Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013390.1 Kokia drynarioides strain JFW-HI SEQ_128414, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 137520
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:136 original size:12 final size:12
Alignment explanation
Indices: 119--178 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
109 AAAATTGAAA
119 TATTAAATAATT
1 TATTAAATAATT
*
131 TATTAAAATAAGT
1 TATT-AAATAATT
* *
144 AATTATATTAATT
1 TATTA-AATAATT
157 ATATT-AATAATT
1 -TATTAAATAATT
*
169 TATTATATAA
1 TATTAAATAA
179 CTAAATATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
11 4 0.11
12 15 0.41
13 15 0.41
14 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
TATTAAATAATT
Found at i:872 original size:25 final size:25
Alignment explanation
Indices: 836--899 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
826 AAAAACTAAT
*
836 TTTTAT-ATTTTTGAATTTTTAAAAA
1 TTTTATGATTTTTCAATTTTT-AAAA
* *
861 TTTTATGATTTTTCAATTTTTCAAT
1 TTTTATGATTTTTCAATTTTTAAAA
886 TTTTATGTATTTTT
1 TTTTATG-ATTTTT
900 TTATAGTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.44
26 19 0.56
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.66
Consensus pattern (25 bp):
TTTTATGATTTTTCAATTTTTAAAA
Found at i:2459 original size:21 final size:21
Alignment explanation
Indices: 2435--2479 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2425 TGAAAAAAAA
*
2435 TTTGTTACTATTTTTT-ACTGT
1 TTTGCTACT-TTTTTTCACTGT
*
2456 TTTGCTACTTTTTTTCATTGT
1 TTTGCTACTTTTTTTCACTGT
2477 TTT
1 TTT
2480 ACTATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (21 bp):
TTTGCTACTTTTTTTCACTGT
Found at i:4558 original size:30 final size:29
Alignment explanation
Indices: 4524--4683 Score: 141
Period size: 30 Copynumber: 5.4 Consensus size: 29
4514 AAACTTTCCA
*
4524 AAAATCATATTTTGACCC-CTAAACTTCTCT
1 AAAATCACATTTTGACCCTC-AAACTTCT-T
* * *
4554 AAAATTACATTTTTG-CCATCAAACTTCTA
1 AAAATCACA-TTTTGACCCTCAAACTTCTT
* *
4583 AAAATCACATTTTTACCCTCGAACTTCTT
1 AAAATCACATTTTGACCCTCAAACTTCTT
*
4612 AAAAATCACATTTTTACCCTCAAACTTCTT
1 -AAAATCACATTTTGACCCTCAAACTTCTT
* *
4642 AAAATTTACATTTTG--CCTCCAAACTTC-C
1 AAAA-TCACATTTTGACCCT-CAAACTTCTT
4670 AAACATCACATTTT
1 AAA-ATCACATTTT
4684 AACCTCGATC
Statistics
Matches: 109, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
28 18 0.17
29 32 0.29
30 53 0.49
31 6 0.06
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATCACATTTTGACCCTCAAACTTCTT
Found at i:4596 original size:29 final size:29
Alignment explanation
Indices: 4510--4741 Score: 172
Period size: 29 Copynumber: 8.0 Consensus size: 29
4500 CCCAAAAGGT
* * *
4510 CCCT-AAACTTTCCAAAAATCATATTTTGA
1 CCCTCAAAC-TTCTAAAAATCACATTTTTA
* * *
4539 CCC-CTAAACTTCTCTAAAATTACATTTTTG
1 CCCTC-AAACTTCT-AAAAATCACATTTTTA
*
4569 CCATCAAACTTCTAAAAATCACATTTTTA
1 CCCTCAAACTTCTAAAAATCACATTTTTA
*
4598 CCCTCGAACTTCTTAAAAATCACATTTTTA
1 CCCTCAAACTTC-TAAAAATCACATTTTTA
* *
4628 CCCTCAAACTTCTTAAAATTTACA-TTTT-
1 CCCTCAAACTTC-TAAAAATCACATTTTTA
* * *
4656 GCCTCCAAACTTCCAAACATCACA-TTTTA
1 CCCT-CAAACTTCTAAAAATCACATTTTTA
* * * * *
4685 ACCTCGATCTTCCAAAAATTACATTTTTA
1 CCCTCAAACTTCTAAAAATCACATTTTTA
*
4714 CCC-CTAAACTT-TCAAAAATCAAATTTTT
1 CCCTC-AAACTTCT-AAAAATCACATTTTT
4742 GTCTCGGACT
Statistics
Matches: 162, Mismatches: 31, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
28 30 0.19
29 68 0.42
30 63 0.39
31 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (29 bp):
CCCTCAAACTTCTAAAAATCACATTTTTA
Found at i:4608 original size:59 final size:59
Alignment explanation
Indices: 4514--4741 Score: 191
Period size: 59 Copynumber: 3.9 Consensus size: 59
4504 AAAGGTCCCT
* * * *
4514 AAACTTTCCAAAAATCATATTTTGACCCCTAAACTTCTCT-AAAATTACATTTTTGCCATC
1 AAAC-TTCTAAAAATCACATTTTGACCCCTAAACTTCT-TAAAAATCACATTTTTACCATC
* * *
4574 AAACTTCTAAAAATCACATTTTTA-CCCTCGAACTTCTTAAAAATCACATTTTTACCCTC
1 AAACTTCTAAAAATCACATTTTGACCCCT-AAACTTCTTAAAAATCACATTTTTACCATC
* * * * *
4633 AAACTTCTTAAAATTTACATTTTG-CCTCC-AAACTTC-CAAACATCACATTTTAACC-TC
1 AAACTTC-TAAAAATCACATTTTGACC-CCTAAACTTCTTAAAAATCACATTTTTACCATC
* * * * * * *
4690 GATCTTCCAAAAATTACATTTTTACCCCTAAACTT-TCAAAAATCAAATTTTT
1 AAACTTCTAAAAATCACATTTTGACCCCTAAACTTCTTAAAAATCACATTTTT
4742 GTCTCGGACT
Statistics
Matches: 138, Mismatches: 22, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
56 15 0.11
57 28 0.20
58 21 0.15
59 54 0.39
60 18 0.13
61 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (59 bp):
AAACTTCTAAAAATCACATTTTGACCCCTAAACTTCTTAAAAATCACATTTTTACCATC
Found at i:4820 original size:30 final size:29
Alignment explanation
Indices: 4777--4841 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
4767 CTTTACATCG
* *
4777 AACTCTCCTAAAATGACATTTTTACTCCTAA
1 AACTTTCCTAAAATGACATTTTAAC-CCT-A
* *
4808 AACTTTCC-AAAATTATATTTTAACCCTA
1 AACTTTCCTAAAATGACATTTTAACCCTA
4836 AACTTT
1 AACTTT
4842 TTGAAGCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 7 0.23
29 3 0.10
30 13 0.43
31 7 0.23
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
AACTTTCCTAAAATGACATTTTAACCCTA
Found at i:14943 original size:39 final size:40
Alignment explanation
Indices: 14894--15535 Score: 428
Period size: 39 Copynumber: 16.5 Consensus size: 40
14884 GAAGATTTTG
*
14894 ATCTCTTACCCCGAGCCTAAGGCAGA-T-CACCATTAGCCA
1 ATCTCTTACCCCGAGCCT-GGGCAGATTGCACCATTAGCCA
* * * *
14933 ATCTTTTACCCTGAGCCTAGGGCAGATTGCAGCCACT---CG
1 ATCTCTTACCCCGAGCCT-GGGCAGATTGCA-CCATTAGCCA
* *
14972 ATCTCTTACCCCGAGCCTAGGGCA-AAT-CACCATCAGCCA
1 ATCTCTTACCCCGAGCCT-GGGCAGATTGCACCATTAGCCA
* * *
15011 ATCTCTTACCTCAAGCCTGGGCAGATTGCAGCCATT---CG
1 ATCTCTTACCCCGAGCCTGGGCAGATTGCA-CCATTAGCCA
*
15049 ATCTCTTACCCCGAGCCTGGGGCA-AAT-CACCATTAGCCA
1 ATCTCTTACCCCGAGCCT-GGGCAGATTGCACCATTAGCCA
* * *
15088 ATCTCTTACCTCGAGCCTGGGCAGATTGTAGCCATT---CG
1 ATCTCTTACCCCGAGCCTGGGCAGATTGCA-CCATTAGCCA
* * *
15126 ATCTCTTACCCCGAACCTTGGACAGATTGGAGCCATT---CA
1 ATCTCTTACCCCGAGCC-TGGGCAGATTGCA-CCATTAGCCA
* * * * *
15165 ATCTCTAACCCCAAGCTTAAGGCAGA-T-CACCATCAGCCA
1 ATCTCTTACCCCGAGCCT-GGGCAGATTGCACCATTAGCCA
* *
15204 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CACCATCAGCCA
1 ATCTCTTACCCCGAGCCT-GGGCAGATTGCACCATTAGCCA
* *
15243 ATCTCTTACCCCGAGCCTGGGTAGATTGCAGCCATT---CG
1 ATCTCTTACCCCGAGCCTGGGCAGATTGCA-CCATTAGCCA
* * *
15281 ATCTCTTACCCCGAGCTTGGGATAGATTGCAGCCATT---CG
1 ATCTCTTACCCCGAGCCTGGG-CAGATTGCA-CCATTAGCCA
* *
15320 ATCTCTTACCCCGAGCCTGGGCAGATTACAACCATT---CG
1 ATCTCTTACCCCGAGCCTGGGCAGATTGC-ACCATTAGCCA
* * ** * *
15358 ATCTCTTACCACGAGCCTGGGGCAGA-T-AATTATCAACCA
1 ATCTCTTACCCCGAGCCT-GGGCAGATTGCACCATTAGCCA
* * *
15397 ATCTCTTACCCCGAGCTTTGGGCAGATTGCAGTCATTCGACC-
1 ATCTCTTACCCCGAGC-CTGGGCAGATTGCA-CCATTAG-CCA
*
15439 -TCT-TTACCCTGAGCCTGTGGCAGA-T-CACCATTAGCCA
1 ATCTCTTACCCCGAGCCTG-GGCAGATTGCACCATTAGCCA
* *
15476 ATCTCTTACCCCGAGCCTGAGGCA-AAT-CACCATCAGCCA
1 ATCTCTTACCCCGAGCCTG-GGCAGATTGCACCATTAGCCA
15515 ATCTCTTACCCCGAGCCTGGG
1 ATCTCTTACCCCGAGCCTGGG
15536 GCTGATTACA
Statistics
Matches: 494, Mismatches: 69, Indels: 81
0.77 0.11 0.13
Matches are distributed among these distances:
36 17 0.03
37 10 0.02
38 115 0.23
39 300 0.61
40 24 0.05
41 19 0.04
42 7 0.01
43 2 0.00
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (40 bp):
ATCTCTTACCCCGAGCCTGGGCAGATTGCACCATTAGCCA
Found at i:15065 original size:116 final size:115
Alignment explanation
Indices: 14894--15563 Score: 500
Period size: 116 Copynumber: 5.8 Consensus size: 115
14884 GAAGATTTTG
* * * *
14894 ATCTCTTACCCCGAGCCTAAGGCAGA-T-CA-CCATTAGCCAATCTTTTACCCTGAGCCTAGGGC
1 ATCTCTTACCCCGAGCCT-GGGCAGATTGCAGCCATT---CGATCTCTTACCCCGAGCCTAGGGC
* *
14956 AGATTGCAGCCACTCGATCTCTTACCCCGAGCCTAGGGCAAATCACCATCAGCCA
62 AGATTGCAGCCATTCGATCTCTTACCCCGAGCCT-GGGCAGATCACCATCAGCCA
* * * *
15011 ATCTCTTACCTCAAGCCTGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCCTGGGGCA-AA
1 ATCTCTTACCCCGAGCCTGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCCTAGGGCAGAT
* * *
15075 T-CA-CCATTAGCCAATCTCTTACCTCGAGCCTGGGCAGATTGTAGCCATTC-G---
66 TGCAGCCATT---CGATCTCTTACCCCGAGCCTGGGCAGA-T-CA-CCA-TCAGCCA
* * * * * * * *
15126 ATCTCTTACCCCGAACCTTGGACAGATTGGAGCCATTCAATCTCTAACCCCAAGCTTAAGGCAGA
1 ATCTCTTACCCCGAGCC-TGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCCTAGGGCAGA
*
15191 -T-CA-CCA-TCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
65 TTGCAGCCATTC-G---ATCTCTTACCCCGAGCCT-GGGCAGATCACCATCAGCCA
* * *
15243 ATCTCTTACCCCGAGCCTGGGTAGATTGCAGCCATTCGATCTCTTACCCCGAG-CTTGGGATAGA
1 ATCTCTTACCCCGAGCCTGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCCTAGGG-CAGA
* * * ** *
15307 TTGCAGCCATTCGATCTCTTACCCCGAGCCTGGGCAGATTACAACCATTCG
65 TTGCAGCCATTCGATCTCTTACCCCGAGCCTGGGCAGATCACCATCAGCCA
* * * ** * * *
15358 ATCTCTTACCACGAGCCTGGGGCAGATAAT-TA-TCAACCAATCTCTTACCCCGAGCTTTGGGCA
1 ATCTCTTACCCCGAGCCT-GGGCAGAT--TGCAGCCATTCGATCTCTTACCCCGAGCCTAGGGCA
* * * *
15421 GATTGCAGTCATTCGACCTCTTTACCCTGAGCCTGTGGCAGATCACCATTAGCCA
63 GATTGCAGCCATTCGATCTC-TTACCCCGAGCCTG-GGCAGATCACCATCAGCCA
* *
15476 ATCTCTTACCCCGAGCCTGAGGCA-AAT-CA-CCA-TCAGCCAATCTCTTACCCCGAGCCTGGGG
1 ATCTCTTACCCCGAGCCTG-GGCAGATTGCAGCCATTC-G---ATCTCTTACCCCGAGCCTAGGG
* * *
15537 CTGATTACAGTCATTCGATCTCTTACC
61 CAGATTGCAGCCATTCGATCTCTTACC
15564 TCGATCACGG
Statistics
Matches: 440, Mismatches: 76, Indels: 74
0.75 0.13 0.13
Matches are distributed among these distances:
112 1 0.00
113 6 0.01
114 7 0.02
115 62 0.14
116 201 0.46
117 69 0.16
118 81 0.18
119 11 0.03
120 2 0.00
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (115 bp):
ATCTCTTACCCCGAGCCTGGGCAGATTGCAGCCATTCGATCTCTTACCCCGAGCCTAGGGCAGAT
TGCAGCCATTCGATCTCTTACCCCGAGCCTGGGCAGATCACCATCAGCCA
Found at i:15072 original size:77 final size:77
Alignment explanation
Indices: 14893--15537 Score: 591
Period size: 77 Copynumber: 8.3 Consensus size: 77
14883 AGAAGATTTT
** * * * *
14893 GATCTCTTACCCCGAGCCTAAGGCAGATCACCATTAGCCAATCTTTTACCCTGAGCCTAGGGCAG
1 GATCTCTTACCCCGAGCCTGGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCT-GGGCAG
*
14958 ATTGCAGCCACTC
65 ATTGCAGCCATTC
* * *
14971 GATCTCTTACCCCGAGCCTAGGGCAAATCACCATCAGCCAATCTCTTACCTCAAGCCTGGGCAGA
1 GATCTCTTACCCCGAGCCTGGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGCAGA
15036 TTGCAGCCATTC
66 TTGCAGCCATTC
* *
15048 GATCTCTTACCCCGAGCCTGGGGCAAATCACCATTAGCCAATCTCTTACCTCGAGCCTGGGCAGA
1 GATCTCTTACCCCGAGCCTGGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGCAGA
*
15113 TTGTAGCCATTC
66 TTGCAGCCATTC
* * * * * * * * * *
15125 GATCTCTTACCCCGAACCTTGGACAGATTGGAGCCAT---TCAATCTCTAACCCCAAGCTTAAGG
1 GATCTCTTACCCCGAGCCTGGGGCA-AAT-CA-CCATCAGCCAATCTCTTACCCCGAGCCT-GGG
15187 CAGA-T-CA-CCA-TC
62 CAGATTGCAGCCATTC
* *
15199 AGCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGG
1 -G---ATCTCTTACCCCGAGCCTGGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTGGG
*
15264 TAGATTGCAGCCATTC
62 CAGATTGCAGCCATTC
* ** *
15280 GATCTCTTACCCCGAGCTTGGGATAGATTGCAGCCATTC-G---ATCTCTTACCCCGAGCCTGGG
1 GATCTCTTACCCCGAGCCTGGGGCA-AAT-CA-CCA-TCAGCCAATCTCTTACCCCGAGCCTGGG
* *
15341 CAGATTACAACCATTC
62 CAGATTGCAGCCATTC
* * * ** * *
15357 GATCTCTTACCACGAGCCTGGGGCAGATAATTATCAACCAATCTCTTACCCCGAGCTTTGGGCAG
1 GATCTCTTACCCCGAGCCTGGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGC-CTGGGCAG
*
15422 ATTGCAGTCATTC
65 ATTGCAGCCATTC
* * * * *
15435 GACCTCTTTACCCTGAGCCTGTGGCAGATCACCATTAGCCAATCTCTTACCCCGAGCCTGAGGCA
1 GATCTC-TTACCCCGAGCCTGGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTG-GGCA
*
15500 -AAT-CA-CCA-TC
64 GATTGCAGCCATTC
15510 AGCCAATCTCTTACCCCGAGCCTGGGGC
1 -G---ATCTCTTACCCCGAGCCTGGGGC
15538 TGATTACAGT
Statistics
Matches: 464, Mismatches: 73, Indels: 60
0.78 0.12 0.10
Matches are distributed among these distances:
73 2 0.00
74 3 0.01
75 11 0.02
76 6 0.01
77 231 0.50
78 140 0.30
79 55 0.12
80 12 0.03
81 4 0.01
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (77 bp):
GATCTCTTACCCCGAGCCTGGGGCAAATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGCAGA
TTGCAGCCATTC
Found at i:16017 original size:17 final size:17
Alignment explanation
Indices: 15995--16098 Score: 127
Period size: 17 Copynumber: 6.1 Consensus size: 17
15985 CCAATTTTTA
*
15995 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
* *
16012 ATTTTAAGTTTAAATAT
1 ATTTTAAATTTAAATTT
*
16029 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* * *
16046 ATTCTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
16063 ATTTTAAAATTTAAATTT
1 ATTTT-AAATTTAAATTT
*
16081 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
16098 A
1 A
16099 AAGTTTATTA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
17 57 0.79
18 15 0.21
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:16105 original size:7 final size:6
Alignment explanation
Indices: 15991--16105 Score: 53
Period size: 6 Copynumber: 19.7 Consensus size: 6
15981 TGAACCAATT
* * * * * *
15991 TTTAAT TTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TAT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
16037 TTTAAA CTT--A TTCTGAG TTTAAA TTT-AT TTTAAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
*
16083 TTTGAA TTTAAA TTTAAA GTTTA
1 TTTAAA TTTAAA TTTAAA -TTTA
16106 TTAAAAGTCC
Statistics
Matches: 81, Mismatches: 19, Indels: 17
0.69 0.16 0.15
Matches are distributed among these distances:
4 2 0.02
5 16 0.20
6 53 0.65
7 10 0.12
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:17918 original size:30 final size:29
Alignment explanation
Indices: 17875--17947 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
17865 AAGGTCTCTG
*
17875 AACTTTCCAAAAATCT-TATTTTGACCCCTA
1 AACTTTCCAAAAAT-TAAATTTT-ACCCCTA
* *
17905 AACTTTTCTAAAATTACAATTTTACCCCTA
1 AACTTTCCAAAAATTA-AATTTTACCCCTA
17935 AAC-TTCCAAAAAT
1 AACTTTCCAAAAAT
17948 CGCATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 9 0.25
30 22 0.61
31 5 0.14
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (29 bp):
AACTTTCCAAAAATTAAATTTTACCCCTA
Found at i:17956 original size:29 final size:30
Alignment explanation
Indices: 17874--18128 Score: 224
Period size: 29 Copynumber: 8.7 Consensus size: 30
17864 AAAGGTCTCT
** *
17874 GAACTTTCCAAAAATCTTATTTTGACCCCT-
1 GAAC-TTCCAAAAATCACATTTTTACCCCTC
* * * * *
17904 AAACTTTTCTAAAATTACAATTTTACCCCT-
1 GAAC-TTCCAAAAATCACATTTTTACCCCTC
* * *
17934 AAACTTCCAAAAATCGCATTTTTA-CCGTC
1 GAACTTCCAAAAATCACATTTTTACCCCTC
17963 GAAC-T-CAAAAATCACATTTTTA-CCCTC
1 GAACTTCCAAAAATCACATTTTTACCCCTC
** *
17990 GAACTTTTAAAAATCTCATTTTTA-CCCTC
1 GAACTTCCAAAAATCACATTTTTACCCCTC
*
18019 GAACTTCTCAAAAATCACATTTTT-GCCCTC
1 GAACTTC-CAAAAATCACATTTTTACCCCTC
*
18049 GAACTTCCAAAAATCACATTTTTACTCCT-
1 GAACTTCCAAAAATCACATTTTTACCCCTC
* * * *
18078 GATCTTACAAAAATTACATTTTTGCCCC-C
1 GAACTTCCAAAAATCACATTTTTACCCCTC
*
18107 AAACTTCCAAAAATCACATTTT
1 GAACTTCCAAAAATCACATTTT
18129 GCCTCAGACT
Statistics
Matches: 185, Mismatches: 33, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
27 24 0.13
28 5 0.03
29 101 0.55
30 55 0.30
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (30 bp):
GAACTTCCAAAAATCACATTTTTACCCCTC
Found at i:18051 original size:59 final size:59
Alignment explanation
Indices: 17935--18167 Score: 250
Period size: 59 Copynumber: 4.1 Consensus size: 59
17925 TTTACCCCTA
* * *
17935 AACTTCCAAAAATCGCATTTTTACCGTCGAA---CTCAAAAATCACATTTTTACCCTCG
1 AACTTCCAAAAATCACATTTTTACCCTCGAACTTCTCAAAAATCACATTTTTGCCCTCG
** *
17991 AACTTTTAAAAATCTCATTTTTACCCTCGAACTTCTCAAAAATCACATTTTTGCCCTCG
1 AACTTCCAAAAATCACATTTTTACCCTCGAACTTCTCAAAAATCACATTTTTGCCCTCG
* * * * *
18050 AACTTCCAAAAATCACATTTTTACTCCT-GATCTT-ACAAAAATTACATTTTTGCCCCCA
1 AACTTCCAAAAATCACATTTTTAC-CCTCGAACTTCTCAAAAATCACATTTTTGCCCTCG
* * * *
18108 AACTTCCAAAAATCACA-TTTT-GCCTC-AGACTTCTCATAAATCACATATTT-ACCTCG
1 AACTTCCAAAAATCACATTTTTACCCTCGA-ACTTCTCAAAAATCACATTTTTGCCCTCG
18164 AACT
1 AACT
18168 CTCCGAAGCT
Statistics
Matches: 148, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
55 4 0.03
56 37 0.25
57 17 0.11
58 37 0.25
59 50 0.34
60 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (59 bp):
AACTTCCAAAAATCACATTTTTACCCTCGAACTTCTCAAAAATCACATTTTTGCCCTCG
Found at i:18568 original size:99 final size:96
Alignment explanation
Indices: 18433--18617 Score: 307
Period size: 99 Copynumber: 1.9 Consensus size: 96
18423 AAATATTTAA
* * *
18433 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAT
1 AAATCAAGGCAATATTCATTTATCTCGGATTTTGAAAATTTGTGCCTTAACTTACTAGGCACGA-
*
18498 TTTTTTTCTTCAAACCGAGATAATCAATACTCTT
65 --CTTTTCTTCAAACCGAGATAATCAATACTCTT
18532 AAATCAAGGCAATATTCATTTATCTCGGATTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
1 AAATCAAGGCAATATTCATTTATCTCGGATTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
18597 TTTTCTTCAAACCGAGATAAT
66 TTTTCTTCAAACCGAGATAAT
18618 TGAATATCCT
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
96 21 0.26
99 61 0.74
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (96 bp):
AAATCAAGGCAATATTCATTTATCTCGGATTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
TTTTCTTCAAACCGAGATAATCAATACTCTT
Found at i:19432 original size:17 final size:17
Alignment explanation
Indices: 19378--19433 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
19368 CTAGTACGGA
*
19378 GATTTTAAAAAATTTA-
1 GATTTTAAAAATTTTAT
19394 -ATTTT-AAAATTTT-T
1 GATTTTAAAAATTTTAT
19408 GAATTTTTAAAAATTTTAT
1 G-A-TTTTAAAAATTTTAT
19427 GATTTTA
1 GATTTTA
19434 CAGTTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
14 7 0.21
15 5 0.15
16 1 0.03
17 9 0.27
18 9 0.27
19 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
GATTTTAAAAATTTTAT
Found at i:21359 original size:24 final size:24
Alignment explanation
Indices: 21341--21415 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
21331 AGTTTGACTC
21341 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
*
21365 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
* * *
21389 AAACAATTAAACAAATTTTAACTG
1 AAACAAATAAACAAAGTTTAATTG
21413 AAA
1 AAA
21416 TATTATTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.57, C:0.09, G:0.08, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:23374 original size:24 final size:24
Alignment explanation
Indices: 23346--23414 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
23336 GACTAATAAG
*
23346 AGTTTGACTCAAACAAATAAACAA
1 AGTTTAACTCAAACAAATAAACAA
* * *
23370 AGTTTAATTGAAACAAATAAACAG
1 AGTTTAACTCAAACAAATAAACAA
* * *
23394 AGTTTAATTGAAACAATTAAA
1 AGTTTAACTCAAACAAATAAA
23415 TAGATTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (24 bp):
AGTTTAACTCAAACAAATAAACAA
Found at i:23423 original size:24 final size:24
Alignment explanation
Indices: 23356--23430 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
23346 AGTTTGACTC
*
23356 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
23380 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* * * *
23404 AAACAATTAAATAGATTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
23428 AAA
1 AAA
23431 GATTATTCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.56, C:0.08, G:0.09, T:0.27
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:24088 original size:23 final size:24
Alignment explanation
Indices: 24044--24094 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
24034 GTTTGAGCAA
*
24044 TTTAATTTTTTTCTTTTATGTTCT
1 TTTAATTTCTTTCTTTTATGTTCT
*
24068 TTTAACTTTCTTT-TTTT-TGTTTT
1 TTTAA-TTTCTTTCTTTTATGTTCT
24091 TTTA
1 TTTA
24095 TTCTCTTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 9 0.38
25 6 0.25
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTAATTTCTTTCTTTTATGTTCT
Found at i:26075 original size:20 final size:21
Alignment explanation
Indices: 26017--26076 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
26007 TCATGAACTT
*
26017 CAAATCTCAAACCCTTAAACC
1 CAAATCTCAAACTCTTAAACC
*
26038 CAAATCTCAAA-TCTTAAATC
1 CAAATCTCAAACTCTTAAACC
*
26058 CGAATCTCAAACTC-TAAAC
1 CAAATCTCAAACTCTTAAAC
26077 TTGAGCCTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.43, C:0.32, G:0.02, T:0.23
Consensus pattern (21 bp):
CAAATCTCAAACTCTTAAACC
Found at i:26426 original size:7 final size:7
Alignment explanation
Indices: 26410--26440 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
26400 GAAGAGGGGG
26410 AAAAGCA
1 AAAAGCA
*
26417 AAAGGCA
1 AAAAGCA
26424 AAAAGCA
1 AAAAGCA
26431 AAAAGCA
1 AAAAGCA
26438 AAA
1 AAA
26441 GAGAGAAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.71, C:0.13, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAGCA
Found at i:31422 original size:19 final size:20
Alignment explanation
Indices: 31398--31437 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
31388 TTCGAAATTG
31398 CCACTATTTTACA-ATTTTA
1 CCACTATTTTACAGATTTTA
*
31417 CCACTATTTTCCAGATTTTA
1 CCACTATTTTACAGATTTTA
31437 C
1 C
31438 AGTTTTACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.28, C:0.25, G:0.03, T:0.45
Consensus pattern (20 bp):
CCACTATTTTACAGATTTTA
Found at i:31464 original size:28 final size:28
Alignment explanation
Indices: 31398--31470 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
31388 TTCGAAATTG
31398 CCACTATTTTACAATTTTACCACTATTTT
1 CCAC-ATTTTACAATTTTACCACTATTTT
* * * *
31427 CCAGATTTTACAGTTTTACCATTGTTTT
1 CCACATTTTACAATTTTACCACTATTTT
31455 CCATCATTTATACAAT
1 CCA-CATTT-TACAAT
31471 ATCAATCGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 24 0.67
29 7 0.19
30 5 0.14
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (28 bp):
CCACATTTTACAATTTTACCACTATTTT
Found at i:35601 original size:21 final size:21
Alignment explanation
Indices: 35570--35636 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
35560 CTATGTGATG
*
35570 CCCTAAATTGCACTACAGTGC
1 CCCTGAATTGCACTACAGTGC
*
35591 CCTTGAATTGCACTA-ATGTGC
1 CCCTGAATTGCACTACA-GTGC
35612 CCCTGAATTGCACTACAGTGC
1 CCCTGAATTGCACTACAGTGC
35633 CCCT
1 CCCT
35637 ATGAATGAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (21 bp):
CCCTGAATTGCACTACAGTGC
Found at i:37397 original size:25 final size:25
Alignment explanation
Indices: 37369--37462 Score: 158
Period size: 25 Copynumber: 3.9 Consensus size: 25
37359 GTACTGGGGA
37369 AACAGAAGCACACACAGTGCTGGGT
1 AACAGAAGCACACACAGTGCTGGGT
37394 AACAGAAGCACACACAGTGCT--G-
1 AACAGAAGCACACACAGTGCTGGGT
*
37416 AACAGAAGCACACATAGTGCTGGGT
1 AACAGAAGCACACACAGTGCTGGGT
37441 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
37463 AACAAAAGCG
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
22 20 0.31
23 1 0.02
24 1 0.02
25 42 0.66
ACGTcount: A:0.38, C:0.24, G:0.26, T:0.12
Consensus pattern (25 bp):
AACAGAAGCACACACAGTGCTGGGT
Found at i:37420 original size:47 final size:47
Alignment explanation
Indices: 37369--37471 Score: 188
Period size: 47 Copynumber: 2.2 Consensus size: 47
37359 GTACTGGGGA
37369 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
*
37416 AACAGAAGCACACATAGTGCTGGGTAACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
*
37463 AACAAAAGC
1 AACAGAAGC
37472 GCGCTAGCGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (47 bp):
AACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGCTG
Found at i:41988 original size:23 final size:23
Alignment explanation
Indices: 41958--42010 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
41948 CGCTAGCGCT
* *
41958 CTTACTGTTTCTCACTTCGTGTG
1 CTTACTGTTTCGCAATTCGTGTG
*
41981 CTTACTGTTTCGCAATTTGTGTG
1 CTTACTGTTTCGCAATTCGTGTG
*
42004 CCTACTG
1 CTTACTG
42011 ATTTGCGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (23 bp):
CTTACTGTTTCGCAATTCGTGTG
Found at i:42046 original size:22 final size:22
Alignment explanation
Indices: 41998--42071 Score: 103
Period size: 23 Copynumber: 3.3 Consensus size: 22
41988 TTTCGCAATT
* *
41998 TGTGTGCCTACTGATTTGCGCTA
1 TGTGTGCCTACTGA-TTGCACTG
*
42021 TGTGCGCCTACTGATTGCACTG
1 TGTGTGCCTACTGATTGCACTG
42043 TGTGTGCCTACTGGATTGCACTG
1 TGTGTGCCTACT-GATTGCACTG
42066 TGTGTG
1 TGTGTG
42072 TTTACTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.37
23 29 0.63
ACGTcount: A:0.12, C:0.22, G:0.30, T:0.36
Consensus pattern (22 bp):
TGTGTGCCTACTGATTGCACTG
Found at i:51757 original size:30 final size:29
Alignment explanation
Indices: 51700--51758 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
51690 GATTGTTTAA
*
51700 TGTGCAATTGTATACATGAACTTTGATTT
1 TGTGCAATTGTATACATAAACTTTGATTT
* *
51729 TGTGCAATTTTATACATAAAATTTTGATTT
1 TGTGCAATTGTATACAT-AAACTTTGATTT
51759 AATCTAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (29 bp):
TGTGCAATTGTATACATAAACTTTGATTT
Found at i:51940 original size:31 final size:29
Alignment explanation
Indices: 51905--51974 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
51895 ATATCAAAAT
* *
51905 TATACATCAACTGTGATTTAATGTGCAATTG
1 TATACATAAACTGTGATTT--TATGCAATTG
* *
51936 TATACATAAACTTTGATTTTATGCAATTT
1 TATACATAAACTGTGATTTTATGCAATTG
51965 TATACATAAA
1 TATACATAAA
51975 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (29 bp):
TATACATAAACTGTGATTTTATGCAATTG
Found at i:51961 original size:29 final size:30
Alignment explanation
Indices: 51905--51985 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
51895 ATATCAAAAT
* * *
51905 TATACATCAACTGTGATTTAATGTGCAATTG
1 TATACATAAACTTTGATTT-ATATGCAATTG
*
51936 TATACATAAACTTTGATTT-TATGCAATTT
1 TATACATAAACTTTGATTTATATGCAATTG
*
51965 TATACATAAAATTTTGATTTA
1 TATACAT-AAACTTTGATTTA
51986 ATCTAATTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 15 0.35
30 11 0.26
31 17 0.40
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (30 bp):
TATACATAAACTTTGATTTATATGCAATTG
Found at i:51999 original size:226 final size:225
Alignment explanation
Indices: 51605--52057 Score: 800
Period size: 226 Copynumber: 2.0 Consensus size: 225
51595 TGACTCAGTG
51605 ATTAAAATATCATAACACAATATCATAAGTAATTAAAACATAACATTTTAAATATAAGAGATAAA
1 ATTAAAATATCATAACACAATATCATAAGTAATTAAAACATAACATTTTAAATATAAGAGATAAA
* *
51670 TATCAAAACTATACATCAACGATTGTTTAATGTGCAATTGTATACATGAACTTTGATTTTGTGCA
66 TATCAAAACTATACATCAACGA-TGTTTAATGTGCAATTGTATACATAAACTTTGATTTTATGCA
* *
51735 ATTTTATACATAAAATTTTGATTTAATCTAATTCTTATAAATTATTAAGACAATTATTGATATAA
130 ATTTTATACATAAAATTTTGATTTAATCTAATTCTTATAAATTATTAAAACAATTATTAATATAA
*
51800 CATTATTTTATGTTTATATATTGCATACATA
195 CATCATTTTATGTTTATATATTGCATACATA
*
51831 ATTAAAATATCATAACACAATATCATAAGTAATTAAAACATAACATTTTAAATATAAGGGATAAA
1 ATTAAAATATCATAACACAATATCATAAGTAATTAAAACATAACATTTTAAATATAAGAGATAAA
*
51896 TATCAAAATTATACATCAACTG-TGATTTAATGTGCAATTGTATACATAAACTTTGATTTTATGC
66 TATCAAAACTATACATCAAC-GATG-TTTAATGTGCAATTGTATACATAAACTTTGATTTTATGC
51960 AATTTTATACATAAAATTTTGATTTAATCTAATTCTTATAAATTATTAAAACAATTATTAATATA
129 AATTTTATACATAAAATTTTGATTTAATCTAATTCTTATAAATTATTAAAACAATTATTAATATA
*
52025 ACATCATTTTATGTTTATATATTGCATGCATA
194 ACATCATTTTATGTTTATATATTGCATACATA
52057 A
1 A
52058 ATAATTATAT
Statistics
Matches: 217, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
225 2 0.01
226 214 0.99
227 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (225 bp):
ATTAAAATATCATAACACAATATCATAAGTAATTAAAACATAACATTTTAAATATAAGAGATAAA
TATCAAAACTATACATCAACGATGTTTAATGTGCAATTGTATACATAAACTTTGATTTTATGCAA
TTTTATACATAAAATTTTGATTTAATCTAATTCTTATAAATTATTAAAACAATTATTAATATAAC
ATCATTTTATGTTTATATATTGCATACATA
Found at i:54343 original size:15 final size:15
Alignment explanation
Indices: 54319--54366 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
54309 GTAATTTAAA
54319 TTTAATACTTAATTT
1 TTTAATACTTAATTT
* *
54334 TTTAACACTTATTTT
1 TTTAATACTTAATTT
*
54349 TTTAGTACTTAATTT
1 TTTAATACTTAATTT
54364 TTT
1 TTT
54367 CAATTTATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTAATACTTAATTT
Found at i:61990 original size:14 final size:13
Alignment explanation
Indices: 61971--62014 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
61961 CAAAAATCTA
61971 TTTTCAAGACTCTG
1 TTTTCAAG-CTCTG
*
61985 TTTTCAAGTTCTG
1 TTTTCAAGCTCTG
* *
61998 TTTTAAAGCTATG
1 TTTTCAAGCTCTG
62011 TTTT
1 TTTT
62015 ATGTGAGCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (13 bp):
TTTTCAAGCTCTG
Found at i:67664 original size:17 final size:17
Alignment explanation
Indices: 67640--67677 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
67630 ATATAAATGA
67640 TTAA-TTTTAATAAAAT
1 TTAATTTTTAATAAAAT
* *
67656 TTAATTTTTTATATAAT
1 TTAATTTTTAATAAAAT
67673 TTAAT
1 TTAAT
67678 ACTTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAATTTTTAATAAAAT
Found at i:71757 original size:26 final size:28
Alignment explanation
Indices: 71728--71784 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
71718 TTTAAAGTTA
71728 TTTTAT-AT-CAAATATTAACAATATCC
1 TTTTATCATACAAATATTAACAATATCC
*
71754 TTTTATCATGAATAAATATTAACAATATCC
1 TTTTATCAT--ACAAATATTAACAATATCC
71784 T
1 T
71785 GCTACCAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 6 0.23
27 2 0.08
30 18 0.69
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (28 bp):
TTTTATCATACAAATATTAACAATATCC
Found at i:85346 original size:24 final size:24
Alignment explanation
Indices: 85272--85389 Score: 112
Period size: 24 Copynumber: 4.9 Consensus size: 24
85262 TTTCAGAAAA
* *
85272 TTAGCTCATACGAGCCCAGACAAA-A
1 TTAGCTCTTACGAGCCCA-A-AAAGG
* * *
85297 TTAGCTCATACAAGCCCAAATAGG
1 TTAGCTCTTACGAGCCCAAAAAGG
* * * *
85321 TTAGCTTTTACGAGTCCAGAATGG
1 TTAGCTCTTACGAGCCCAAAAAGG
*
85345 TTAGCTCTTACAAGCCCAAAAAGG
1 TTAGCTCTTACGAGCCCAAAAAGG
*
85369 TTAGCTCTTACGAGCCGAAAA
1 TTAGCTCTTACGAGCCCAAAA
85390 TCAGAATAAT
Statistics
Matches: 75, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
23 2 0.03
24 56 0.75
25 17 0.23
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAAAAAGG
Found at i:85430 original size:27 final size:27
Alignment explanation
Indices: 85372--85500 Score: 186
Period size: 27 Copynumber: 4.7 Consensus size: 27
85362 AAAAAGGTTA
* *
85372 GCTCTTACGAGCCGAAAATCAGAATAAT
1 GCTCTTTCGAGCC-AAAATCAGAATAAC
* *
85400 GCTCTTTCGAGCCAGAATCAAAATAAC
1 GCTCTTTCGAGCCAAAATCAGAATAAC
*
85427 GCTCTTTCGACCCAAAATCAGAATAAC
1 GCTCTTTCGAGCCAAAATCAGAATAAC
85454 GCTCTTTCGAGCCAAAATCAGAATAAC
1 GCTCTTTCGAGCCAAAATCAGAATAAC
* *
85481 GCTATTTCGAGCCAGAATCA
1 GCTCTTTCGAGCCAAAATCA
85501 AATTACTCCT
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 79 0.87
28 12 0.13
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (27 bp):
GCTCTTTCGAGCCAAAATCAGAATAAC
Found at i:92296 original size:57 final size:57
Alignment explanation
Indices: 92206--92317 Score: 134
Period size: 57 Copynumber: 2.0 Consensus size: 57
92196 ACAAGGGCTA
*** * * * *
92206 GAGATAGCCACAAATTTTTCTTTTAACAGAGATTAGACATAAAGGCTTCCTTTAATG
1 GAGATAGCCACAAAGACTTCCTTTAACAAAGATTAGACACAAAAGCTTCCTTTAATG
* * *
92263 GAGATAGCCACAAAGACTTCCTTTAATAAAGATTAGCCACAAAAGCTTCTTTTAA
1 GAGATAGCCACAAAGACTTCCTTTAACAAAGATTAGACACAAAAGCTTCCTTTAA
92318 CAGAGATTAG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (57 bp):
GAGATAGCCACAAAGACTTCCTTTAACAAAGATTAGACACAAAAGCTTCCTTTAATG
Found at i:92311 original size:29 final size:29
Alignment explanation
Indices: 92204--92328 Score: 112
Period size: 29 Copynumber: 4.4 Consensus size: 29
92194 CCACAAGGGC
*** *
92204 TAGAGA-TAGCCACAAATTTTTCTTTTAA
1 TAGAGATTAGCCACAAAAGCTTCCTTTAA
* * * *
92232 CAGAGATTAGACATAAAGGCTTCCTTTAA
1 TAGAGATTAGCCACAAAAGCTTCCTTTAA
*
92261 TGGAGA-TAGCCAC-AAAGACTTCCTTTAA
1 TAGAGATTAGCCACAAAAG-CTTCCTTTAA
* *
92289 TAAAGATTAGCCACAAAAGCTTCTTTTAA
1 TAGAGATTAGCCACAAAAGCTTCCTTTAA
*
92318 CAGAGATTAGC
1 TAGAGATTAGC
92329 TTCAAAGGCC
Statistics
Matches: 76, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
27 3 0.04
28 24 0.32
29 45 0.59
30 4 0.05
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (29 bp):
TAGAGATTAGCCACAAAAGCTTCCTTTAA
Found at i:92334 original size:29 final size:29
Alignment explanation
Indices: 92223--92345 Score: 83
Period size: 29 Copynumber: 4.2 Consensus size: 29
92213 CCACAAATTT
* *
92223 TTCTTTTAACAGAGATTAG-ACATAAAGGC
1 TTCTTTTAACAGAGATTAGCTCA-AAAGAC
* **
92252 TTCCTTTAATGGAGA-TAGC-CACAAAGAC
1 TTCTTTTAACAGAGATTAGCTCA-AAAGAC
* * * *
92280 TTCCTTTAATAAAGATTAGCCACAAAAG-C
1 TTCTTTTAACAGAGATTAG-CTCAAAAGAC
* *
92309 TTCTTTTAACAGAGATTAGCTTCAAAGGCC
1 TTCTTTTAACAGAGATTAGC-TCAAAAGAC
92339 TTCTTTT
1 TTCTTTT
92346 TAAAAATCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
28 24 0.32
29 37 0.49
30 13 0.17
31 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (29 bp):
TTCTTTTAACAGAGATTAGCTCAAAAGAC
Found at i:98344 original size:22 final size:20
Alignment explanation
Indices: 98316--98355 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
98306 TCATGATTAA
98316 CTTAATTAATCACTTATTTAGC
1 CTTAATTAATC-C-TATTTAGC
98338 CTTAATTAATCCTATTTA
1 CTTAATTAATCCTATTTA
98356 TAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (20 bp):
CTTAATTAATCCTATTTAGC
Found at i:101946 original size:24 final size:24
Alignment explanation
Indices: 101913--101963 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
101903 AGAAATAATC
* * * *
101913 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTATTTAGTTG
101937 TTTCAATTAAACTCTATTTAGTTG
1 TTTCAATTAAACTCTATTTAGTTG
101961 TTT
1 TTT
101964 GAGTCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAGTTG
Found at i:103922 original size:24 final size:24
Alignment explanation
Indices: 103889--103939 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
103879 AGAAATAATC
* * *
103889 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
103913 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
103937 TTT
1 TTT
103940 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:103948 original size:24 final size:24
Alignment explanation
Indices: 103897--103951 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
103887 TCTTTCAGTT
* * *
103897 AAACTTTGTTTATTTGTTTCAATT
1 AAACTCTGTTTAGTTGTTTCAATC
* *
103921 AAACTCTGTTTAGTTGTTTGAGTC
1 AAACTCTGTTTAGTTGTTTCAATC
103945 AAACTCT
1 AAACTCT
103952 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTAGTTGTTTCAATC
Found at i:104680 original size:30 final size:28
Alignment explanation
Indices: 104569--104684 Score: 88
Period size: 30 Copynumber: 3.9 Consensus size: 28
104559 TAAAAGTTGG
** *
104569 TAAAAAAAAATTTTGGACCCTTAAAAGCT
1 TAAAAAAATTTTTTGGACCTTTAAAAG-T
* * *
104598 AAAAAAAATTTTTGGGAGCTCTTAAAAGT
1 TAAAAAAATTTTTTGGACCT-TTAAAAGT
** * *
104627 TGGTAAAACTCTTTTTTGACCTTTAAAAGT
1 T-AAAAAAAT-TTTTTGGACCTTTAAAAGT
104657 TAAACAAAATTTTTTGGACCCTTTAAAA
1 TAAA-AAAATTTTTTGGA-CCTTTAAAA
104685 ACTAGAAAAC
Statistics
Matches: 65, Mismatches: 17, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
29 23 0.35
30 34 0.52
31 8 0.12
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (28 bp):
TAAAAAAATTTTTTGGACCTTTAAAAGT
Found at i:111641 original size:31 final size:32
Alignment explanation
Indices: 111603--111662 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
111593 ACCTGAACTC
* *
111603 GACACTTTTTCTTA-AATTGGTATTTAAATTT
1 GACACTTTTTCTTAGAATTGATACTTAAATTT
*
111634 GACACTTTTTTTTAGAATTGATACTTAAA
1 GACACTTTTTCTTAGAATTGATACTTAAA
111663 CTTTTTGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (32 bp):
GACACTTTTTCTTAGAATTGATACTTAAATTT
Found at i:112870 original size:32 final size:32
Alignment explanation
Indices: 112833--112893 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
112823 GAATCAGTAC
*
112833 GAGTTAGTAAATTAAACTAATTAATTTATCTT
1 GAGTTAGTAAATTAAACTAATCAATTTATCTT
* *
112865 GAGTTATTAAATTCAACTAATCAATTTAT
1 GAGTTAGTAAATTAAACTAATCAATTTAT
112894 AAATTTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (32 bp):
GAGTTAGTAAATTAAACTAATCAATTTATCTT
Found at i:113221 original size:13 final size:13
Alignment explanation
Indices: 113205--113247 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
113195 TAAATATTGA
*
113205 TTTTAAAAAATAT
1 TTTTAAATAATAT
*
113218 TTTTTAATAAT-T
1 TTTTAAATAATAT
113230 TTATTAAATAATAT
1 TT-TTAAATAATAT
113244 TTTT
1 TTTT
113248 TTATTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 3 0.12
13 19 0.76
14 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTTAAATAATAT
Found at i:113236 original size:26 final size:26
Alignment explanation
Indices: 113207--113257 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
113197 AATATTGATT
113207 TTAAAAAATATTTTTTAATAATTTTA
1 TTAAAAAATATTTTTTAATAATTTTA
* * *
113233 TTAAATAATATTTTTTTATTATTTT
1 TTAAAAAATATTTTTTAATAATTTT
113258 GGATAGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTAAAAAATATTTTTTAATAATTTTA
Found at i:113801 original size:22 final size:22
Alignment explanation
Indices: 113742--113801 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
113732 TAATAAGATT
113742 ATTATTAAATATAATTTAATAAA
1 ATTATT-AATATAATTTAATAAA
* * *
113765 AATAAT-ATTTAAATTTAATAAA
1 ATTATTAATAT-AATTTAATAAA
113787 ATTATTAATATAATT
1 ATTATTAATATAATT
113802 ATTTTTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 3 0.10
22 19 0.66
23 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTATTAATATAATTTAATAAA
Found at i:114453 original size:26 final size:25
Alignment explanation
Indices: 114416--114464 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
114406 ATATTGTTCT
*
114416 TATTAGTAGTAATAGTAGTTTATAA
1 TATTAGTAGTAATAATAGTTTATAA
* *
114441 TATTGGTATGTAATAATATTTTAT
1 TATTAGTA-GTAATAATAGTTTAT
114465 TATCTATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (25 bp):
TATTAGTAGTAATAATAGTTTATAA
Found at i:121981 original size:14 final size:13
Alignment explanation
Indices: 121940--121979 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
121930 GTGATATTTA
121940 AATTATTATTTTTT
1 AATTA-TATTTTTT
121954 AATTATATTTTTT
1 AATTATATTTTTT
* *
121967 AGTTCTATTTTTT
1 AATTATATTTTTT
121980 TAACAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (13 bp):
AATTATATTTTTT
Found at i:127984 original size:47 final size:47
Alignment explanation
Indices: 127950--128108 Score: 152
Period size: 41 Copynumber: 3.5 Consensus size: 47
127940 TCGTTTTCGA
127950 CAAATATGTGGTGGCTTGTCCACGATGTGTTATGTGACTGTTATCAG
1 CAAATATGTGGTGGCTTGTCCACGATGTGTTATGTGACTGTTATCAG
*
127997 CAAATATGTGGTGGCTTGTCCATGATG-G---TG-G-CTGTTATC-G
1 CAAATATGTGGTGGCTTGTCCACGATGTGTTATGTGACTGTTATCAG
* * ** * * *
128037 ACAATTATGTGGTGGTTTACCCATGATGTGCTATGTGACCGTTTATCAG
1 -CAAATATGTGGTGGCTTGTCCACGATGTGTTATGTGACTG-TTATCAG
* **
128086 TACCTATGTGGTGGCTTGTCCAC
1 CAAATATGTGGTGGCTTGTCCAC
128109 AAATGGTGTG
Statistics
Matches: 90, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
40 1 0.01
41 31 0.34
42 2 0.02
43 2 0.02
45 2 0.02
46 2 0.02
47 28 0.31
48 21 0.23
49 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (47 bp):
CAAATATGTGGTGGCTTGTCCACGATGTGTTATGTGACTGTTATCAG
Found at i:128050 original size:88 final size:89
Alignment explanation
Indices: 127946--128107 Score: 227
Period size: 88 Copynumber: 1.8 Consensus size: 89
127936 GTGATCGTTT
** * *
127946 TCGACAAATATGTGGTGGCTTGTCCACGATGTGTTATGTGACTG-TTATCAGCAAATATGTGGTG
1 TCGACAAATATGTGGTGGCTTACCCACGATGTGCTATGTGACCGTTTATCAGCAAATATGTGGTG
128010 GCTTGTCCATGATGGTGGCTGTTA
66 GCTTGTCCATGATGGTGGCTGTTA
* * * * **
128034 TCGACAATTATGTGGTGGTTTACCCATGATGTGCTATGTGACCGTTTATCAGTACCTATGTGGTG
1 TCGACAAATATGTGGTGGCTTACCCACGATGTGCTATGTGACCGTTTATCAGCAAATATGTGGTG
128099 GCTTGTCCA
66 GCTTGTCCA
128108 CAAATGGTGT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
88 37 0.59
89 26 0.41
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.36
Consensus pattern (89 bp):
TCGACAAATATGTGGTGGCTTACCCACGATGTGCTATGTGACCGTTTATCAGCAAATATGTGGTG
GCTTGTCCATGATGGTGGCTGTTA
Found at i:130078 original size:23 final size:23
Alignment explanation
Indices: 130003--130067 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
129993 AATTTTATTT
130003 AATACAAAACCCAAACCCTTTTTA
1 AATA-AAAACCCAAACCCTTTTTA
*
130027 AATAAAAAACCAAACCCTTTTTA
1 AATAAAAACCCAAACCCTTTTTA
130050 AATAAAAACCCAAACCCT
1 AATAAAAACCCAAACCCT
130068 GTCAAAGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 35 0.90
24 4 0.10
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.22
Consensus pattern (23 bp):
AATAAAAACCCAAACCCTTTTTA
Found at i:130142 original size:17 final size:17
Alignment explanation
Indices: 130116--130157 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
130106 CCAACCCAAC
*
130116 TCGACTCGACCTGTTGA
1 TCGACCCGACCTGTTGA
130133 TCGACCCGACCTGTTGA
1 TCGACCCGACCTGTTGA
*
130150 TCAACCCG
1 TCGACCCG
130158 TTGGCCGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.19, C:0.36, G:0.21, T:0.24
Consensus pattern (17 bp):
TCGACCCGACCTGTTGA
Found at i:130196 original size:14 final size:14
Alignment explanation
Indices: 130179--130215 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
130169 CCATTGACAA
130179 TTGATCGTTAATAG
1 TTGATCGTTAATAG
*
130193 TTGATCGTTGATAG
1 TTGATCGTTAATAG
*
130207 TTGACCGTT
1 TTGATCGTT
130216 GACTTTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (14 bp):
TTGATCGTTAATAG
Found at i:130216 original size:14 final size:14
Alignment explanation
Indices: 130164--130217 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
130154 CCCGTTGGCC
* *
130164 GTTGACCATTGACA
1 GTTGACCGTTGATA
* * *
130178 ATTGATCGTTAATA
1 GTTGACCGTTGATA
*
130192 GTTGATCGTTGATA
1 GTTGACCGTTGATA
130206 GTTGACCGTTGA
1 GTTGACCGTTGA
130218 CTTTTCCTGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (14 bp):
GTTGACCGTTGATA
Found at i:136465 original size:23 final size:23
Alignment explanation
Indices: 136430--136574 Score: 116
Period size: 23 Copynumber: 6.3 Consensus size: 23
136420 AAGTGCTGGG
136430 TAAT-AGAGAGCACACAAAGTGC
1 TAATCAGAGAGCACACAAAGTGC
* *
136452 TAATCAGAGGGCACACGAAGTGC
1 TAATCAGAGAGCACACAAAGTGC
* *
136475 TAATAACAGAGGGCACACAAAGTGT
1 TAAT--CAGAGAGCACACAAAGTGC
* * * *
136500 TGATCAGAGGGCATGA-AACGTGC
1 TAATCAGAGAGCA-CACAAAGTGC
* * *
136523 TAAACAGAGAGCACACACAGTGG
1 TAATCAGAGAGCACACAAAGTGC
* *
136546 TAAACAGA-AGCACACACAGTGC
1 TAATCAGAGAGCACACAAAGTGC
*
136568 TGATCAG
1 TAATCAG
136575 TAAGTGCACT
Statistics
Matches: 100, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
22 23 0.23
23 56 0.56
24 1 0.01
25 20 0.20
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (23 bp):
TAATCAGAGAGCACACAAAGTGC
Found at i:136490 original size:25 final size:25
Alignment explanation
Indices: 136405--136498 Score: 104
Period size: 25 Copynumber: 3.8 Consensus size: 25
136395 CCGAAGTACT
* **
136405 TAACAGAGGGCACA-TAAGTGCTGGG
1 TAACAGAGGGCACACAAAGTGCT-AA
* *
136430 TAATAGAGAGCACACAAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
*
136455 T--CAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
136478 TAACAGAGGGCACACAAAGTG
1 TAACAGAGGGCACACAAAGTG
136499 TTGATCAGAG
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
23 20 0.35
25 30 0.53
26 7 0.12
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.14
Consensus pattern (25 bp):
TAACAGAGGGCACACAAAGTGCTAA
Found at i:136491 original size:48 final size:48
Alignment explanation
Indices: 136408--136570 Score: 131
Period size: 48 Copynumber: 3.4 Consensus size: 48
136398 AAGTACTTAA
* ** *
136408 CAGAGGGCACATAAGTGCTGGGTAATAGAGAGCACACAAAGTGCTAAT
1 CAGAGGGCACAGAAGTGCTGAATAACAGAGAGCACACAAAGTGCTAAT
* * *
136456 CAGAGGGCACACGAAGTGCT-AATAACAGAGGGCACACAAAGTGTTGAT
1 CAGAGGGCACA-GAAGTGCTGAATAACAGAGAGCACACAAAGTGCTAAT
* * * *
136504 CAGAGGGCA-TGAAACGTGCT--A-AACAGAGAGCACACACAGTGGTAAA
1 CAGAGGGCACAG-AA-GTGCTGAATAACAGAGAGCACACAAAGTGCTAAT
* *
136550 CAGA-AGCACACACAGTGCTGA
1 CAGAGGGCACAGA-AGTGCTGA
136571 TCAGTAAGTG
Statistics
Matches: 92, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
45 9 0.10
46 26 0.28
47 3 0.03
48 47 0.51
49 7 0.08
ACGTcount: A:0.39, C:0.20, G:0.28, T:0.13
Consensus pattern (48 bp):
CAGAGGGCACAGAAGTGCTGAATAACAGAGAGCACACAAAGTGCTAAT
Done.