Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015011.1 Kokia drynarioides strain JFW-HI SEQ_130055, 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: 27149
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:2285 original size:27 final size:29
Alignment explanation
Indices: 2254--2325 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
2244 ACTAATATGT
2254 TATATAATTTATAAT-TAAATTT-ACATAA
1 TATATAATTTATAATATAAATTTGAC-TAA
*
2282 -ATAT-ATTCTATATATAATTAATTTGACTAA
1 TATATAATT-TATA-AT-ATAAATTTGACTAA
2312 TATATAATTTATAA
1 TATATAATTTATAA
2326 AACAAGTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
26 3 0.08
27 8 0.22
28 2 0.06
30 10 0.28
31 10 0.28
32 3 0.08
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (29 bp):
TATATAATTTATAATATAAATTTGACTAA
Found at i:2324 original size:29 final size:30
Alignment explanation
Indices: 2254--2324 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 30
2244 ACTAATATGT
2254 TATATAA-TT-TATAATTAAATTTACATAA
1 TATATAATTTATATAATTAAATTTACATAA
*
2282 -ATATATTCTATATATAATT-AATTTGAC-TAA
1 TATATAAT-T-TATATAATTAAATTT-ACATAA
2312 TATATAATTTATA
1 TATATAATTTATA
2325 AAACAAGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
27 5 0.14
29 5 0.14
30 10 0.29
31 15 0.43
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (30 bp):
TATATAATTTATATAATTAAATTTACATAA
Found at i:4918 original size:17 final size:17
Alignment explanation
Indices: 4896--4929 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4886 TATTTATAGA
4896 CAGTTATAAGTAAGTAT
1 CAGTTATAAGTAAGTAT
4913 CAGTTATAAGTAAGTAT
1 CAGTTATAAGTAAGTAT
4930 ACTTCTCGAA
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:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
CAGTTATAAGTAAGTAT
Found at i:5781 original size:3 final size:3
Alignment explanation
Indices: 5775--5807 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5765 TTTGAAAAGG
5775 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5808 AGGATATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6776 original size:6 final size:6
Alignment explanation
Indices: 6752--6823 Score: 69
Period size: 6 Copynumber: 12.5 Consensus size: 6
6742 ATTTGATAAG
* * * *
6752 AAATTT AAACTT AAA-TT AAATTT AAGTTT AAA-AT AAATTT AAACTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* *
6798 AAACTT AAA-AT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
6824 AACAAATTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
5 13 0.24
6 42 0.76
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (6 bp):
AAATTT
Found at i:6793 original size:23 final size:23
Alignment explanation
Indices: 6763--6823 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
6753 AATTTAAACT
**
6763 TAAA-TTAAATTTAAGTTTAAAA
1 TAAATTTAAATTTAAACTTAAAA
*
6785 TAAATTTAAACTTAAACTTAAAA
1 TAAATTTAAATTTAAACTTAAAA
6808 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
6824 AACAAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 4 0.12
23 30 0.88
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAATTTAAATTTAAACTTAAAA
Found at i:6794 original size:34 final size:36
Alignment explanation
Indices: 6733--6814 Score: 107
Period size: 34 Copynumber: 2.4 Consensus size: 36
6723 ATATTTAGGA
*
6733 TAAATTTAAATTTGATAAGAAATTTAAACTTAAA-T
1 TAAATTTAAATTTGAAAAGAAATTTAAACTTAAACT
* *
6768 TAAATTTAAGTTT-AAAATAAATTTAAACTTAAACT
1 TAAATTTAAATTTGAAAAGAAATTTAAACTTAAACT
*
6803 TAAA-ATAAATTT
1 TAAATTTAAATTT
6815 AAATTTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 24 0.59
35 17 0.41
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (36 bp):
TAAATTTAAATTTGAAAAGAAATTTAAACTTAAACT
Found at i:6822 original size:17 final size:17
Alignment explanation
Indices: 6718--6852 Score: 90
Period size: 17 Copynumber: 7.5 Consensus size: 17
6708 GGACTTTATT
* **
6718 AATTTATATTTAGGATA
1 AATTTAAATTTAAAATA
* *
6735 AATTTAAATTTGATAAGA
1 AATTTAAATTT-AAAATA
* *
6753 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
*
6770 AATTTAAGTTTAAAATA
1 AATTTAAATTTAAAATA
6787 AATTTAAACTTAAACTTAAAATA
1 AATTTAAA--T----TTAAAATA
*
6810 AATTTAAATTTAAAAACA
1 AATTTAAATTT-AAAATA
* * *
6828 AATTCAAACTTAAGATA
1 AATTTAAATTTAAAATA
6845 AATTTAAA
1 AATTTAAA
6853 GCAAAATAGG
Statistics
Matches: 92, Mismatches: 18, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
17 47 0.51
18 27 0.29
19 1 0.01
21 1 0.01
23 16 0.17
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:7631 original size:209 final size:209
Alignment explanation
Indices: 7284--7836 Score: 791
Period size: 209 Copynumber: 2.6 Consensus size: 209
7274 AGATGACCAT
* * * * * * *
7284 TTTATTTCTTCGACCTGCTTCTCCGTATCTCACCGGGAAGCTAGGGTTCGAAGTTTTGCTTACAT
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACTT
* * * * * *
7349 CGAGCTTTGATTTCATTAATTTGGTCTACTTCTCAGTATCTCATTAAGAAGATGACCGTATCACT
66 TGAGC-CTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACT
* * * *
7414 TATTTTGATCCACTTCTTTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTTTGTATCTCAT
130 TGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCAT
* *
7479 CAGGAAGGTTACTGC
195 CAGGAAGGTAACCGC
* * *
7494 TTTATTGCTTCGACCTGCTTCTCAGTTTCTCATCAGGAAGTTAGGGTTCGAAGATTTACTCACTT
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACTT
* *
7559 TGAGCCTGGTTTTATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTT
66 TGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTT
*
7624 GTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGATAGATCTGGTTCACTTCTCTGTATCTCATC
131 GTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATC
7689 AGGAAGGTAACCGC
196 AGGAAGGTAACCGC
* * * * ** *
7703 TTGATTGCTTCGACTTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTTAAAGAGTTGCTCACTT
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACTT
* *
7768 TGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACTGCATCACTT
66 TGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTT
7833 GTTT
131 GTTT
7837 CAATCTGCTT
Statistics
Matches: 304, Mismatches: 39, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
209 245 0.81
210 59 0.19
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (209 bp):
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACTT
TGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTT
GTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACAGATCTGGTTCACTTCTCTGTATCTCATC
AGGAAGGTAACCGC
Found at i:7905 original size:45 final size:47
Alignment explanation
Indices: 7795--7911 Score: 132
Period size: 45 Copynumber: 2.5 Consensus size: 47
7785 ATTTGGTCTA
* * * *
7795 CTTCTCAGTATCTCATCAAGAAGATGACTGCATCACTTGTTTCAATCTG
1 CTTCTTAGTATCTCATCAAGAAGATGAAT--ATCACTTGCTTCAACCTG
* *
7844 CTTC-TATGTATCTCATCAAGAAGATGAAT-TTA-TTGCTTCGACCTG
1 CTTCTTA-GTATCTCATCAAGAAGATGAATATCACTTGCTTCAACCTG
7889 CTTCTTAGTATCTCATCAAGAAG
1 CTTCTTAGTATCTCATCAAGAAG
7912 TAGGGGTTCG
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
45 30 0.50
46 4 0.07
48 1 0.02
49 25 0.42
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (47 bp):
CTTCTTAGTATCTCATCAAGAAGATGAATATCACTTGCTTCAACCTG
Found at i:7992 original size:167 final size:168
Alignment explanation
Indices: 7706--8034 Score: 482
Period size: 167 Copynumber: 2.0 Consensus size: 168
7696 TAACCGCTTG
* * *
7706 ATTGCTTCGACTTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTTAAAGAGTTGCTCACTTTGA
1 ATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGTTCAAAGAGTTGCTCACTTT-A
7771 GCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACTGCATCACTTGTT
65 GCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACTGCATCACTTGTT
*
7836 TCAATCTGCTTCTATGTATCTCATCAAGAAGATGAATTT
130 TCAATCCGCTTCTATGTATCTCATCAAGAAGATGAATTT
* * * *
7875 ATTGCTTCGACCTGCTTCTTAGTATCTCATCAAGAAG-TAGGGGTTCGAAGATTTGCTCACTTT-
1 ATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCT-GGGGTTCAAAGAGTTGCTCACTTTA
* * * * * *
7938 GTCTGGTTTCATTGATTTGGTCTCCTTCTTAGTATCTCATTAGGAAGATGACTGCATCACTTGTT
65 GCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACTGCATCACTTGTT
* *
8003 TCAATCCGCTTCTCTGTATCTCATCAGGAAGA
130 TCAATCCGCTTCTATGTATCTCATCAAGAAGA
8035 CGGATTTGGT
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
167 88 0.62
168 1 0.01
169 54 0.38
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (168 bp):
ATTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGTTCAAAGAGTTGCTCACTTTAG
CCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACTGCATCACTTGTTT
CAATCCGCTTCTATGTATCTCATCAAGAAGATGAATTT
Found at i:8189 original size:376 final size:376
Alignment explanation
Indices: 7494--8242 Score: 1079
Period size: 376 Copynumber: 2.0 Consensus size: 376
7484 AGGTTACTGC
* *
7494 TTTATTGCTTCGACCTGCTTCTCAGTTTCTCATCAGGAAGTTAGGGTTCGAAGATTTACTCACTT
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGTTAGGGTTCGAAGATTTACTCACTT
*
7559 TGAGCCTGGTTTTATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTT
66 T-AGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTT
** * * *
7624 GTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGATAGATCTGGTTCACTTCTCTGTATCTCATC
130 GTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATCTGGTTCACTTCTCTATATCTCATC
* *
7689 AGGAAGGTAACCGCTTGATTGCTTCGACTTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTTAA
195 AGGAAGGTAACCGCTTGATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCAA
* *
7754 AGAGTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGA
260 AGAGTTGCTCACTTTGAACCTAGTTTCATCGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGA
* **
7819 TGACTGCATCACTTGTTTCAATCTGCTTCTATGTATCTCATCAAGAAGATGAA
325 TGACCGCATC-CTTGTTTCAATCCACTTCTATGTATCTCATCAAGAAGATGAA
* *
7872 TTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAAGAAG-TAGGGGTTCGAAGATTTGCTCACT
1 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGTTA-GGGTTCGAAGATTTACTCACT
* * * * *
7936 TT-GTCTGGTTTCATTGATTTGGTCTCCTTCTTAGTATCTCATTAGGAAGATGACTGCATCACTT
65 TTAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTT
* * * *
8000 GTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTCACTTCTCTATATCTCGTC
130 GTTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATCTGGTTCACTTCTCTATATCTCATC
* * * * * *
8065 AGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCATGAAGTTGGGGTTCGA
195 AGGAAGGTAACCGCTTGATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCAA
* * * *
8130 AGATTTGCTTACTTTGAACCTGGTTTCATCGATTTGGTCTACTTCTCAGTATTTCATCAAGAAGA
260 AGAGTTGCTCACTTTGAACCTAGTTTCATCGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGA
* * ** * *
8195 TGACCGCCTCGTTGTTTTGATCCACTTCTCTGTATCTTATCAAGAAGA
325 TGACCGCATCCTTGTTTCAATCCACTTCTATGTATCTCATCAAGAAGA
8243 CGGATCTGGT
Statistics
Matches: 328, Mismatches: 42, Indels: 5
0.87 0.11 0.01
Matches are distributed among these distances:
375 31 0.09
376 236 0.72
377 2 0.01
378 59 0.18
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (376 bp):
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGTTAGGGTTCGAAGATTTACTCACTT
TAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG
TTTCAATCCACTTCTCTGTATCTCATCAGGAAGACAGATCTGGTTCACTTCTCTATATCTCATCA
GGAAGGTAACCGCTTGATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCAAA
GAGTTGCTCACTTTGAACCTAGTTTCATCGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGAT
GACCGCATCCTTGTTTCAATCCACTTCTATGTATCTCATCAAGAAGATGAA
Found at i:8291 original size:208 final size:207
Alignment explanation
Indices: 7872--8293 Score: 612
Period size: 208 Copynumber: 2.0 Consensus size: 207
7862 AGAAGATGAA
7872 TTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAAGAAGTAGGGGTTCGAAGATTTGCTCACTT
1 TTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAAGAAGTAGGGGTTCGAAGATTTGCTCACTT
* * * * * * *
7937 TGTCTGGTTTCATTGATTTGGTCTCCTTCTTAGTATCTCATTAGGAAGATGACTGCATCACTTGT
66 TGCCTGGTTTCATCGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGT
* * * *
8002 TTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTCACTTCTCTATATCTCGTCAG
131 TTCAATCCACTTCTCTGTATCTCATCAAGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAG
8067 GAAGGTAACCGC
196 GAAGGTAACCGC
* * *
8079 TTTATTGCTTCGACCTGCTTCTTAGTATCTCATCATGAAGTTGGGGTTCGAAGATTTGCTTACTT
1 TTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAAGAAGTAGGGGTTCGAAGATTTGCTCACTT
* * *
8144 TGAACCTGGTTTCATCGATTTGGTCTACTTCTCAGTATTTCATCAAGAAGATGACCGCCTC-GTT
66 TG--CCTGGTTTCATCGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTT
** * * *
8208 GTTTTGATCCACTTCTCTGTATCTTATCAAGAAGACGGATCTGGTTCACTTCTTTGTATCTCATC
129 GTTTCAATCCACTTCTCTGTATCTCATCAAGAAGACGGATCTGGTTCACTTCTCTATATCTCATC
*
8273 AGGAAGGTAACTGC
194 AGGAAGGTAACCGC
8287 TTTATTG
1 TTTATTG
8294 TTTTGGATAA
Statistics
Matches: 190, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
207 64 0.34
208 78 0.41
209 48 0.25
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (207 bp):
TTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAAGAAGTAGGGGTTCGAAGATTTGCTCACTT
TGCCTGGTTTCATCGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGT
TTCAATCCACTTCTCTGTATCTCATCAAGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAG
GAAGGTAACCGC
Found at i:8436 original size:39 final size:38
Alignment explanation
Indices: 8309--8561 Score: 144
Period size: 39 Copynumber: 6.7 Consensus size: 38
8299 GATAACTAGA
* * *
8309 ATCTGCTCCATGATC-GGGTAAGAGATTG-GATGACAGTG
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGCGATGGC--TG
*
8347 ATCTGCCCCA---T-GGGGTAAAAGA-T-CGAATGGCTG
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGCG-ATGGCTG
* * *
8380 CAATCTACCTCAGGCTCGGGGTAAGAGATTGGCTGATGG-TG
1 --ATCTGCCCCATGCTCGGGGTAAGAGATT-GC-GATGGCTG
* *
8421 ATCTGCCCCATGCTCGGGGTAAAAGATTG-GATGGCTACA
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGCGATGGCT--G
*
8460 ATCTGCCCCA---T-GGGGTAAAAGA-T-CGAATGGCTG
1 ATCTGCCCCATGCTCGGGGTAAGAGATTGCG-ATGGCTG
*
8493 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGG-TG
1 --ATCTGCCCCATGCTCGGGGTAAGAGATT-GC-GATGGCTG
*
8534 ATCTGCCCCATGGCTTGGGGTAAGAGAT
1 ATCTGCCCCAT-GCTCGGGGTAAGAGAT
8562 CGAATCTTCA
Statistics
Matches: 171, Mismatches: 15, Indels: 56
0.71 0.06 0.23
Matches are distributed among these distances:
33 2 0.01
34 4 0.02
35 49 0.29
36 6 0.04
37 1 0.01
38 12 0.07
39 64 0.37
40 17 0.10
41 4 0.02
42 10 0.06
43 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.23
Consensus pattern (38 bp):
ATCTGCCCCATGCTCGGGGTAAGAGATTGCGATGGCTG
Found at i:8475 original size:74 final size:75
Alignment explanation
Indices: 8324--8524 Score: 177
Period size: 74 Copynumber: 2.7 Consensus size: 75
8314 CTCCATGATC
* ** * * *
8324 GGGTAAGAGATTGGATGACAGTGATCTGCCCCA--T-GGGGTAAAAGATCGAATGGCTGCAATCT
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGCTCGGGGTAAAAGATTGGATGGCTACAATCT
*
8386 ACCTCAGGCTCG
66 ACCCCA-G-TCG
8398 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCATGCTCGGGGTAAAAGATTGGATGGCTACAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCA-GCTCGGGGTAAAAGATTGGATGGCTACAATC
*
8463 TGCCCCA-T-G
65 TACCCCAGTCG
* *
8472 GGGTAAAAGA-T--C-GAATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGG
1 GGGTAAGAGATTGGCTG-ATGG-TG--ATCTGCCCC-AGCTCGGGGTAAAAGATTGG
8525 CTGATGGTGA
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
70 1 0.01
71 5 0.05
72 2 0.02
73 1 0.01
74 67 0.62
75 2 0.02
77 1 0.01
78 29 0.27
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (75 bp):
GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGCTCGGGGTAAAAGATTGGATGGCTACAATCT
ACCCCAGTCG
Found at i:8482 original size:35 final size:35
Alignment explanation
Indices: 8436--8504 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
8426 CCCCATGCTC
* *
8436 GGGGTAAAAGATTGGATGGCTACAATCTGCCCCAT
1 GGGGTAAAAGATCGAATGGCTACAATCTGCCCCAT
*
8471 GGGGTAAAAGATCGAATGGCTGCAATCTGCCCCA
1 GGGGTAAAAGATCGAATGGCTACAATCTGCCCCA
8505 AGCTCGGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (35 bp):
GGGGTAAAAGATCGAATGGCTACAATCTGCCCCAT
Found at i:8510 original size:113 final size:114
Alignment explanation
Indices: 8347--8561 Score: 378
Period size: 113 Copynumber: 1.9 Consensus size: 114
8337 GATGACAGTG
* *
8347 ATCTGCCCCATGGGGTAAAAGATCGAATGGCTGCAATCTACCTCAGGCTCGGGGTAAGAGATTGG
1 ATCTGCCCCATGGGGTAAAAGATCGAATGGCTGCAATCTACCCCAAGCTCGGGGTAAGAGATTGG
8412 CTGATGGTGATCTGCCCCAT-GCTCGGGGTAAAAGATTGGATGGCTACA
66 CTGATGGTGATCTGCCCCATGGCTCGGGGTAAAAGATTGGATGGCTACA
*
8460 ATCTGCCCCATGGGGTAAAAGATCGAATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGG
1 ATCTGCCCCATGGGGTAAAAGATCGAATGGCTGCAATCTACCCCAAGCTCGGGGTAAGAGATTGG
* *
8525 CTGATGGTGATCTGCCCCATGGCTTGGGGTAAGAGAT
66 CTGATGGTGATCTGCCCCATGGCTCGGGGTAAAAGAT
8562 CGAATCTTCA
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 82 0.85
114 14 0.15
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (114 bp):
ATCTGCCCCATGGGGTAAAAGATCGAATGGCTGCAATCTACCCCAAGCTCGGGGTAAGAGATTGG
CTGATGGTGATCTGCCCCATGGCTCGGGGTAAAAGATTGGATGGCTACA
Found at i:8952 original size:48 final size:49
Alignment explanation
Indices: 8834--9014 Score: 150
Period size: 48 Copynumber: 3.7 Consensus size: 49
8824 TGTTTTCTAA
* *
8834 GGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCC-TTCATATCTTCAT
1 GGTACCGGATTCACCATTGCGGCCTCAACCTTTCCCATT-ACATCTTCAT
* *** * * *
8883 GGTACCGGGTTTGTCACTGCTGCCTCAACCTATCCCATTACAT-TTCAT
1 GGTACCGGATTCACCATTGCGGCCTCAACCTTTCCCATTACATCTTCAT
* * * * * * *
8931 GGTACCGGATTCGCCGTTGCTGCCTCAATCTTTCTCATCACATCTTCTT
1 GGTACCGGATTCACCATTGCGGCCTCAACCTTTCCCATTACATCTTCAT
* *
8980 GAGGTACCGGATTCACCGTCGCGGCCTCAATCCTT
1 --GGTACCGGATTCACCATTGCGGCCTCAA-CCTT
9015 CCTTTCAAAA
Statistics
Matches: 106, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
48 39 0.37
49 37 0.35
50 2 0.02
51 25 0.24
52 3 0.03
ACGTcount: A:0.17, C:0.33, G:0.18, T:0.32
Consensus pattern (49 bp):
GGTACCGGATTCACCATTGCGGCCTCAACCTTTCCCATTACATCTTCAT
Found at i:10803 original size:20 final size:20
Alignment explanation
Indices: 10779--10817 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10769 TTCATCTTGA
10779 CTTTTT-CTTTCTTT-TCTTT
1 CTTTTTCCTTT-TTTCTCTTT
10798 CTTTTTCCTTTTTTCTCTTT
1 CTTTTTCCTTTTTTCTCTTT
10818 TTATTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
CTTTTTCCTTTTTTCTCTTT
Found at i:10874 original size:3 final size:3
Alignment explanation
Indices: 10866--10894 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10856 CCATATTTTG
10866 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
10895 TTGATAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:16254 original size:6 final size:6
Alignment explanation
Indices: 16245--16335 Score: 73
Period size: 6 Copynumber: 15.7 Consensus size: 6
16235 ATATTTAGGA
* * * *
16245 TAAATT TAAATT T-AATAA TAAATT TAAACT TAAA-C TAAATT TAAGTT
1 TAAATT TAAATT TAAAT-T TAAATT TAAATT TAAATT TAAATT TAAATT
* * * *
16292 TAAA-A TAAATT TAAACT TAAACT TAAA-A TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
16336 AATAAATTCA
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
5 15 0.22
6 50 0.74
7 3 0.04
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (6 bp):
TAAATT
Found at i:16304 original size:34 final size:35
Alignment explanation
Indices: 16245--16328 Score: 127
Period size: 34 Copynumber: 2.4 Consensus size: 35
16235 ATATTTAGGA
16245 TAAATTTAAATTTAATAATAAATTTAAACTTAAAC
1 TAAATTTAAATTTAATAATAAATTTAAACTTAAAC
*
16280 TAAATTTAAGTTTAA-AATAAATTTAAACTTAAAC
1 TAAATTTAAATTTAATAATAAATTTAAACTTAAAC
*
16314 TTAAA-ATAAATTTAA
1 -TAAATTTAAATTTAA
16329 ATTTAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.60
35 18 0.40
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (35 bp):
TAAATTTAAATTTAATAATAAATTTAAACTTAAAC
Found at i:16306 original size:23 final size:23
Alignment explanation
Indices: 16280--16335 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
16270 AAACTTAAAC
**
16280 TAAATTTAAGTTTAAAATAAATT
1 TAAATTTAAACTTAAAATAAATT
*
16303 TAAACTTAAACTTAAAATAAATT
1 TAAATTTAAACTTAAAATAAATT
16326 TAAATTTAAA
1 TAAATTTAAA
16336 AATAAATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAATTTAAACTTAAAATAAATT
Found at i:16334 original size:17 final size:17
Alignment explanation
Indices: 16230--16343 Score: 102
Period size: 17 Copynumber: 6.2 Consensus size: 17
16220 GGACTTTATT
* **
16230 AATTTATATTTAGGATA
1 AATTTAAATTTAAAATA
16247 AATTTAAATTTAATAATA
1 AATTTAAATTTAA-AATA
* *
16265 AATTTAAACTTAAACTA
1 AATTTAAATTTAAAATA
*
16282 AATTTAAGTTTAAAATA
1 AATTTAAATTTAAAATA
16299 AATTTAAACTTAAACTTAAAATA
1 AATTTAAA--T----TTAAAATA
16322 AATTTAAATTTAAAAATA
1 AATTTAAATTT-AAAATA
16340 AATT
1 AATT
16344 CAAACTTAGG
Statistics
Matches: 80, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
17 37 0.46
18 25 0.31
19 1 0.01
21 1 0.01
23 16 0.20
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.40
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:16341 original size:23 final size:23
Alignment explanation
Indices: 16292--16341 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
16282 AATTTAAGTT
**
16292 TAAAATAAATTTAAACTTAAACT
1 TAAAATAAATTTAAACTTAAAAA
*
16315 TAAAATAAATTTAAATTTAAAAA
1 TAAAATAAATTTAAACTTAAAAA
16338 TAAA
1 TAAA
16342 TTCAAACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAAATAAATTTAAACTTAAAAA
Found at i:16601 original size:25 final size:25
Alignment explanation
Indices: 16554--16601 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16544 AATCTAAAAA
* *
16554 CACGTTTTACATTAATGCGTAGGAC
1 CACGTTTTACATTAATACATAGGAC
*
16579 CACGTTTTGCATTAATACATAGG
1 CACGTTTTACATTAATACATAGG
16602 TAGTCCTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (25 bp):
CACGTTTTACATTAATACATAGGAC
Found at i:18884 original size:27 final size:29
Alignment explanation
Indices: 18853--18924 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
18843 ACTAATATTT
18853 TATATAATTTATAAT-TAAATTT-ACATAA
1 TATATAATTTATAATATAAATTTGAC-TAA
*
18881 -ATAT-ATTCTATATATAATTAATTTGACTAA
1 TATATAATT-TATA-AT-ATAAATTTGACTAA
18911 TATATAATTTATAA
1 TATATAATTTATAA
18925 AACAAGTAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
26 3 0.08
27 8 0.22
28 2 0.06
30 10 0.28
31 10 0.28
32 3 0.08
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (29 bp):
TATATAATTTATAATATAAATTTGACTAA
Found at i:18923 original size:29 final size:30
Alignment explanation
Indices: 18853--18923 Score: 71
Period size: 31 Copynumber: 2.4 Consensus size: 30
18843 ACTAATATTT
18853 TATATAA-TT-TATAATTAAATTTACATAA
1 TATATAATTTATATAATTAAATTTACATAA
*
18881 -ATATATTCTATATATAATT-AATTTGAC-TAA
1 TATATAAT-T-TATATAATTAAATTT-ACATAA
18911 TATATAATTTATA
1 TATATAATTTATA
18924 AAACAAGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
27 5 0.14
29 5 0.14
30 10 0.29
31 15 0.43
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (30 bp):
TATATAATTTATATAATTAAATTTACATAA
Found at i:20983 original size:20 final size:20
Alignment explanation
Indices: 20955--20993 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20945 GAACGAAGCT
20955 TCTTATAAACCTTCTTCAAG
1 TCTTATAAACCTTCTTCAAG
* **
20975 TCTTCTAAATTTTCTTCAA
1 TCTTATAAACCTTCTTCAA
20994 CTTTGTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.03, T:0.46
Consensus pattern (20 bp):
TCTTATAAACCTTCTTCAAG
Found at i:24253 original size:28 final size:30
Alignment explanation
Indices: 24141--24254 Score: 94
Period size: 29 Copynumber: 3.9 Consensus size: 30
24131 ATTTTCGAGG
*
24141 AATTTGAGGGTCAAAAT-TGAATTTTTTGGAA
1 AATTTGAGGATCAAAATGTG-A-TTTTTGGAA
* *** *
24172 AATTTG-GGATTAAAATCAAACTTTTGGAA
1 AATTTGAGGATCAAAATGTGATTTTTGGAA
*
24201 AATTTGAGGTTCAAAATGTGATTTTTGG-A
1 AATTTGAGGATCAAAATGTGATTTTTGGAA
*
24230 AATTTGGGGAT-AAAATG-GTATTTTT
1 AATTTGAGGATCAAAATGTG-ATTTTT
24255 TGGATGTTCA
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.01
28 12 0.18
29 24 0.36
30 24 0.36
31 6 0.09
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (30 bp):
AATTTGAGGATCAAAATGTGATTTTTGGAA
Found at i:24311 original size:30 final size:30
Alignment explanation
Indices: 24241--24371 Score: 124
Period size: 30 Copynumber: 4.5 Consensus size: 30
24231 ATTTGGGGAT
* * *
24241 AAAATGGT-ATTTTTTGGATGTTCAAGGGC
1 AAAATGATAATTTTTTGGATATTCAGGGGC
** * *
24270 AAAAAAATAATTTTTTAGATATTCGGGGGC
1 AAAATGATAATTTTTTGGATATTCAGGGGC
* **
24300 AAAATGGTAA-TTTTTGGAT-TTTGGGGGC
1 AAAATGATAATTTTTTGGATATTCAGGGGC
* *
24328 AAAATGATAATTTCTTGGATATTCAGAGGC
1 AAAATGATAATTTTTTGGATATTCAGGGGC
*
24358 AAAATCATAATTTT
1 AAAATGATAATTTT
24372 GGAGAAGTTT
Statistics
Matches: 80, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
28 17 0.21
29 21 0.26
30 42 0.52
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (30 bp):
AAAATGATAATTTTTTGGATATTCAGGGGC
Found at i:24313 original size:88 final size:87
Alignment explanation
Indices: 24212--24371 Score: 198
Period size: 88 Copynumber: 1.8 Consensus size: 87
24202 ATTTGAGGTT
* * * * *
24212 CAAAATGTGATTTTTGGAAATTTGGGGATAAAATGGT-ATTTTTTGGATGTTCA-AGGGCAAAAA
1 CAAAATGTAATTTTTGG-AATTTGGGGACAAAATGATAATTTCTTGGATATTCAGA-GGCAAAAA
24275 AATAATTTTTTAGATATTCGGGGG
64 AATAATTTTTTAGATATTCGGGGG
* * **
24299 CAAAATGGTAATTTTTGGATTTTGGGGGCAAAATGATAATTTCTTGGATATTCAGAGGCAAAATC
1 CAAAAT-GTAATTTTTGGAATTTGGGGACAAAATGATAATTTCTTGGATATTCAGAGGCAAAAAA
24364 ATAATTTT
65 ATAATTTT
24372 GGAGAAGTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
87 21 0.34
88 39 0.64
89 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (87 bp):
CAAAATGTAATTTTTGGAATTTGGGGACAAAATGATAATTTCTTGGATATTCAGAGGCAAAAAAA
TAATTTTTTAGATATTCGGGGG
Found at i:24325 original size:28 final size:29
Alignment explanation
Indices: 24212--24371 Score: 117
Period size: 30 Copynumber: 5.5 Consensus size: 29
24202 ATTTGAGGTT
* * * *
24212 CAAAAT-GTGATTTTTGGAAATTTGGGGA
1 CAAAATGGTAATTTTTGGATATTCGGGGG
* * * **
24240 TAAAATGGTATTTTTTGGATGTTCAAGGG
1 CAAAATGGTAATTTTTGGATATTCGGGGG
*** *
24269 CAAAAAAATAATTTTTTAGATATTCGGGGG
1 CAAAATGGTAA-TTTTTGGATATTCGGGGG
*
24299 CAAAATGGTAATTTTTGGAT-TTTGGGGG
1 CAAAATGGTAATTTTTGGATATTCGGGGG
* * *
24327 CAAAATGATAATTTCTTGGATATTCAGAGG
1 CAAAATGGTAATTT-TTGGATATTCGGGGG
**
24357 CAAAATCATAATTTT
1 CAAAATGGTAATTTT
24372 GGAGAAGTTT
Statistics
Matches: 100, Mismatches: 28, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
28 25 0.25
29 35 0.35
30 40 0.40
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (29 bp):
CAAAATGGTAATTTTTGGATATTCGGGGG
Found at i:24338 original size:58 final size:59
Alignment explanation
Indices: 24241--24371 Score: 147
Period size: 58 Copynumber: 2.2 Consensus size: 59
24231 ATTTGGGGAT
* * * *
24241 AAAATGGTATTTTTTGGATGTTCAAGGGCAAAAAAATAATTTTTTAGATATTCGGGGGC
1 AAAATGGTAATTTTTGGATGTTCAAGGGCAAAAAAATAATTTCTTAGATATTCAGAGGC
*** ** *
24300 AAAATGGTAATTTTTGGAT-TTTGGGGGCAAAATGATAATTTCTTGGATATTCAGAGGC
1 AAAATGGTAATTTTTGGATGTTCAAGGGCAAAAAAATAATTTCTTAGATATTCAGAGGC
**
24358 AAAATCATAATTTT
1 AAAATGGTAATTTT
24372 GGAGAAGTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
58 42 0.70
59 18 0.30
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGATGTTCAAGGGCAAAAAAATAATTTCTTAGATATTCAGAGGC
Found at i:24486 original size:90 final size:88
Alignment explanation
Indices: 24365--24550 Score: 227
Period size: 90 Copynumber: 2.1 Consensus size: 88
24355 GGCAAAATCA
* * *
24365 TAATTTTGGAGAAGTTTGGGTCAAAATGTAA-TTTTA-GAAAAGTTTAAGG-GTTAAAATGTGAT
1 TAATTTTAGAAAAGTTTGGGTCAAAATGTAATTTTTATG--AA-TTTAAGGAGTCAAAATGTGAT
24427 TTTGGA-AAAGTTTAGGGCTCAAAATG
63 TTTGGAGAAA-TTTAGGGCTCAAAATG
*
24453 TAATTTTAGAAAAGTTTAGGTGTCAAAATGTAATTTTTATGAATTTAGGGAGTCAAAATGTGATT
1 TAATTTTAGAAAAGTTT-GG-GTCAAAATGTAATTTTTATGAATTTAAGGAGTCAAAATGTGATT
* *
24518 TTTGAGAAATTTAGGGGTCAAAATG
64 TTGGAGAAATTTAGGGCTCAAAATG
24543 TAAATTTT
1 T-AATTTT
24551 GAGTTTAAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
88 15 0.18
89 8 0.09
90 47 0.55
91 14 0.16
92 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (88 bp):
TAATTTTAGAAAAGTTTGGGTCAAAATGTAATTTTTATGAATTTAAGGAGTCAAAATGTGATTTT
GGAGAAATTTAGGGCTCAAAATG
Found at i:24551 original size:30 final size:31
Alignment explanation
Indices: 24365--24553 Score: 193
Period size: 30 Copynumber: 6.3 Consensus size: 31
24355 GGCAAAATCA
*
24365 TAATTTTG-GAGAAGTTT--GGGTCAAAATG
1 TAATTTTGAGAAAAGTTTAGGGGTCAAAATG
* *
24393 TAATTTT-AGAAAAGTTTAAGGGTTAAAATG
1 TAATTTTGAGAAAAGTTTAGGGGTCAAAATG
* *
24423 TGATTTTG-GAAAAGTTTAGGGCTCAAAATG
1 TAATTTTGAGAAAAGTTTAGGGGTCAAAATG
*
24453 TAATTTT-AGAAAAGTTTAGGTGTCAAAATG
1 TAATTTTGAGAAAAGTTTAGGGGTCAAAATG
*
24483 TAATTTTTATG--AA-TTTAGGGAGTCAAAATG
1 TAATTTTGA-GAAAAGTTTAGGG-GTCAAAATG
*
24513 TGATTTTTGAG-AAA-TTTAGGGGTCAAAATG
1 T-AATTTTGAGAAAAGTTTAGGGGTCAAAATG
24543 TAAATTTTGAG
1 T-AATTTTGAG
24554 TTTAAATAAT
Statistics
Matches: 137, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
28 15 0.11
29 6 0.04
30 99 0.72
31 16 0.12
32 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (31 bp):
TAATTTTGAGAAAAGTTTAGGGGTCAAAATG
Found at i:24594 original size:30 final size:30
Alignment explanation
Indices: 24560--24670 Score: 116
Period size: 30 Copynumber: 3.7 Consensus size: 30
24550 TGAGTTTAAA
*
24560 TAATTTTTGAGAAGTTTAAGGGTTAAAATG
1 TAATTTTTGAGAAGTTTAAGGGTCAAAATG
* *
24590 TAATTTTTAAGAAGTTTAGGGGTCAAAATG
1 TAATTTTTGAGAAGTTTAAGGGTCAAAATG
* * ** *
24620 AAATTTTTGAGAAATTTGTGAGTCAAAATG
1 TAATTTTTGAGAAGTTTAAGGGTCAAAATG
* *
24650 TGATTTATG-GATAGTTTAAGG
1 TAATTTTTGAGA-AGTTTAAGG
24671 ACTTATTGGA
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
29 2 0.03
30 62 0.97
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (30 bp):
TAATTTTTGAGAAGTTTAAGGGTCAAAATG
Found at i:24645 original size:107 final size:107
Alignment explanation
Indices: 24453--24650 Score: 285
Period size: 107 Copynumber: 1.9 Consensus size: 107
24443 GCTCAAAATG
* **
24453 TAATTTTAGAAAAGTTTAGGTGTCAAAATGTAATTTTTATGAATTTAGGGAGTCAAAATGTGATT
1 TAATTTTAGAAAAGTTTAGGTGTCAAAATGTAATTTTTAAGAATTTAGGGAGTCAAAATGAAATT
*
24518 TTTGAGAAATTTAGGGGTCAAAATGTAAATTTTGAGTTTAAA
66 TTTGAGAAATTTAGGAGTCAAAATGTAAATTTTGAGTTTAAA
* * *
24560 TAATTTTTGAGAAGTTTAAGG-GTTAAAATGTAATTTTTAAGAAGTTTAGGG-GTCAAAATGAAA
1 TAATTTTAGAAAAGTTT-AGGTGTCAAAATGTAATTTTTAAGAA-TTTAGGGAGTCAAAATGAAA
24623 TTTTTGAGAAATTT-GTGAGTCAAAATGT
64 TTTTTGAGAAATTTAG-GAGTCAAAATGT
24651 GATTTATGGA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
106 1 0.01
107 70 0.86
108 10 0.12
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (107 bp):
TAATTTTAGAAAAGTTTAGGTGTCAAAATGTAATTTTTAAGAATTTAGGGAGTCAAAATGAAATT
TTTGAGAAATTTAGGAGTCAAAATGTAAATTTTGAGTTTAAA
Found at i:26473 original size:2 final size:2
Alignment explanation
Indices: 26466--26506 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
26456 AAAGTTCTTT
* * *
26466 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26507 GACTCAAGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26507 original size:12 final size:12
Alignment explanation
Indices: 26466--26506 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
26456 AAAGTTCTTT
*
26466 TATATATATATA
1 TATATATATATG
26478 TATATATATATG
1 TATATATATATG
*
26490 TATATGTATATG
1 TATATATATATG
26502 TATAT
1 TATAT
26507 GACTCAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Done.