Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 163 of 208
Found at i:49762247 original size:17 final size:18
Alignment explanation
Indices: 49762217--49762250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49762207 GCCAGTCCGA
*
49762217 TTAAAAAACTATTAAAAT
1 TTAAAAAACAATTAAAAT
49762235 TTAAAAAA-AATTAAAA
1 TTAAAAAACAATTAAAA
49762251 AATACCGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAAAACAATTAAAAT
Found at i:49769848 original size:24 final size:25
Alignment explanation
Indices: 49769828--49769874 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
49769818 TAGATTATAT
49769828 TTTTTATT-ATAATTTTTATTAATA
1 TTTTTATTAATAATTTTTATTAATA
*
49769852 TTTTTATTAATATTTTTTATTAA
1 TTTTTATTAATAATTTTTATTAA
49769875 AAATTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTTATTAATAATTTTTATTAATA
Found at i:49769874 original size:13 final size:13
Alignment explanation
Indices: 49769824--49769874 Score: 79
Period size: 12 Copynumber: 4.1 Consensus size: 13
49769814 TATCTAGATT
49769824 ATATTTTTTATT-
1 ATATTTTTTATTA
*
49769836 ATAATTTTTATTA
1 ATATTTTTTATTA
49769849 ATA-TTTTTATTA
1 ATATTTTTTATTA
49769861 ATATTTTTTATTA
1 ATATTTTTTATTA
49769874 A
1 A
49769875 AAATTAATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
12 23 0.64
13 13 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATATTTTTTATTA
Found at i:49770054 original size:24 final size:23
Alignment explanation
Indices: 49770010--49770054 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
49770000 TTTTATTTCA
* *
49770010 TTGTTATATTTTAACTTAATATT
1 TTGTTATATTTTAAATAAATATT
*
49770033 TTGTATATTTTTTAAATAAATA
1 TTGT-TATATTTTAAATAAATA
49770055 GGCAGAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
TTGTTATATTTTAAATAAATATT
Found at i:49779109 original size:27 final size:27
Alignment explanation
Indices: 49779079--49779163 Score: 127
Period size: 27 Copynumber: 3.1 Consensus size: 27
49779069 TATAACAGTT
* *
49779079 ATTTTATCCTATGAGGGTATTTCGGTC
1 ATTTTACCCTATGAGGGTAATTCGGTC
49779106 ATTTTACCCTATTGA-GGTAATTCGGTC
1 ATTTTACCCTA-TGAGGGTAATTCGGTC
*
49779133 ATTTTACCCTATGGGGGTAATTCGGTC
1 ATTTTACCCTATGAGGGTAATTCGGTC
49779160 ATTT
1 ATTT
49779164 ATTGACCTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 2 0.04
27 48 0.91
28 3 0.06
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTATGAGGGTAATTCGGTC
Found at i:49785073 original size:14 final size:14
Alignment explanation
Indices: 49785050--49785084 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
49785040 ATCGAATTAT
*
49785050 AAAGTATTGGGTTA
1 AAAGTCTTGGGTTA
49785064 AAAGTCTTGGGTTA
1 AAAGTCTTGGGTTA
49785078 AAAGTCT
1 AAAGTCT
49785085 AGGAAGTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (14 bp):
AAAGTCTTGGGTTA
Found at i:49792546 original size:9 final size:9
Alignment explanation
Indices: 49792517--49792553 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
49792507 TGAGTTTTAG
49792517 AATTCGAAT
1 AATTCGAAT
*
49792526 AACTCGAAT
1 AATTCGAAT
49792535 AATTCGAAT
1 AATTCGAAT
*
49792544 AATTTGAAT
1 AATTCGAAT
49792553 A
1 A
49792554 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:49798282 original size:28 final size:28
Alignment explanation
Indices: 49798242--49798297 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
49798232 ATTTCCATTT
49798242 GATGAAATTTAGTACGTAGTTGTAGTAA
1 GATGAAATTTAGTACGTAGTTGTAGTAA
49798270 GATGAAATTTAGTACGTAGTTGTAGTAA
1 GATGAAATTTAGTACGTAGTTGTAGTAA
49798298 TAATACTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (28 bp):
GATGAAATTTAGTACGTAGTTGTAGTAA
Found at i:49798801 original size:51 final size:52
Alignment explanation
Indices: 49798718--49798857 Score: 255
Period size: 51 Copynumber: 2.7 Consensus size: 52
49798708 TTGACGTTGA
49798718 TTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTCGTTTAGGGTGCAGGCT
1 TTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTCGTTTAGGGTGCAGGCT
* *
49798770 TTTTTAGGGTTTAGGGGTGCCG-AAAAAATTATTTCGTTTAGGGTGCAGGTT
1 TTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTCGTTTAGGGTGCAGGCT
49798821 TTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTCG
1 TTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTCG
49798858 AGTTGACGTT
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
51 49 0.58
52 35 0.42
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.38
Consensus pattern (52 bp):
TTTTTAGGGTTTAGGGGTCCCGAAAAAAATTATTTCGTTTAGGGTGCAGGCT
Found at i:49799088 original size:125 final size:124
Alignment explanation
Indices: 49798860--49799265 Score: 638
Period size: 125 Copynumber: 3.2 Consensus size: 124
49798850 TTATTTCGAG
**
49798860 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCA-GAGAAGAAATTG
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTAT-ATGAGAAGAAATTG
** * * *
49798923 TGAAATCGTACCCTCGTGGACGCCATTTCAGC-ACAGTTGGTCATGTAAGAAATAATTCTTT
64 TGAAATCGCGCCCTCGTGGACGCGATTTC-GCTACAGTTGGTCATGTAGGAAATAATTTTTT
49798984 TTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
49799049 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTT
* *
49799109 TTGACGTTTCTGAGCAAATAGTGTAAAATCGCTGATACCCAGGATGCTATATGAGAAGAAATCGT
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATA-CCAGGATGCTATATGAGAAGAAATTGT
*
49799174 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAGGAAATAAATTTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAAT-AATTTTTT
*
49799235 TTGACGTTTCTGAGCAAATAGTTTAAAATCG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCG
49799266 TGCCCTCGTG
Statistics
Matches: 265, Mismatches: 11, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
124 39 0.15
125 187 0.71
126 39 0.15
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTT
Found at i:49800458 original size:23 final size:23
Alignment explanation
Indices: 49800431--49800492 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
49800421 TAAGATTATC
49800431 AAATTAGGTTAGGGTTTTAAATT
1 AAATTAGGTTAGGGTTTTAAATT
49800454 AAATTAGGTTAGGGTTTTAAATT
1 AAATTAGGTTAGGGTTTTAAATT
49800477 AAATTAGGTTAGGGTT
1 AAATTAGGTTAGGGTT
49800493 AGGGTTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (23 bp):
AAATTAGGTTAGGGTTTTAAATT
Found at i:49800493 original size:29 final size:29
Alignment explanation
Indices: 49800434--49800797 Score: 410
Period size: 29 Copynumber: 12.5 Consensus size: 29
49800424 GATTATCAAA
49800434 TTAGGTTAGGGTTTTA-AATT-AA--A--
1 TTAGGTTAGGGTTTTATAATTAAATTAGG
49800457 TTAGGTTAGGGTTTTA-AATTAAATTAGG
1 TTAGGTTAGGGTTTTATAATTAAATTAGG
49800485 TTAGGGTTAGGG-TTTATAATTAAATTAGG
1 TTA-GGTTAGGGTTTTATAATTAAATTAGG
**
49800514 TTAGAGTTAGGGTTTTATAATTAAATTAAA
1 TTAG-GTTAGGGTTTTATAATTAAATTAGG
*
49800544 TTAGGTTAGGGTTTTATAATTGAATTAGG
1 TTAGGTTAGGGTTTTATAATTAAATTAGG
* **
49800573 TTAGGGATAGGG-TTTATAATTAAATTAAA
1 TTA-GGTTAGGGTTTTATAATTAAATTAGG
*
49800602 TTAGGTTTGGGTTTTTAATTAAATTAAATTAGG
1 TTAGGTTAGGG-TTTT-A-T-AATTAAATTAGG
49800635 TTAGGGTTTAGGGTTTT-TAATTAAATTAGG
1 TTA-GG-TTAGGGTTTTATAATTAAATTAGG
*
49800665 TTAGGTTAGGGTTTT-TAATTAAATTATG
1 TTAGGTTAGGGTTTTATAATTAAATTAGG
49800693 TTAGGTTAGGGTTTATAATTAAATTAAATTAGG
1 TTAGGTTAGGGTTT-T-A-T-AATTAAATTAGG
*
49800726 TTAGGTTAGGGTTTTATAATTGAATTAGG
1 TTAGGTTAGGGTTTTATAATTAAATTAGG
**
49800755 TTAGGGTTAGGG-TTTATAATTAAATTAAA
1 TTA-GGTTAGGGTTTTATAATTAAATTAGG
*
49800784 TTAGGTTTGGGTTT
1 TTAGGTTAGGGTTT
49800798 ACTGCCCGGA
Statistics
Matches: 296, Mismatches: 21, Indels: 42
0.82 0.06 0.12
Matches are distributed among these distances:
23 20 0.07
24 2 0.01
26 1 0.00
28 57 0.19
29 108 0.36
30 53 0.18
31 3 0.01
32 3 0.01
33 38 0.13
34 6 0.02
35 5 0.02
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.45
Consensus pattern (29 bp):
TTAGGTTAGGGTTTTATAATTAAATTAGG
Found at i:49800656 original size:63 final size:61
Alignment explanation
Indices: 49800447--49800797 Score: 363
Period size: 63 Copynumber: 5.9 Consensus size: 61
49800437 GGTTAGGGTT
** * **
49800447 TTAAATTAAATTA-GGTTAGGGTTTTAAATTAAATTAGGTTAGGGTTAGGG--TTTA-T-AA
1 TTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTATTAAA
*
49800504 TTAAATTAGGTTAGAGTTAGGGTTTTATAATTAAATTAAATTAGGTTAGGG-TTTTA-T-AA
1 TTAAATTAGGTTAGGGTTAGGGTTTT-TAATTAAATTAAATTAGGTTAGGGTTTTTATTAAA
* * * *
49800563 TTGAATTAGGTTAGGGATAGGGTTTATAATTAAATTAAATTAGGTTTGGGTTTTTAATTAAA
1 TTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTT-ATTAAA
**
49800625 TTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGG--TTT-TT-AA
1 TTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTATTAAA
* * *
49800683 TTAAATTATGTTA-GGTTAGGGTTTATAATTAAATTAAATTAGGTTA-GGTTAGGGTT-TTATAA
1 TTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTT---TTTATTA-AA
* * *
49800745 TTGAATTAGGTTAGGGTTAGGGTTTATAATTAAATTAAATTAGGTTTGGGTTT
1 TTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTT
49800798 ACTGCCCGGA
Statistics
Matches: 251, Mismatches: 26, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
55 2 0.01
56 28 0.11
57 13 0.05
58 56 0.22
59 48 0.19
60 5 0.02
61 4 0.02
62 30 0.12
63 61 0.24
64 4 0.02
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.44
Consensus pattern (61 bp):
TTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTATTAAA
Found at i:49800695 original size:23 final size:25
Alignment explanation
Indices: 49800431--49800718 Score: 125
Period size: 28 Copynumber: 10.2 Consensus size: 25
49800421 TAAGATTATC
*
49800431 AAATTAG--GTTAGGGTTTTAAATT
1 AAATTAGTAGTTAGGGTTTTTAATT
*
49800454 AAATTAG--GTTAGGGTTTTAAATT
1 AAATTAGTAGTTAGGGTTTTTAATT
*
49800477 AAATTAGGTTAGGGTTAGGGTTTATAATT
1 AAATTA-G-TA--GTTAGGGTTTTTAATT
49800506 AAATTAGGTTAGAGTTAGGGTTTTATAATT
1 AAATTA-G-T--AGTTAGGGTTTT-TAATT
*
49800536 AAATTAAATTAGGTTAGGGTTTTATAATT
1 AAATT--AGTA-GTTAGGGTTTT-TAATT
* * *
49800565 GAATTAGGTTAGGGATAGGGTTTATAATT
1 AAATTA-G-TA--GTTAGGGTTTTTAATT
* *
49800594 AAATTAAATTAGGTTTGGGTTTTTAATT
1 AAATT--AGTA-GTTAGGGTTTTTAATT
*
49800622 AAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATT--AGTA-GTTA-------GGGTTTTTAATT
49800657 AAATTAGGTTAGGTTAGGGTTTTTAATT
1 AAATTA-G-TA-GTTAGGGTTTTTAATT
*
49800685 AAATTATGTTAGGTTAGGGTTTATAATT
1 AAATTA-G-TA-GTTAGGGTTTTTAATT
49800713 AAATTA
1 AAATTA
49800719 AATTAGGTTA
Statistics
Matches: 222, Mismatches: 17, Indels: 47
0.78 0.06 0.16
Matches are distributed among these distances:
23 29 0.13
24 1 0.00
27 1 0.00
28 74 0.33
29 68 0.31
30 21 0.09
31 2 0.01
32 1 0.00
33 1 0.00
35 24 0.11
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (25 bp):
AAATTAGTAGTTAGGGTTTTTAATT
Found at i:49800885 original size:7 final size:7
Alignment explanation
Indices: 49800875--49800899 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49800865 ATATATACAT
49800875 AATACTA
1 AATACTA
49800882 AATACTA
1 AATACTA
49800889 AATACTA
1 AATACTA
49800896 AATA
1 AATA
49800900 TCAATCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:49802052 original size:29 final size:29
Alignment explanation
Indices: 49801988--49802046 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
49801978 CAGAAAATAC
49801988 TAAAAA-TTTTAAAATTATTTTAAAAAAA
1 TAAAAATTTTTAAAATTATTTTAAAAAAA
*
49802016 TAAAAATTTTTAAAATTTTCTTTAAAAAAA
1 TAAAAATTTTTAAAATTAT-TTTAAAAAAA
49802046 T
1 T
49802047 GAAATTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 6 0.21
29 11 0.39
30 11 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAAATTTTTAAAATTATTTTAAAAAAA
Found at i:49802155 original size:52 final size:51
Alignment explanation
Indices: 49802077--49802182 Score: 140
Period size: 52 Copynumber: 2.1 Consensus size: 51
49802067 ATTTAATATG
* * * *
49802077 GAGTTTAGAGATTTTTTGAAGGAAATTGTGAGGATTTTGGAAGGAATTCGA
1 GAGTTTAGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
* * *
49802128 GAGTTTAAGAGAATTTTGGAAGGAAATTGAGAGAATTTTTGAAGGACTTTGA
1 GAGTTT-AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
49802180 GAG
1 GAG
49802183 AATTTTTGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 6 0.13
52 41 0.87
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (51 bp):
GAGTTTAGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTCGA
Found at i:49802162 original size:22 final size:22
Alignment explanation
Indices: 49802135--49802203 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
49802125 CGAGAGTTTA
*
49802135 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
**
49802157 AGAGAATTTTTGAAGGACTTTG
1 AGAGAATTTTTGAAGGAAATTG
*
49802179 AGAGAATTTTTGAATGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
49802201 AGA
1 AGA
49802204 TAGGATTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.39, C:0.01, G:0.28, T:0.32
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:49802461 original size:29 final size:27
Alignment explanation
Indices: 49802420--49802473 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
49802410 CGGGGAAAAT
49802420 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCGGTAAAT--TTAAAAAACC
* *
49802449 GGCCTATTTCGGTAAATTTAAAAAA
1 GGCCCATTCCGGTAAATTTAAAAAA
49802474 AAGGGCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
29 15 0.65
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (27 bp):
GGCCCATTCCGGTAAATTTAAAAAACC
Found at i:49806431 original size:25 final size:25
Alignment explanation
Indices: 49806393--49806509 Score: 71
Period size: 25 Copynumber: 4.7 Consensus size: 25
49806383 TCATATACAT
*
49806393 GTATGCTCATACGAGTTATGAATCG
1 GTATGCTCATACGAGCTATGAATCG
* *
49806418 GTATGCTC-TCACGAGCTGTGAATCA
1 GTATGCTCAT-ACGAGCTATGAATCG
* *
49806443 GT-CGACTCATATGAGCTGA-GAATCG
1 GTATG-CTCATACGAGCT-ATGAATCG
* * **
49806468 GTAAGCTC-TCATGAGCTACAAATCG
1 GTATGCTCAT-ACGAGCTATGAATCG
* *
49806493 ATAAGCTCATACGAGCT
1 GTATGCTCATACGAGCT
49806510 GTGGTATGTC
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
24 4 0.05
25 66 0.90
26 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCG
Found at i:49808461 original size:36 final size:36
Alignment explanation
Indices: 49808414--49808519 Score: 194
Period size: 36 Copynumber: 2.9 Consensus size: 36
49808404 TGCTCGACTA
49808414 AAAACTATTATTATACGCAAATTCGACTAATGGTCG
1 AAAACTATTATTATACGCAAATTCGACTAATGGTCG
49808450 AAAACTATTATTATACGCAAATTCGACTAATGGTCG
1 AAAACTATTATTATACGCAAATTCGACTAATGGTCG
* *
49808486 AAAACTATTATTATATGCAAATTCGACTAGTGGT
1 AAAACTATTATTATACGCAAATTCGACTAATGGT
49808520 AAGTATTTCT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (36 bp):
AAAACTATTATTATACGCAAATTCGACTAATGGTCG
Found at i:49814588 original size:44 final size:44
Alignment explanation
Indices: 49814524--49814635 Score: 161
Period size: 44 Copynumber: 2.5 Consensus size: 44
49814514 TTAATCCGCC
* *
49814524 CCACTGCAACTTCAGGGAGATAGGATTAGTAACTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAGTAACTTCAACCTGCT
* * * *
49814568 CCACTGCAATTTCAGAGAGATAAGATTGGTATCTTCAACCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTAGTAACTTCAACCTGCT
*
49814612 CCACTCCAACTTCAGGGAGATAAG
1 CCACTGCAACTTCAGGGAGATAAG
49814636 GTTTGTTATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTAGTAACTTCAACCTGCT
Found at i:49814720 original size:44 final size:44
Alignment explanation
Indices: 49814562--49815158 Score: 330
Period size: 44 Copynumber: 13.8 Consensus size: 44
49814552 GTAACTTCAA
* *
49814562 TCTGCTCCACTGCAATTTCAGAGAGATAAGAT-TGGTATCTTCAA-
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGG-AT-TTTAAT
* * * * * * * *
49814606 CCTGCTCCACTCCAACTTCAGGGAGATAAGGTTTGTTATGGTGTGA-
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG-GAT--TTTAAT
* * *
49814652 TCTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGATTTTAAT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG-GATTTTAAT
* * **
49814697 TC-GCTCCACTGCAACTTCCGAGAGATAGGAT-TGG-TTTCTTTT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGGATTT-TAAT
* * * ***
49814739 GTCTACTCTACTGCAACTTCAGGGAGATAAGAT-TGGA-TGCGA-
1 -TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGGATTTTAAT
* * *
49814781 TCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTAA-
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG-GATTTTAAT
* * * * **
49814825 TCCGCTCTACTGCAACTTCAGGGAGATAGGAT-T-GATTTCTTTT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGGATTT-TAAT
* ***
49814868 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGGA-TGCGA-
1 -TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGGATTTTAAT
* *
49814910 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA-
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG-GATTTTAAT
* * * * **
49814954 TATGCTCCACTGCAACTTCCGAAAGATAGGAT-TGG-TTTCTTTT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGGATTT-TAAT
* ***
49814997 GTCTGCTCCACTGTAACTTCAGAGAGATAAGA-CTGGA-TACGA-
1 -TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGGATTTTAAT
* *
49815039 TCTTCTCTACTGCAACTTCAGAGAGATAAGATCTATGG-TTTTAA-
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATC--TGGATTTTAAT
* * * ***
49815083 TCCGCTCCACTGCAACTTCA-AGGAGATAGGA-GTGGA-TGCGA-
1 TCTGCTCCACTGCAACTTCAGA-GAGATAAGATCTGGATTTTAAT
* *
49815124 TCTGCTCTACTGCAACCTCAGAGAGATAAGATCTG
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTG
49815159 TGGTGTATGG
Statistics
Matches: 423, Mismatches: 98, Indels: 66
0.72 0.17 0.11
Matches are distributed among these distances:
41 126 0.30
42 15 0.04
43 10 0.02
44 231 0.55
45 8 0.02
46 33 0.08
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGGATTTTAAT
Found at i:49814831 original size:129 final size:129
Alignment explanation
Indices: 49814560--49815113 Score: 741
Period size: 129 Copynumber: 4.3 Consensus size: 129
49814550 TAGTAACTTC
* * * * **** *
49814560 AATCTGCTCCACTGCAATTTCAGAGAGATAAGATTGGTATCTTCAACCTGCTCCACTCCAACTTC
1 AATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAACTTC
** * * * * *
49814625 AGGGAGATAAGGTTTGTTATGGTGTGATCTGCTCTACTACAACTTTAGAGAGATAAGATCTGTGA
66 AGGGAGATAA-GACTG----GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
49814690 TTTT
126 TTTT
* * * *
49814694 AATTCGCTCCACTGCAACTTCCGAGAGATAGGATTGGTTTCTTTTGTCTACTCTACTGCAACTTC
1 AATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAACTTC
* *
49814759 AGGGAGATAAGATTGGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTT
66 AGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
* * *
49814823 AATCCGCTCTACTGCAACTTCAGGGAGATAGGATTGATTTCTTTTGTCTGCTCCACTGCAACTTC
1 AATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAACTTC
49814888 AGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
66 AGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
** * * *
49814952 AATATGCTCCACTGCAACTTCCGAAAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGTAACTTC
1 AATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAACTTC
* * * *
49815017 AGAGAGATAAGACTGGATACGATCTTCTCTACTGCAACTTCAGAGAGATAAGATCTATGGTTTT
66 AGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
49815081 AATCCGCTCCACTGCAACTTCA-AGGAGATAGGA
1 AATCCGCTCCACTGCAACTTCAGA-GAGATAGGA
49815114 GTGGATGCGA
Statistics
Matches: 374, Mismatches: 45, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
128 1 0.00
129 307 0.82
133 4 0.01
134 62 0.17
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (129 bp):
AATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTTTGTCTGCTCCACTGCAACTTC
AGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
Found at i:49814838 original size:85 final size:85
Alignment explanation
Indices: 49814744--49815162 Score: 375
Period size: 85 Copynumber: 4.9 Consensus size: 85
49814734 CTTTTGTCTA
*
49814744 CTCTACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGTAACTTCAGAGAGATA
1 CTCTACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATA
49814809 AGATCTGTGGTTTTAATCCG
66 AGATCTGTGGTTTTAATCCG
* * * *
49814829 CTCTACTGCAACTTCAGGGAGATAGGATT-GATTTCTTTTG-TCTGCTCCACTGCAACTTCAGGG
1 CTCTACTGCAACTTCAGGGAGATAAGATTGGA-TGC----GATCTGCTCTACTGCAACTTCAGAG
* *** *
49814892 AGATAAGA-C--TGGATGCGATCTG
61 AGATAAGATCTGTGGTTTTAATCCG
* * *** * * * *
49814914 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATATGCTCCACTGCAACTTCCGAAAG
1 CTCTACTGCAACTTCAGGGAGATAAGA--T-TGGATGCGATCTGCTCTACTGCAACTTCAGAGAG
* * ** *
49814979 ATAGGAT-TG-GTTTCTTTTGTCTG
63 ATAAGATCTGTG-GT-TTTAATCCG
* * * * * *
49815002 CTCCACTGTAACTTCAGAGAGATAAGACTGGATACGATCTTCTCTACTGCAACTTCAGAGAGATA
1 CTCTACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATA
*
49815067 AGATCTATGGTTTTAATCCG
66 AGATCTGTGGTTTTAATCCG
* * * * *
49815087 CTCCACTGCAACTTCAAGGAGATAGGAGTGGATGCGATCTGCTCTACTGCAACCTCAGAGAGATA
1 CTCTACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATA
49815152 AGATCTGTGGT
66 AGATCTGTGGT
49815163 GTATGGCTTC
Statistics
Matches: 264, Mismatches: 53, Indels: 34
0.75 0.15 0.10
Matches are distributed among these distances:
84 2 0.01
85 193 0.73
86 3 0.01
87 3 0.01
88 61 0.23
89 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.30
Consensus pattern (85 bp):
CTCTACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATA
AGATCTGTGGTTTTAATCCG
Found at i:49815439 original size:101 final size:100
Alignment explanation
Indices: 49815166--49815581 Score: 584
Period size: 101 Copynumber: 4.2 Consensus size: 100
49815156 CTGTGGTGTA
**
49815166 TGGCTTCAATCTTTTAAAATGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTAT
1 TGGCTTCAATCTTTTAAAATGCAATGTC-GGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
* * * ** *
49815231 TCCACTGCGAAC-TCAGGGAGGTAAGATTCATAGTCG
65 TCCACTGC-ACCGCCAGGGAAGTAAGATTCACCGTTG
* * *
49815267 TGGCTTCAATCTTTTAAATTGCAATATCGGGGAAGCAAGATTCACCGGCGTAGCTTCAATCTGCT
1 TGGCTTCAATCTTTTAAAATGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCT
*
49815332 CCACTGCACCGCTAGGGAAGTAAGATTCACCGTTG
66 CCACTGCACCGCCAGGGAAGTAAGATTCACCGTTG
49815367 TGGCTTCAATCTTTTAAAATGCAATGTCGAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
1 TGGCTTCAATCTTTTAAAATGCAATGTCG-GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
* *
49815432 TCTACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
65 TCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTG
* * * * * * *
49815468 CGGCTTCAATCTTTTTAATTGCGATGTCGGGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGTT
1 TGGCTTCAATCTTTTAAAATGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCT
*
49815532 CCACTGCACCGCCAGGGAAGTAAGATTCACCATTG
66 CCACTGCACCGCCAGGGAAGTAAGATTCACCGTTG
*
49815567 CGGCTTCAATCTTTT
1 TGGCTTCAATCTTTT
49815582 TAACCGTAAT
Statistics
Matches: 285, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
99 76 0.27
100 91 0.32
101 118 0.41
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (100 bp):
TGGCTTCAATCTTTTAAAATGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCT
CCACTGCACCGCCAGGGAAGTAAGATTCACCGTTG
Found at i:49815576 original size:50 final size:50
Alignment explanation
Indices: 49815196--49815578 Score: 259
Period size: 50 Copynumber: 7.7 Consensus size: 50
49815186 GCAATGTCAG
* * * * * * *
49815196 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTATTCCACTGCGAAC-TCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCAACTGC-ACCGCCA
* ** * * * * **** *
49815246 GGGAGGTAAGATTCATAGTCGTGGCTTCAATCTTTTAAATTGCAATATCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCAACTGCACCGCCA
* ** * * * *
49815296 GGGAAGCAAGATTCACCGGCGTAGCTTCAATCTGCTCCACTGCACCGCTA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCAACTGCACCGCCA
* * * ** *
49815346 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAAATGCAATGTCGA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCAACTGCACCG-CCA
* * * * *
49815397 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCTACTGCACCGCCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCAACTGCACCGCCA
* * * * * * * *
49815447 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCGA-TGTCG
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCAACTGC-ACCGCCA
* * * *
49815497 GGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCA
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCAACTGCACCGCCA
* *
49815546 GGGAAGTAAGATTCACCATTGCGGCTTCAATCT
1 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
49815579 TTTTAACCGT
Statistics
Matches: 249, Mismatches: 79, Indels: 10
0.74 0.23 0.03
Matches are distributed among these distances:
48 1 0.00
49 39 0.16
50 169 0.68
51 40 0.16
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (50 bp):
GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTGTTCAACTGCACCGCCA
Found at i:49818036 original size:42 final size:42
Alignment explanation
Indices: 49817977--49818080 Score: 190
Period size: 42 Copynumber: 2.5 Consensus size: 42
49817967 ACCCCTCGGG
49817977 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGAT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGAT
* *
49818019 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGAT
49818061 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
49818081 ACCAATGAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGAT
Found at i:49818121 original size:26 final size:27
Alignment explanation
Indices: 49818092--49818143 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
49818082 CCAATGAATC
49818092 GGGGAATCAACACTTAGC-AACCCCTT
1 GGGGAATCAACACTTAGCAAACCCCTT
*
49818118 GGGGAATCAGCACTTAGCAAACCCCT
1 GGGGAATCAACACTTAGCAAACCCCT
49818144 CTATATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (27 bp):
GGGGAATCAACACTTAGCAAACCCCTT
Found at i:49818141 original size:144 final size:144
Alignment explanation
Indices: 49817875--49818143 Score: 468
Period size: 144 Copynumber: 1.9 Consensus size: 144
49817865 AATCAGTCAG
* *
49817875 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATCAGTACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACC
* * *
49817940 AGTGATTCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTTCAC
66 AATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTTCAC
49818005 ATTTAAGATACGAT
131 ATTTAAGATACGAT
49818019 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACC
* *
49818084 AATGAATCGGGGAATCAACACTTAGCAACCCCT-TGGGGAATCAGCACTTAGCAAACCCCT
66 AATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCT
49818144 CTATATTCAA
Statistics
Matches: 118, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
143 25 0.21
144 93 0.79
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.21
Consensus pattern (144 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACC
AATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTTCAC
ATTTAAGATACGAT
Found at i:49818441 original size:22 final size:22
Alignment explanation
Indices: 49818413--49818565 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
49818403 TTTATTGTTC
*
49818413 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
49818435 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
49818457 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
49818479 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
49818501 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
49818523 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
49818545 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
49818566 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:49820066 original size:11 final size:11
Alignment explanation
Indices: 49820042--49820091 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
49820032 CCGGTAGAGG
49820042 TTTTTTTTCTT
1 TTTTTTTTCTT
49820053 TTTTATTTTCTT
1 TTTT-TTTTCTT
49820065 TTTTGTTTT-TT
1 TTTT-TTTTCTT
*
49820076 TGTTTTTTGCTT
1 T-TTTTTTTCTT
49820088 TTTT
1 TTTT
49820092 GCTTTTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 13 0.38
12 21 0.62
ACGTcount: A:0.02, C:0.06, G:0.06, T:0.86
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:49820089 original size:16 final size:16
Alignment explanation
Indices: 49820058--49820102 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
49820048 TTCTTTTTTA
*
49820058 TTTTCTTTTTTG-TTT
1 TTTTGTTTTTTGCTTT
49820073 TTTTGTTTTTTGC-TT
1 TTTTGTTTTTTGCTTT
49820088 TTTTGCTTTTTTGCT
1 TTTTG-TTTTTTGCT
49820103 CTCTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (16 bp):
TTTTGTTTTTTGCTTT
Found at i:49820100 original size:8 final size:8
Alignment explanation
Indices: 49820058--49820102 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
49820048 TTCTTTTTTA
49820058 TTTT-CTT
1 TTTTGCTT
*
49820065 TTTTGTTT
1 TTTTGCTT
49820073 TTTTG-TT
1 TTTTGCTT
49820080 TTTTGCTT
1 TTTTGCTT
49820088 TTTTGCTT
1 TTTTGCTT
49820096 TTTTGCT
1 TTTTGCT
49820103 CTCTTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
7 11 0.31
8 24 0.69
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (8 bp):
TTTTGCTT
Found at i:49829619 original size:25 final size:25
Alignment explanation
Indices: 49829591--49829697 Score: 112
Period size: 25 Copynumber: 4.3 Consensus size: 25
49829581 GTATGCTCAA
*
49829591 ACGAGCTATGAATCGGTATGCTCTC
1 ACGAGCTATGAATCGGTAAGCTCTC
*
49829616 ACGAGCTGTGAATCGGTAAGCTCAT-
1 ACGAGCTATGAATCGGTAAGCTC-TC
*
49829641 ACGAGCTGA-GAATCGATAAGCTCTC
1 ACGAGCT-ATGAATCGGTAAGCTCTC
***
49829666 ACGAGCTGCAAATCGGTAAGCTCAT-
1 ACGAGCTATGAATCGGTAAGCTC-TC
49829691 ACGAGCT
1 ACGAGCT
49829698 GTGGTGTGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
24 1 0.01
25 67 0.96
26 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.22
Consensus pattern (25 bp):
ACGAGCTATGAATCGGTAAGCTCTC
Found at i:49829664 original size:50 final size:51
Alignment explanation
Indices: 49829585--49829698 Score: 169
Period size: 50 Copynumber: 2.3 Consensus size: 51
49829575 ATACATGTAT
* * * **
49829585 GCTCAAACGAGCT-ATGAATCGGTATGCTCTCACGAGCTGTGAATCGGTAA
1 GCTCATACGAGCTGATGAATCGATAAGCTCTCACGAGCTGCAAATCGGTAA
49829635 GCTCATACGAGCTGA-GAATCGATAAGCTCTCACGAGCTGCAAATCGGTAA
1 GCTCATACGAGCTGATGAATCGATAAGCTCTCACGAGCTGCAAATCGGTAA
49829685 GCTCATACGAGCTG
1 GCTCATACGAGCTG
49829699 TGGTGTGTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 57 0.98
51 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (51 bp):
GCTCATACGAGCTGATGAATCGATAAGCTCTCACGAGCTGCAAATCGGTAA
Found at i:49842705 original size:20 final size:20
Alignment explanation
Indices: 49842665--49842705 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
49842655 AAACAAAAAT
*
49842665 ATTAAAAATATAAAAATTAA
1 ATTAAAAATATAAAAAATAA
49842685 ATTAAAAATA-AATAAAATAA
1 ATTAAAAATATAA-AAAATAA
49842705 A
1 A
49842706 AAATGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
ATTAAAAATATAAAAAATAA
Found at i:49853146 original size:19 final size:20
Alignment explanation
Indices: 49853122--49853161 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
49853112 TTTAAGCTTT
49853122 TTTA-TTTTTAATTAATAAA
1 TTTATTTTTTAATTAATAAA
49853141 TTTATTGTTTTTAATTAATAA
1 TTTA-T-TTTTTAATTAATAA
49853162 TTCTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTATTTTTTAATTAATAAA
Found at i:49856689 original size:22 final size:22
Alignment explanation
Indices: 49856629--49856686 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
49856619 AATCTTCAAG
49856629 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
49856648 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
49856670 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
49856687 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:49858412 original size:22 final size:22
Alignment explanation
Indices: 49858387--49858430 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
49858377 TTACTAATTA
*
49858387 ATTTAATAATATTATTATTATT
1 ATTTAATAATACTATTATTATT
* *
49858409 ATTTATTAATCCTATTATTATT
1 ATTTAATAATACTATTATTATT
49858431 TGTACTATTA
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:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTAATAATACTATTATTATT
Found at i:49863833 original size:41 final size:41
Alignment explanation
Indices: 49863776--49863858 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
49863766 TCAGCAATAG
49863776 AGCAGTCGATTGTTAACTGACTGGTCGTAGGTTCGAATCCT
1 AGCAGTCGATTGTTAACTGACTGGTCGTAGGTTCGAATCCT
*
49863817 AGCAGTCGATTGTTAACTGACTGGTTGTAGGTTCGAATCCT
1 AGCAGTCGATTGTTAACTGACTGGTCGTAGGTTCGAATCCT
49863858 A
1 A
49863859 CTTGAGGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (41 bp):
AGCAGTCGATTGTTAACTGACTGGTCGTAGGTTCGAATCCT
Found at i:49873304 original size:27 final size:27
Alignment explanation
Indices: 49873266--49873320 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
49873256 TCACTAACTG
*
49873266 ATACTAATCTAATACTAATAGATTAGA
1 ATACTAATCTAATACTAATAGAATAGA
49873293 ATACTAATCTAATACTAATAGAATAGA
1 ATACTAATCTAATACTAATAGAATAGA
49873320 A
1 A
49873321 AAATATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (27 bp):
ATACTAATCTAATACTAATAGAATAGA
Found at i:49876939 original size:16 final size:16
Alignment explanation
Indices: 49876918--49876950 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
49876908 TTTTATTGCT
*
49876918 TTGCTACTATAGAATA
1 TTGCTACTATAAAATA
49876934 TTGCTACTATAAAATA
1 TTGCTACTATAAAATA
49876950 T
1 T
49876951 AGAATATCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTGCTACTATAAAATA
Found at i:49878535 original size:33 final size:33
Alignment explanation
Indices: 49878493--49878561 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
49878483 CATACATGTG
*
49878493 AATATGAATCCATTTTCCTTTTTCTCCGTAATC
1 AATACGAATCCATTTTCCTTTTTCTCCGTAATC
*
49878526 AATACGAATCTATTTTCCTTTTTCTCCGTAATC
1 AATACGAATCCATTTTCCTTTTTCTCCGTAATC
49878559 AAT
1 AAT
49878562 CTTCTCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (33 bp):
AATACGAATCCATTTTCCTTTTTCTCCGTAATC
Found at i:49885354 original size:23 final size:23
Alignment explanation
Indices: 49885321--49885381 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
49885311 CCACAACTCG
*
49885321 TATGA-GCTTACTGTTTCAGCTC
1 TATGAGGCTTACCGTTTCAGCTC
49885343 TATGAGGCTTACCG-TTCAGCTC
1 TATGAGGCTTACCGTTTCAGCTC
*
49885365 GAT-AGAGCTTACCGTTT
1 TATGAG-GCTTACCGTTT
49885382 ACCGGCACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 2 0.06
22 23 0.68
23 9 0.26
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (23 bp):
TATGAGGCTTACCGTTTCAGCTC
Found at i:49889197 original size:8 final size:8
Alignment explanation
Indices: 49889184--49889210 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
49889174 ACACAATTAA
49889184 TAATATAG
1 TAATATAG
49889192 TAATATAG
1 TAATATAG
49889200 TAATATAG
1 TAATATAG
49889208 TAA
1 TAA
49889211 CATATCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (8 bp):
TAATATAG
Found at i:49890323 original size:13 final size:13
Alignment explanation
Indices: 49890307--49890341 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
49890297 AGTATTCAAT
*
49890307 CCAACCTAATTAC
1 CCAACCCAATTAC
49890320 CCAACCCAATTAC
1 CCAACCCAATTAC
49890333 CCAACCCAA
1 CCAACCCAA
49890342 CCCAATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.40, C:0.46, G:0.00, T:0.14
Consensus pattern (13 bp):
CCAACCCAATTAC
Found at i:49890465 original size:9 final size:9
Alignment explanation
Indices: 49890448--49890541 Score: 109
Period size: 9 Copynumber: 10.4 Consensus size: 9
49890438 TGTATGATTC
*
49890448 AATTAGGTT
1 AATTCGGTT
49890457 AATTCGGTT
1 AATTCGGTT
*
49890466 AATTCGGGT
1 AATTCGGTT
49890475 AATTCGAG-T
1 AATTCG-GTT
*
49890484 AATTCGGGT
1 AATTCGGTT
49890493 AATTCGGTT
1 AATTCGGTT
* *
49890502 TATTCGGGT
1 AATTCGGTT
49890511 AATTCGGTT
1 AATTCGGTT
*
49890520 AATTTGGTT
1 AATTCGGTT
*
49890529 AATTCGGCT
1 AATTCGGTT
49890538 AATT
1 AATT
49890542 TTTAACCAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
8 1 0.01
9 71 0.97
10 1 0.01
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:49890542 original size:18 final size:18
Alignment explanation
Indices: 49890456--49890541 Score: 120
Period size: 18 Copynumber: 4.8 Consensus size: 18
49890446 TCAATTAGGT
49890456 TAATTCGGTTAATTCGGG
1 TAATTCGGTTAATTCGGG
49890474 TAATTCGAG-TAATTCGGG
1 TAATTCG-GTTAATTCGGG
*
49890492 TAATTCGGTTTATTCGGG
1 TAATTCGGTTAATTCGGG
* *
49890510 TAATTCGGTTAATTTGGT
1 TAATTCGGTTAATTCGGG
*
49890528 TAATTCGGCTAATT
1 TAATTCGGTTAATT
49890542 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
17 1 0.02
18 59 0.97
19 1 0.02
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.42
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGG
Found at i:49890640 original size:29 final size:29
Alignment explanation
Indices: 49890603--49890682 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
49890593 CGAATTAACC
*
49890603 GAAAAAATTTCAGTTCGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
*
49890632 GAAAAAATTTCGGTTAGGTTAATTTTTTT
1 GAAAAAATTTCGGTTCGGTTAATTTTTTT
49890661 GAAAAAATTTCGGTTCGGTTAA
1 GAAAAAATTTCGGTTCGGTTAA
49890683 CGGTTAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (29 bp):
GAAAAAATTTCGGTTCGGTTAATTTTTTT
Found at i:49890747 original size:12 final size:12
Alignment explanation
Indices: 49890730--49890754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49890720 TGCTATTTCG
49890730 GGTCGGTTAACC
1 GGTCGGTTAACC
49890742 GGTCGGTTAACC
1 GGTCGGTTAACC
49890754 G
1 G
49890755 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:49891900 original size:8 final size:8
Alignment explanation
Indices: 49891887--49891918 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
49891877 ATATTAATTG
49891887 CAACATTA
1 CAACATTA
49891895 CAACATTA
1 CAACATTA
*
49891903 CAATATTA
1 CAACATTA
49891911 CAACATTA
1 CAACATTA
49891919 AAACTTGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (8 bp):
CAACATTA
Found at i:49891953 original size:14 final size:14
Alignment explanation
Indices: 49891934--49891962 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
49891924 TGGAACAAAC
49891934 TTTGTAATATAAAT
1 TTTGTAATATAAAT
49891948 TTTGTAATATAAAT
1 TTTGTAATATAAAT
49891962 T
1 T
49891963 AAATACATTA
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:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:49900241 original size:16 final size:16
Alignment explanation
Indices: 49900220--49900257 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
49900210 TTTGGTTCGC
49900220 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
49900236 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
49900252 CGTAAT
1 TGTAAT
49900258 AGTAACTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:49900303 original size:45 final size:44
Alignment explanation
Indices: 49900239--49900331 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
49900229 ATAGAGGTGT
*
49900239 AATGGAATAGAGGCGTAATAGTAACTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAGACGTAATAGT-ACTC-ATGTGTTTGGTTGAATGG
* *
49900284 AATGGAATAGA-ACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGAC-GTAATAGTACTCATGTGTTTGGTTGAATGG
49900328 AATG
1 AATG
49900332 ATGCTGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.34
Consensus pattern (44 bp):
AATGGAATAGAGACGTAATAGTACTCATGTGTTTGGTTGAATGG
Found at i:49900874 original size:17 final size:17
Alignment explanation
Indices: 49900852--49900885 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49900842 TTATTATTAA
49900852 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
49900869 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
49900886 TCAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:49900927 original size:63 final size:63
Alignment explanation
Indices: 49900740--49900927 Score: 168
Period size: 53 Copynumber: 3.1 Consensus size: 63
49900730 AAATATAATT
*
49900740 TAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAAT
1 TAAT-AAAATATATAATTTAATAAAATTC--AATA-TAATTATTCTTATATGAATTTACTAAAAT
49900805 CA
62 CA
* * * *
49900807 TAATATATAATACTATAA---AATATAATTTAAAATAATTA---TTAT-T-AA---A-TATAAT-
1 TAATA-A-AATA-TATAATTTAATAAAATTCAATATAATTATTCTTATATGAATTTACTAAAATC
*
49900859 T
63 A
49900860 TAATAAAATATATAATTTAATAAAATTCAATATAATTATTCTTATATGAATTTACTAAAATCA
1 TAATAAAATATATAATTTAATAAAATTCAATATAATTATTCTTATATGAATTTACTAAAATCA
49900923 TAATA
1 TAATA
49900928 TATAATACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 36
0.67 0.08 0.26
Matches are distributed among these distances:
50 5 0.05
51 4 0.04
52 1 0.01
53 22 0.23
54 5 0.05
55 1 0.01
56 4 0.04
57 1 0.01
58 4 0.04
59 1 0.01
60 4 0.04
61 1 0.01
62 5 0.05
63 10 0.11
64 3 0.03
66 9 0.10
67 5 0.05
68 4 0.04
69 5 0.05
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (63 bp):
TAATAAAATATATAATTTAATAAAATTCAATATAATTATTCTTATATGAATTTACTAAAATCA
Found at i:49900955 original size:21 final size:21
Alignment explanation
Indices: 49900912--49900955 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
49900902 TATATGAATT
*
49900912 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATAAAA
*
49900933 TACTAAAAAT-ATAATTTAAAA
1 TACT-AAAATCATAATATAAAA
49900954 TA
1 TA
49900956 ATCTACTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (21 bp):
TACTAAAATCATAATATAAAA
Found at i:49903246 original size:27 final size:29
Alignment explanation
Indices: 49903210--49903280 Score: 103
Period size: 27 Copynumber: 2.5 Consensus size: 29
49903200 ATAAAAAATA
*
49903210 ACCAAAATATTATAA-CTTTTT-TTATTT
1 ACCAAAATATTATAATATTTTTATTATTT
49903237 ACCAAAATATTATAATTATTTTTATTATTT
1 ACCAAAATATTATAA-TATTTTTATTATTT
49903267 ACCAAAATA-TATAA
1 ACCAAAATATTATAA
49903281 AAAAACAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 15 0.38
29 10 0.25
30 15 0.38
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (29 bp):
ACCAAAATATTATAATATTTTTATTATTT
Found at i:49903413 original size:27 final size:27
Alignment explanation
Indices: 49903344--49903420 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
49903334 AGGCCAATGG
*
49903344 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAATGGTGCCAAAAC
*
49903371 CATTGGCGGCACCAATGGTGCCAAAGC
1 CATTGGCGGCACCAATGGTGCCAAAAC
*
49903398 CATTGGCGGCACCAATGGAGCCA
1 CATTGGCGGCACCAATGGTGCCA
49903421 TACAGATTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.29, C:0.30, G:0.29, T:0.13
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAAC
Found at i:49903433 original size:27 final size:26
Alignment explanation
Indices: 49903343--49903436 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 26
49903333 CAGGCCAATG
* * *
49903343 GCATTGGCGGCACCAAAGGTGCCAAAA
1 GCATTAGCGGCACCAATGGAGCC-AAA
* * *
49903370 CCATTGGCGGCACCAATGGTGCCAAA
1 GCATTAGCGGCACCAATGGAGCCAAA
*
49903396 GCCATTGGCGGCACCAATGGAGCCATACA
1 G-CATTAGCGGCACCAATGGAGCCA-A-A
49903425 G-ATTAGCGGCAC
1 GCATTAGCGGCAC
49903437 TACTCGTGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
26 3 0.05
27 53 0.90
28 1 0.02
29 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (26 bp):
GCATTAGCGGCACCAATGGAGCCAAA
Found at i:49903535 original size:11 final size:11
Alignment explanation
Indices: 49903519--49903557 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
49903509 GGTGTTGCGG
49903519 AAAAGAAGAGA
1 AAAAGAAGAGA
49903530 AAAAG-AGAGA
1 AAAAGAAGAGA
*
49903540 AAGAGAAGAGA
1 AAAAGAAGAGA
49903551 AAAAGAA
1 AAAAGAA
49903558 TGTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:49903547 original size:21 final size:20
Alignment explanation
Indices: 49903518--49903556 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
49903508 AGGTGTTGCG
49903518 GAAAAGAAGAGAAAAAGAGA
1 GAAAAGAAGAGAAAAAGAGA
49903538 GAAAGAGAAGAGAAAAAGA
1 GAAA-AGAAGAGAAAAAGA
49903557 ATGTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
GAAAAGAAGAGAAAAAGAGA
Found at i:49903690 original size:3 final size:3
Alignment explanation
Indices: 49903684--49903733 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
49903674 ATTATTATTA
49903684 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
49903732 TT
1 TT
49903734 AGTATTAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:49904559 original size:18 final size:18
Alignment explanation
Indices: 49904536--49904572 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
49904526 GGTTGGTGGT
49904536 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
49904554 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
49904572 G
1 G
49904573 GTCATTGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.49, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:49910426 original size:18 final size:17
Alignment explanation
Indices: 49910405--49910482 Score: 66
Period size: 18 Copynumber: 4.4 Consensus size: 17
49910395 TTCTCTTCTC
49910405 CTTTCCTTTTCTTTCCTT
1 CTTTCC-TTTCTTTCCTT
*
49910423 CTTTTTCTTTCTTTCCTCT
1 C-TTTCCTTTCTTTCCT-T
* *
49910442 CCTTCCTTTCTTTCTTT
1 CTTTCCTTTCTTTCCTT
* * *
49910459 CCTCTCCTTCCTTTCTTT
1 -CTTTCCTTTCTTTCCTT
49910477 CTTTCC
1 CTTTCC
49910483 CTCTCCTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
17 6 0.12
18 37 0.76
19 6 0.12
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (17 bp):
CTTTCCTTTCTTTCCTT
Found at i:49910492 original size:18 final size:22
Alignment explanation
Indices: 49910437--49910491 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
49910427 TTCTTTCTTT
49910437 CCTCTCCTTCCTTTCTTTCTTT
1 CCTCTCCTTCCTTTCTTTCTTT
49910459 CCTCTCCTTCCTTTCTTTCTTT
1 CCTCTCCTTCCTTTCTTTCTTT
49910481 CCCTCTCCTTC
1 -CCTCTCCTTC
49910492 TCCCCTCCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (22 bp):
CCTCTCCTTCCTTTCTTTCTTT
Found at i:49910554 original size:27 final size:27
Alignment explanation
Indices: 49910522--49910590 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
49910512 CCTATTATGG
*
49910522 CATTGGTGCCGCCAATGGTTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
*
49910549 CATTGGTGCCACCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
*
49910576 CTTTGGTGCCGCCAA
1 CATTGGTGCCGCCAA
49910591 GTATTGGCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.28
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTTTGGCAC
Found at i:49910710 original size:27 final size:29
Alignment explanation
Indices: 49910655--49910721 Score: 102
Period size: 27 Copynumber: 2.3 Consensus size: 29
49910645 TTTTTTTGAT
*
49910655 ATATTTTGGTAAATAATAAAAAAATTTATA
1 ATATTTTGGT-AATAATAAAAAAAGTTATA
49910685 ATATTTTGGT-A-AATAAAAAAAGTTATA
1 ATATTTTGGTAATAATAAAAAAAGTTATA
49910712 ATATTTTGGT
1 ATATTTTGGT
49910722 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 25 0.69
28 1 0.03
30 10 0.28
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (29 bp):
ATATTTTGGTAATAATAAAAAAAGTTATA
Found at i:49915763 original size:31 final size:29
Alignment explanation
Indices: 49915694--49915767 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
49915684 AATAAATGAT
**
49915694 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGGCA
*
49915723 AACATAAGTGACTAAAATGTAACCTGAGGCA
1 AACATAAGTGACTAAAATGTAACAT--GGCA
*
49915754 AACAAAAGTGACTA
1 AACATAAGTGACTA
49915768 TTTTGGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGGCA
Found at i:49937152 original size:19 final size:18
Alignment explanation
Indices: 49937128--49937163 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
49937118 TTATTTATAA
*
49937128 AAATAAATTATATAAAATC
1 AAATAAAATATA-AAAATC
49937147 AAATAAAATATAAAAAT
1 AAATAAAATATAAAAAT
49937164 TAGATTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAAAATATAAAAATC
Found at i:49937450 original size:34 final size:34
Alignment explanation
Indices: 49937344--49937450 Score: 83
Period size: 34 Copynumber: 3.1 Consensus size: 34
49937334 ATGAAAATAC
*
49937344 AAAAGTATCACCATAATAATACTGATTATCATTT
1 AAAAGTATCACCATAATAATATTGATTATCATTT
* ** * * * ** **
49937378 AAAAGAAAT-ATGAAAATAA-ATCGCATGAAAATAC
1 AAAAG-TATCACCATAATAATATTG-ATTATCATTT
49937412 AAAAGTATCACCATAATAATATTGATTATCATTT
1 AAAAGTATCACCATAATAATATTGATTATCATTT
49937446 AAAAG
1 AAAAG
49937451 AAATATGTAA
Statistics
Matches: 48, Mismatches: 21, Indels: 8
0.62 0.27 0.10
Matches are distributed among these distances:
33 4 0.08
34 39 0.81
35 5 0.10
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.29
Consensus pattern (34 bp):
AAAAGTATCACCATAATAATATTGATTATCATTT
Found at i:49937488 original size:68 final size:68
Alignment explanation
Indices: 49937332--49937468 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
49937322 TCATATAAAA
49937332 GCATGAAAATACAAAAGTATCACCATAATAATACTGATTATCATTTAAAAGAAATATGAAAATAA
1 GCATGAAAATACAAAAGTATCACCATAATAATACTGATTATCATTTAAAAGAAATATGAAAATAA
49937397 ATC
66 ATC
* *
49937400 GCATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGTAAATAA
1 GCATGAAAATACAAAAGTATCACCATAATAATACTGATTATCATTTAAAAGAAATATGAAAATAA
49937465 ATC
66 ATC
49937468 G
1 G
49937469 TTTTCAATTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.28
Consensus pattern (68 bp):
GCATGAAAATACAAAAGTATCACCATAATAATACTGATTATCATTTAAAAGAAATATGAAAATAA
ATC
Found at i:49939512 original size:25 final size:26
Alignment explanation
Indices: 49939484--49939532 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
49939474 AATTAGGCAA
*
49939484 AAAATA-ATAATGATTAAAAAAAGAG
1 AAAATAGATAATGACTAAAAAAAGAG
* *
49939509 AAAATAGGTTATGACTAAAAAAAG
1 AAAATAGATAATGACTAAAAAAAG
49939533 GGTATTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.63, C:0.02, G:0.14, T:0.20
Consensus pattern (26 bp):
AAAATAGATAATGACTAAAAAAAGAG
Found at i:49941151 original size:17 final size:16
Alignment explanation
Indices: 49941131--49941164 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
49941121 ATATTAAGAT
49941131 AAAAAAAATCTTATGGG
1 AAAAAAAATCTTA-GGG
*
49941148 AAAAAAATTCTTAGGG
1 AAAAAAAATCTTAGGG
49941164 A
1 A
49941165 CGGAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (16 bp):
AAAAAAAATCTTAGGG
Found at i:49943286 original size:24 final size:24
Alignment explanation
Indices: 49943257--49943313 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
49943247 AAAAAGAACG
*
49943257 TCCCGTTATTAGCTCTCAT-GAGCA
1 TCCCGTTATTAGCCCTC-TCGAGCA
* *
49943281 TCCCGTTAATAGCCCTCTCGAGCT
1 TCCCGTTATTAGCCCTCTCGAGCA
49943305 TCCCGTTAT
1 TCCCGTTAT
49943314 ATAGTTCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.18, C:0.33, G:0.16, T:0.33
Consensus pattern (24 bp):
TCCCGTTATTAGCCCTCTCGAGCA
Found at i:49943327 original size:25 final size:25
Alignment explanation
Indices: 49943276--49943358 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 25
49943266 TAGCTCTCAT
* *
49943276 GAGCATCCCGTTAATAGC-CCTCT-C
1 GAGCTTCCCGTTAATAGCTTCT-TGC
49943300 GAGCTTCCCGTTATATAG-TTCTTGC
1 GAGCTTCCCGTTA-ATAGCTTCTTGC
* *
49943325 GAGCTTCCCATTAATAGCTTTTTG-
1 GAGCTTCCCGTTAATAGCTTCTTGC
*
49943349 GAGCATCCCG
1 GAGCTTCCCG
49943359 ATTGGTTGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
24 25 0.51
25 24 0.49
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCGTTAATAGCTTCTTGC
Found at i:49943439 original size:26 final size:25
Alignment explanation
Indices: 49943404--49943488 Score: 91
Period size: 26 Copynumber: 3.4 Consensus size: 25
49943394 ACAGCTCTTA
*
49943404 TGAGCGTCCTATTATATGGCTCTTCG
1 TGAGCTTCCTATTA-ATGGCTCTTCG
* *
49943430 TGAGCTTCCTGATTAAAGGCTCTTTG
1 TGAGCTTCCT-ATTAATGGCTCTTCG
** *
49943456 TGAGCTTCCCGTTAATGGCTCTCCG
1 TGAGCTTCCTATTAATGGCTCTTCG
49943481 -GAGCTTCC
1 TGAGCTTCC
49943489 CGATATGGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 8 0.16
25 11 0.22
26 27 0.54
27 4 0.08
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCTATTAATGGCTCTTCG
Found at i:49943489 original size:24 final size:24
Alignment explanation
Indices: 49943419--49943557 Score: 91
Period size: 25 Copynumber: 5.7 Consensus size: 24
49943409 GTCCTATTAT
* *
49943419 ATGGCTCTTCGTGAGCTTCCTGATTA
1 ATGGCTCTCCG-GAGCTTCCCG-TTA
* **
49943445 AAGGCTCTTTGTGAGCTTCCCGTTA
1 ATGGCTCTCCG-GAGCTTCCCGTTA
*
49943470 ATGGCTCTCCGGAGCTTCCCGAT-
1 ATGGCTCTCCGGAGCTTCCCGTTA
* ** * *
49943493 ATGGCTCGCTTGAACTTCCCGATA
1 ATGGCTCTCCGGAGCTTCCCGTTA
* **
49943517 TATGGCTATCCGGAGCTTCTTGTTA
1 -ATGGCTCTCCGGAGCTTCCCGTTA
* *
49943542 ATGGCTATTCGGAGCT
1 ATGGCTCTCCGGAGCT
49943558 ACTCGTTATT
Statistics
Matches: 91, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
23 19 0.21
24 26 0.29
25 27 0.30
26 19 0.21
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (24 bp):
ATGGCTCTCCGGAGCTTCCCGTTA
Found at i:49943565 original size:24 final size:24
Alignment explanation
Indices: 49943518--49943565 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
49943508 TTCCCGATAT
* *
49943518 ATGGCTATCCGGAGCTTCTTGTTA
1 ATGGCTATCCGGAGCTACTCGTTA
*
49943542 ATGGCTATTCGGAGCTACTCGTTA
1 ATGGCTATCCGGAGCTACTCGTTA
49943566 TTAGCCCGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (24 bp):
ATGGCTATCCGGAGCTACTCGTTA
Found at i:49946097 original size:33 final size:33
Alignment explanation
Indices: 49946022--49946148 Score: 129
Period size: 33 Copynumber: 4.0 Consensus size: 33
49946012 GCATCCACAT
* **
49946022 AATAGAGATAGTCCGTTGGGACAGTAAACACAG
1 AATAGAGATAGTCCGTTGGGACAATAAACATGG
* * *
49946055 AACATAGATAGTTCGTTGGGACAATAAACATGG
1 AATAGAGATAGTCCGTTGGGACAATAAACATGG
* * * *
49946088 AATAGAGATAATCTGTTAGGACAATTAACATGG
1 AATAGAGATAGTCCGTTGGGACAATAAACATGG
49946121 -AT--A-A-AGTCCGTTGGGACAATAAACATGG
1 AATAGAGATAGTCCGTTGGGACAATAAACATGG
49946149 GATAAGTTCG
Statistics
Matches: 77, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
28 20 0.26
29 1 0.01
30 1 0.01
32 2 0.03
33 53 0.69
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (33 bp):
AATAGAGATAGTCCGTTGGGACAATAAACATGG
Found at i:49946155 original size:28 final size:28
Alignment explanation
Indices: 49946068--49946155 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
49946058 ATAGATAGTT
*
49946068 CGTTGGGACAATAAACATGGAATAGAGATAATC
1 CGTTGGGACAATAAACATGGGATA-AG----TC
* * *
49946101 TGTTAGGACAATTAACAT-GGATAAAGTC
1 CGTTGGGACAATAAACATGGGAT-AAGTC
49946129 CGTTGGGACAATAAACATGGGATAAGT
1 CGTTGGGACAATAAACATGGGATAAGT
49946156 TCGACGAGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 21 0.46
29 4 0.09
32 5 0.11
33 16 0.35
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (28 bp):
CGTTGGGACAATAAACATGGGATAAGTC
Found at i:49947551 original size:16 final size:17
Alignment explanation
Indices: 49947513--49947554 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
49947503 TTCACCATTT
*
49947513 TTTTTGTATTTTTCCAAA
1 TTTTT-TATTTTTCAAAA
*
49947531 CTTTTTATTTTT-AAAA
1 TTTTTTATTTTTCAAAA
49947547 TTTTTTAT
1 TTTTTTAT
49947555 AACATTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 10 0.48
17 7 0.33
18 4 0.19
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTTATTTTTCAAAA
Found at i:49949593 original size:42 final size:40
Alignment explanation
Indices: 49949519--49949606 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 40
49949509 TTTATTATTC
* *
49949519 TAAAAATTTTAGATTAAATAACGTTAATAACAATAAAACTA
1 TAAAAAGTTTAGATTAAATAACGTTAATAACAA-AAAAATA
* ** *
49949560 TTAAAAGTTTAGATTAAATAAATTTTATTAACAAAAAAATA
1 TAAAAAGTTTAGATTAAAT-AACGTTAATAACAAAAAAATA
49949601 TAAAAA
1 TAAAAA
49949607 TTGAAAATTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 28 0.72
42 11 0.28
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (40 bp):
TAAAAAGTTTAGATTAAATAACGTTAATAACAAAAAAATA
Found at i:49957606 original size:15 final size:16
Alignment explanation
Indices: 49957574--49957607 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49957564 ATTTTGTGTG
49957574 TTTATTATGTGTAAAT
1 TTTATTATGTGTAAAT
*
49957590 TTTATTGTGTG-AAAT
1 TTTATTATGTGTAAAT
49957605 TTT
1 TTT
49957608 CGTGTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (16 bp):
TTTATTATGTGTAAAT
Found at i:49958785 original size:43 final size:43
Alignment explanation
Indices: 49958707--49958788 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
49958697 TTCTGATAAA
* ***
49958707 TGTTTTCGTGTAAGACCACTTCTGGGACGTTGGCATCGACTTG
1 TGTTTTCGTGTAAGACCACTTCCGGGACAACGGCATCGACTTG
49958750 TGTTTTCGTGTAAGACC-CTGTCCGGGACAACGGCATCGA
1 TGTTTTCGTGTAAGACCACT-TCCGGGACAACGGCATCGA
49958789 TCAGTGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.06
43 32 0.94
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.30
Consensus pattern (43 bp):
TGTTTTCGTGTAAGACCACTTCCGGGACAACGGCATCGACTTG
Found at i:49959099 original size:2 final size:2
Alignment explanation
Indices: 49959092--49959125 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
49959082 AGGTTATAAT
49959092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49959126 AGTTTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49962563 original size:21 final size:21
Alignment explanation
Indices: 49962539--49962650 Score: 98
Period size: 21 Copynumber: 5.3 Consensus size: 21
49962529 TCTTAAGAGC
49962539 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAACCCTTATGGGT
* * * * *
49962560 TTCTATTTAGCTCTTTTGGGC
1 TTCTGTTTAACCCTTATGGGT
*
49962581 TTATGTTTAACCCTTATGGGT
1 TTCTGTTTAACCCTTATGGGT
** * * * * *
49962602 TTCCATTCAGCTCTTATGAGC
1 TTCTGTTTAACCCTTATGGGT
*
49962623 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTTAACCCTTATGGGT
49962644 TTCTGTT
1 TTCTGTT
49962651 AAGCTCTCAT
Statistics
Matches: 66, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (21 bp):
TTCTGTTTAACCCTTATGGGT
Found at i:49962588 original size:42 final size:42
Alignment explanation
Indices: 49962523--49962671 Score: 208
Period size: 42 Copynumber: 3.5 Consensus size: 42
49962513 TTACTTTCCG
*
49962523 TTTAGCTCTTAAGAGCTTCTGTTTAACCCTTATGGGTTTCTA
1 TTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTCTA
* * * *
49962565 TTTAGCTCTTTTGGGCTTATGTTTAACCCTTATGGGTTTCCA
1 TTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTCTA
* * *
49962607 TTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTCTG
1 TTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTCTA
* *
49962649 TTAAGCTCTCATGAGCTTCTGTT
1 TTTAGCTCTTATGAGCTTCTGTT
49962672 CAGCTTTCGA
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (42 bp):
TTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTCTA
Found at i:49962668 original size:21 final size:21
Alignment explanation
Indices: 49962610--49962692 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
49962600 GTTTCCATTC
*
49962610 AGCTCTTATGAGCTTCTGTTCA
1 AGCTCTCATGAGCTTCTGTT-A
* * * *
49962632 A-CCCTTATGGGTTTCTGTTA
1 AGCTCTCATGAGCTTCTGTTA
*
49962652 AGCTCTCATGAGCTTCTGTTC
1 AGCTCTCATGAGCTTCTGTTA
*
49962673 AGCTTTC--GAGCTTCTGTTA
1 AGCTCTCATGAGCTTCTGTTA
49962692 A
1 A
49962693 TGATGTACTC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 12 0.24
20 2 0.04
21 35 0.70
22 1 0.02
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (21 bp):
AGCTCTCATGAGCTTCTGTTA
Found at i:49964765 original size:12 final size:13
Alignment explanation
Indices: 49964741--49964769 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
49964731 TTTTTAAAGA
49964741 AAAATTATCTTTT
1 AAAATTATCTTTT
49964754 AAAATT-TCTTTT
1 AAAATTATCTTTT
49964766 AAAA
1 AAAA
49964770 AAGTCGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATTATCTTTT
Found at i:49965404 original size:11 final size:11
Alignment explanation
Indices: 49965388--49965418 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
49965378 TTGGGATCCC
49965388 TTTTCTTTTTT
1 TTTTCTTTTTT
49965399 TTTTC-TTTTT
1 TTTTCTTTTTT
49965409 TTTTCTTTTT
1 TTTTCTTTTT
49965419 CTACCTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:49965412 original size:16 final size:16
Alignment explanation
Indices: 49965387--49965420 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49965377 CTTGGGATCC
*
49965387 CTTTTCTTTTTTTTTT
1 CTTTTCTTTTCTTTTT
*
49965403 CTTTTTTTTTCTTTTT
1 CTTTTCTTTTCTTTTT
49965419 CT
1 CT
49965421 ACCTATTGGG
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
CTTTTCTTTTCTTTTT
Found at i:49965760 original size:18 final size:17
Alignment explanation
Indices: 49965737--49965792 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
49965727 TATATATATA
49965737 TTTTTATTTTTTCTTTCC
1 TTTTTATTTTTTCTTT-C
49965755 TTTTTATTTTTTCCTTTC
1 TTTTTATTTTTT-CTTTC
*
49965773 TTTTTTTCTTTTTC-TTC
1 TTTTTAT-TTTTTCTTTC
49965790 TTT
1 TTT
49965793 CTTTTGCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
17 6 0.17
18 20 0.57
19 9 0.26
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTATTTTTTCTTTC
Found at i:49965769 original size:14 final size:13
Alignment explanation
Indices: 49965743--49965785 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
49965733 TATATTTTTA
*
49965743 TTTTTTCTTTCCT
1 TTTTTTTTTTCCT
49965756 TTTTATTTTTTCCT
1 TTTT-TTTTTTCCT
*
49965770 TTCTTTTTTT-CT
1 TTTTTTTTTTCCT
49965782 TTTT
1 TTTT
49965786 CTTCTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 11 0.42
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTTCCT
Found at i:49965793 original size:13 final size:13
Alignment explanation
Indices: 49965743--49965797 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
49965733 TATATTTTTA
49965743 TTTTTTCTTTCCT
1 TTTTTTCTTTCCT
*
49965756 TTTTATTTTTTCCT
1 TTTT-TTCTTTCCT
49965770 TTCTTTT-TTT-CT
1 TT-TTTTCTTTCCT
49965782 TTTTCTTCTTT-CT
1 TTTT-TTCTTTCCT
49965795 TTT
1 TTT
49965798 GCAAACCCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
11 2 0.05
12 6 0.16
13 15 0.41
14 12 0.32
15 2 0.05
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTCTTTCCT
Found at i:49965891 original size:20 final size:20
Alignment explanation
Indices: 49965866--49965920 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
49965856 CCGGTCTCCC
49965866 TCTTTTTCTCCTTCTATTTT
1 TCTTTTTCTCCTTCTATTTT
*
49965886 TCTTTTCTCTCC-TCTTTTTT
1 TCTTTT-TCTCCTTCTATTTT
49965906 TCTTCCTTTCTCCTT
1 TCTT--TTTCTCCTT
49965921 TCCTTTCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.57
21 10 0.33
22 3 0.10
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (20 bp):
TCTTTTTCTCCTTCTATTTT
Found at i:49968563 original size:21 final size:21
Alignment explanation
Indices: 49968403--49968605 Score: 92
Period size: 21 Copynumber: 9.8 Consensus size: 21
49968393 CTGTTTAGCT
* * *
49968403 CTTACGAGCTTCTATTTAACC
1 CTTATGAGCTTCTGTTCAACC
* * * *
49968424 CTTATG-GGTTTTCGGTCAACT
1 CTTATGAGCTTCT-GTTCAACC
* **
49968445 CTTTTGAGCTTCTGTTTTACC
1 CTTATGAGCTTCTGTTCAACC
* * ** * *
49968466 CTTATGGGTTTCCATTCAGCT
1 CTTATGAGCTTCTGTTCAACC
*
49968487 CTTTTGAGCTTCTAGTT-AACC
1 CTTATGAGCTTCT-GTTCAACC
* * * * *
49968508 CTTATGGGTTTCTATTCAGCT
1 CTTATGAGCTTCTGTTCAACC
*
49968529 CTTACGAGCTTCTGTTCAACC
1 CTTATGAGCTTCTGTTCAACC
* * * *
49968550 CTTATGGGTTTCTGTTAAACT
1 CTTATGAGCTTCTGTTCAACC
*
49968571 CTCATGAGCTTCTGTTCAA--
1 CTTATGAGCTTCTGTTCAACC
49968590 CTT-TCGAGCTTCTGTT
1 CTTAT-GAGCTTCTGTT
49968606 AACGATGTAC
Statistics
Matches: 125, Mismatches: 52, Indels: 12
0.66 0.28 0.06
Matches are distributed among these distances:
18 1 0.01
19 13 0.10
20 6 0.05
21 99 0.79
22 6 0.05
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (21 bp):
CTTATGAGCTTCTGTTCAACC
Found at i:49968587 original size:42 final size:42
Alignment explanation
Indices: 49968390--49968590 Score: 217
Period size: 42 Copynumber: 4.8 Consensus size: 42
49968380 CATGTTTTAA
* * * *
49968390 TTTCTGTTTAGCTCTTACGAGCTTCTATTTAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* * * **
49968432 TTT-TCGGTCAACTCTTTTGAGCTTCTGTTTTACCCTTATGGG
1 TTTCT-GTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
** *
49968474 TTTCCATTCAGCTCTTTTGAGCTTCTAGTT-AACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCT-GTTCAACCCTTATGGG
* *
49968516 TTTCTATTCAGCTCTTACGAGCTTCTGTTCAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* * *
49968558 TTTCTGTTAAACTCTCATGAGCTTCTGTTCAAC
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAAC
49968591 TTTCGAGCTT
Statistics
Matches: 135, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.03
42 128 0.95
43 3 0.02
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.44
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
Found at i:49973146 original size:26 final size:26
Alignment explanation
Indices: 49973117--49973176 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
49973107 TTCCCCCAAC
49973117 AAAATTTTGATGATTTTA-CTCCTAGT
1 AAAATTTTGATGATTTTACCT-CTAGT
* *
49973143 AAAATTTTGATGATTTTGCCTCTGGT
1 AAAATTTTGATGATTTTACCTCTAGT
49973169 AAAATTTT
1 AAAATTTT
49973177 TAGAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 29 0.94
27 2 0.06
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAATTTTGATGATTTTACCTCTAGT
Found at i:49979829 original size:13 final size:14
Alignment explanation
Indices: 49979804--49979832 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49979794 GTTTGTTGTT
49979804 TGTTTTTCTTTATG
1 TGTTTTTCTTTATG
49979818 TGTTTTTC-TTATG
1 TGTTTTTCTTTATG
49979831 TG
1 TG
49979833 CAGCAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69
Consensus pattern (14 bp):
TGTTTTTCTTTATG
Found at i:49982089 original size:11 final size:10
Alignment explanation
Indices: 49982071--49982124 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
49982061 GTTTTAGGTT
49982071 TAGTTTTCTC
1 TAGTTTTCTC
*
49982081 TAGGTTTTCTT
1 TA-GTTTTCTC
49982092 TAGTTTTCTC
1 TAGTTTTCTC
*
49982102 TAGGTTTTCTT
1 TA-GTTTTCTC
*
49982113 TAGTTTGCTC
1 TAGTTTTCTC
49982123 TA
1 TA
49982125 TACTTTTCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 19 0.51
11 18 0.49
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59
Consensus pattern (10 bp):
TAGTTTTCTC
Found at i:49982094 original size:21 final size:21
Alignment explanation
Indices: 49982069--49982124 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
49982059 TAGTTTTAGG
49982069 TTTAGTTTTCTCTAGGTTTTC
1 TTTAGTTTTCTCTAGGTTTTC
49982090 TTTAGTTTTCTCTAGGTTTTC
1 TTTAGTTTTCTCTAGGTTTTC
*
49982111 TTTAGTTTGCTCTA
1 TTTAGTTTTCTCTA
49982125 TACTTTTCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.61
Consensus pattern (21 bp):
TTTAGTTTTCTCTAGGTTTTC
Found at i:49982099 original size:10 final size:10
Alignment explanation
Indices: 49982069--49982118 Score: 64
Period size: 11 Copynumber: 4.8 Consensus size: 10
49982059 TAGTTTTAGG
49982069 TTTAGTTTTC
1 TTTAGTTTTC
*
49982079 TCTAGGTTTTC
1 TTTA-GTTTTC
49982090 TTTAGTTTTC
1 TTTAGTTTTC
*
49982100 TCTAGGTTTTC
1 TTTA-GTTTTC
49982111 TTTAGTTT
1 TTTAGTTT
49982119 GCTCTATACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 16 0.47
11 18 0.53
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (10 bp):
TTTAGTTTTC
Found at i:49987231 original size:24 final size:24
Alignment explanation
Indices: 49987203--49987266 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
49987193 TTTCTAGAAG
* *
49987203 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
49987227 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
49987251 ATTT-GACATTTATTAG
1 ATTTAG-CATTTATTAG
49987267 AAATAGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:49991706 original size:23 final size:23
Alignment explanation
Indices: 49991680--49991725 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
49991670 TTCTAGAAGA
* *
49991680 TTTAGTATTTATTAGTATAATAT
1 TTTAGCATTTATTAGCATAATAT
49991703 TTTAGCATTTATTAGCATAATAT
1 TTTAGCATTTATTAGCATAATAT
49991726 ATTTGACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (23 bp):
TTTAGCATTTATTAGCATAATAT
Found at i:49991740 original size:24 final size:23
Alignment explanation
Indices: 49991680--49991740 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
49991670 TTCTAGAAGA
* * *
49991680 TTTAGTATTTATTAGTATAATAT
1 TTTAGCATTGATTAGCATAATAT
*
49991703 TTTAGCATTTATTAGCATAATAT
1 TTTAGCATTGATTAGCATAATAT
49991726 ATTT-GACATTGATTA
1 -TTTAG-CATTGATTA
49991741 AAATCAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 22 0.67
24 11 0.33
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (23 bp):
TTTAGCATTGATTAGCATAATAT
Found at i:49998889 original size:5 final size:5
Alignment explanation
Indices: 49998879--49998903 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
49998869 TGAGCATTCG
49998879 ATCGA ATCGA ATCGA ATCGA ATCGA
1 ATCGA ATCGA ATCGA ATCGA ATCGA
49998904 CAATTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
ATCGA
Found at i:50004311 original size:3 final size:3
Alignment explanation
Indices: 50004303--50004354 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
50004293 ACCCAATCTC
50004303 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
50004351 CAT C
1 CAT C
50004355 TTTATCTACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:50007791 original size:19 final size:19
Alignment explanation
Indices: 50007717--50007788 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
50007707 AATCTTCAAG
*
50007717 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
*
50007736 GGTATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
50007755 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
50007776 GATATGCAATCTT
1 GATATGCAATCTT
50007789 GGAAGATATG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 30 0.64
21 17 0.36
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:50011422 original size:20 final size:19
Alignment explanation
Indices: 50011392--50011478 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
50011382 ATCAACTATG
50011392 ATTAAACTTAATCATTTTAAT
1 ATTAAA-TTAATCA-TTTAAT
* *
50011413 ATTAAATTAATGA-TAAAT
1 ATTAAATTAATCATTTAAT
* *
50011431 ATTAGACTAA--ATTTAAT
1 ATTAAATTAATCATTTAAT
50011448 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAATCA-TTTAAT
50011468 ATTAAATTAAT
1 ATTAAATTAAT
50011479 AAAATACTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.02
17 11 0.20
18 13 0.24
19 2 0.04
20 21 0.39
21 6 0.11
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTAAATTAATCATTTAAT
Found at i:50015766 original size:16 final size:17
Alignment explanation
Indices: 50015739--50015773 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
50015729 AGAGATTTGA
50015739 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
50015756 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
50015772 GA
1 GA
50015774 TTGAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:50028218 original size:25 final size:26
Alignment explanation
Indices: 50028189--50028240 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
50028179 AATTGTAAAT
50028189 TAGAAAAATATC-TCTAGA-AATTTTC
1 TAGAAAAATATCTTC-AGAGAATTTTC
* *
50028214 TAGAATAATCTCTTCAGAGAATTTTC
1 TAGAAAAATATCTTCAGAGAATTTTC
50028240 T
1 T
50028241 CTCTATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (26 bp):
TAGAAAAATATCTTCAGAGAATTTTC
Found at i:50028456 original size:54 final size:54
Alignment explanation
Indices: 50028349--50028458 Score: 136
Period size: 54 Copynumber: 2.0 Consensus size: 54
50028339 ACCACTTTAA
* *
50028349 TATTAAATTAATATAATATTTATCAACATAAATATTAAATTTAGTATTAAATAT
1 TATTAAAATAATATAATATTTATCAACATAAATATTAAATTTAGAATTAAATAT
* *
50028403 TATTAAAATAATATAAT-TTTATCTACAAGATAAATATTAAA-TTA-AATTTAATAT
1 TATTAAAATAATATAATATTTA--T-CAACATAAATATTAAATTTAGAATTAAATAT
50028457 TA
1 TA
50028459 AGATAATTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
53 4 0.08
54 26 0.53
55 4 0.08
56 15 0.31
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (54 bp):
TATTAAAATAATATAATATTTATCAACATAAATATTAAATTTAGAATTAAATAT
Found at i:50028485 original size:20 final size:18
Alignment explanation
Indices: 50028435--50028486 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
50028425 CTACAAGATA
50028435 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
50028452 AATATTAAGA-TAATTACTTT
1 AATATTAA-ATTAA-TA-TTT
50028472 AATATTAAATTAATA
1 AATATTAAATTAATA
50028487 AAATATTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 4 0.13
20 14 0.47
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:50030104 original size:16 final size:16
Alignment explanation
Indices: 50030079--50030111 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
50030069 TATGTATACA
*
50030079 AAATATAAAAGACATG
1 AAATAAAAAAGACATG
50030095 AAATAAAAAAGACATG
1 AAATAAAAAAGACATG
50030111 A
1 A
50030112 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (16 bp):
AAATAAAAAAGACATG
Found at i:50033877 original size:51 final size:52
Alignment explanation
Indices: 50033802--50033905 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 52
50033792 TCTAAATTTG
* *
50033802 ATTTGATTTGGTTTCGTTAATGGTAAACTATAAAAGAAAGA-TTGAGTTAAA
1 ATTTGATTTGATTTCGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
*
50033853 ATTTGATTTGATTTGGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
1 ATTTGATTTGATTTCGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
50033905 A
1 A
50033906 GAAAATTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 38 0.78
52 11 0.22
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (52 bp):
ATTTGATTTGATTTCGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
Found at i:50042378 original size:25 final size:26
Alignment explanation
Indices: 50042335--50042404 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
50042325 TTTTCTCGAC
*
50042335 ATTTTACCAGGGGTAAAATCATCATA
1 ATTTTACCAGAGGTAAAATCATCATA
* *
50042361 ATTTTACC-GAGGTAAAATCGTTATA
1 ATTTTACCAGAGGTAAAATCATCATA
*
50042386 ATTTTATCA-AGGGTAAAAT
1 ATTTTACCAGA-GGTAAAAT
50042405 TGGGATTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 22 0.58
26 16 0.42
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (26 bp):
ATTTTACCAGAGGTAAAATCATCATA
Found at i:50053259 original size:24 final size:24
Alignment explanation
Indices: 50053229--50053279 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
50053219 TGGGATACTC
50053229 AGTTCATGCTTGAGCTTGGATGTA
1 AGTTCATGCTTGAGCTTGGATGTA
50053253 AGTTCATGCTTGAGCTTGGATGTA
1 AGTTCATGCTTGAGCTTGGATGTA
50053277 AGT
1 AGT
50053280 GATTTTGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (24 bp):
AGTTCATGCTTGAGCTTGGATGTA
Found at i:50064026 original size:10 final size:10
Alignment explanation
Indices: 50064011--50064035 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
50064001 TTAGTAACTA
50064011 TATTTTATAT
1 TATTTTATAT
50064021 TATTTTATAT
1 TATTTTATAT
50064031 TATTT
1 TATTT
50064036 ATTTGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTATAT
Done.