Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_14 ID=scaffold_14-JGI_221_v2.0
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: 2042280
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 64439 characters in sequence are not A, C, G, or T
File 4 of 7
Found at i:885059 original size:125 final size:124
Alignment explanation
Indices: 884827--885074 Score: 279
Period size: 125 Copynumber: 2.0 Consensus size: 124
884817 GATTGAATGT
** * *
884827 AATACAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAGTAG
1 AATACAGACTTTACGTCTAGCAGGCTTAATGCCACTGAAATAATTTCAGACTATACGTCTAGCAG
*** *
884892 GCTTAATGCCGATGAAATAATTTCAGACTTTACGTCTAGCAGGCTTAA-TGTCGGTGAAAC
66 GCTTAATGCCGATGAAATAA-TTCAGACTTTAAACCTAGCAGGC-TAAGTGCCGGTGAAAC
* *
884952 AATATCAGACTTTACGTCTAGCAGGCTTAATGCCACTGAAA-CATTTCAGACTATATGTCTAGCA
1 AATA-CAGACTTTACGTCTAGCAGGCTTAATGCCACTGAAATAATTTCAGACTATACGTCTAGCA
* * * **
885016 GGC-TAAGTGCCGGTGTACTGAA-TCAGGTTTTAAAACCTAGCAGGCTAAGTGCCGGTGAA
65 GGCTTAA-TGCCGATGAAAT-AATTCAGACTTT-AAACCTAGCAGGCTAAGTGCCGGTGAA
885075 TCTATTTAAA
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
124 13 0.13
125 54 0.52
126 36 0.35
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (124 bp):
AATACAGACTTTACGTCTAGCAGGCTTAATGCCACTGAAATAATTTCAGACTATACGTCTAGCAG
GCTTAATGCCGATGAAATAATTCAGACTTTAAACCTAGCAGGCTAAGTGCCGGTGAAAC
Found at i:904257 original size:19 final size:18
Alignment explanation
Indices: 904211--904265 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
904201 AAATTACATA
* *
904211 ATATATTATATATGAAGT
1 ATATATAATATATGATGT
904229 ATATATAATATATGATGT
1 ATATATAATATATGATGT
*
904247 ATATCATAATATATCATGT
1 ATAT-ATAATATATGATGT
904266 TAGAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 20 0.61
19 13 0.39
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (18 bp):
ATATATAATATATGATGT
Found at i:905654 original size:13 final size:13
Alignment explanation
Indices: 905636--905712 Score: 84
Period size: 13 Copynumber: 5.9 Consensus size: 13
905626 AGTTCTTCAT
905636 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
905649 TGCTTTTCAAAAG
1 TGCTTTTGAAAAG
*
905662 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
* *
905675 TGCTTTTCAGAAG
1 TGCTTTTGAAAAG
*
905688 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
905701 TACTTTTGAAAA
1 TGCTTTTGAAAA
905713 TTTTGAGTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
12 2 0.04
13 49 0.92
14 2 0.04
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:905701 original size:26 final size:26
Alignment explanation
Indices: 905636--905712 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
905626 AGTTCTTCAT
905636 TGCTTTTGAAAAGTGCTTTTCAAAAG
1 TGCTTTTGAAAAGTGCTTTTCAAAAG
* *
905662 TG-TTGTGGAAAAGTGCTTTTCAGAAG
1 TGCTT-TTGAAAAGTGCTTTTCAAAAG
* * *
905688 TGCTTTTGAGAAGTACTTTTGAAAA
1 TGCTTTTGAAAAGTGCTTTTCAAAA
905713 TTTTGAGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.05
26 38 0.90
27 2 0.05
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTTTTCAAAAG
Found at i:907957 original size:72 final size:72
Alignment explanation
Indices: 907764--907931 Score: 223
Period size: 72 Copynumber: 2.3 Consensus size: 72
907754 AAAATCACAT
* * * * *
907764 ATAAACAACTATTGATAAAACTA-ATTT-AGTAAAAAATAAGTAGAATATAAATTCAATATCTAA
1 ATAAACAACTATTAATAAAACTAGATTTCA--CATAAATAAGTAGAACATAAATTCAATATCCAA
*
907827 AGACCAAAC
64 AAACCAAAC
*
907836 ATAAACAACTTTTAATAAAACTAGATTTCACATAAATAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTAATAAAACTAGATTTCACATAAATAAGTAGAACATAAATTCAATATCCAAAA
907901 ACCAAAC
66 ACCAAAC
* *
907908 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTAATAAAACTAG
907932 TTTAGCATTG
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
72 79 0.94
73 4 0.05
74 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTAATAAAACTAGATTTCACATAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:909313 original size:15 final size:15
Alignment explanation
Indices: 909293--909345 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
909283 GGCACAAGTT
909293 TGTAATTAATATTTA
1 TGTAATTAATATTTA
*
909308 TGTAATT-ATAAGTT-
1 TGTAATTAAT-ATTTA
909322 TGTAATTAATATTTA
1 TGTAATTAATATTTA
909337 TGTAATTAA
1 TGTAATTAA
909346 AAATAGTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 12 0.36
15 21 0.64
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (15 bp):
TGTAATTAATATTTA
Found at i:909320 original size:29 final size:30
Alignment explanation
Indices: 909288--909362 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 30
909278 TTATAGGCAC
*
909288 AAGTTTGTAATTAATATTTATGTAATT-AT
1 AAGTTTGTAATTAATATTTATGTAATTAAA
909317 AAGTTTGTAATTAATATTTATGTAATTAAAA
1 AAGTTTGTAATTAATATTTATGTAATT-AAA
909348 ATAGTTTGTAATTAA
1 A-AGTTTGTAATTAA
909363 GATGATTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
29 27 0.64
31 2 0.05
32 13 0.31
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (30 bp):
AAGTTTGTAATTAATATTTATGTAATTAAA
Found at i:909327 original size:14 final size:13
Alignment explanation
Indices: 909288--909346 Score: 55
Period size: 15 Copynumber: 4.2 Consensus size: 13
909278 TTATAGGCAC
909288 AAGTTTGTAATTA
1 AAGTTTGTAATTA
*
909301 ATATTTATGTAATTA
1 A-AGTT-TGTAATTA
909316 TAAGTTTGTAATTA
1 -AAGTTTGTAATTA
*
909330 ATATTTATGTAATTA
1 A-AGTT-TGTAATTA
909345 AA
1 AA
909347 AATAGTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.05
14 15 0.39
15 20 0.53
16 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (13 bp):
AAGTTTGTAATTA
Found at i:912478 original size:19 final size:19
Alignment explanation
Indices: 912454--912571 Score: 71
Period size: 19 Copynumber: 6.2 Consensus size: 19
912444 GTGGTGGAGA
*
912454 AGAGGAACAAAGCACCAGC
1 AGAGGAACAAAGAACCAGC
912473 AGAGGAACAAAGAACCAGC
1 AGAGGAACAAAGAACCAGC
* * * * * *
912492 ACCAGCACCAGCAGAA-GAAC
1 A-GAGGAACA-AAGAACCAGC
* * *
912512 A-AAGAAC-CAGCACCAGC
1 AGAGGAACAAAGAACCAGC
* * *
912529 AGAGGATCAAAGGAGCAGC
1 AGAGGAACAAAGAACCAGC
912548 AGAGGAACAAAGAACCAGC
1 AGAGGAACAAAGAACCAGC
912567 GAGAG
1 -AGAG
912572 AAGAGATGAG
Statistics
Matches: 72, Mismatches: 21, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
16 4 0.06
17 3 0.04
18 7 0.10
19 42 0.58
20 12 0.17
21 4 0.06
ACGTcount: A:0.47, C:0.25, G:0.27, T:0.01
Consensus pattern (19 bp):
AGAGGAACAAAGAACCAGC
Found at i:912492 original size:25 final size:25
Alignment explanation
Indices: 912464--912566 Score: 92
Period size: 31 Copynumber: 4.1 Consensus size: 25
912454 AGAGGAACAA
912464 AGCACCAGCAGAGGAACAAAGAACC
1 AGCACCAGCAGAGGAACAAAGAACC
912489 AGCACCAGCACCAGCAGAAGAACAAAGAACC
1 AGCACCAG---CAG-AG--GAACAAAGAACC
*
912520 AGCACCAGCAGAGGATCAAAG----
1 AGCACCAGCAGAGGAACAAAGAACC
*
912541 -G-AGCAGCAGAGGAACAAAGAACC
1 AGCACCAGCAGAGGAACAAAGAACC
912564 AGC
1 AGC
912567 GAGAGAAGAG
Statistics
Matches: 63, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
19 16 0.25
20 1 0.02
24 1 0.02
25 15 0.24
27 2 0.03
28 6 0.10
29 2 0.03
31 20 0.32
ACGTcount: A:0.47, C:0.27, G:0.25, T:0.01
Consensus pattern (25 bp):
AGCACCAGCAGAGGAACAAAGAACC
Found at i:912499 original size:31 final size:31
Alignment explanation
Indices: 912464--912529 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
912454 AGAGGAACAA
*
912464 AGCACCAGCAGAGGAACAAAGAACCAGCACC
1 AGCACCAGCAGAAGAACAAAGAACCAGCACC
912495 AGCACCAGCAGAAGAACAAAGAACCAGCACC
1 AGCACCAGCAGAAGAACAAAGAACCAGCACC
912526 AGCA
1 AGCA
912530 GAGGATCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.47, C:0.32, G:0.21, T:0.00
Consensus pattern (31 bp):
AGCACCAGCAGAAGAACAAAGAACCAGCACC
Found at i:913650 original size:18 final size:17
Alignment explanation
Indices: 913629--913662 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
913619 AAGAAGAGAG
*
913629 TGAGAAGGAAGAAAGAAA
1 TGAGAA-GAAAAAAGAAA
913647 TGAGAAGAAAAAAGAA
1 TGAGAAGAAAAAAGAA
913663 GGATAAGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (17 bp):
TGAGAAGAAAAAAGAAA
Found at i:913872 original size:102 final size:101
Alignment explanation
Indices: 913758--914007 Score: 332
Period size: 102 Copynumber: 2.5 Consensus size: 101
913748 TTTTATGTTG
*
913758 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAACTATTATAAATTGTTTGTTTAGTTTAATGTT
1 TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAACTATTATAAATTGTTTGTTTAGTTTAATGTT
* *
913823 TATTGTGATTTGTTAGGTTATGAATGTAATTTTTTTA
66 CATTGTGATTTGTTAGGTTATGAATGTAA-TCTTTTA
* *
913860 TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTTGTGATTAGGTTAATTGTTTGTTTAGTT
1 TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAA----CT-ATTA--TAAATTGTTTGTTTAGTT
913925 TAATGTTCATTGTGATTTGTTAGGTTATGAATGTAATCTTTTA
59 TAATGTTCATTGTGATTTGTTAGGTTATGAATGTAATCTTTTA
*
913968 ---TT--ATT-TTTTAAATTTATTTTGTTAGTAACTATTATAAATT
1 TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAACTATTATAAATT
914008 AATTGTTAGT
Statistics
Matches: 133, Mismatches: 8, Indels: 21
0.82 0.05 0.13
Matches are distributed among these distances:
95 5 0.04
97 4 0.03
98 1 0.01
102 55 0.41
103 3 0.02
105 2 0.02
106 1 0.01
107 4 0.03
108 6 0.05
109 52 0.39
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.58
Consensus pattern (101 bp):
TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAACTATTATAAATTGTTTGTTTAGTTTAATGTT
CATTGTGATTTGTTAGGTTATGAATGTAATCTTTTA
Found at i:913942 original size:109 final size:105
Alignment explanation
Indices: 913758--913987 Score: 331
Period size: 109 Copynumber: 2.1 Consensus size: 105
913748 TTTTATGTTG
*
913758 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAACTATTATAAATTGTTTGTTTAGTTTAATGTT
1 TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAACTATTATAAATTGTTTGTTTAGTTTAATGTT
*
913823 TATTGTGATTTGTTAGGTTATGAATGTAAT-TTTT-TTA-
66 CATTGTGATTTGTTAGGTTATGAATGTAATCTTTTATTAT
* *
913860 TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTTGTGATTAGGTTAATTGTTTGTTTAGTT
1 TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAA----CT-ATTA--TAAATTGTTTGTTTAGTT
913925 TAATGTTCATTGTGATTTGTTAGGTTATGAATGTAATCTTTTATTAT
59 TAATGTTCATTGTGATTTGTTAGGTTATGAATGTAATCTTTTATTAT
913972 TTTTTAAATTTATTTT
1 TTTTTAAA-TTATTTT
913988 GTTAGTAACT
Statistics
Matches: 113, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
102 33 0.29
106 1 0.01
107 4 0.04
109 53 0.47
110 4 0.04
111 3 0.03
112 8 0.07
113 7 0.06
ACGTcount: A:0.26, C:0.01, G:0.14, T:0.59
Consensus pattern (105 bp):
TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAACTATTATAAATTGTTTGTTTAGTTTAATGTT
CATTGTGATTTGTTAGGTTATGAATGTAATCTTTTATTAT
Found at i:917695 original size:48 final size:47
Alignment explanation
Indices: 917613--917778 Score: 171
Period size: 48 Copynumber: 3.5 Consensus size: 47
917603 ACTCCAATGT
* **
917613 ATCTAATTTATATTACAAAGGTTTTTCCTCGTTTTAATGTTGCAATTA
1 ATCTAATTTAAATTACAAA-GTTTTTCCAAGTTTTAATGTTGCAATTA
* *
917661 ATCTAATTTAAATTACAAAGTTTATTCCAAGTTTTAATGTTGCGATGA
1 ATCTAATTTAAATTACAAAGTTT-TTCCAAGTTTTAATGTTGCAATTA
* *
917709 ATCTCAATTAATTAAA-TACAAAGTTTGTCTAGAG--TT--TGTTGCAATTA
1 ATCT-AA-T--TTAAATTACAAAGTTTTTCCA-AGTTTTAATGTTGCAATTA
917756 ATCTAATTTAAATTACAAAGTTT
1 ATCTAATTTAAATTACAAAGTTT
917779 GTATTTTTGC
Statistics
Matches: 102, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
43 5 0.05
44 10 0.10
45 1 0.01
46 2 0.02
47 17 0.17
48 42 0.41
49 4 0.04
50 4 0.04
51 12 0.12
52 5 0.05
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (47 bp):
ATCTAATTTAAATTACAAAGTTTTTCCAAGTTTTAATGTTGCAATTA
Found at i:918067 original size:38 final size:38
Alignment explanation
Indices: 918025--918105 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
918015 GGGAGGAAAA
*
918025 GAGTACTGCGGTGGATATAGGCCGGGCCAGGAGGAGTG
1 GAGTACTGCGGTGGATACAGGCCGGGCCAGGAGGAGTG
* * ***
918063 GAGTACTGTGGTGGATACAGGCTGGGTTGGGAGGAGTG
1 GAGTACTGCGGTGGATACAGGCCGGGCCAGGAGGAGTG
918101 GAGTA
1 GAGTA
918106 ATACGATGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.11, G:0.48, T:0.20
Consensus pattern (38 bp):
GAGTACTGCGGTGGATACAGGCCGGGCCAGGAGGAGTG
Found at i:920581 original size:9 final size:8
Alignment explanation
Indices: 920563--920614 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
920553 ATAATACCTT
920563 AAAAAATA
1 AAAAAATA
*
920571 AAAAAATT
1 AAAAAATA
**
920579 AAAATCTA
1 AAAAAATA
920587 AAACAAATA
1 AAA-AAATA
920596 AAATAACATA
1 AAA-AA-ATA
920606 AAAAAATA
1 AAAAAATA
920614 A
1 A
920615 CATTTATAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
8 19 0.54
9 10 0.29
10 6 0.17
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAAATA
Found at i:920810 original size:17 final size:17
Alignment explanation
Indices: 920784--920823 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
920774 AATTAAATCC
* *
920784 CTTTTTCTTCCCTTTCT
1 CTTTTCCTTCCCTCTCT
920801 CTTTTCCTTCCCTCTCT
1 CTTTTCCTTCCCTCTCT
920818 CTTTTC
1 CTTTTC
920824 TTTCTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (17 bp):
CTTTTCCTTCCCTCTCT
Found at i:923279 original size:18 final size:19
Alignment explanation
Indices: 923256--923330 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 19
923246 TTTCTAAAAA
*
923256 ATAAAT-TTTAGAATTTTT
1 ATAAATATTTTGAATTTTT
* *
923274 ATAAATATTTTTAATTTTA
1 ATAAATATTTTGAATTTTT
*
923293 AAAAATATTTTGAACTTTTT
1 ATAAATATTTTGAA-TTTTT
* *
923313 A-AAATTTTTTTAATTTTT
1 ATAAATATTTTGAATTTTT
923331 TAATTTTTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
18 11 0.23
19 31 0.66
20 5 0.11
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (19 bp):
ATAAATATTTTGAATTTTT
Found at i:923331 original size:19 final size:19
Alignment explanation
Indices: 923269--923333 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
923259 AATTTTAGAA
923269 TTTTTATAAATATTTTTAAT
1 TTTTTA-AAATATTTTTAAT
** * *
923289 TTTAAAAAATATTTTGAAC
1 TTTTTAAAATATTTTTAAT
*
923308 TTTTTAAAATTTTTTTAAT
1 TTTTTAAAATATTTTTAAT
923327 TTTTTAA
1 TTTTTAA
923334 TTTTTGTTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 32 0.89
20 4 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTAAAATATTTTTAAT
Found at i:933174 original size:71 final size:66
Alignment explanation
Indices: 933034--933167 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
933024 TAGTTATTCA
933034 TTATAGTTTTTAAGTTAGGTTTTCTTTTCTTTTCTTTTCTTTTTTAAATTAGGTTTAGAAGAGAT
1 TTATAGTTTTTAAGTTAGGTTTTCTTTTCTTTTCTTTTCTTTTTTAAATTAGGTTTAGAAGAGAT
933099 T
66 T
933100 TTATAGTTTTTAAGTTAGGTTTTCTTTTCTTTTCTTTTCTTTTTTAAATTAGGTTTAGAAGAGAT
1 TTATAGTTTTTAAGTTAGGTTTTCTTTTCTTTTCTTTTCTTTTTTAAATTAGGTTTAGAAGAGAT
933165 T
66 T
933166 TT
1 TT
933168 TTTTTATTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.21, C:0.06, G:0.13, T:0.60
Consensus pattern (66 bp):
TTATAGTTTTTAAGTTAGGTTTTCTTTTCTTTTCTTTTCTTTTTTAAATTAGGTTTAGAAGAGAT
T
Found at i:936495 original size:28 final size:29
Alignment explanation
Indices: 936458--936513 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
936448 AAATTAATCT
* *
936458 AAAATATTATAATTT-TTAATATTATTATG
1 AAAATATTAT-ATTTAATAATATAATTATG
936487 AAAAT-TTATATTTAATAATATAATTAT
1 AAAATATTATATTTAATAATATAATTAT
936514 TTATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.17
28 15 0.62
29 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
AAAATATTATATTTAATAATATAATTATG
Found at i:936555 original size:19 final size:18
Alignment explanation
Indices: 936531--936566 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
936521 AATGAAATTA
*
936531 TTTAATATTACAATTTTAT
1 TTTAATAATA-AATTTTAT
936550 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
936567 ACATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:936605 original size:20 final size:20
Alignment explanation
Indices: 936547--936612 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
936537 ATTACAATTT
*
936547 TATTTTAATAATAAATTTTAA
1 TATTTTAAAAAT-AATTTTAA
*
936568 CA--TTAAAAATAATTTTAA
1 TATTTTAAAAATAATTTTAA
*
936586 -ATTTTAAAAGATATTTTTAA
1 TATTTTAAAA-ATAATTTTAA
936606 TATTTTA
1 TATTTTA
936613 TTGAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.03
18 8 0.21
19 13 0.34
20 9 0.24
21 7 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TATTTTAAAAATAATTTTAA
Found at i:937073 original size:19 final size:17
Alignment explanation
Indices: 937049--937098 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
937039 CATCCAAATA
937049 TTAAAAAATATTAGCATTT
1 TTAAAAAATATTA--ATTT
937068 TTAAAAAATAATCTAATTT
1 TTAAAAAAT-AT-TAATTT
*
937087 TTAAAAATTATT
1 TTAAAAAATATT
937099 TTTTGAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 2 0.07
19 21 0.75
20 2 0.07
21 2 0.07
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAAAAAATATTAATTT
Found at i:937261 original size:25 final size:23
Alignment explanation
Indices: 937219--937265 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
937209 CCTTAACGTT
*
937219 TATATTTTTTTGTCAATTTGACC
1 TATATTTTTTTGTAAATTTGACC
937242 TATATTTTTTTAGCTAAATTTGAC
1 TATATTTTTTT-G-TAAATTTGAC
937266 AATTACCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 1 0.05
25 9 0.43
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (23 bp):
TATATTTTTTTGTAAATTTGACC
Found at i:937461 original size:12 final size:12
Alignment explanation
Indices: 937428--937472 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
937418 CAAATGATTT
*
937428 AAAA-TCTATAA
1 AAAATTCTAAAA
*
937439 AATATTC-AAAA
1 AAAATTCTAAAA
937450 AAAATTCTAAAA
1 AAAATTCTAAAA
937462 AAAATTCTAAA
1 AAAATTCTAAA
937473 CAATAGTGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 12 0.41
12 17 0.59
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATTCTAAAA
Found at i:937562 original size:28 final size:28
Alignment explanation
Indices: 937520--937576 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
937510 CTTTTTGGGC
*
937520 TAAATTAGCCATATATGCCTTTATTTTT
1 TAAATTAGCCATATAAGCCTTTATTTTT
* * * *
937548 TAAATTAGGCTTATAAGTCTTTTTTTTT
1 TAAATTAGCCATATAAGCCTTTATTTTT
937576 T
1 T
937577 GAAAATTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (28 bp):
TAAATTAGCCATATAAGCCTTTATTTTT
Found at i:955191 original size:23 final size:23
Alignment explanation
Indices: 955162--955215 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
955152 TATTCAAATT
955162 ATTCGAGTCAACTCGAATAAGTA
1 ATTCGAGTCAACTCGAATAAGTA
955185 ATTCGAGTCAACTCGAATAAGTA
1 ATTCGAGTCAACTCGAATAAGTA
955208 ATTCGAGT
1 ATTCGAGT
955216 TTTGAGTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (23 bp):
ATTCGAGTCAACTCGAATAAGTA
Found at i:955369 original size:19 final size:19
Alignment explanation
Indices: 955342--955400 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
955332 CAAAAATTAC
955342 TAAATAATTCAAAATAATTT-
1 TAAA-AATTCAAAAT-ATTTA
*
955362 TTAAAATTCAAAATATTTA
1 TAAAAATTCAAAATATTTA
*
955381 TAAAAATTCCAAA-ATTTA
1 TAAAAATTCAAAATATTTA
955399 TA
1 TA
955401 TTATCTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.31
19 21 0.60
20 3 0.09
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAAATTCAAAATATTTA
Found at i:961568 original size:3 final size:3
Alignment explanation
Indices: 961553--961624 Score: 53
Period size: 3 Copynumber: 24.3 Consensus size: 3
961543 CATTTTAATA
* * * *
961553 TAT TAT TAC TAT TAT TAT TAT TAT TAT TGCT TGT TAT TTT TAGT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA-T TAT
961599 TAT T-T TAT T-T TCAT TAT T-T TAT TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT T
961625 TCATGAATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
2 8 0.15
3 41 0.75
4 6 0.11
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:961744 original size:12 final size:12
Alignment explanation
Indices: 961727--961751 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
961717 ATACTTTCAA
961727 ACTATTATTATT
1 ACTATTATTATT
961739 ACTATTATTATT
1 ACTATTATTATT
961751 A
1 A
961752 TCATACTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
ACTATTATTATT
Found at i:963249 original size:17 final size:17
Alignment explanation
Indices: 963224--963265 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
963214 TATTCAAATA
* *
963224 CATGAATCTTTCAA-TT
1 CATGTATCTTCCAAGTT
963240 CAATGTATCTTCCAAGTT
1 C-ATGTATCTTCCAAGTT
963258 CATGTATC
1 CATGTATC
963266 CTCTTTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 18 0.82
18 3 0.14
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (17 bp):
CATGTATCTTCCAAGTT
Found at i:965195 original size:17 final size:17
Alignment explanation
Indices: 965173--965207 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
965163 ATAATAGAGA
965173 GTGTTTGATTGACCTCC
1 GTGTTTGATTGACCTCC
965190 GTGTTTGATTGACCTCC
1 GTGTTTGATTGACCTCC
965207 G
1 G
965208 AATTAAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.40
Consensus pattern (17 bp):
GTGTTTGATTGACCTCC
Found at i:968460 original size:22 final size:21
Alignment explanation
Indices: 968415--968472 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
968405 AATTTTAAAA
* *
968415 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
968435 TATTTTTAAAATAAATTTTTGG
1 TATTTTTAAAATAAATTTTT-G
968457 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
968473 AGGCCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.36
21 6 0.18
22 9 0.27
23 6 0.18
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:974977 original size:101 final size:103
Alignment explanation
Indices: 974862--975089 Score: 270
Period size: 101 Copynumber: 2.3 Consensus size: 103
974852 GCACGAACTG
* ** * *
974862 TGTGTAGGCCACTATGTAAAAGTGAA-AGTGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTAC
1 TGTGTAGGCTACTATGTAAAACCGAATAGT-ATCGATCACGGGTGTAGTACTATGTGCAGGCTAC
* * *
974925 TACGTGTGCCGGA-A-TGATAGGTCGCATGTGTAGTACTA
65 TACGTGTACCGGATAGTAAT-GGTCACATGTGTAGTACTA
* * *
974963 TGTGTAGGCTACTATG-CATACCGAATAGTTTCGATCACGGGTGTAGTACTATGTGCAGGCTACT
1 TGTGTAGGCTACTATGTAAAACCGAATAGTATCGATCACGGGTGTAGTACTATGTGCAGGCTACT
*
975027 ACGTGTATCGGATAGTAATGGTCACATGTGTAGTACTA
66 ACGTGTACCGGATAGTAATGGTCACATGTGTAGTACTA
* *
975065 TGTGCAGGCTACTATGT-GAACCGAA
1 TGTGTAGGCTACTATGTAAAACCGAA
975090 CATCATTGAT
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
100 6 0.06
101 58 0.54
102 40 0.37
103 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (103 bp):
TGTGTAGGCTACTATGTAAAACCGAATAGTATCGATCACGGGTGTAGTACTATGTGCAGGCTACT
ACGTGTACCGGATAGTAATGGTCACATGTGTAGTACTA
Found at i:975016 original size:51 final size:51
Alignment explanation
Indices: 974952--975080 Score: 152
Period size: 51 Copynumber: 2.5 Consensus size: 51
974942 TAGGTCGCAT
* * *
974952 GTGTAGTACTATGTGTAGGCTACTATGCATACCGAATAGT-TTCGATCACGG
1 GTGTAGTACTATGTGCAGGCTACTATGCATACCGAATAGTAAT-GATCACAG
* ** * * * *
975003 GTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTAATGGTCACAT
1 GTGTAGTACTATGTGCAGGCTACTATGCATACCGAATAGTAATGATCACAG
975054 GTGTAGTACTATGTGCAGGCTACTATG
1 GTGTAGTACTATGTGCAGGCTACTATG
975081 TGAACCGAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
51 65 0.98
52 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (51 bp):
GTGTAGTACTATGTGCAGGCTACTATGCATACCGAATAGTAATGATCACAG
Found at i:975082 original size:26 final size:26
Alignment explanation
Indices: 975003--975082 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 26
974993 TCGATCACGG
*
975003 GTGTAGTACTATGTGCAGGCTACTAC
1 GTGTAGTACTATGTGCAGGCTACTAT
* *
975029 GTGTA-T-CGGATAGT-AATGG-TCAC-AT
1 GTGTAGTAC-TAT-GTGCA-GGCT-ACTAT
975054 GTGTAGTACTATGTGCAGGCTACTAT
1 GTGTAGTACTATGTGCAGGCTACTAT
975080 GTG
1 GTG
975083 AACCGAACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 18
0.63 0.08 0.29
Matches are distributed among these distances:
24 1 0.03
25 17 0.43
26 21 0.52
27 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.33
Consensus pattern (26 bp):
GTGTAGTACTATGTGCAGGCTACTAT
Found at i:975140 original size:45 final size:45
Alignment explanation
Indices: 975084--975178 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
975074 TACTATGTGA
* *
975084 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTAATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCC
* *
975129 ACCGGACATCATTGATTAATGAGGTGGTTGCTATGTGCTAAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCC
975174 ACCGA
1 ACCGA
975179 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCC
Found at i:983068 original size:30 final size:29
Alignment explanation
Indices: 983034--983107 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
983024 GATATTTTAA
* *
983034 TATTTTATGATTATTTAATTAGATAAATAT
1 TATTTTATTATTATTTAATGAGAT-AATAT
* *
983064 TATTTTATTAATATTTTAATGAGATATTAT
1 TATTTTATTATTA-TTTAATGAGATAATAT
983094 TATTTTATTATTAT
1 TATTTTATTATTAT
983108 ATTTATTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 1 0.03
30 27 0.71
31 10 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (29 bp):
TATTTTATTATTATTTAATGAGATAATAT
Found at i:983104 original size:11 final size:12
Alignment explanation
Indices: 983088--983116 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
983078 TTTAATGAGA
983088 TATTATTAT-TT
1 TATTATTATATT
983099 TATTATTATATT
1 TATTATTATATT
983111 TATTAT
1 TATTAT
983117 ATGAGCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTATTATATT
Found at i:988700 original size:25 final size:25
Alignment explanation
Indices: 988650--988700 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
988640 ACGTTAAGCA
* **
988650 TTTGAATAAGGAAATAATTTTGTTT
1 TTTGAACAAGGAAATAATTTAATTT
*
988675 TTTGAACATGGAAATAATTTAATTT
1 TTTGAACAAGGAAATAATTTAATTT
988700 T
1 T
988701 GTAATTTCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (25 bp):
TTTGAACAAGGAAATAATTTAATTT
Found at i:989799 original size:24 final size:23
Alignment explanation
Indices: 989744--989791 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
989734 ATTTCTAGCC
989744 TTCCATTCTTTTTCAGCGAGAAT
1 TTCCATTCTTTTTCAGCGAGAAT
989767 TTCCATTCTTTTTCAGCGAGAAT
1 TTCCATTCTTTTTCAGCGAGAAT
989790 TT
1 TT
989792 TTAGTTCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (23 bp):
TTCCATTCTTTTTCAGCGAGAAT
Found at i:991818 original size:2 final size:2
Alignment explanation
Indices: 991811--991835 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
991801 GACTGAAGAT
991811 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
991836 ATTTGTATTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:991916 original size:15 final size:17
Alignment explanation
Indices: 991896--991928 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
991886 ACTATTATTT
991896 TAGTTT-TTG-ATTTCA
1 TAGTTTATTGTATTTCA
991911 TAGTTTATTGTATTTCA
1 TAGTTTATTGTATTTCA
991928 T
1 T
991929 TTGAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.61
Consensus pattern (17 bp):
TAGTTTATTGTATTTCA
Found at i:992150 original size:22 final size:21
Alignment explanation
Indices: 992119--992160 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
992109 AATTATTATA
*
992119 AAACAAAGAGAATTATAGAAT
1 AAACAAAGAGAATAATAGAAT
992140 AAACAAGAGAGAATAATAGAA
1 AAACAA-AGAGAATAATAGAA
992161 AAATGAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.05, G:0.17, T:0.14
Consensus pattern (21 bp):
AAACAAAGAGAATAATAGAAT
Found at i:992813 original size:15 final size:15
Alignment explanation
Indices: 992793--992821 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
992783 TTCACTATTA
992793 TATCTTTTATGTTTC
1 TATCTTTTATGTTTC
992808 TATCTTTTATGTTT
1 TATCTTTTATGTTT
992822 TGCATGCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.10, G:0.07, T:0.69
Consensus pattern (15 bp):
TATCTTTTATGTTTC
Found at i:997574 original size:16 final size:16
Alignment explanation
Indices: 997549--997582 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
997539 ATTTATTTGC
*
997549 ATTTAGTATAATAATA
1 ATTTAATATAATAATA
*
997565 ATTTAATATAATTATA
1 ATTTAATATAATAATA
997581 AT
1 AT
997583 ATAAATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTTAATATAATAATA
Found at i:997696 original size:19 final size:19
Alignment explanation
Indices: 997642--997697 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
997632 AAAATCTCGT
* *
997642 TATTATAATTTTAAGAATA
1 TATTATAATTTTAAAAACA
997661 TATTGTATTAA-TTTAAAAACA
1 TA-T-TA-TAATTTTAAAAACA
997682 TATTATAATTTTAAAA
1 TATTATAATTTTAAAA
997698 TATTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 3 0.10
19 11 0.35
20 2 0.06
21 12 0.39
22 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
TATTATAATTTTAAAAACA
Found at i:997704 original size:19 final size:18
Alignment explanation
Indices: 997642--997706 Score: 67
Period size: 18 Copynumber: 3.3 Consensus size: 18
997632 AAAATCTCGT
997642 TATTATAATTTTAAGAATA
1 TATTATAATTTTAA-AATA
* *
997661 TATTGTATTAATTTAAAAACA
1 TA-T-TA-TAATTTTAAAATA
997682 TATTATAATTTTAAAATA
1 TATTATAATTTTAAAATA
997700 TTATTAT
1 -TATTAT
997707 TTACTAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 11 0.29
19 10 0.26
20 2 0.05
21 7 0.18
22 8 0.21
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (18 bp):
TATTATAATTTTAAAATA
Found at i:998218 original size:30 final size:30
Alignment explanation
Indices: 998184--998246 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
998174 GCTTAATAAG
998184 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
** * *
998214 CAAATGTCTTTAAAATAATAACAAACTTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
998244 CAA
1 CAA
998247 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:998674 original size:21 final size:21
Alignment explanation
Indices: 998649--998718 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
998639 ATAAACAAAA
998649 TGTTAACTTCTAAAAATGTTC
1 TGTTAACTTCTAAAAATGTTC
* * *
998670 TGTTAAATCTT-TAGAATTAGAT-
1 TGTT-AA-CTTCTAAAAAT-GTTC
998692 TGTTAACTTCTAAAAATGTTC
1 TGTTAACTTCTAAAAATGTTC
*
998713 TATTAA
1 TGTTAA
998719 ATCTTTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
20 5 0.14
21 16 0.43
22 11 0.30
23 5 0.14
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
TGTTAACTTCTAAAAATGTTC
Found at i:998696 original size:43 final size:43
Alignment explanation
Indices: 998649--998734 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
998639 ATAAACAAAA
* *
998649 TGTTAACTTCTAAAAATGTTCTGTTAAATCTTTAGAATTAGAT
1 TGTTAACTTCTAAAAATGTTCTATTAAATCTTTAAAATTAGAT
998692 TGTTAACTTCTAAAAATGTTCTATTAAATCTTTAAAATTAGAT
1 TGTTAACTTCTAAAAATGTTCTATTAAATCTTTAAAATTAGAT
998735 CGGTGATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (43 bp):
TGTTAACTTCTAAAAATGTTCTATTAAATCTTTAAAATTAGAT
Found at i:1008087 original size:85 final size:85
Alignment explanation
Indices: 1007987--1008157 Score: 342
Period size: 85 Copynumber: 2.0 Consensus size: 85
1007977 TAAAGTGTCA
1007987 GTACTATATCAAAATTTAGTGAGATTAATTATTCCAAATAAATTATAATTTTGGTAGAGTTTGCT
1 GTACTATATCAAAATTTAGTGAGATTAATTATTCCAAATAAATTATAATTTTGGTAGAGTTTGCT
1008052 TTTCGATTTCTAGCATTTGG
66 TTTCGATTTCTAGCATTTGG
1008072 GTACTATATCAAAATTTAGTGAGATTAATTATTCCAAATAAATTATAATTTTGGTAGAGTTTGCT
1 GTACTATATCAAAATTTAGTGAGATTAATTATTCCAAATAAATTATAATTTTGGTAGAGTTTGCT
1008137 TTTCGATTTCTAGCATTTGG
66 TTTCGATTTCTAGCATTTGG
1008157 G
1 G
1008158 AGTTATTGAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (85 bp):
GTACTATATCAAAATTTAGTGAGATTAATTATTCCAAATAAATTATAATTTTGGTAGAGTTTGCT
TTTCGATTTCTAGCATTTGG
Found at i:1008551 original size:38 final size:39
Alignment explanation
Indices: 1008509--1008591 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 39
1008499 AAAATTTATT
* *
1008509 AAAAATTAGAAAAAAAATATAAAAATCGTAAAAAATAA-A
1 AAAAATT-GAAAAAAAATATAAAAATCATAAAAAAAAATA
* ***
1008548 AAAAATTGTAAAATTTTATAAAAATCAT-AAAAAAAATA
1 AAAAATTGAAAAAAAATATAAAAATCATAAAAAAAAATA
1008586 AAAAAT
1 AAAAAT
1008592 GCGTCAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
37 7 0.19
38 23 0.62
39 7 0.19
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (39 bp):
AAAAATTGAAAAAAAATATAAAAATCATAAAAAAAAATA
Found at i:1008560 original size:58 final size:59
Alignment explanation
Indices: 1008480--1008601 Score: 160
Period size: 58 Copynumber: 2.1 Consensus size: 59
1008470 TATAATAAAT
* *
1008480 AAAAATAAATAAAAGTTATAAAA-TTTATTAAAAATTAGAAAAAAAATATAAAAAT-CGTA
1 AAAAATAAATAAAAATTATAAAATTTTA-TAAAAATCAGAAAAAAAATA-AAAAATGCGTA
* * *
1008539 AAAAATAAA-AAAAATTGTAAAATTTTATAAAAATCATAAAAAAAATAAAAAATGCGTC
1 AAAAATAAATAAAAATTATAAAATTTTATAAAAATCAGAAAAAAAATAAAAAATGCGTA
1008597 AAAAA
1 AAAAA
1008602 CGCCTTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
57 6 0.11
58 37 0.66
59 13 0.23
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (59 bp):
AAAAATAAATAAAAATTATAAAATTTTATAAAAATCAGAAAAAAAATAAAAAATGCGTA
Found at i:1008814 original size:329 final size:328
Alignment explanation
Indices: 1008418--1009072 Score: 1150
Period size: 329 Copynumber: 2.0 Consensus size: 328
1008408 CCCTAATTTT
*
1008418 TTTAATTAAAGTCACCTTGTATCACAACCACGGCGTGACATGTGAAAAAAATTATAATAAATAAA
1 TTTAATTAAAGTCACCTTGTATCACAACCACGGCGTGACATGTGAAAAAAATTATAAAAAATAAA
**
1008483 AATAAATAAAAGTTATAAAATTTATTAAAAATTAGAAAAAAAATATAAAAATCGTAAAAAATAAA
66 AATAAATAAAAGTTATAAAA-TTAGAAAAAATTAGAAAAAAAATATAAAAATCGTAAAAAATAAA
* *
1008548 AAAAATTGTAAAATTTTATAAAAATCATAAAAAAAATAAAAAATGCGTCAAAAACGCCTTTTATA
130 AAAAATTGCAAAATTTTATAAAAATCAT-AAAAAAATAAAAAATGCATCAAAAACGCCTTTTATA
1008613 ACTGTAACTGTTGACCATTAAAGCCATCACGTGTTGCAACACAGCATGACATGTGGTGAAAAATG
194 ACTGTAACTGTTGACCATTAAAGCCATCACGTGTTGCAACACAGCATGACATGTGGTGAAAAATG
* *
1008678 ATAAAAA-AATAAAAAATCAATAAAAGTTATAGAAAAATTATAAAATGTTTCTTCTGGTACGATA
259 ATAAAAACAATAAAAAATCAATAAAAGTTATAGAAAAATTATAAAATGATTCTTCTAGTACGATA
1008742 ATATA
324 ATATA
* *
1008747 TTTAATTAAAGTCACCTTGTGTCACAACCACGGCGTGACATGTGAAAAGAATTATAAAAAATAAA
1 TTTAATTAAAGTCACCTTGTATCACAACCACGGCGTGACATGTGAAAAAAATTATAAAAAATAAA
* * *
1008812 AATCAATAAAATTTATAAAATTAGAAAAAATTAGAAAAAAAATATATAAATCGTAAAAAATAAAA
66 AATAAATAAAAGTTATAAAATTAGAAAAAATTAGAAAAAAAATATAAAAATCGTAAAAAATAAAA
*
1008877 AAAATTGCAAAATTTTATAAAAATCATAAAAAAATATAAAATGCATCAAAAACGCCTTTTATAAC
131 AAAATTGCAAAATTTTATAAAAATCATAAAAAAATAAAAAATGCATCAAAAACGCCTTTTATAAC
*
1008942 TGTAACTGTTGACCATTAAAGCCATCACGTGTTGCAACACAGCGTGACATGTGGTGAAAAATGAT
196 TGTAACTGTTGACCATTAAAGCCATCACGTGTTGCAACACAGCATGACATGTGGTGAAAAATGAT
1009007 AAAAATCAATAAAAAATCAATAAAAGTTATAGAAAAATTATAAAATGATTCTTCTAGTACGATAA
261 AAAAA-CAATAAAAAATCAATAAAAGTTATAGAAAAATTATAAAATGATTCTTCTAGTACGATAA
1009072 T
325 T
1009073 TTTTATATTT
Statistics
Matches: 310, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
327 105 0.34
328 68 0.22
329 137 0.44
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (328 bp):
TTTAATTAAAGTCACCTTGTATCACAACCACGGCGTGACATGTGAAAAAAATTATAAAAAATAAA
AATAAATAAAAGTTATAAAATTAGAAAAAATTAGAAAAAAAATATAAAAATCGTAAAAAATAAAA
AAAATTGCAAAATTTTATAAAAATCATAAAAAAATAAAAAATGCATCAAAAACGCCTTTTATAAC
TGTAACTGTTGACCATTAAAGCCATCACGTGTTGCAACACAGCATGACATGTGGTGAAAAATGAT
AAAAACAATAAAAAATCAATAAAAGTTATAGAAAAATTATAAAATGATTCTTCTAGTACGATAAT
ATA
Found at i:1009023 original size:11 final size:11
Alignment explanation
Indices: 1009007--1009031 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1008997 GAAAAATGAT
1009007 AAAAATCAATA
1 AAAAATCAATA
1009018 AAAAATCAATA
1 AAAAATCAATA
1009029 AAA
1 AAA
1009032 GTTATAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATCAATA
Found at i:1009112 original size:18 final size:18
Alignment explanation
Indices: 1009071--1009112 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1009061 TAGTACGATA
*
1009071 ATTTTTATATTTTTTATG
1 ATTTTTATATTTTTTATC
*
1009089 AATTTTATATTTCTTTA-C
1 ATTTTTATATTT-TTTATC
1009107 ATTTTT
1 ATTTTT
1009113 TTATAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTATATTTTTTATC
Found at i:1009192 original size:18 final size:18
Alignment explanation
Indices: 1009169--1009217 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1009159 TTTCTCTATA
1009169 TTTTATATTTTTTAC-AAT
1 TTTTATATTTTTT-CTAAT
1009187 TTTTATATTTTTTCTAAT
1 TTTTATATTTTTTCTAAT
*
1009205 TTTAAATATTTTT
1 TTT-TATATTTTT
1009218 GTATTTCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 1 0.04
18 19 0.68
19 8 0.29
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTATATTTTTTCTAAT
Found at i:1009216 original size:17 final size:17
Alignment explanation
Indices: 1009155--1009216 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
1009145 TAATTTTCTC
1009155 TATATTTCTCTATATTTTA
1 TATATTT-TCTA-ATTTTA
*
1009174 TATTTTTTAC-AATTTTTA
1 TATATTTT-CTAA-TTTTA
*
1009192 TATTTTTTCTAATTTTA
1 TATATTTTCTAATTTTA
*
1009209 AATATTTT
1 TATATTTT
1009217 TGTATTTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 13 0.35
18 17 0.46
19 7 0.19
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.66
Consensus pattern (17 bp):
TATATTTTCTAATTTTA
Found at i:1011314 original size:122 final size:122
Alignment explanation
Indices: 1010992--1011320 Score: 388
Period size: 123 Copynumber: 2.7 Consensus size: 122
1010982 GAAACGCCGC
** * * * **
1010992 AAAAAATAAGTATTAGTGGCATTTTTAGCAAAAACGCCGCAAAATAATAAAACCCAACAACGTCG
1 AAAAAATAACCATTAGTGGCGTTTTTAGAAAAAACGCCGC-AAATAATAAAAGCCAACGGCGTCG
* * * *
1011057 TTTGGTGGCCTTTCGGGGGATTTAGTGGAGCATCAGCTGCGTTACACTAAAATCATCG
65 TTTGGTGACCTTTCGGGGGATTTAGTGGACCATCAGCAGCGTTACACTAAAATCACCG
* * ** *
1011115 AAAAAAGTAATCATTAGTGGCGTTTTTGGGGAAAACGCCGCAAATATTAAAAGCCAACGGCGTCG
1 AAAAAA-TAACCATTAGTGGCGTTTTTAGAAAAAACGCCGCAAATAATAAAAGCCAACGGCGTCG
* * * * ** *
1011180 TTTGATGCCCTTTCGGGGGATTTAGTGGACCATTAGCAGCGTTTCTTTAAAATCGCCG
65 TTTGGTGACCTTTCGGGGGATTTAGTGGACCATCAGCAGCGTTACACTAAAATCACCG
* * * *
1011238 TAAAAATAACCATTAGTGGCGTTTTTTGAAAAAACGCTGCACATAATAAAAGCCAACGGCGTCGT
1 AAAAAATAACCATTAGTGGCGTTTTTAGAAAAAACGCCGCAAATAATAAAAGCCAACGGCGTCGT
*
1011303 TTGGTGACCTTTTGGGGG
66 TTGGTGACCTTTCGGGGG
1011321 GAATTAGCGG
Statistics
Matches: 174, Mismatches: 31, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
122 67 0.39
123 79 0.45
124 28 0.16
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (122 bp):
AAAAAATAACCATTAGTGGCGTTTTTAGAAAAAACGCCGCAAATAATAAAAGCCAACGGCGTCGT
TTGGTGACCTTTCGGGGGATTTAGTGGACCATCAGCAGCGTTACACTAAAATCACCG
Found at i:1011459 original size:41 final size:41
Alignment explanation
Indices: 1011405--1011511 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 41
1011395 TGCTCGGGGT
*
1011405 TTTTAGCGGCGTTTTTCATGAAGCGCCGCTAATGCTTA-GAC
1 TTTTAGCGGCGTTTTTCATGAAGCGCCACTAATGC-TAGGAC
* ** * **
1011446 TTTTAGCGGCGTTTTTTATGATTCGCCACTAATTCTAGGGG
1 TTTTAGCGGCGTTTTTCATGAAGCGCCACTAATGCTAGGAC
* *
1011487 TTTTAGCGGCATTTTTGATGAAGCG
1 TTTTAGCGGCGTTTTTCATGAAGCG
1011512 TCGCAAACAC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 2 0.04
41 52 0.96
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCATGAAGCGCCACTAATGCTAGGAC
Found at i:1012655 original size:15 final size:14
Alignment explanation
Indices: 1012631--1012698 Score: 55
Period size: 15 Copynumber: 4.7 Consensus size: 14
1012621 TAGGGGGTAT
*
1012631 GGATTTAGGGTTTG
1 GGATTAAGGGTTTG
*
1012645 GGATATAAGGGTTAG
1 GGAT-TAAGGGTTTG
* *
1012660 GGGTTAAGGGTTTA
1 GGATTAAGGGTTTG
* *
1012674 TGATTTAAGGGTTAG
1 GGA-TTAAGGGTTTG
*
1012689 GGGTTAAGGG
1 GGATTAAGGG
1012699 GTTAATGATT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
14 20 0.49
15 21 0.51
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.34
Consensus pattern (14 bp):
GGATTAAGGGTTTG
Found at i:1012682 original size:29 final size:30
Alignment explanation
Indices: 1012650--1012710 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
1012640 GTTTGGGATA
*
1012650 TAAGGGTTAGGGGTTAA-GGGTTTATGATT
1 TAAGGGTTAGGGGTTAAGGGGTTAATGATT
1012679 TAAGGGTTAGGGGTTAAGGGGTTAATGATT
1 TAAGGGTTAGGGGTTAAGGGGTTAATGATT
1012709 TA
1 TA
1012711 GGATTTAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.36
Consensus pattern (30 bp):
TAAGGGTTAGGGGTTAAGGGGTTAATGATT
Found at i:1012697 original size:14 final size:14
Alignment explanation
Indices: 1012650--1012698 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1012640 GTTTGGGATA
1012650 TAAGGGTTAGGGGT
1 TAAGGGTTAGGGGT
* **
1012664 TAAGGGTTTATGATT
1 TAAGGG-TTAGGGGT
1012679 TAAGGGTTAGGGGT
1 TAAGGGTTAGGGGT
1012693 TAAGGG
1 TAAGGG
1012699 GTTAATGATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (14 bp):
TAAGGGTTAGGGGT
Found at i:1012700 original size:15 final size:15
Alignment explanation
Indices: 1012653--1012702 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1012643 TGGGATATAA
1012653 GGGTTAGGGGTTAAG
1 GGGTTAGGGGTTAAG
* * **
1012668 GGTTTATGATTTAA-
1 GGGTTAGGGGTTAAG
1012682 GGGTTAGGGGTTAAG
1 GGGTTAGGGGTTAAG
1012697 GGGTTA
1 GGGTTA
1012703 ATGATTTAGG
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (15 bp):
GGGTTAGGGGTTAAG
Found at i:1013611 original size:270 final size:270
Alignment explanation
Indices: 1013161--1013727 Score: 771
Period size: 270 Copynumber: 2.1 Consensus size: 270
1013151 TTCTCTCCAC
* * * **
1013161 GATTTTTAACTTATAAAAAGTTTAGAATTATTTACTTAAAACGTCACCGTTTGGCTTAAAGTACG
1 GATTTTTAACTTAGAAAAATTTTAGAATTATTTACTTAAAACATCACCGTTTGGCTTAAAGTAAA
* *
1013226 TTAAGTATTAGTGGCATTTTAACATAAAACGCCAGAAACAATGCAATTTGAGAGTAGCAAAACGG
66 TTAAGTATTAGTGGCATTTTAACATAAAAAGCCAGAAACAATGCAATTTGAGAGTAGAAAAACGG
* * ** * * * * *
1013291 CGCTGTTTCTGTTTACGATTTTAAATATTTGTGGCGTTTTTGGCAAAACGCCGGAACTTTGAAAG
131 CACCGTTTCCCTTTACAACTTTAAATATTTGTGGCGTTTTAGGCAAAACGCCGGAAATGTGAAAG
* * * *
1013356 CAATAGCGGCGTTTGTATAGTAAACGCCACAAAAGGGTATTAAAATAATGTCTAAATGGCGCCGT
196 CAATAGCGGCGTTTGTACAGTAAACGCCACAAAAGGATATTAAAATAATGGCTAAACGGCGCCGT
*
1013421 TTCTGTACAT
261 TTCTGTACAA
* *
1013431 GATTTTTAACTTAGAAAAATTTTAGAATTATTTATTTAAAACATCACCGTTTGGGTTAAAGTAAA
1 GATTTTTAACTTAGAAAAATTTTAGAATTATTTACTTAAAACATCACCGTTTGGCTTAAAGTAAA
* * *
1013496 TTAAGTATTAGTGGCGTTTTTACATAAAAAGCCAGAAATAATGCAATTTGAGAGTA-AAAAATCG
66 TTAAGTATTAGTGGCATTTTAACATAAAAAGCCAGAAACAATGCAATTTGAGAGTAGAAAAA-CG
*
1013560 GCACCGTTTCCCTTTACAACTTT-AATATTTAGTGGCGGTTTTAGG-AAAACGCCGGAAATGTGG
130 GCACCGTTTCCCTTTACAACTTTAAATATTT-GTGGC-GTTTTAGGCAAAACGCCGGAAATGTGA
* * * * * *
1013623 AAGCAATAGCGGCGTTTTTACAGTAAACGCCGCAAAAGGATATTAGAGTAATGGGTAAACGGTGC
193 AAGCAATAGCGGCGTTTGTACAGTAAACGCCACAAAAGGATATTAAAATAATGGCTAAACGGCGC
**
1013688 CGTTTCTGTGTAA
258 CGTTTCTGTACAA
1013701 GATTTTTAACTTAGAAAAATTTTAGAA
1 GATTTTTAACTTAGAAAAATTTTAGAA
1013728 ATCAAGTATT
Statistics
Matches: 259, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
269 11 0.04
270 241 0.93
271 7 0.03
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (270 bp):
GATTTTTAACTTAGAAAAATTTTAGAATTATTTACTTAAAACATCACCGTTTGGCTTAAAGTAAA
TTAAGTATTAGTGGCATTTTAACATAAAAAGCCAGAAACAATGCAATTTGAGAGTAGAAAAACGG
CACCGTTTCCCTTTACAACTTTAAATATTTGTGGCGTTTTAGGCAAAACGCCGGAAATGTGAAAG
CAATAGCGGCGTTTGTACAGTAAACGCCACAAAAGGATATTAAAATAATGGCTAAACGGCGCCGT
TTCTGTACAA
Found at i:1013908 original size:233 final size:233
Alignment explanation
Indices: 1013493--1013960 Score: 654
Period size: 233 Copynumber: 2.0 Consensus size: 233
1013483 GGGTTAAAGT
* * *
1013493 AAATTAAGTATTAGTGGCGTTTTTACATAAAAAGCCAGAAATAATGCAATTTGAGAGTAAAAAAT
1 AAATCAAGTATTAGTGGCGTTTTTACATAAAAAGCCAGAAAAAATGCAATTTGAGACTAAAAAAT
* * *
1013558 CGGCACCGTTTCCCTTTACAACTTTAATATTTAGTGGCGGTTTTAGGAAAACGCCGGAAATGTGG
66 CGGCACCGTTTCCCTTTACAAATTTAATATTTAGTCGCGGTTTTAGGAAAACACCGGAAATGTGG
* * * * ***
1013623 AAGCAATAGCGGCGTTTTTACAGTAAACGCCGCAAAAGGATATTAGAGTAATGGGTAAACGGTGC
131 AAGCAATAGCGGCGTTTGTACAGAAAACGCCGCAAAAGGATATTAAAGTAATGGCTAAACAACGC
* *
1013688 CGTTTCTGTGTAA-GATTTTTAACTTAGAAAAATTTTAG
196 CGTTTCCGT-AAACGATTTTTAACTTAGAAAAATTTTAG
** *
1013726 AAATCAAGTATTAGTGGCGTTTTTATGTAAAATGCCAGAAAAAATGCAATTTGAGACTAACAAAA
1 AAATCAAGTATTAGTGGCGTTTTTACATAAAAAGCCAGAAAAAATGCAATTTGAGACTAA-AAAA
* * **
1013791 -CGGCGCCG-TTCCTCTTTACAAATTTAATATTTAGTCGCGTTTTTAGGAAAACATTGGAAATGT
65 TCGGCACCGTTTCC-CTTTACAAATTTAATATTTAGTCGCGGTTTTAGGAAAACACCGGAAATGT
* * * *
1013854 GTAAGCAATAGCGGCGTTTGTACCGAAAATGCCGCAAAAGGGTATTAAAGTAATGGCTAAACAAC
129 GGAAGCAATAGCGGCGTTTGTACAGAAAACGCCGCAAAAGGATATTAAAGTAATGGCTAAACAAC
1013919 GCCGTTTCCGTAAACGATTTTTAACTTAGAAAAATTTTAG
194 GCCGTTTCCGTAAACGATTTTTAACTTAGAAAAATTTTAG
1013959 AA
1 AA
1013961 TTATTTATTT
Statistics
Matches: 206, Mismatches: 26, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
232 6 0.03
233 196 0.95
234 4 0.02
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (233 bp):
AAATCAAGTATTAGTGGCGTTTTTACATAAAAAGCCAGAAAAAATGCAATTTGAGACTAAAAAAT
CGGCACCGTTTCCCTTTACAAATTTAATATTTAGTCGCGGTTTTAGGAAAACACCGGAAATGTGG
AAGCAATAGCGGCGTTTGTACAGAAAACGCCGCAAAAGGATATTAAAGTAATGGCTAAACAACGC
CGTTTCCGTAAACGATTTTTAACTTAGAAAAATTTTAG
Found at i:1014768 original size:60 final size:60
Alignment explanation
Indices: 1014696--1014819 Score: 205
Period size: 60 Copynumber: 2.1 Consensus size: 60
1014686 GTGAATTTTG
* * *
1014696 TGAATTTCGGTTACAGTGTGTGAGGGATTTAGGTATAATTTGTTTATTTAGTAGTTGCCC
1 TGAATTTCGGTTACAGTGTATGAGGGATTTAGGTATAAATTGTTTATTTAGCAGTTGCCC
*
1014756 TGAATTTTGGTTACAGTGTATGAGGGATTTAGGTATAAATTGTTTATTTAGCAGTTGCCC
1 TGAATTTCGGTTACAGTGTATGAGGGATTTAGGTATAAATTGTTTATTTAGCAGTTGCCC
1014816 -GAAT
1 TGAAT
1014820 GAATTTTGTG
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 4 0.07
60 56 0.93
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (60 bp):
TGAATTTCGGTTACAGTGTATGAGGGATTTAGGTATAAATTGTTTATTTAGCAGTTGCCC
Found at i:1014884 original size:13 final size:13
Alignment explanation
Indices: 1014860--1014900 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1014850 ATTTTGCGAG
*
1014860 ATTTTCTAAATGA
1 ATTTTCTTAATGA
1014873 ATTTT-TTGAATGA
1 ATTTTCTT-AATGA
1014886 ATTTTCTTAATGA
1 ATTTTCTTAATGA
1014899 AT
1 AT
1014901 ATAGTAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.88
14 2 0.08
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (13 bp):
ATTTTCTTAATGA
Found at i:1015253 original size:23 final size:22
Alignment explanation
Indices: 1015202--1015253 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
1015192 TCATTTTTTT
* *
1015202 TTTGCT-TGCATTTTTTGCTTA
1 TTTGCTCTACATTTTTGGCTTA
1015223 TCTT-CTCTACATTTCTTGGCTTA
1 T-TTGCTCTACATTT-TTGGCTTA
1015246 TTTGCTCT
1 TTTGCTCT
1015254 TTGTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 10 0.40
23 12 0.48
ACGTcount: A:0.10, C:0.21, G:0.12, T:0.58
Consensus pattern (22 bp):
TTTGCTCTACATTTTTGGCTTA
Found at i:1016339 original size:13 final size:13
Alignment explanation
Indices: 1016323--1016421 Score: 101
Period size: 13 Copynumber: 7.5 Consensus size: 13
1016313 TTACTAAAAT
*
1016323 TTACTTTAATATA
1 TTACTTAAATATA
*
1016336 TTACTTGAATATA
1 TTACTTAAATATA
*
1016349 TTACTTAAATAAA
1 TTACTTAAATATA
*
1016362 TTACTTAAATACA
1 TTACTTAAATATA
*
1016375 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
1016389 TTGGTTAAATTTA
1 TTACTTAAATATA
1016402 TTACTTAAATATA
1 TTACTTAAATATA
1016415 TTACTTA
1 TTACTTA
1016422 CTAAAATTTA
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
12 3 0.04
13 59 0.84
14 5 0.07
15 3 0.04
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:1016397 original size:40 final size:40
Alignment explanation
Indices: 1016353--1016430 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
1016343 AATATATTAC
1016353 TTAAATAAATTACTTAAATACATTACTTACTAAAATTTGG
1 TTAAATAAATTACTTAAATACATTACTTACTAAAATTTGG
** *
1016393 TTAAATTTATTACTTAAATATATTACTTACTAAAATTT
1 TTAAATAAATTACTTAAATACATTACTTACTAAAATTT
1016431 AAGTATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.45
Consensus pattern (40 bp):
TTAAATAAATTACTTAAATACATTACTTACTAAAATTTGG
Found at i:1016454 original size:9 final size:9
Alignment explanation
Indices: 1016440--1016809 Score: 206
Period size: 9 Copynumber: 42.4 Consensus size: 9
1016430 TAAGTATATA
*
1016440 TTACATTAC
1 TTACATAAC
1016449 TTACATAAC
1 TTACATAAC
*
1016458 TTAAATAAC
1 TTACATAAC
*
1016467 TTACACAAC
1 TTACATAAC
1016476 TTACATAAC
1 TTACATAAC
1016485 TTACATAAC
1 TTACATAAC
1016494 TTACATAA-
1 TTACATAAC
*
1016502 -TGCATAAC
1 TTACATAAC
*
1016510 TCT-GATAAC
1 T-TACATAAC
* *
1016519 TAACATTA-
1 TTACATAAC
*
1016527 -TACACAAC
1 TTACATAAC
*
1016535 TTATATAA-
1 TTACATAAC
* *
1016543 -GACATTAC
1 TTACATAAC
1016551 TTACATAAC
1 TTACATAAC
*
1016560 TTACATTA-
1 TTACATAAC
*
1016568 -TACACAAC
1 TTACATAAC
*
1016576 TTACATAAT
1 TTACATAAC
*** *
1016585 TTTTTTAATA
1 TTACATAA-C
1016595 TTACACATAAC
1 TT--ACATAAC
* *
1016606 GTACATTA-
1 TTACATAAC
1016614 -TACATAAC
1 TTACATAAC
1016622 TTACATAAC
1 TTACATAAC
1016631 -T-CATAAC
1 TTACATAAC
1016638 TTACATAAC
1 TTACATAAC
*
1016647 TTA-ATTAC
1 TTACATAAC
**
1016655 ATTATGCA-CCC
1 -TTA--CATAAC
1016666 TTTACATAAC
1 -TTACATAAC
1016676 TTACATAAC
1 TTACATAAC
*
1016685 TTACATAGC
1 TTACATAAC
*
1016694 TTACAT-TC
1 TTACATAAC
*
1016702 -TACACAAC
1 TTACATAAC
1016710 TTACATAAC
1 TTACATAAC
* *
1016719 ATACATTAC
1 TTACATAAC
**
1016728 TTTGATAAC
1 TTACATAAC
1016737 TTACATAAC
1 TTACATAAC
*
1016746 TTACATAGC
1 TTACATAAC
*
1016755 TTACTTAA-
1 TTACATAAC
1016763 -TACATAAC
1 TTACATAAC
1016771 TTACATAAC
1 TTACATAAC
1016780 TT--ATACAC
1 TTACATA-AC
*
1016788 GTACATAAC
1 TTACATAAC
*
1016797 TTACATAAT
1 TTACATAAC
1016806 TTAC
1 TTAC
1016810 TTAATACATA
Statistics
Matches: 270, Mismatches: 62, Indels: 58
0.69 0.16 0.15
Matches are distributed among these distances:
7 44 0.16
8 11 0.04
9 199 0.74
10 7 0.03
11 5 0.02
12 4 0.01
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:1016618 original size:16 final size:16
Alignment explanation
Indices: 1016594--1016643 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1016584 TTTTTTTAAT
1016594 ATTACACATAACGTAC
1 ATTACACATAACGTAC
* *
1016610 ATTATACATAACTTAC
1 ATTACACATAACGTAC
* * *
1016626 ATAACTCATAACTTAC
1 ATTACACATAACGTAC
1016642 AT
1 AT
1016644 AACTTAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (16 bp):
ATTACACATAACGTAC
Found at i:1016793 original size:51 final size:52
Alignment explanation
Indices: 1016711--1016820 Score: 152
Period size: 51 Copynumber: 2.1 Consensus size: 52
1016701 CTACACAACT
* * *
1016711 TACATAACATACATTACTTTGATAACTTACATAACTTACATAGCTTACTTAA
1 TACATAACATACATAACTTTGATAACGTACATAACTTACATAACTTACTTAA
* *
1016763 TACATAACTTACATAAC-TT-ATACACGTACATAACTTACATAATTTACTTAA
1 TACATAACATACATAACTTTGATA-ACGTACATAACTTACATAACTTACTTAA
1016814 TACATAA
1 TACATAA
1016821 ATATATATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 3 0.06
51 34 0.65
52 15 0.29
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (52 bp):
TACATAACATACATAACTTTGATAACGTACATAACTTACATAACTTACTTAA
Found at i:1022320 original size:21 final size:21
Alignment explanation
Indices: 1022294--1022343 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1022284 CTACAACTTA
1022294 AAGCAGAGGCGGCAGTGAGGG
1 AAGCAGAGGCGGCAGTGAGGG
1022315 AAGCAGAGGCGGCAGTGAGGG
1 AAGCAGAGGCGGCAGTGAGGG
1022336 AAGCAGAG
1 AAGCAGAG
1022344 CAAAGCAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.50, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGTGAGGG
Found at i:1022772 original size:43 final size:43
Alignment explanation
Indices: 1022690--1022991 Score: 244
Period size: 43 Copynumber: 7.1 Consensus size: 43
1022680 CGCCAAACAA
* * ** *
1022690 TAGCGGCATTTTTG-GAAAAAGTGCCGCTAAA-AGTTATGACATT
1 TAGCGGCATTTGTGAG-AAAAGCGCCGCTAAAGA-ACATGACCTT
*
1022733 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCATTTGTGAGAAAAGCGCCGCTAAAGAACATGACCTT
* * *
1022776 TAGGGGCATTT-TCGGGAAAAGCACCGCTAAAGAACATGACCTT
1 TAGCGGCATTTGT-GAGAAAAGCGCCGCTAAAGAACATGACCTT
* * * *
1022819 TAGAGGCGTTTGTGTA-AAAAGCGTCGCTAAAGAACATGACATT
1 TAGCGGCATTTGTG-AGAAAAGCGCCGCTAAAGAACATGACCTT
* * **
1022862 TAGCGGCATTTGTG-GGAAAGCGCCGCTAAAGATCATGTTCTT
1 TAGCGGCATTTGTGAGAAAAGCGCCGCTAAAGAACATGACCTT
* * * *
1022904 TAGCGGCATTT-TTATGGAAA-CGCCGCTAATGAACTTGACCTT
1 TAGCGGCATTTGTGA-GAAAAGCGCCGCTAAAGAACATGACCTT
* * *** *
1022946 TAGCGGCGTTT-TTATG-GTTGTGCCGCTAAAGAACATGACCTT
1 TAGCGGCATTTGTGA-GAAAAGCGCCGCTAAAGAACATGACCTT
1022988 TAGC
1 TAGC
1022992 AGCGTTTATA
Statistics
Matches: 213, Mismatches: 37, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.00
42 88 0.41
43 121 0.57
44 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (43 bp):
TAGCGGCATTTGTGAGAAAAGCGCCGCTAAAGAACATGACCTT
Found at i:1022997 original size:42 final size:42
Alignment explanation
Indices: 1022725--1022998 Score: 212
Period size: 42 Copynumber: 6.5 Consensus size: 42
1022715 GCTAAAAGTT
* * *
1022725 ATGACATTTAGCGGCGTTTGTGA-GAAAAGCGCCGCTAAAGAAC
1 ATGACCTTTAGCGGCGTTT-TTATGGAAA-CGCCGCTAAAGAAC
* * ** *
1022768 ATGACCTTTAGGGGC-ATTTTCGGGAAAAGCACCGCTAAAGAAC
1 ATGACCTTTAGCGGCGTTTTTATGG-AAA-CGCCGCTAAAGAAC
* * * ** *
1022811 ATGACCTTTAGAGGCGTTTGTGTAAAAAGCGTCGCTAAAGAAC
1 ATGACCTTTAGCGGCGTTTTTATGGAAA-CGCCGCTAAAGAAC
* * * * *
1022854 ATGACATTTAGCGGCATTTGT-GGGAAAGCGCCGCTAAAGATC
1 ATGACCTTTAGCGGCGTTTTTATGGAAA-CGCCGCTAAAGAAC
** * *
1022896 ATGTTCTTTAGCGGCATTTTTATGGAAACGCCGCTAATGAAC
1 ATGACCTTTAGCGGCGTTTTTATGGAAACGCCGCTAAAGAAC
* ****
1022938 TTGACCTTTAGCGGCGTTTTTATGGTTGTGCCGCTAAAGAAC
1 ATGACCTTTAGCGGCGTTTTTATGGAAACGCCGCTAAAGAAC
*
1022980 ATGACCTTTAGCAGCGTTT
1 ATGACCTTTAGCGGCGTTT
1022999 ATAAATGTTA
Statistics
Matches: 185, Mismatches: 42, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
41 1 0.01
42 98 0.53
43 83 0.45
44 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (42 bp):
ATGACCTTTAGCGGCGTTTTTATGGAAACGCCGCTAAAGAAC
Found at i:1046284 original size:25 final size:25
Alignment explanation
Indices: 1046243--1046292 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1046233 AGTTGTAGAG
1046243 AGAAAATTCTCTAAAGAAATTATTTC
1 AGAAAATTCTCTAAAGAAATT-TTTC
*
1046269 AGAAAATT-TCTAAAGATATTTTTC
1 AGAAAATTCTCTAAAGAAATTTTTC
1046293 TTATTTACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.17
25 11 0.48
26 8 0.35
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (25 bp):
AGAAAATTCTCTAAAGAAATTTTTC
Found at i:1050561 original size:24 final size:23
Alignment explanation
Indices: 1050525--1050586 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 23
1050515 TTAATATTTG
* *
1050525 TTTTTAATATGTCTAGCT-ACAGCA
1 TTTTAAATGTGTCTAGCTGA-A-CA
1050549 TTTTAAATGTGTCTTTAGCTGAACA
1 TTTTAAATGTGTC--TAGCTGAACA
1050574 -TTTAAATGTGTCT
1 TTTTAAATGTGTCT
1050587 TAGTTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 1 0.03
24 23 0.70
25 2 0.06
26 6 0.18
27 1 0.03
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (23 bp):
TTTTAAATGTGTCTAGCTGAACA
Found at i:1060937 original size:36 final size:36
Alignment explanation
Indices: 1060897--1060967 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1060887 AGTTTGAGCT
* *
1060897 TGTGGCTATGGAGTC-GTGACTACAGAATCTGAGGTG
1 TGTGGATATGGAATCTG-GACTACAGAATCTGAGGTG
* *
1060933 TGTGGATATGGAATCTGGACTATAGAATTTGAGGT
1 TGTGGATATGGAATCTGGACTACAGAATCTGAGGT
1060968 ACAAAATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.25, C:0.10, G:0.34, T:0.31
Consensus pattern (36 bp):
TGTGGATATGGAATCTGGACTACAGAATCTGAGGTG
Found at i:1061227 original size:27 final size:28
Alignment explanation
Indices: 1061178--1061249 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 28
1061168 AACAATAGAG
** *
1061178 AAAGCTTCAAGAAAAACATAAAATAGGA
1 AAAGCTTCAAGAAATCCATAAAATAAGA
*
1061206 AAAGTTTCAAGAAATCCA-AAAATAAGA
1 AAAGCTTCAAGAAATCCATAAAATAAGA
*
1061233 AAAGCATCAAGAAATCC
1 AAAGCTTCAAGAAATCC
1061250 CCAAAACTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.15
Consensus pattern (28 bp):
AAAGCTTCAAGAAATCCATAAAATAAGA
Found at i:1082346 original size:21 final size:21
Alignment explanation
Indices: 1082286--1082346 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
1082276 CATTTCAATC
1082286 AAACTTATATTTAATTTT-TT
1 AAACTTATATTTAATTTTATT
* ** *
1082306 AAAATT-TATTGCATAATTATT
1 AAACTTATATTTAAT-TTTATT
1082327 AAACTTATATTTAATTTTAT
1 AAACTTATATTTAATTTTAT
1082347 AAGTGTATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
21 11 0.37
22 6 0.20
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (21 bp):
AAACTTATATTTAATTTTATT
Found at i:1087518 original size:32 final size:32
Alignment explanation
Indices: 1087482--1087552 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
1087472 ACAAGGTAAA
**
1087482 TAAAAAATTTAAAATAAAAATATTTAATTAAC
1 TAAAAAATAAAAAATAAAAATATTTAATTAAC
* **
1087514 TAAAAAATAAAAAATAAAATTATTTAATTATG
1 TAAAAAATAAAAAATAAAAATATTTAATTAAC
1087546 TAAAAAA
1 TAAAAAA
1087553 AATTAGAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (32 bp):
TAAAAAATAAAAAATAAAAATATTTAATTAAC
Found at i:1089865 original size:18 final size:19
Alignment explanation
Indices: 1089833--1089868 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1089823 GTAAAAATGA
1089833 ATGTCAAATTTTTTATTTT
1 ATGTCAAATTTTTTATTTT
1089852 ATGTCAAA-TTTTTATTT
1 ATGTCAAATTTTTTATTT
1089869 AGAACTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (19 bp):
ATGTCAAATTTTTTATTTT
Found at i:1091109 original size:30 final size:30
Alignment explanation
Indices: 1091070--1091134 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1091060 TAGTTTGGCC
* * *
1091070 CAAGATTCGTGTCTTATCCCTGAACCTTCA
1 CAAGTTTCGTGTCTTAGCCCCGAACCTTCA
1091100 CAAGTTTCGTGTCTTAGCCCCGAACCTTCA
1 CAAGTTTCGTGTCTTAGCCCCGAACCTTCA
*
1091130 AAAGT
1 CAAGT
1091135 AGGCCAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (30 bp):
CAAGTTTCGTGTCTTAGCCCCGAACCTTCA
Found at i:1099593 original size:19 final size:20
Alignment explanation
Indices: 1099551--1099593 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1099541 TTCGAAAAAT
1099551 TATTTCTGAAAAATAGTATG
1 TATTTCTGAAAAATAGTATG
1099571 -ATTTCTTGAAAAAT-GT-TG
1 TATTTC-TGAAAAATAGTATG
1099589 TATTT
1 TATTT
1099594 TTTGGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.10
19 11 0.52
20 8 0.38
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (20 bp):
TATTTCTGAAAAATAGTATG
Found at i:1099850 original size:14 final size:14
Alignment explanation
Indices: 1099833--1099861 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1099823 TAAATTTAGC
1099833 CCCTAGCATTTACT
1 CCCTAGCATTTACT
1099847 CCCTAGCATTTACT
1 CCCTAGCATTTACT
1099861 C
1 C
1099862 ATTTTGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.38, G:0.07, T:0.34
Consensus pattern (14 bp):
CCCTAGCATTTACT
Found at i:1100696 original size:29 final size:29
Alignment explanation
Indices: 1100653--1100716 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1100643 GGGTAGATTG
* *
1100653 AAAGATTGAATATTTGAAGTTGACTGGAT
1 AAAGATTGAAGATTTGAAATTGACTGGAT
**
1100682 AAAGATTGAAGATTTGAAATTGGTTGGAT
1 AAAGATTGAAGATTTGAAATTGACTGGAT
1100711 AAAGAT
1 AAAGAT
1100717 CAAATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAGATTGAAGATTTGAAATTGACTGGAT
Found at i:1103031 original size:20 final size:20
Alignment explanation
Indices: 1102993--1103032 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1102983 CTAACATCTC
* *
1102993 TTTCGAGAATAAGAGCAACT
1 TTTCAAGAATAAGAACAACT
*
1103013 TTTCAAGAATAATAACAACT
1 TTTCAAGAATAAGAACAACT
1103033 GACTTTAGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (20 bp):
TTTCAAGAATAAGAACAACT
Found at i:1105523 original size:11 final size:11
Alignment explanation
Indices: 1105486--1105544 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
1105476 GAAGTCTAAG
*
1105486 AAAATAAAAGT
1 AAAATAAAAAT
* *
1105497 AAAACAACAA-
1 AAAATAAAAAT
1105507 AAAATAAAAAT
1 AAAATAAAAAT
*
1105518 AAAATAAAGAT
1 AAAATAAAAAT
*
1105529 AAAAGTAAAACT
1 AAAA-TAAAAAT
1105541 AAAA
1 AAAA
1105545 AGAAAAGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
10 8 0.21
11 21 0.55
12 9 0.24
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:1105532 original size:17 final size:18
Alignment explanation
Indices: 1105510--1105543 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1105500 ACAACAAAAA
1105510 ATAAAAATAAAA-TAAAG
1 ATAAAAATAAAACTAAAG
*
1105527 ATAAAAGTAAAACTAAA
1 ATAAAAATAAAACTAAA
1105544 AAGAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (18 bp):
ATAAAAATAAAACTAAAG
Found at i:1108659 original size:2 final size:2
Alignment explanation
Indices: 1108652--1108682 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1108642 TTAGAAGGTG
1108652 AT AT AT 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 AT AT AT A
1108683 AATAAAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1115241 original size:21 final size:22
Alignment explanation
Indices: 1115217--1115257 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1115207 TTATGCATAC
*
1115217 AGTC-CTAAATATGAGTTTACA
1 AGTCTCTAAAAATGAGTTTACA
*
1115238 AGTCTCTAAAAATGATTTTA
1 AGTCTCTAAAAATGAGTTTA
1115258 GAACTAACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (22 bp):
AGTCTCTAAAAATGAGTTTACA
Found at i:1125602 original size:22 final size:21
Alignment explanation
Indices: 1125560--1125602 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1125550 TATTATTTTA
*
1125560 ATTTAATTATATTTTTAGGTT
1 ATTTAATTATATTATTAGGTT
* *
1125581 ATTTTATTACTATTATTCGGTT
1 ATTTAATTA-TATTATTAGGTT
1125603 TTGGATTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (21 bp):
ATTTAATTATATTATTAGGTT
Found at i:1127613 original size:5 final size:5
Alignment explanation
Indices: 1127606--1127640 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
1127596 GGAAAACTGA
*
1127606 ATCTA ATCTG ATCTG ATCTG ATCTG ATCTG ATCTG
1 ATCTG ATCTG ATCTG ATCTG ATCTG ATCTG ATCTG
1127641 GAAGTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (5 bp):
ATCTG
Found at i:1135160 original size:18 final size:19
Alignment explanation
Indices: 1135139--1135180 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1135129 TTTTCACATA
*
1135139 TTTTCCTTTTATTT-TTAT
1 TTTTCATTTTATTTCTTAT
* *
1135157 TTTTAATTTTATTTCTTTT
1 TTTTCATTTTATTTCTTAT
1135176 TTTTC
1 TTTTC
1135181 TTCACAGTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTCATTTTATTTCTTAT
Found at i:1135519 original size:21 final size:23
Alignment explanation
Indices: 1135476--1135520 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1135466 AAACCCCTTA
*
1135476 TCTTCTTTCTTTTTTGATGCTTTT
1 TCTTCTTTCTTTTCTGA-GCTTTT
1135500 TCTT-TTTCTTTTCTGA-CTTTT
1 TCTTCTTTCTTTTCTGAGCTTTT
1135521 GTTTTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.04, C:0.18, G:0.07, T:0.71
Consensus pattern (23 bp):
TCTTCTTTCTTTTCTGAGCTTTT
Found at i:1137393 original size:20 final size:18
Alignment explanation
Indices: 1137346--1137452 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
1137336 TTTACCAAAC
1137346 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
1137363 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
**
1137383 ATTAAATTAATAAAATAAT
1 ATTAAATTAAT-ATTTAAT
* *
1137402 ACTAAGA-TAAGTATTAAAT
1 ATTAA-ATTAA-TATTTAAT
* *
1137421 -TTAATTTAATATTAAACT
1 ATTAAATTAATATTTAA-T
*
1137439 ATTAAAATAATATT
1 ATTAAATTAATATT
1137453 ATTTTTGGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
17 15 0.22
18 8 0.12
19 28 0.41
20 18 0.26
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:1140827 original size:217 final size:217
Alignment explanation
Indices: 1140452--1140885 Score: 832
Period size: 217 Copynumber: 2.0 Consensus size: 217
1140442 CAATGGTATA
1140452 ATCGACATATTATATGTTGTGTGATAGACAGTATTTGTTGGAGAATTGTTGTATATGTTATGCAT
1 ATCGACATATTATATGTTGTGTGATAGACAGTATTTGTTGGAGAATTGTTGTATATGTTATGCAT
* *
1140517 GATATTTATGTGGCTTTGCAAAGGTTCGGATGGCCATATACGGGATTGCATATGCATTTTATTTA
66 GATATTTATGTGGCTTTGCAAAGGTTCGAATGGCCATATACGGGATTGCATATGCATTTTATCTA
*
1140582 TGTGGCTTTGAAGGAGGTTCGGTTGACTAAGCCAGGAAAGGAAATTAAATGATACGGAGACTCAA
131 TGTGGCTTTGAAGGAGGTTCGGTTGACTAAGCCAGGAAAGGAAATTAAATGATACGAAGACTCAA
*
1140647 TGTGCACCTTTATATGAGAGAC
196 TGCGCACCTTTATATGAGAGAC
1140669 ATCGACATATTATATGTTGTGTGATAGACAGTATTTGTTGGAGAATTGTTGTATATGTTATGCAT
1 ATCGACATATTATATGTTGTGTGATAGACAGTATTTGTTGGAGAATTGTTGTATATGTTATGCAT
1140734 GATATTTATGTGGCTTTGCAAAGGTTCGAATGGCCATATACGGGATTGCATATGCATTTTATCTA
66 GATATTTATGTGGCTTTGCAAAGGTTCGAATGGCCATATACGGGATTGCATATGCATTTTATCTA
1140799 TGTGGCTTTGAAGGAGGTTCGGTTGACTAAGCCAGGAAAGGAAATTAAATGATACGAAGACTCAA
131 TGTGGCTTTGAAGGAGGTTCGGTTGACTAAGCCAGGAAAGGAAATTAAATGATACGAAGACTCAA
1140864 TGCGCACCTTTATATGAGAGAC
196 TGCGCACCTTTATATGAGAGAC
1140886 CCTTGTGTGG
Statistics
Matches: 213, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
217 213 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (217 bp):
ATCGACATATTATATGTTGTGTGATAGACAGTATTTGTTGGAGAATTGTTGTATATGTTATGCAT
GATATTTATGTGGCTTTGCAAAGGTTCGAATGGCCATATACGGGATTGCATATGCATTTTATCTA
TGTGGCTTTGAAGGAGGTTCGGTTGACTAAGCCAGGAAAGGAAATTAAATGATACGAAGACTCAA
TGCGCACCTTTATATGAGAGAC
Found at i:1142754 original size:6 final size:6
Alignment explanation
Indices: 1142731--1142774 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
1142721 ATGAAATCTG
* *
1142731 TGATAT TGTTAA TGATAT TGATAT TGATAT TGATAT TGATAT TG
1 TGATAT TGATAT TGATAT TGATAT TGATAT TGATAT TGATAT TG
1142775 TATGTATAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
TGATAT
Found at i:1143689 original size:203 final size:203
Alignment explanation
Indices: 1143333--1143735 Score: 725
Period size: 203 Copynumber: 2.0 Consensus size: 203
1143323 AGAGTTGCAC
* ** *
1143333 ACTGAGTTTTGTAAGCCCACCTAATTATTTTTCTTCTCAGGTAATCAGTTAACTTAGGATTGGAC
1 ACTGAGCTTTGTAAGCCCACCTAATTATTTTTCTTCTCAGGTAATCAGCAAACTTAGGATCGGAC
*
1143398 GGTGTGTGGAAGCTCGAGTTGGATTCTCAGTAATAAAATGGTTTATAACAGTCTTATTGTTTAAT
66 GGTGTGTGGAAGCTCGAGTTGGATTCTCAGTAATAAAATGGTTTATAAAAGTCTTATTGTTTAAT
*
1143463 ATGGACTTTTTAAACTGTTGGTACTTTTGGACTTGTTTTTCGGTTTTTGGTTTATTTTGTTAGAC
131 ATGGACTTTTTAAACTGTTGGTACTTTTGGACTTGTTTTTCGATTTTTGGTTTATTTTGTTAGAC
1143528 TTTTTATT
196 TTTTTATT
1143536 ACTGAGCTTTGTAAGCCCACCTAATTATTTTTCTTCTCAGGTAATCAGCAAACTTAGGATCGGAC
1 ACTGAGCTTTGTAAGCCCACCTAATTATTTTTCTTCTCAGGTAATCAGCAAACTTAGGATCGGAC
* *
1143601 GGTGTGTGGAAGCTCGAGTTGGATTCTCAGTAATAAGATGGTTTTTAAAAGTCTTATTGTTTAAT
66 GGTGTGTGGAAGCTCGAGTTGGATTCTCAGTAATAAAATGGTTTATAAAAGTCTTATTGTTTAAT
*
1143666 ATGGACTTTTTAGACTGTTGGTACTTTTGGACTTGTTTTTCGATTTTTGGTTTATTTTGTTAGAC
131 ATGGACTTTTTAAACTGTTGGTACTTTTGGACTTGTTTTTCGATTTTTGGTTTATTTTGTTAGAC
1143731 TTTTT
196 TTTTT
1143736 GATATACTTA
Statistics
Matches: 191, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
203 191 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (203 bp):
ACTGAGCTTTGTAAGCCCACCTAATTATTTTTCTTCTCAGGTAATCAGCAAACTTAGGATCGGAC
GGTGTGTGGAAGCTCGAGTTGGATTCTCAGTAATAAAATGGTTTATAAAAGTCTTATTGTTTAAT
ATGGACTTTTTAAACTGTTGGTACTTTTGGACTTGTTTTTCGATTTTTGGTTTATTTTGTTAGAC
TTTTTATT
Found at i:1148567 original size:27 final size:29
Alignment explanation
Indices: 1148513--1148573 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 29
1148503 AATAGTATAG
1148513 ATATTATATAGGATATGTAAAAAATATATT
1 ATATTATATA-GATATGTAAAAAATATATT
**
1148543 ATATTATATA-A-ATGTAAAATCTATATT
1 ATATTATATAGATATGTAAAAAATATATT
1148570 ATAT
1 ATAT
1148574 ATTAAGTGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 18 0.62
28 1 0.03
30 10 0.34
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.43
Consensus pattern (29 bp):
ATATTATATAGATATGTAAAAAATATATT
Found at i:1148805 original size:24 final size:25
Alignment explanation
Indices: 1148778--1148830 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1148768 AAACCTAATT
* *
1148778 CTAATC-AATGTTAAATATATTATG
1 CTAATCAAATGCTAAATATATTATA
1148802 CTAA-CAAATGCTAAATATATTATA
1 CTAATCAAATGCTAAATATATTATA
1148826 CTAAT
1 CTAAT
1148831 ATATACTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (25 bp):
CTAATCAAATGCTAAATATATTATA
Found at i:1148839 original size:24 final size:24
Alignment explanation
Indices: 1148789--1148841 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1148779 TAATCAATGT
* *
1148789 TAAATATATTATGCTAACAAATGC
1 TAAATATATTATACTAACAAATAC
* *
1148813 TAAATATATTATACTAATATATAC
1 TAAATATATTATACTAACAAATAC
1148837 TAAAT
1 TAAAT
1148842 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
TAAATATATTATACTAACAAATAC
Found at i:1157540 original size:25 final size:27
Alignment explanation
Indices: 1157512--1157608 Score: 89
Period size: 25 Copynumber: 3.8 Consensus size: 27
1157502 ATTATGTGAT
1157512 TTAAATTG-GTCTTA-GTTTAGACAAA
1 TTAAATTGTGTCTTATGTTTAGACAAA
* * * *
1157537 TTAAATT-AGTCTT-GGTTCAGAC-AC
1 TTAAATTGTGTCTTATGTTTAGACAAA
* *
1157561 TTTAATTGTGTC-TATGTTTTAGAAAAA
1 TTAAATTGTGTCTTATG-TTTAGACAAA
1157588 TTAAATTGTGTCTTATGTTTA
1 TTAAATTGTGTCTTATGTTTA
1157609 CATTTAAGTC
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
24 8 0.14
25 23 0.41
26 5 0.09
27 16 0.29
28 4 0.07
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.45
Consensus pattern (27 bp):
TTAAATTGTGTCTTATGTTTAGACAAA
Found at i:1159077 original size:13 final size:13
Alignment explanation
Indices: 1159053--1159108 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
1159043 ATTTTTAGTC
*
1159053 ACACGGGCAGGGG
1 ACACGAGCAGGGG
*
1159066 ACACGAGTAGGGG
1 ACACGAGCAGGGG
1159079 ACAC-AGGCAGGGG
1 ACACGA-GCAGGGG
*
1159092 ACACGAGCAGGGA
1 ACACGAGCAGGGG
1159105 ACAC
1 ACAC
1159109 AATGTAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
12 1 0.03
13 35 0.95
14 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.43, T:0.02
Consensus pattern (13 bp):
ACACGAGCAGGGG
Found at i:1159089 original size:26 final size:26
Alignment explanation
Indices: 1159053--1159109 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
1159043 ATTTTTAGTC
* * *
1159053 ACACGGGCAGGGGACACGAGTAGGGG
1 ACACAGGCAGGGGACACGAGCAGGGA
1159079 ACACAGGCAGGGGACACGAGCAGGGA
1 ACACAGGCAGGGGACACGAGCAGGGA
1159105 ACACA
1 ACACA
1159110 ATGTAAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.23, G:0.42, T:0.02
Consensus pattern (26 bp):
ACACAGGCAGGGGACACGAGCAGGGA
Found at i:1164605 original size:2 final size:2
Alignment explanation
Indices: 1164598--1164630 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1164588 TGATATTCTA
1164598 AT AT AT AT 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 AT AT AT AT A
1164631 AGTTAATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1165350 original size:7 final size:8
Alignment explanation
Indices: 1165334--1165377 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
1165324 ATTATGTTAA
1165334 AAAAATTT
1 AAAAATTT
*
1165342 AAAAATTAA
1 AAAAATT-T
1165351 AAAAATTT
1 AAAAATTT
1165359 -AAAATTT
1 AAAAATTT
*
1165366 AAAATTTT
1 AAAAATTT
1165374 AAAA
1 AAAA
1165378 CTATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 7 0.23
8 17 0.55
9 7 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAAATTT
Found at i:1165352 original size:17 final size:17
Alignment explanation
Indices: 1165330--1165369 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1165320 AAATATTATG
1165330 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
*
1165347 TTAAAAAAATTTAAAAT
1 TTAAAAAAATTTAAAAA
1165364 TTAAAA
1 TTAAAA
1165370 TTTTAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:1170045 original size:22 final size:22
Alignment explanation
Indices: 1170020--1170074 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1170010 CGTGTAACGC
1170020 TACCAGTGCATACATGTAAGGT
1 TACCAGTGCATACATGTAAGGT
1170042 TACCAGTGCATACATGTAAGGT
1 TACCAGTGCATACATGTAAGGT
1170064 TACCAGTGCAT
1 TACCAGTGCAT
1170075 GCTAAACCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (22 bp):
TACCAGTGCATACATGTAAGGT
Found at i:1188459 original size:51 final size:50
Alignment explanation
Indices: 1188320--1188503 Score: 150
Period size: 51 Copynumber: 3.6 Consensus size: 50
1188310 AAAGTGATGG
* * *
1188320 TCACGTGTGTAGTACTATGTGCAGGCTACTA-CATGTACCGGAAT-G--ATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATC--GTATC-GAATAGTAAT-GA
* *
1188370 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTATC-AGATAGT-TTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTAT-CGTATCGA-ATAGTAAT-GA
* * *
1188421 TCACGTGTGTAGTACTATGTGCAGAATGCTACT-T-GTATCGAATGGTAATGG
1 TCACATGTGTAGTACTATGTGCAG---GCTACTATCGTATCGAATAGTAATGA
1188472 TCACATGTGTAGTACTATGTGCAGGCTACTAT
1 TCACATGTGTAGTACTATGTGCAGGCTACTAT
1188504 GTGAACCAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
48 7 0.06
49 3 0.03
50 34 0.31
51 57 0.51
52 3 0.03
53 1 0.01
54 6 0.05
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATCGTATCGAATAGTAATGA
Found at i:1188503 original size:102 final size:101
Alignment explanation
Indices: 1188320--1188504 Score: 282
Period size: 101 Copynumber: 1.8 Consensus size: 101
1188310 AAAGTGATGG
** *
1188320 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGAATACTACATGTACCGGAATGATAGGTCACATGTGTAGTAC
1188385 TATGTGCAGGCTACTATGCGTATCAGATAGTTTCGA
66 TATGTGCAGGCTACTATGCGTATCAGATAGTTTCGA
* * * *
1188421 TCACGTGTGTAGTACTATGTGCAGAATGCTACTTGTATC-GAATGGTAATGGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGAATACTACATGTACCGGAATGAT-A-GGTCACATGTGTAGT
1188485 ACTATGTGCAGGCTACTATG
64 ACTATGTGCAGGCTACTATG
1188505 TGAACCAAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 6 0.08
101 35 0.47
102 34 0.45
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGAATACTACATGTACCGGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTATCAGATAGTTTCGA
Found at i:1188615 original size:45 final size:45
Alignment explanation
Indices: 1188513--1188601 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
1188503 TGTGAACCAA
* * *
1188513 ACATCATTGATTAGTAAGGTGGTTGTTATGTGCTGATTCCACCGG
1 ACATCATTTATTAATAAGGTGGTTGTTATGTGCTGAATCCACCGG
1188558 ACATCATTTATTAATAAGGTGGTTGTTATGTGCTGAATCCACCG
1 ACATCATTTATTAATAAGGTGGTTGTTATGTGCTGAATCCACCG
1188602 AGTATCGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.36
Consensus pattern (45 bp):
ACATCATTTATTAATAAGGTGGTTGTTATGTGCTGAATCCACCGG
Found at i:1196115 original size:22 final size:20
Alignment explanation
Indices: 1196075--1196122 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1196065 AGGGGCCTCG
1196075 ATTTT-TTTTATTTTATTAC
1 ATTTTATTTTATTTTATTAC
1196094 TAGTTTTATTTTATTGTT-TTAC
1 -A-TTTTATTTTATT-TTATTAC
1196116 ATTTTAT
1 ATTTTAT
1196123 AATTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.28
21 5 0.20
22 11 0.44
23 2 0.08
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (20 bp):
ATTTTATTTTATTTTATTAC
Found at i:1196955 original size:16 final size:16
Alignment explanation
Indices: 1196934--1196964 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1196924 GTCAAATTAA
*
1196934 AAAATTATTAAAATTC
1 AAAATTAATAAAATTC
1196950 AAAATTAATAAAATT
1 AAAATTAATAAAATT
1196965 TGATTCAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTAATAAAATTC
Found at i:1200270 original size:13 final size:13
Alignment explanation
Indices: 1200248--1200309 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
1200238 TTCTTCATTA
1200248 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
1200261 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
* *
1200274 CTATGGAAAAGTG
1 CTTTTGAAAAGTG
* *
1200287 CTTTTGAGAAGTA
1 CTTTTGAAAAGTG
1200300 CTTTTGAAAA
1 CTTTTGAAAA
1200310 TTTTGAGTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.35
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Done.