26255 Score: 125
Period size: 35 Copynumber: 2.9 Consensus size: 36
26144 TCAAAGGTTT
* *
26154 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-
1 TGTTCCAAGAGAAACTGTCTCAAGAGAGACAAAATG
* * * *
26189 TTTTTCAAGAGTAATTGTCTCAAGAGAGACAAAATG
1 TGTTCCAAGAGAAACTGTCTCAAGAGAGACAAAATG
* *
26225 TGTTCCATGAGAAACTATCTCAAGAGAGACA
1 TGTTCCAAGAGAAACTGTCTCAAGAGAGACA
26256 GAACTTTGTT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 31 0.55
36 25 0.45
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (36 bp):
TGTTCCAAGAGAAACTGTCTCAAGAGAGACAAAATG
Found at i:26764 original size:106 final size:106
Alignment explanation
Indices: 26533--27608 Score: 1701
Period size: 106 Copynumber: 10.2 Consensus size: 106
26523 TGGATGGCCA
** * *
26533 CTTCGTCGTGAAGTTGAACTTGTATTGTTTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* * *
26598 GCTCCGAAATT-GGAAATTGTTTATTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
* * * * *
26638 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTTCAATATCCTTCGTTGTGCAGTTAAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
*
26703 GCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
* * *
26744 CGTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCTAATATCCTTTGCTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
*
26809 GCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
*
26850 CTTCGTCGTGAAGTTGAACTTGCGTTGTCAT-GAGTCCAATATCATTCGCTGTGAAGTTGAAATT
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
*
26914 GGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCC
65 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
* * *
26956 CTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATTCTTCACTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* *
27021 GCTCTAAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
*
27062 CTTCGTCTTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* * * *
27127 GCTTTGAAATTGAGAAGTTGTTTGTTGACAACCAGTGATCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
* * * *
27168 CTTCCTCGTAAAGTTGAACTTGCGTTATCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* *
27233 GCTTTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
*
27274 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* * *
27339 GCTATGAAATT-GGAAGTTGTTTATTGACAACCAGTGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
*
27379 CTTCGTCGTGAAGTTGAACTTGCATTGTCAT-GAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* *
27443 GGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTTC
65 GGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
* *
27485 CTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCATTCGCTGTGAAGTTGAAATTG
1 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
*
27550 GCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCC
66 GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
27591 CTTCGTCGTGAAGTTGAA
1 CTTCGTCGTGAAGTTGAA
27609 ATCTACTCTC
Statistics
Matches: 896, Mismatches: 69, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
105 167 0.19
106 728 0.81
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
GCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCC
Found at i:28993 original size:15 final size:14
Alignment explanation
Indices: 28982--29013 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28972 TTCTTTTTGA
28982 TTTTTGCT-TTTTT
1 TTTTTGCTCTTTTT
28995 TTTTTGCTCTTTTT
1 TTTTTGCTCTTTTT
29009 TTTTT
1 TTTTT
29014 TTTTTGCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.84
Consensus pattern (14 bp):
TTTTTGCTCTTTTT
Found at i:28998 original size:13 final size:13
Alignment explanation
Indices: 28969--29013 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
28959 TTTTTTTCCC
*
28969 TTTTT-CTTTTTGA
1 TTTTTGCTTTTT-T
28982 TTTTTGCTTTTTT
1 TTTTTGCTTTTTT
28995 TTTTTGCTCTTTTT
1 TTTTTGCT-TTTTT
29009 TTTTT
1 TTTTT
29014 TTTTTGCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 13 0.45
14 16 0.55
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.82
Consensus pattern (13 bp):
TTTTTGCTTTTTT
Found at i:29050 original size:21 final size:20
Alignment explanation
Indices: 28969--29050 Score: 78
Period size: 20 Copynumber: 4.0 Consensus size: 20
28959 TTTTTTTCCC
*
28969 TTTTTCTTTTTGATTTTTGCT
1 TTTTTC-TTTTGATTTTTTCT
* *
28990 TTTTTTTTTTGCTCTTTTT-T
1 TTTTTCTTTTGAT-TTTTTCT
*
29010 TTTTT-TTTTGCTTCTTTTCT
1 TTTTTCTTTTGATT-TTTTCT
29030 TTTTTCTTTTGATTTTGTTCT
1 TTTTTCTTTTGATTTT-TTCT
29051 GATTGAAACT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.02
19 11 0.21
20 20 0.38
21 20 0.38
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTGATTTTTTCT
Found at i:30216 original size:27 final size:26
Alignment explanation
Indices: 30181--30231 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
30171 AAGAAATTTC
*
30181 ATGTTTATG-AAAATGCTTAAAAATGAA
1 ATGTATATGCAAAATGC--AAAAATGAA
30208 ATGTATATGCAAAATGCAAAAATG
1 ATGTATATGCAAAATGCAAAAATG
30232 CATGAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.29
Consensus pattern (26 bp):
ATGTATATGCAAAATGCAAAAATGAA
Found at i:32001 original size:11 final size:11
Alignment explanation
Indices: 31987--32017 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31977 AAATGTTATA
*
31987 AAATATATATT
1 AAATAAATATT
31998 AAATAAATATT
1 AAATAAATATT
32009 AAATAAATA
1 AAATAAATA
32018 AGAAACGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAAATATT
Found at i:33193 original size:3 final size:3
Alignment explanation
Indices: 33187--33230 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
33177 TTAATAGAAT
* *
33187 TAA TAA TAA TTAA TAA TAA TAA TAA TAAA TAA TTA TTA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
33231 CATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:33199 original size:19 final size:17
Alignment explanation
Indices: 33175--33218 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
33165 CTTCAAAAAA
33175 AATTAATAGAATTAATAAT
1 AATTAATA-AA-TAATAAT
33194 AATTAAT-AATAATAAT
1 AATTAATAAATAATAAT
*
33210 AATAAATAA
1 AATTAATAA
33219 TTATTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 13 0.57
17 3 0.13
19 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AATTAATAAATAATAAT
Found at i:33208 original size:16 final size:16
Alignment explanation
Indices: 33187--33230 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
33177 TTAATAGAAT
*
33187 TAATAATAATTAATAA
1 TAATAATAATAAATAA
33203 TAATAATAATAAATAA
1 TAATAATAATAAATAA
* *
33219 TTATTATAATAA
1 TAATAATAATAA
33231 CATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:33219 original size:19 final size:19
Alignment explanation
Indices: 33187--33230 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
33177 TTAATAGAAT
*
33187 TAATAATAATTAATAATAA
1 TAATAATAAATAATAATAA
* *
33206 TAATAATAAATAATTATTA
1 TAATAATAAATAATAATAA
33225 TAATAA
1 TAATAA
33231 CATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAATAAATAATAATAA
Found at i:37058 original size:41 final size:41
Alignment explanation
Indices: 37001--37078 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
36991 AGGACAATGA
37001 AAAAATACAGATCCAGTAAATCCTACTCAAAAG-AAAAGTAC
1 AAAAATACAGATCCAGTAAATCCTACT-AAAAGCAAAAGTAC
* *
37042 AAAAATATAGATCCAGTAGATCCTACTAAAAGCAAAA
1 AAAAATACAGATCCAGTAAATCCTACTAAAAGCAAAA
37079 CTGCTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 5 0.15
41 29 0.85
ACGTcount: A:0.54, C:0.18, G:0.10, T:0.18
Consensus pattern (41 bp):
AAAAATACAGATCCAGTAAATCCTACTAAAAGCAAAAGTAC
Found at i:38520 original size:23 final size:23
Alignment explanation
Indices: 38476--38523 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
38466 TAATTTTTAA
* * * *
38476 TTTTAAATCTTTATTAACTGTAT
1 TTTTAAATATGTATAAAATGTAT
38499 TTTTAAATATGTATAAAATGTAT
1 TTTTAAATATGTATAAAATGTAT
38522 TT
1 TT
38524 AATTATAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (23 bp):
TTTTAAATATGTATAAAATGTAT
Found at i:38935 original size:20 final size:20
Alignment explanation
Indices: 38905--39079 Score: 97
Period size: 20 Copynumber: 8.7 Consensus size: 20
38895 ATTTTCAGAT
*
38905 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
38925 TCGCATTGCGATT-TTACAAA
1 TCGCAATGCGATTCTGAC-TA
**
38945 TTCGCGTTGCGATTTTCTGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * * *
38968 TTGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
38988 TCGTAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
** * * *
39008 TCGCAATGTAAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
39028 TCGCAATGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
* *
39048 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
39068 TCGCAAT-CGATT
1 TCGCAATGCGATT
39080 TTCAAAGCGC
Statistics
Matches: 111, Mismatches: 35, Indels: 19
0.67 0.21 0.12
Matches are distributed among these distances:
19 9 0.08
20 76 0.68
21 12 0.11
22 8 0.07
23 3 0.03
24 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:39014 original size:40 final size:40
Alignment explanation
Indices: 38905--39058 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
38895 ATTTTCAGAT
* * * * **
38905 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTACAAA
1 TCGCAATGCGATTCTGACTATCGCAATGCGAATATGTAAA
** *
38945 TTCGCGTTGCGATTTTCTGACTATTGCAATGCGAATATGTAAA
1 -TCGCAATGCGA--TTCTGACTATCGCAATGCGAATATGTAAA
* **
38988 TCGTAATGCGATTCTGACTATCGCAATGTAAATATGTAAA
1 TCGCAATGCGATTCTGACTATCGCAATGCGAATATGTAAA
* *
39028 TCGCAATGCGATTCTGACTGTCGCAACGCGA
1 TCGCAATGCGATTCTGACTATCGCAATGCGA
39059 TGCTGACTAT
Statistics
Matches: 91, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
40 52 0.57
41 8 0.09
42 8 0.09
43 23 0.25
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (40 bp):
TCGCAATGCGATTCTGACTATCGCAATGCGAATATGTAAA
Found at i:39280 original size:22 final size:22
Alignment explanation
Indices: 39255--39297 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
39245 GGCAACATCC
39255 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
39277 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
39298 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:39757 original size:20 final size:20
Alignment explanation
Indices: 39683--39750 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
39673 AGAATCGCAA
*
39683 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGTGT
**
39702 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
39722 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
39742 TGCGATTTT
1 TGCGATTTT
39751 AAGTTTCAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 9 0.21
20 34 0.79
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:41405 original size:18 final size:18
Alignment explanation
Indices: 41382--41431 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
41372 TTTACTCATA
41382 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
41400 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
41418 ATTTCACTTAGATT
1 ATTTCACTTAGATT
41432 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:41609 original size:20 final size:20
Alignment explanation
Indices: 41579--41626 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
41569 TAGTTTACTT
41579 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* * **
41599 TTGCAATGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
41619 TCGCAACG
1 TCGCAACG
41627 AAAGAATCGC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:42229 original size:21 final size:21
Alignment explanation
Indices: 42204--42286 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 21
42194 GACTCACTTG
*
42204 TCATCATTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
** * *
42225 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* * * *
42246 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTA
* *
42267 TCATCGTTGAAGAGGTCCCT
1 TCATCGTTCAAGAGGCCCCT
42287 CCCAACATTC
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:42280 original size:42 final size:42
Alignment explanation
Indices: 42210--42290 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
42200 CTTGTCATCA
*
42210 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCG
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACCG
* ** *
42252 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
42291 ACATTCTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.21
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACCG
Found at i:43716 original size:14 final size:14
Alignment explanation
Indices: 43679--43717 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
43669 TTGCTTGTTT
*
43679 AATTGATTTATAAA
1 AATTGATTTGTAAA
43693 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
43707 AGTTGATTTGT
1 AATTGATTTGT
43718 TTAATATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:43960 original size:20 final size:20
Alignment explanation
Indices: 43933--44196 Score: 230
Period size: 20 Copynumber: 13.8 Consensus size: 20
43923 GCGATTTTCT
* *
43933 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
43953 CATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
43973 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
43993 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
* *
44012 CGTTTCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
44032 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
**
44052 CGTTGCGATAGAAAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
44072 AGTTGC-A-A-T---TTTTG
1 CGTTGCGATAGTCAAATTCG
*
44086 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
44106 TGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
44126 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
44140 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
44160 TGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
44180 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
44197 GAATGTGTAA
Statistics
Matches: 193, Mismatches: 38, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
14 19 0.10
15 1 0.01
16 2 0.01
17 1 0.01
18 2 0.01
19 16 0.08
20 152 0.79
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:44034 original size:59 final size:60
Alignment explanation
Indices: 43933--44062 Score: 208
Period size: 59 Copynumber: 2.2 Consensus size: 60
43923 GCGATTTTCT
43933 CGTTGCGATAGTCAAATACCCATTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATACCCATTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCA
* * * **
43993 CGTTGCGATAGTCAAATA-GCGTTTCGATAATCAAATTCGCGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATACCCATTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCA
44052 CGTTGCGATAG
1 CGTTGCGATAG
44063 AAAAATTCGA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 47 0.72
60 18 0.28
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (60 bp):
CGTTGCGATAGTCAAATACCCATTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCA
Found at i:44171 original size:54 final size:54
Alignment explanation
Indices: 43974--44188 Score: 216
Period size: 54 Copynumber: 3.9 Consensus size: 54
43964 TCAAATTCGC
** * * * *
43974 GTTGCGATAGTCAAATTCACGTTGCGATAGTCAAA-TAGCGTTTCGATAATCAAATTCGC
1 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTTGA
* * ** * * *
44033 GTTGCGATAGTCAAATTTGCGTTGCGATAGAAAAATTCGAGTTGCAATTTTTGC
1 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
* *
44087 GTTGCGATAGTCATATTCGTGTTACGATAGTCAAATTCGCGTTGCGATTTTTGA
1 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
* *
44141 GTTGCGATAATCAAATTCGTGTTGCGATAGTCAAATTCCCGTTGCGAT
1 GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
44189 ATTCAAATGA
Statistics
Matches: 133, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
54 93 0.70
58 1 0.01
59 31 0.23
60 8 0.06
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (54 bp):
GTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGA
Found at i:44419 original size:140 final size:140
Alignment explanation
Indices: 44167--44436 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
44157 TCGTGTTGCG
*
44167 ATAGTCAAATTCCCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCCCGTTGCGATATTCAAATGAATGTGAAATAAGTGATAACAACTGAACATATCA
44232 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
44297 AATACACATA
131 AATACACATA
*
44307 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGAAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCCCGTTGCGATATTCAAATGAATGTGAAATAAGTGATAACAACTGAACATATCA
44372 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
44437 TACAACGTTT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCCCGTTGCGATATTCAAATGAATGTGAAATAAGTGATAACAACTGAACATATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:46796 original size:24 final size:24
Alignment explanation
Indices: 46759--46811 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
46749 CTGAAACATC
*
46759 ATCAAAATCCGAGTATTGACTAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
46783 ATCAAAGTCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
46807 ATCAA
1 ATCAA
46812 GTTTCGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:47770 original size:22 final size:22
Alignment explanation
Indices: 47745--47800 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
47735 TATTCGCATT
47745 GCGATAGTCAGAAAATCGCAAC
1 GCGATAGTCAGAAAATCGCAAC
* ** *
47767 GCGA-ATTTGGAAAATCGCAAT
1 GCGATAGTCAGAAAATCGCAAC
47788 GCGATAGTCAGAA
1 GCGATAGTCAGAA
47801 TCGCGTTGCG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (22 bp):
GCGATAGTCAGAAAATCGCAAC
Found at i:47804 original size:20 final size:20
Alignment explanation
Indices: 47623--47811 Score: 114
Period size: 20 Copynumber: 9.3 Consensus size: 20
47613 AAATTCAGTG
* * *
47623 TTGCGACAGTCAGAATTGCG
1 TTGCGATAGTCAGAATCGCA
* * *
47643 TTGTGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCA
47663 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
* *
47683 TTGCAATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
* * *
47703 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
* * *
47723 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGAATCGCA
47743 TTGCGATAGTCAGAAAATCGCA
1 TTGCGATAGTCAG--AATCGCA
** * * *
47765 ACGCGA-ATTTGGAAAATCGCA
1 TTGCGATA-GT-CAGAATCGCA
* *
47786 ATGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
47806 TTGCGA
1 TTGCGA
47812 ATCTGGAAAC
Statistics
Matches: 136, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.01
20 107 0.79
21 15 0.11
22 12 0.09
23 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:47819 original size:41 final size:42
Alignment explanation
Indices: 47738--47820 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 42
47728 ATTTACATAT
* *
47738 TCGCATTGCGATAGTCAGAAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATAGTCAG-AAATCGCAACGCGAATCTGGAAAA
***
47781 TCGCAATGCGATAGTCAG-AATCGCGTTGCGAATCTGGAAA
1 TCGCAATGCGATAGTCAGAAATCGCAACGCGAATCTGGAAA
47821 CTAATTTGCG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 18 0.51
43 17 0.49
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (42 bp):
TCGCAATGCGATAGTCAGAAATCGCAACGCGAATCTGGAAAA
Found at i:48019 original size:2 final size:2
Alignment explanation
Indices: 48012--48063 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
48002 AAATATTGTA
48012 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
48054 AT AT AT -T AT A
1 AT AT AT AT AT A
48064 AAAGTCATTC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48706 original size:15 final size:16
Alignment explanation
Indices: 48686--48718 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
48676 ACTTTTATTC
48686 ATTATTATTTA-AAAA
1 ATTATTATTTATAAAA
48701 ATTATTATTTATAAAA
1 ATTATTATTTATAAAA
48717 AT
1 AT
48719 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATTATTTATAAAA
Found at i:49494 original size:179 final size:182
Alignment explanation
Indices: 49194--49557 Score: 689
Period size: 179 Copynumber: 2.0 Consensus size: 182
49184 TTGTTTTATT
49194 TTGTCCACTTTTAATAAATGATTTAAGAAAATAATTTTTTGGTCACTTACATTATTTATAATGTT
1 TTGTCCACTTTTAATAAATGATTTAAGAAAATAATTTTTTGGTCACTTACATTATTTATAATGTT
49259 TCAGTTATTGCAACATTAAATGTCGGTAGTTTGAAGACATGACACATTAATAGAAGAGATTA-TT
66 TCAGTTATTGCAACATTAAATGTCGGTAGTTTGAAGACATGACACATTAATAGAAGAGATTATTT
49323 T-TTTGACCTTAAATTCTAGATAAAACGTTAATTTAATTTCTAAAC-TTAAA
131 TATTTGACCTTAAATTCTAGATAAAACGTTAATTTAATTTCTAAACTTTAAA
49373 TTGTCCACTTTTAATAAATGATTTAAGAAAATAATTTTTTGGTCACTTACATTATTTATAATGTT
1 TTGTCCACTTTTAATAAATGATTTAAGAAAATAATTTTTTGGTCACTTACATTATTTATAATGTT
49438 TCAGTTATTGCAACATTAAATGTCGGTAGTTTGAAGACATGACACATTAATAGAAGAGATTATTT
66 TCAGTTATTGCAACATTAAATGTCGGTAGTTTGAAGACATGACACATTAATAGAAGAGATTA--T
49503 TTTATTTGACCTTAAATTCTAGATAAAACGTTAATTTAATTTCTAAACTTTAAA
129 TTTATTTGACCTTAAATTCTAGATAAAACGTTAATTTAATTTCTAAACTTTAAA
49557 T
1 T
49558 AAAATAATTG
Statistics
Matches: 180, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
179 127 0.71
182 3 0.02
183 44 0.24
184 6 0.03
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (182 bp):
TTGTCCACTTTTAATAAATGATTTAAGAAAATAATTTTTTGGTCACTTACATTATTTATAATGTT
TCAGTTATTGCAACATTAAATGTCGGTAGTTTGAAGACATGACACATTAATAGAAGAGATTATTT
TATTTGACCTTAAATTCTAGATAAAACGTTAATTTAATTTCTAAACTTTAAA
Found at i:50300 original size:20 final size:19
Alignment explanation
Indices: 50267--50304 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
50257 TAATATAATA
50267 AATAAATTAAAAATAATTG
1 AATAAATTAAAAATAATTG
*
50286 AATAAATATATAAATAATT
1 AATAAAT-TAAAAATAATT
50305 AAATCATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AATAAATTAAAAATAATTG
Found at i:51244 original size:37 final size:37
Alignment explanation
Indices: 51202--51280 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
51192 AATATTAGGG
* * *
51202 AAAATATTAATAATAGTATA-G-AAAAAATAATAGAAAT
1 AAAATA-TAATAATAATAAAGGTAAAAAACAATA-AAAT
*
51239 AAAATATATTAATAATAAAGGTAAAAAACAATAAAAT
1 AAAATATAATAATAATAAAGGTAAAAAACAATAAAAT
51276 AAAAT
1 AAAAT
51281 TAGTAAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 10 0.28
37 16 0.44
38 10 0.28
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.25
Consensus pattern (37 bp):
AAAATATAATAATAATAAAGGTAAAAAACAATAAAAT
Found at i:53503 original size:106 final size:106
Alignment explanation
Indices: 53318--53791 Score: 732
Period size: 106 Copynumber: 4.5 Consensus size: 106
53308 GTATTGCTCC
* * * * * * *
53318 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGTCTCTGGAACTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAG
53383 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * *
53424 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAG
*
53489 TCAGTCGCCCCTTCGCTGTGAAGTCGAGCTTGTGCTGTCTT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* *
53530 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAG
* * *
53595 TCAGCCGCCCCTTTGCTATGAAGTTGAGCTTGTGCTGTCTT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * * *
53636 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAG
* * *
53701 TCAATCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTATCTT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
*
53742 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
53792 GCCCCTTTGT
Statistics
Matches: 336, Mismatches: 32, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 336 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAG
TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:58585 original size:60 final size:60
Alignment explanation
Indices: 58513--58635 Score: 228
Period size: 60 Copynumber: 2.0 Consensus size: 60
58503 CCCACACAAA
58513 ACAGTCAAAGAATTAAATTTGAAAGAAAATGGAAATGAAGTGCTGGAATGAAGAAAACAG
1 ACAGTCAAAGAATTAAATTTGAAAGAAAATGGAAATGAAGTGCTGGAATGAAGAAAACAG
* *
58573 ACAGTCAAAGAATTAAATTTGAAAGAAAATGGAAATGAAGTGTTGGAATGAAGAAAATAG
1 ACAGTCAAAGAATTAAATTTGAAAGAAAATGGAAATGAAGTGCTGGAATGAAGAAAACAG
58633 ACA
1 ACA
58636 ATGAATTCGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.20
Consensus pattern (60 bp):
ACAGTCAAAGAATTAAATTTGAAAGAAAATGGAAATGAAGTGCTGGAATGAAGAAAACAG
Found at i:72198 original size:23 final size:23
Alignment explanation
Indices: 72086--72194 Score: 139
Period size: 23 Copynumber: 4.7 Consensus size: 23
72076 GTGCAACATA
72086 TTTGTCCCGAAGGACCACATAAG-
1 TTTGTCCCGAAGGACCACAT-AGT
* * *
72109 ATTATCCCGAAGGAGCACATAGT
1 TTTGTCCCGAAGGACCACATAGT
72132 TTTGTCCCGAAGGACCACATAGT
1 TTTGTCCCGAAGGACCACATAGT
*
72155 TTTGTCCCGAAGGACCATATAGT
1 TTTGTCCCGAAGGACCACATAGT
* * *
72178 TTTCTTCTGAAGGACCA
1 TTTGTCCCGAAGGACCA
72195 TATAAAACCC
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
22 2 0.03
23 73 0.97
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (23 bp):
TTTGTCCCGAAGGACCACATAGT
Found at i:76904 original size:40 final size:41
Alignment explanation
Indices: 76848--76928 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 41
76838 CTTTTAATCC
76848 TCTCAATTTTAGCATTTATGCACAATTATTTTGAAACCATT
1 TCTCAATTTTAGCATTTATGCACAATTATTTTGAAACCATT
76889 TCTCAA-TTTAGCATTTATGCACAATTATTTTGAAACCATT
1 TCTCAATTTTAGCATTTATGCACAATTATTTTGAAACCATT
76929 ATATGGGGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 34 0.85
41 6 0.15
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.43
Consensus pattern (41 bp):
TCTCAATTTTAGCATTTATGCACAATTATTTTGAAACCATT
Found at i:77308 original size:80 final size:80
Alignment explanation
Indices: 77218--77388 Score: 326
Period size: 80 Copynumber: 2.1 Consensus size: 80
77208 AGATCAAGTC
77218 AAAAAATATTTTTCCCTTATTTGTTATATTAAATATAGGTTCAACAATCTCCCCCTTTTTGATAT
1 AAAAAATATTTTTCCCTTATTTGTTATATTAAATATAGGTTCAACAATCTCCCCCTTTTTGATAT
77283 AACAAAACATTTGAA
66 AACAAAACATTTGAA
77298 AAAAAATATTTTTCCCTTATTTGTTATATTAAATATAGGTTCAACAATCTCCCCCTTTTTGATAT
1 AAAAAATATTTTTCCCTTATTTGTTATATTAAATATAGGTTCAACAATCTCCCCCTTTTTGATAT
77363 AACAAAACATTTGAA
66 AACAAAACATTTGAA
*
77378 AAATAAT-TTTT
1 AAAAAATATTTT
77389 GACAAAAGCT
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 4 0.04
80 86 0.96
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (80 bp):
AAAAAATATTTTTCCCTTATTTGTTATATTAAATATAGGTTCAACAATCTCCCCCTTTTTGATAT
AACAAAACATTTGAA
Found at i:79555 original size:12 final size:12
Alignment explanation
Indices: 79534--79565 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
79524 GAGTGATTCT
*
79534 GATGAAGATAAC
1 GATGACGATAAC
79546 GATGACGATAAC
1 GATGACGATAAC
79558 GATGACGA
1 GATGACGA
79566 AGATGACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.28, T:0.16
Consensus pattern (12 bp):
GATGACGATAAC
Found at i:83837 original size:14 final size:14
Alignment explanation
Indices: 83818--83844 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
83808 TTGTGCAAAG
83818 TGTATCGATACATA
1 TGTATCGATACATA
83832 TGTATCGATACAT
1 TGTATCGATACAT
83845 CCTCGCTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
TGTATCGATACATA
Found at i:85013 original size:15 final size:15
Alignment explanation
Indices: 84993--85022 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
84983 TAACACCTTT
84993 GGTTTAGATAACGAG
1 GGTTTAGATAACGAG
85008 GGTTTAGATAACGAG
1 GGTTTAGATAACGAG
85023 AGAGAGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.27
Consensus pattern (15 bp):
GGTTTAGATAACGAG
Found at i:90149 original size:14 final size:14
Alignment explanation
Indices: 90081--90150 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 14
90071 TTTGTATCAC
90081 TAAAAAATATTTTT
1 TAAAAAATATTTTT
*
90095 AAAAAAATATTTTTT
1 TAAAAAATA-TTTTT
90110 ATAAAATAAATTAATTGTTT
1 -T-AAA-AAA-T-ATT-TTT
*
90130 TGAAAAATATTTTT
1 TAAAAAATATTTTT
90144 TAAAAAA
1 TAAAAAA
90151 CGTTTTACGA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
14 17 0.38
15 8 0.18
16 1 0.02
17 6 0.13
18 5 0.11
19 4 0.09
20 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
TAAAAAATATTTTT
Found at i:90262 original size:26 final size:26
Alignment explanation
Indices: 90233--90294 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
90223 TTTAATACAA
90233 TTATTAAATAAAATAAATAATATTAT
1 TTATTAAATAAAATAAATAATATTAT
* * *
90259 TTATCATAA-AAACTAAATAGTATTAT
1 TTATTA-AATAAAATAAATAATATTAT
90285 TT-TTGAAATA
1 TTATT-AAATA
90295 TTAAAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
25 3 0.10
26 24 0.83
27 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (26 bp):
TTATTAAATAAAATAAATAATATTAT
Found at i:90476 original size:24 final size:24
Alignment explanation
Indices: 90425--90477 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
90415 TATTATAATT
*
90425 ATATTTTTAAAATTATTAATTAAT
1 ATATTTTTAAAATTATTAATTAAA
90449 ATATTTTTAAATATCT-TT-ATTAAA
1 ATATTTTTAAA-AT-TATTAATTAAA
90473 ATATT
1 ATATT
90478 ATTATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 21 0.81
25 4 0.15
26 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATTTTTAAAATTATTAATTAAA
Found at i:90688 original size:26 final size:24
Alignment explanation
Indices: 90659--90721 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
90649 ATTAAAAAAT
90659 ATAATATTATATTATTAGAA-ATATTA
1 ATAATA-TATATT-TTA-AATATATTA
*
90685 ATAA-ATATATTTTAAATATTTTA
1 ATAATATATATTTTAAATATATTA
90708 ATAAT-TAATATTTT
1 ATAATAT-ATATTTT
90722 GATTAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 13 0.39
24 13 0.39
25 1 0.03
26 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATAATATATATTTTAAATATATTA
Found at i:94103 original size:14 final size:14
Alignment explanation
Indices: 94084--94117 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
94074 GTGTATAACC
94084 AATGAAGTAAATAA
1 AATGAAGTAAATAA
*
94098 AATGAATTAAATAA
1 AATGAAGTAAATAA
*
94112 GATGAA
1 AATGAA
94118 AAAAAATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (14 bp):
AATGAAGTAAATAA
Found at i:94870 original size:39 final size:41
Alignment explanation
Indices: 94819--94913 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 41
94809 TTCGGTTTGC
* *
94819 AAAAAACTGGTTTTTAAAAAAAACCGGATTTTT-T-CGGTT
1 AAAAAACCGGTTTTTAAAAAAAACCGGATTTTTATCCGGAT
* *
94858 AAAAAACCGGTTTTTTAAAAAAACCGGTTTTTTATCCGGAT
1 AAAAAACCGGTTTTTAAAAAAAACCGGATTTTTATCCGGAT
*
94899 AAAAAATCGGTTTTT
1 AAAAAACCGGTTTTT
94914 TTATCCGGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 30 0.61
40 1 0.02
41 18 0.37
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (41 bp):
AAAAAACCGGTTTTTAAAAAAAACCGGATTTTTATCCGGAT
Found at i:94880 original size:17 final size:17
Alignment explanation
Indices: 94819--94891 Score: 74
Period size: 17 Copynumber: 4.0 Consensus size: 17
94809 TTCGGTTTGC
* *
94819 AAAAAACTGGTTTTTAA
1 AAAAAACCGGTTTTTTA
*
94836 AAAAAACCGGATTTTTTCGGTT
1 AAAAAACCGG--TTTTT---TA
94858 AAAAAACCGGTTTTTTA
1 AAAAAACCGGTTTTTTA
94875 AAAAAACCGGTTTTTTA
1 AAAAAACCGGTTTTTTA
94892 TCCGGATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
17 27 0.57
19 5 0.11
20 5 0.11
22 10 0.21
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (17 bp):
AAAAAACCGGTTTTTTA
Found at i:94913 original size:25 final size:23
Alignment explanation
Indices: 94836--94961 Score: 97
Period size: 24 Copynumber: 5.5 Consensus size: 23
94826 TGGTTTTTAA
*
94836 AAAAAACCGGATTTTT-T-CGGTT
1 AAAAAACCGGTTTTTTATCCGG-T
94858 AAAAAACCGGTTTTTTA------
1 AAAAAACCGGTTTTTTATCCGGT
94875 AAAAAACCGGTTTTTTATCCGGAT
1 AAAAAACCGGTTTTTTATCCGG-T
*
94899 AAAAAATCGGTTTTTTTATCCGGTTT
1 AAAAAACCGG-TTTTTTATCCGG--T
*
94925 GAAAAAAACCGGTTTTTAATCCGGT
1 --AAAAAACCGGTTTTTTATCCGGT
94950 AAAAAAACCGGT
1 -AAAAAACCGGT
94962 CGTTCAATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 22
0.76 0.04 0.19
Matches are distributed among these distances:
17 17 0.20
22 15 0.17
24 21 0.24
25 13 0.15
26 1 0.01
27 11 0.13
28 9 0.10
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (23 bp):
AAAAAACCGGTTTTTTATCCGGT
Found at i:96513 original size:19 final size:20
Alignment explanation
Indices: 96489--96544 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
96479 ACTGCTTTTC
96489 ATAATTT-TTAAATTTTTAT
1 ATAATTTATTAAATTTTTAT
*
96508 ATAATTTAGTTAATTTTTTAT
1 ATAATTTA-TTAAATTTTTAT
**
96529 ATTTCTTTATTAAATT
1 A-TAATTTATTAAATT
96545 AATTTTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.23
21 18 0.60
22 5 0.17
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
ATAATTTATTAAATTTTTAT
Found at i:112267 original size:2 final size:2
Alignment explanation
Indices: 112260--112303 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
112250 AATTGTTAGC
* *
112260 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
112302 TA
1 TA
112304 CGTACGTACG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:113506 original size:21 final size:21
Alignment explanation
Indices: 113460--113501 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
113450 ATACATGATA
113460 AAATTTAGAGTTTAAATTATG
1 AAATTTAGAGTTTAAATTATG
113481 AAATTTAAGAAGTTT-AATTAT
1 AAATTT-AG-AGTTTAAATTAT
113502 CAATTGTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (21 bp):
AAATTTAGAGTTTAAATTATG
Found at i:113811 original size:13 final size:14
Alignment explanation
Indices: 113793--113822 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
113783 TAGATTCATG
113793 TTTCTCTTTTCT-T
1 TTTCTCTTTTCTCT
113806 TTTCTCTTTTCTCT
1 TTTCTCTTTTCTCT
113820 TTT
1 TTT
113823 GGTAAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTCTTTTCTCT
Found at i:113815 original size:7 final size:7
Alignment explanation
Indices: 113793--113822 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
113783 TAGATTCATG
113793 TTTCTCT
1 TTTCTCT
113800 TTTCT-T
1 TTTCTCT
113806 TTTCTCT
1 TTTCTCT
113813 TTTCTCT
1 TTTCTCT
113820 TTT
1 TTT
113823 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTCTCT
Found at i:114396 original size:15 final size:15
Alignment explanation
Indices: 114376--114407 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
114366 GTTCGCGAAC
*
114376 TCTAAACGAATATGT
1 TCTAAACGAACATGT
114391 TCTAAACGAACATGT
1 TCTAAACGAACATGT
114406 TC
1 TC
114408 ACAAACGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (15 bp):
TCTAAACGAACATGT
Found at i:114452 original size:23 final size:23
Alignment explanation
Indices: 114392--114459 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
114382 CGAATATGTT
*
114392 CTAAACGAACATGTTCACAAACG
1 CTAAACGAACATGTTCACGAACG
* *
114415 TTAAAAGAACATGTTCACGAACG
1 CTAAACGAACATGTTCACGAACG
*
114438 CTAAACGAAGC-TGTTCGCGAAC
1 CTAAACGAA-CATGTTCACGAAC
114460 ATATTCGCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (23 bp):
CTAAACGAACATGTTCACGAACG
Found at i:114460 original size:35 final size:35
Alignment explanation
Indices: 114421--114496 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
114411 AACGTTAAAA
* * *
114421 GAACATGTTCACGAACGCTAAACGAAGCTGTTCGC
1 GAACATATTCACGAACGCTAAACGAAACTATTCGC
*
114456 GAACATATTCGCGAACGCTAAACGAAACTATTCGC
1 GAACATATTCACGAACGCTAAACGAAACTATTCGC
114491 GAACAT
1 GAACAT
114497 TAAATGAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (35 bp):
GAACATATTCACGAACGCTAAACGAAACTATTCGC
Found at i:114524 original size:23 final size:24
Alignment explanation
Indices: 114456--114529 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 24
114446 AGCTGTTCGC
* *
114456 GAACA-TATTCGCGAACGCTAAAC
1 GAACACTATTCGCGAACGTTAAAT
*
114479 GAA-ACTATTCGCGAACATTAAAT
1 GAACACTATTCGCGAACGTTAAAT
*
114502 GAACAC-GTTCGCGAACGTTAAAT
1 GAACACTATTCGCGAACGTTAAAT
*
114525 AAACA
1 GAACA
114530 AACACAAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.02
23 40 0.93
24 2 0.05
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (24 bp):
GAACACTATTCGCGAACGTTAAAT
Found at i:116115 original size:20 final size:21
Alignment explanation
Indices: 116092--116146 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
116082 CTCAAATGTT
116092 AGTATCGATACCTACAGGC-A
1 AGTATCGATACCTACAGGCTA
* *
116112 AGTACCGATA-CTGA-AGGCTT
1 AGTATCGATACCT-ACAGGCTA
116132 AGTATCGATACCTAC
1 AGTATCGATACCTAC
116147 GAACAGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 20 0.71
21 2 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
AGTATCGATACCTACAGGCTA
Found at i:116295 original size:16 final size:16
Alignment explanation
Indices: 116254--116297 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
116244 ATAATAAACT
116254 CATAACAACTA-GAAA
1 CATAACAACTAGGAAA
116269 CAGTAACAACTAGGATAA
1 CA-TAACAACTAGGA-AA
116287 CATAA-AACTAG
1 CATAACAACTAG
116298 CCTTGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.08
16 15 0.58
17 5 0.19
18 4 0.15
ACGTcount: A:0.55, C:0.18, G:0.11, T:0.16
Consensus pattern (16 bp):
CATAACAACTAGGAAA
Found at i:119769 original size:23 final size:23
Alignment explanation
Indices: 119743--119811 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
119733 CACCACAACT
*
119743 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
119766 CGTAGAATTGCATCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
119789 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
119812 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:120088 original size:22 final size:23
Alignment explanation
Indices: 120026--120092 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
120016 CATTTTACAT
120026 TTTCACATAAACACGTAGTTCAC
1 TTTCACATAAACACGTAGTTCAC
120049 TTTCACATAAACACGTAGTTCAC
1 TTTCACATAAACACGTAGTTCAC
* *
120072 TTTCACGT-AGCACGTAGTTCA
1 TTTCACATAAACACGTAGTTCA
120093 TATCAACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 12 0.29
23 30 0.71
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (23 bp):
TTTCACATAAACACGTAGTTCAC
Found at i:120744 original size:17 final size:19
Alignment explanation
Indices: 120705--120746 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
120695 TCTTTTATAT
*
120705 TCATATAATTTCTTATCATA
1 TCATATAATTTCATATCA-A
120725 TCATATAATTT-ATATC-A
1 TCATATAATTTCATATCAA
120742 TCATA
1 TCATA
120747 ACATAGCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
19 4 0.19
20 11 0.52
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (19 bp):
TCATATAATTTCATATCAA
Found at i:121180 original size:24 final size:20
Alignment explanation
Indices: 121127--121184 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
121117 TTCCCCTTGA
*
121127 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
121147 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
121170 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
121185 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:121259 original size:64 final size:64
Alignment explanation
Indices: 121172--121293 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
121162 TCTTTAACAT
* *
121172 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
* * * * **
121236 GTGCATTGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTT
1 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCGATGTTTCCATTTT
121294 TAATGGGTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 2 0.04
64 47 0.96
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
Found at i:123197 original size:32 final size:33
Alignment explanation
Indices: 123136--123222 Score: 97
Period size: 32 Copynumber: 2.6 Consensus size: 33
123126 TTTGTATTTG
* *
123136 TATTTGTATTTGAATGACTATTTGATTTTT-T-T
1 TATTT-TATTTGAATGAATGTTTGATTTTTCTAT
*
123168 TATTTCTATTTGAATGAATGTTTGGTTTTTCCTAT
1 TATTT-TATTTGAATGAATGTTTGATTTTT-CTAT
*
123203 TATTTTTTTTGAATGAATGT
1 TATTTTATTTGAATGAATGT
123223 AATGGATTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 26 0.55
34 15 0.32
35 6 0.13
ACGTcount: A:0.22, C:0.05, G:0.14, T:0.60
Consensus pattern (33 bp):
TATTTTATTTGAATGAATGTTTGATTTTTCTAT
Found at i:123233 original size:34 final size:35
Alignment explanation
Indices: 123167--123233 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
123157 TTGATTTTTT
* *
123167 TTATTTCTATTTGAATGAATGTTTGGTTTTTCCTA
1 TTATTTCTATTTGAATGAATGTATGGTATTTCCTA
*
123202 TTATTT-TTTTTGAATGAATGTAATGG-ATTTCC
1 TTATTTCTATTTGAATGAATGT-ATGGTATTTCC
123234 ATGTTTGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 19 0.68
35 9 0.32
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.55
Consensus pattern (35 bp):
TTATTTCTATTTGAATGAATGTATGGTATTTCCTA
Found at i:126500 original size:212 final size:212
Alignment explanation
Indices: 126133--126558 Score: 852
Period size: 212 Copynumber: 2.0 Consensus size: 212
126123 GATCAAGCTG
126133 ATGGATATTGAATTATATTATTATATAGTTAAGTTAAGCGTTCAAGGAAATTACCTGAAAGTCTT
1 ATGGATATTGAATTATATTATTATATAGTTAAGTTAAGCGTTCAAGGAAATTACCTGAAAGTCTT
126198 AATTGAAGGGTCATGAACCATCTTTGGCCTTTGCATTACTGTCAAACGGTGGTAATCGACTTCCA
66 AATTGAAGGGTCATGAACCATCTTTGGCCTTTGCATTACTGTCAAACGGTGGTAATCGACTTCCA
126263 ACCTTCTCAAGACTCCCCCAGTTGCATAATGGCATGGATTTGCCTTCCGAGACTACCCATTACTT
131 ACCTTCTCAAGACTCCCCCAGTTGCATAATGGCATGGATTTGCCTTCCGAGACTACCCATTACTT
126328 TATACAAATGAAGTCTT
196 TATACAAATGAAGTCTT
126345 ATGGATATTGAATTATATTATTATATAGTTAAGTTAAGCGTTCAAGGAAATTACCTGAAAGTCTT
1 ATGGATATTGAATTATATTATTATATAGTTAAGTTAAGCGTTCAAGGAAATTACCTGAAAGTCTT
126410 AATTGAAGGGTCATGAACCATCTTTGGCCTTTGCATTACTGTCAAACGGTGGTAATCGACTTCCA
66 AATTGAAGGGTCATGAACCATCTTTGGCCTTTGCATTACTGTCAAACGGTGGTAATCGACTTCCA
126475 ACCTTCTCAAGACTCCCCCAGTTGCATAATGGCATGGATTTGCCTTCCGAGACTACCCATTACTT
131 ACCTTCTCAAGACTCCCCCAGTTGCATAATGGCATGGATTTGCCTTCCGAGACTACCCATTACTT
126540 TATACAAATGAAGTCTT
196 TATACAAATGAAGTCTT
126557 AT
1 AT
126559 TGAAGCCATC
Statistics
Matches: 214, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 214 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (212 bp):
ATGGATATTGAATTATATTATTATATAGTTAAGTTAAGCGTTCAAGGAAATTACCTGAAAGTCTT
AATTGAAGGGTCATGAACCATCTTTGGCCTTTGCATTACTGTCAAACGGTGGTAATCGACTTCCA
ACCTTCTCAAGACTCCCCCAGTTGCATAATGGCATGGATTTGCCTTCCGAGACTACCCATTACTT
TATACAAATGAAGTCTT
Found at i:129466 original size:188 final size:187
Alignment explanation
Indices: 129150--129523 Score: 658
Period size: 188 Copynumber: 2.0 Consensus size: 187
129140 AAAGCCTTTG
*
129150 ATCGCCTCTGCTGGGGCTTTATCTTGGACACTCTTCAAGAATTTGGGTTTTCCCCTCCCTCATTC
1 ATCGCCTCTGCTGGGGCTTTATCTTGGACACTCTTCAAGAAGTTGGGTTTTCCCCTCCCTCATTC
* * *
129215 ATCGGATTTTGCATTGCATTTTCACTTCTACCATGCATATTCAAATCAATGGAACCCTCACTAGC
66 ATCGGATTTCGCATTGCATTTCCACTTCCACCATGCATATTCAAATCAATGGAACCCTCACTAGC
129280 TCATTTGCTCCTAACAGTGGAATTCATCAGGGAGACCCCTTTCTCCCTACCTTTTTT
131 TCATTTGCTCCTAACAGTGGAATTCATCAGGGAGACCCCTTTCTCCCTACCTTTTTT
129337 ATCGCCTCTGCTGGGGCTTTATCTTGGACACTCTTCAAGAAGTTGGGTTTTCCCCCTCCCTCATT
1 ATCGCCTCTGCTGGGGCTTTATCTTGGACACTCTTCAAGAAGTTGGGTTTT-CCCCTCCCTCATT
* **
129402 CGTTTGATTTCGCATTGCATTTCCACTTCCACCATGCATATTCAAATCAATGGAACCCTCACTAG
65 CATCGGATTTCGCATTGCATTTCCACTTCCACCATGCATATTCAAATCAATGGAACCCTCACTAG
* *
129467 CTCATTTTCTCCTAACCGTGGAATTCATCAGGGAGACCCCTTTCTCCCTACCTTTTT
130 CTCATTTGCTCCTAACAGTGGAATTCATCAGGGAGACCCCTTTCTCCCTACCTTTTT
129524 GTTCTGGCCA
Statistics
Matches: 177, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
187 50 0.28
188 127 0.72
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (187 bp):
ATCGCCTCTGCTGGGGCTTTATCTTGGACACTCTTCAAGAAGTTGGGTTTTCCCCTCCCTCATTC
ATCGGATTTCGCATTGCATTTCCACTTCCACCATGCATATTCAAATCAATGGAACCCTCACTAGC
TCATTTGCTCCTAACAGTGGAATTCATCAGGGAGACCCCTTTCTCCCTACCTTTTTT
Found at i:132057 original size:33 final size:35
Alignment explanation
Indices: 132003--132078 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 35
131993 CTTAATATTA
*
132003 AAAAATAAATAAATATTAATAAAATAT-T-TTTAT
1 AAAAATAAATAAATATAAATAAAATATATATTTAT
*
132036 AAAAATAATTAAA-ATAAAATAAAATATATAATTTAT
1 AAAAATAAATAAATAT-AAATAAAATATAT-ATTTAT
132072 AAAAATA
1 AAAAATA
132079 GGATATTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
32 2 0.05
33 22 0.59
34 1 0.03
36 12 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (35 bp):
AAAAATAAATAAATATAAATAAAATATATATTTAT
Found at i:132337 original size:24 final size:24
Alignment explanation
Indices: 132293--132339 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
132283 AATAATAATA
**
132293 ATAATAATTAAATATTTTAAACAT
1 ATAATAATTAAATATACTAAACAT
132317 ATAA-AATTAAATATAACTAAACA
1 ATAATAATTAAATAT-ACTAAACA
132340 GTGACTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (24 bp):
ATAATAATTAAATATACTAAACAT
Found at i:133541 original size:3 final size:3
Alignment explanation
Indices: 133533--133595 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
133523 ATTTTTTATT
*
133533 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-G TATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
133578 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
133596 AAACAAACTG
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 1 0.02
3 53 0.95
4 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:134006 original size:121 final size:121
Alignment explanation
Indices: 133740--134232 Score: 696
Period size: 121 Copynumber: 4.1 Consensus size: 121
133730 TTTTGCCCAG
* * * *
133740 AGGTCTTATGAATGGCCATGAGGTATTATTATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
* *
133805 CTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTTTTTTTGAAAACATCATGCGCTGT
66 CTTTAAAAATATCAAAAAGCTCCCGAAGG---GTTTTTTTTGAAAACATCATGCGCTGT
* *
133864 AGGTCTTATGGATGGCTCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGG
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
* * *
133929 TTTTAAAAATATCAAAAAGCTCCCAAAGGGTTTTTTTTGAAAACATCATGCGTTGT
66 CTTTAAAAATATCAAAAAGCTCCCGAAGGGTTTTTTTTGAAAACATCATGCGCTGT
*
133985 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTATAGATGACCCGGAGG
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
* * * **
134050 CTTTAAAAATATCAAAAAGATCCCGAA-GG--CTTTTTGAAAACATCCTGAACTGT
66 CTTTAAAAATATCAAAAAGCTCCCGAAGGGTTTTTTTTGAAAACATCATGCGCTGT
*
134103 AGGTCTTATGGATGACCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
* * * * *
134168 CTTT-AAAA-ATCAAAAAGCTCCCGAA-GG--CTTTTTGTAAACATCCTACACTGT
66 CTTTAAAAATATCAAAAAGCTCCCGAAGGGTTTTTTTTGAAAACATCATGCGCTGT
134219 AGGTCTTATGGATG
1 AGGTCTTATGGATG
134233 TGGGAAATAG
Statistics
Matches: 341, Mismatches: 28, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
116 53 0.16
117 4 0.01
118 86 0.25
120 2 0.01
121 111 0.33
124 85 0.25
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (121 bp):
AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
CTTTAAAAATATCAAAAAGCTCCCGAAGGGTTTTTTTTGAAAACATCATGCGCTGT
Found at i:134175 original size:239 final size:238
Alignment explanation
Indices: 133740--134200 Score: 708
Period size: 245 Copynumber: 1.9 Consensus size: 238
133730 TTTTGCCCAG
*
133740 AGGTCTTATGAATGGCCATGAGGTATTATTATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
1 AGGTCTTATGAATGGCCATGAGGTATTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
* * **
133805 CTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTTTTTTTGAAAACATCATGCGCTGTAGGTCT
66 CTTTAAAAATATCAAAAAGATCCCGAAGGC-----TTTTTTGAAAACATCATGAACTGTAGGTCT
* * *
133870 TATGGATGGCTCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGGTTTTAA
126 TATGGATGACCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGGCTTT-A
*
133935 AAATATCAAAAAGCTCCCAAAGGGTTTTTTTTGAAAACATCATGCGTTGT
190 AAA-ATCAAAAAGCTCCCAAAGGCTTTTTTTTGAAAACATCATGCGTTGT
* * * *
133985 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTATAGATGACCCGGAGG
1 AGGTCTTATGAATGGCCATGAGGTATTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
*
134050 CTTTAAAAATATCAAAAAGATCCCGAAGGC-TTTTTGAAAACATCCTGAACTGTAGGTCTTATGG
66 CTTTAAAAATATCAAAAAGATCCCGAAGGCTTTTTTGAAAACATCATGAACTGTAGGTCTTATGG
*
134114 ATGACCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAAAATC
131 ATGACCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGGCTTTAAAAATC
*
134179 AAAAAGCTCCCGAAGGCTTTTT
196 AAAAAGCTCCCAAAGGCTTTTT
134201 GTAAACATCC
Statistics
Matches: 200, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
237 23 0.12
238 4 0.02
239 85 0.43
245 88 0.44
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (238 bp):
AGGTCTTATGAATGGCCATGAGGTATTATCATCTTGCACTGTAGGTCTTACAGATGACCCGGAGG
CTTTAAAAATATCAAAAAGATCCCGAAGGCTTTTTTGAAAACATCATGAACTGTAGGTCTTATGG
ATGACCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGGCTTTAAAAATC
AAAAAGCTCCCAAAGGCTTTTTTTTGAAAACATCATGCGTTGT
Found at i:134947 original size:22 final size:22
Alignment explanation
Indices: 134893--134948 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
134883 ATAAAGCTTT
* *
134893 CATCTTTGAAAAGAGAATCTAT
1 CATCTTTGAAGAGAGAATCTAC
134915 CATCTTTGAAGAGAGAATCTAC
1 CATCTTTGAAGAGAGAATCTAC
*
134937 CATTTTTGAAGA
1 CATCTTTGAAGA
134949 ATGTAGATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (22 bp):
CATCTTTGAAGAGAGAATCTAC
Found at i:135450 original size:54 final size:54
Alignment explanation
Indices: 135321--135519 Score: 236
Period size: 54 Copynumber: 3.7 Consensus size: 54
135311 CGTAAAATAT
* * *
135321 TTTGACAACACATTCATCCTTTTATGTGGTTTCTGCTCAAATGTCCGTAAAGCA
1 TTTGACAACACATTCATCATTTCATGTGGTTTCTGCTCAAATGTTCGTAAAGCA
* * * * * *
135375 TTTTGACAACATATTCATCATTTCCTATGGTTTCTACCCATATGTTCGTAAAGCA
1 -TTTGACAACACATTCATCATTTCATGTGGTTTCTGCTCAAATGTTCGTAAAGCA
* * * *
135430 TTTGACAACACATTCATCATTTCTTGTGGTTTCTGCTCAGATGTTAGTAAAACA
1 TTTGACAACACATTCATCATTTCATGTGGTTTCTGCTCAAATGTTCGTAAAGCA
* * * *
135484 TTTGACAACACATTCTTCCTTTTATGTGGCTTCTGC
1 TTTGACAACACATTCATCATTTCATGTGGTTTCTGC
135520 CTATATTTCT
Statistics
Matches: 122, Mismatches: 22, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
54 77 0.63
55 45 0.37
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (54 bp):
TTTGACAACACATTCATCATTTCATGTGGTTTCTGCTCAAATGTTCGTAAAGCA
Found at i:136554 original size:76 final size:75
Alignment explanation
Indices: 136435--136618 Score: 226
Period size: 76 Copynumber: 2.4 Consensus size: 75
136425 TTCAAAATGT
* * *
136435 TATTCCAATTTCTGATTGAAATGAGCTTTCAGCATGCCCCAACATTTGTTAATACAGACGTTCAA
1 TATTCCAATTTCTGATTGAAATGAGCTTTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAA
136500 AATGTGCCAA
66 AATGTGCCAA
* * *
136510 TATTTCAATTTCTGATTGAAATGGGACTTTCATCATGCCCCAACATTGGCTAATACAAACGTTCA
1 TATTCCAATTTCTGATTGAAATGAG-CTTTCAGCATGCCCCAACATTGGCTAATACAAACGTTCA
* * *
136575 AAAAGTGTCAG
65 AAATGTGCCAA
* * * *
136586 TATTCCTGA-TTATGATTGGAATGGGCTTTCAGC
1 TATTCC-AATTTCTGATTGAAATGAGCTTTCAGC
136619 GTGCTCTATC
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
75 30 0.32
76 62 0.67
77 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (75 bp):
TATTCCAATTTCTGATTGAAATGAGCTTTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAA
AATGTGCCAA
Found at i:140118 original size:16 final size:16
Alignment explanation
Indices: 140097--140128 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
140087 TATTGATTCA
140097 ATTTTTTCCTTTTTTT
1 ATTTTTTCCTTTTTTT
140113 ATTTTTTCCTTTTTTT
1 ATTTTTTCCTTTTTTT
140129 GATGGATGAG
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:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (16 bp):
ATTTTTTCCTTTTTTT
Found at i:141545 original size:19 final size:18
Alignment explanation
Indices: 141512--141548 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
141502 TTGTTGATCA
*
141512 CATTTTCAATTAATTCTC
1 CATTTTCAATAAATTCTC
141530 CATTTATCAATAAATTCTC
1 CATTT-TCAATAAATTCTC
141549 GAATTCCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (18 bp):
CATTTTCAATAAATTCTC
Found at i:145684 original size:22 final size:21
Alignment explanation
Indices: 145656--145702 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
145646 AAAATAAAAT
145656 AATATATA-TAATTTA-TAAA
1 AATATATATTAATTTATTAAA
*
145675 AATATGATATTTATTTATTTAAA
1 AATAT-ATATTAATTTA-TTAAA
145698 AATAT
1 AATAT
145703 CAAAAAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 5 0.22
20 3 0.13
21 6 0.26
23 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AATATATATTAATTTATTAAA
Found at i:145890 original size:3 final size:3
Alignment explanation
Indices: 145882--145939 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
145872 ATATGACTAC
145882 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
145930 ATA ATA ATA A
1 ATA ATA ATA A
145940 ATATTTTAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:147086 original size:3 final size:3
Alignment explanation
Indices: 147078--147130 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
147068 ATTTTTTATT
* * *
147078 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TGTA TAT TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
147123 TAA TAA TA
1 TAA TAA TA
147131 GAACAAACTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:147684 original size:16 final size:16
Alignment explanation
Indices: 147663--147694 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
147653 ACTATTTACA
*
147663 TGAATAGTAAATTTTG
1 TGAATAGTAAAATTTG
147679 TGAATAGTAAAATTTG
1 TGAATAGTAAAATTTG
147695 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (16 bp):
TGAATAGTAAAATTTG
Found at i:154487 original size:16 final size:16
Alignment explanation
Indices: 154450--154505 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 16
154440 GATTCGAAAT
*
154450 AAATATATTTATAA-AA
1 AAATAT-TTTTTAATAA
*
154466 ATATATTTTTTAATAA
1 AAATATTTTTTAATAA
154482 AAATATGTTTTTTAATAA
1 AAATA--TTTTTTAATAA
154500 AAATAT
1 AAATAT
154506 GTATATGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.18
16 12 0.35
18 16 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATATTTTTTAATAA
Found at i:154506 original size:18 final size:18
Alignment explanation
Indices: 154460--154507 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
154450 AAATATATTT
*
154460 ATAAAAATATATTTTTTA
1 ATAAAAATATGTTTTTTA
154478 ATAAAAATATGTTTTTTA
1 ATAAAAATATGTTTTTTA
154496 ATAAAAATATGT
1 ATAAAAATATGT
154508 ATATGATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
ATAAAAATATGTTTTTTA
Found at i:158572 original size:17 final size:17
Alignment explanation
Indices: 158552--158585 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
158542 AATCCTCATA
158552 AGACTTTAATAACAATT
1 AGACTTTAATAACAATT
*
158569 AGACTTTAATAATAATT
1 AGACTTTAATAACAATT
158586 GGGAACCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (17 bp):
AGACTTTAATAACAATT
Found at i:161096 original size:21 final size:20
Alignment explanation
Indices: 161067--161107 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
161057 ATGAATCAGA
*
161067 TGAATAGTATCAATATTGAT
1 TGAATAGTATCAATACTGAT
*
161087 TGAAGTAGTATCGATACTGAT
1 TGAA-TAGTATCAATACTGAT
161108 GTGGAGGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (20 bp):
TGAATAGTATCAATACTGAT
Found at i:161598 original size:23 final size:23
Alignment explanation
Indices: 161566--161715 Score: 114
Period size: 23 Copynumber: 6.4 Consensus size: 23
161556 GAGTCGAGGG
*
161566 TTCTACGTGGTCCTTCGGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
161589 TTCTATGTGGTCCTTCGGGAC-A
1 TTCTATGTGGTCCTTCGGGACAA
* *
161611 TT-TATGTATGGACCTTTGGGAC-A
1 TTCTATG--TGGTCCTTCGGGACAA
* *
161634 TT-TATGTATGGACCTTTGGGACAGA
1 TTCTATG--TGGTCCTTCGGGACA-A
* *
161659 TTCTACGTGGTCCTTCTGGACAA
1 TTCTATGTGGTCCTTCGGGACAA
*
161682 ATCTATGTGG-CACTTCGGTG-CATA
1 TTCTATGTGGTC-CTTCGG-GACA-A
161706 TTCTATGTGG
1 TTCTATGTGG
161716 CACTTCGATA
Statistics
Matches: 108, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.04
22 4 0.04
23 71 0.66
24 23 0.21
25 3 0.03
26 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAA
Found at i:161736 original size:24 final size:24
Alignment explanation
Indices: 161678--161736 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
161668 GTCCTTCTGG
*
161678 ACAAA-TCTATGTGGCACTTCGGT
1 ACAAATTCTATGTGGCACTTCGAT
* *
161701 GCATATTCTATGTGGCACTTCGAT
1 ACAAATTCTATGTGGCACTTCGAT
*
161725 ACAAATTTTATG
1 ACAAATTCTATG
161737 AGCAGTGGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (24 bp):
ACAAATTCTATGTGGCACTTCGAT
Found at i:170699 original size:21 final size:21
Alignment explanation
Indices: 170671--170711 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
170661 CATTGCAGGA
170671 ATTTATGGCCTCAA-AAAAAG
1 ATTTATGGCCTCAACAAAAAG
*
170691 ATTTCATGGCTTCAACAAAAA
1 ATTT-ATGGCCTCAACAAAAA
170712 CCTTGATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (21 bp):
ATTTATGGCCTCAACAAAAAG
Found at i:175247 original size:22 final size:22
Alignment explanation
Indices: 175209--175250 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
175199 TATGTATGAG
175209 TTATTTATTTTTATTTTATTCT
1 TTATTTATTTTTATTTTATTCT
*
175231 TTATTT-TTGTTTTTTTTATT
1 TTATTTATT-TTTATTTTATT
175251 TAGGGTACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (22 bp):
TTATTTATTTTTATTTTATTCT
Found at i:176151 original size:13 final size:13
Alignment explanation
Indices: 176133--176160 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
176123 AGCCAGTTAC
176133 CAAGCTTTGGAAT
1 CAAGCTTTGGAAT
176146 CAAGCTTTGGAAT
1 CAAGCTTTGGAAT
176159 CA
1 CA
176161 TTTTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (13 bp):
CAAGCTTTGGAAT
Found at i:180306 original size:24 final size:24
Alignment explanation
Indices: 180273--180329 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
180263 TGTTATGTGG
*
180273 GTATCAATATTTTCCTTACCTTGA
1 GTATCGATATTTTCCTTACCTTGA
180297 GTATCGATATTTTCCTTACCTTGA
1 GTATCGATATTTTCCTTACCTTGA
180321 GTATCGATA
1 GTATCGATA
180330 CTACAAGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (24 bp):
GTATCGATATTTTCCTTACCTTGA
Found at i:181840 original size:18 final size:18
Alignment explanation
Indices: 181817--181860 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
181807 AAGTTGGCTA
181817 CTTCATCATCGGAGTTGT
1 CTTCATCATCGGAGTTGT
181835 CTTCATCATCGGAGTTGT
1 CTTCATCATCGGAGTTGT
181853 CTTCATCA
1 CTTCATCA
181861 CTCCAACCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (18 bp):
CTTCATCATCGGAGTTGT
Found at i:184810 original size:20 final size:20
Alignment explanation
Indices: 184767--184837 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
184757 CAGTTAGTAG
* * **
184767 GTATCGATACCAAAAGGTGG
1 GTATCGATACTAAAGGGTCA
* *
184787 GTATCGATACTCAGGGGTCA
1 GTATCGATACTAAAGGGTCA
*
184807 GTATCGATACTAAAGGTTCA
1 GTATCGATACTAAAGGGTCA
*
184827 ATATCGATACT
1 GTATCGATACT
184838 GACGAACAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (20 bp):
GTATCGATACTAAAGGGTCA
Found at i:188384 original size:3 final size:3
Alignment explanation
Indices: 188376--188433 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
188366 GTCTAAAAAA
188376 TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
188422 TA- TAT T-T TAT TA
1 TAT TAT TAT TAT TA
188434 AATATTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:188403 original size:22 final size:22
Alignment explanation
Indices: 188378--188433 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
188368 CTAAAAAATA
188378 TTATTATTATTATTATTATTAT
1 TTATTATTATTATTATTATTAT
188400 TTATTATTATTATTATTATTAT
1 TTATTATTATTATTATTATTAT
188422 TATATT-TTATTA
1 T-TATTATTATTA
188434 AATATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTATTATTATTATTATTAT
Found at i:188410 original size:25 final size:26
Alignment explanation
Indices: 188376--188433 Score: 102
Period size: 25 Copynumber: 2.3 Consensus size: 26
188366 GTCTAAAAAA
188376 TATTATTATTATTATTATTATTAT-T
1 TATTATTATTATTATTATTATTATAT
188401 TATTATTATTATTATTATTATTATAT
1 TATTATTATTATTATTATTATTATAT
188427 T-TTATTA
1 TATTATTA
188434 AATATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTATTATTATTATTATTATTATAT
Found at i:188764 original size:22 final size:22
Alignment explanation
Indices: 188734--188788 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
188724 AAATCTACAC
*
188734 CAAAAAGTGACAACAAATCCAT
1 CAAACAGTGACAACAAATCCAT
**
188756 CAAACAGTGACCCCAAATCCAT
1 CAAACAGTGACAACAAATCCAT
188778 CAAACAGTGAC
1 CAAACAGTGAC
188789 CTCAAATCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.47, C:0.29, G:0.11, T:0.13
Consensus pattern (22 bp):
CAAACAGTGACAACAAATCCAT
Found at i:188789 original size:22 final size:22
Alignment explanation
Indices: 188747--188796 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
188737 AAAGTGACAA
188747 CAAATCCATCAAACAGTGACCC
1 CAAATCCATCAAACAGTGACCC
*
188769 CAAATCCATCAAACAGTGACCT
1 CAAATCCATCAAACAGTGACCC
188791 CAAATC
1 CAAATC
188797 AGTTAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.34, G:0.08, T:0.16
Consensus pattern (22 bp):
CAAATCCATCAAACAGTGACCC
Found at i:192290 original size:17 final size:17
Alignment explanation
Indices: 192266--192313 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
192256 GATCACATCG
192266 AAGCAAAGAAAGAA-AAA
1 AAGCAAAGAAA-AAGAAA
*
192283 AAGTAAAGAAAAAGAAA
1 AAGCAAAGAAAAAGAAA
192300 AAGCAAAGAAAAAG
1 AAGCAAAGAAAAAG
192314 CAAAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 2 0.07
17 26 0.93
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (17 bp):
AAGCAAAGAAAAAGAAA
Done.