Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2158
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: 70958
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5267 original size:21 final size:22
Alignment explanation
Indices: 5243--5292 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
5233 ATCAAATCTT
* *
5243 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
5264 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
5286 --TCAAAAT
1 CTTCAAAAT
5293 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:6805 original size:13 final size:13
Alignment explanation
Indices: 6787--6811 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6777 CATTATGCTT
6787 TGTATCGATACAA
1 TGTATCGATACAA
6800 TGTATCGATACA
1 TGTATCGATACA
6812 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6811 original size:33 final size:32
Alignment explanation
Indices: 6766--6830 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
6756 ACACACCTAG
*
6766 ATGTATCAATACAT-TATGCTTTGTATCGATACA
1 ATGTATCAATACATGT-T-CATTGTATCGATACA
*
6799 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCAATACATGTTCATTGTATCGATACA
6831 TGGATAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (32 bp):
ATGTATCAATACATGTTCATTGTATCGATACA
Found at i:6842 original size:20 final size:20
Alignment explanation
Indices: 6800--6852 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
6790 ATCGATACAA
* *
6800 TGTATCGATACAT-GTTCAT
1 TGTATCGATACATGGATAAT
6819 TGTATCGATACATGGATAAT
1 TGTATCGATACATGGATAAT
6839 TGTATCGATACATG
1 TGTATCGATACATG
6853 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGGATAAT
Found at i:6907 original size:20 final size:20
Alignment explanation
Indices: 6882--6935 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
6872 TAACCACTGT
6882 TTGTATCGATACATGA-CACA
1 TTGTATCGATACATGATCA-A
*
6902 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATCAA
*
6922 TTTTATCGATACAT
1 TTGTATCGATACAT
6936 TGCTTCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATCAA
Found at i:7000 original size:62 final size:66
Alignment explanation
Indices: 6903--7069 Score: 234
Period size: 72 Copynumber: 2.5 Consensus size: 66
6893 CATGACACAT
* *
6903 TGTATCGATACATGATGAATTTTATCGATACATTGC-T-T-C-AAACGGCTATAATTTCAAATGC
1 TGTATCGATACATTATGAATTGTATCGATACATTGCTTATGCTAAACGGCTATAATTTCAAATGC
6964 A
66 A
6965 TGTATCGATACATTATGAATTGTATCGATACATTGCTTCAAATGGCTGTAAACGGCTATAATTTC
1 TGTATCGATACATTATGAATTGTATCGATACATTGCTT---AT-GC--TAAACGGCTATAATTTC
7030 AAATGCA
60 AAATGCA
7037 TGTATCGATACATTATGAATTGTATCGATACAT
1 TGTATCGATACATTATGAATTGTATCGATACAT
7070 AGCTACAGGA
Statistics
Matches: 93, Mismatches: 2, Indels: 10
0.89 0.02 0.10
Matches are distributed among these distances:
62 34 0.37
63 1 0.01
67 1 0.01
69 1 0.01
72 56 0.60
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (66 bp):
TGTATCGATACATTATGAATTGTATCGATACATTGCTTATGCTAAACGGCTATAATTTCAAATGC
A
Found at i:11413 original size:13 final size:13
Alignment explanation
Indices: 11395--11419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11385 ACAACACTTA
11395 TGTATCGATACAT
1 TGTATCGATACAT
11408 TGTATCGATACA
1 TGTATCGATACA
11420 AATTGTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14061 original size:22 final size:20
Alignment explanation
Indices: 14013--14085 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
14003 CAAGAAAATG
* * *
14013 TATCGATACATTAATAAATG
1 TATCGATACATTTATAATTA
14033 TATCGATACATGCTTCA-AATTA
1 TATCGATACAT--TT-ATAATTA
*
14055 TATCGATACATTTATCATTA
1 TATCGATACATTTATAATTA
14075 TATCGATACAT
1 TATCGATACAT
14086 ACAGGCAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 28 0.62
22 15 0.33
23 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (20 bp):
TATCGATACATTTATAATTA
Found at i:15481 original size:52 final size:49
Alignment explanation
Indices: 15403--16186 Score: 434
Period size: 43 Copynumber: 16.3 Consensus size: 49
15393 ATCATTTTTC
* ** * *
15403 TCATCTTTAAGCCCAATGTCATTGGCCTTAAATCAGCACATTGGCATCTTTT
1 TCATC-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-CTT
* *
15455 TCTTTCTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCA-C--
1 TC-ATCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
15502 -C-T-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
1 TCATCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TT
* * * * *
15549 ATCATCTTTAAGTTCAATGTCGCTAGACTTAAATCAGCACATTAGCA----
1 -TCATC-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
15596 -CAT-TTAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
1 TCATCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
15643 TACCACCTCTTAATTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTT
1 T--CA--TCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * * * * * *
15696 TAAGTC-TAA-T---AT-T-ACTAGCCTTGAATCAACATATTGGCGTCTTT
1 TCA-TCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC-ACCTT
* * * *
15740 GTCATTTTTAAGTCTAATGTCGTTAGCCTTGAATCAGCACATTGGCA-C--
1 -TCA-TCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * * * * *
15788 -C-T-TTAAGTCCAATATCGTTAGCCTTGAATCAGCATATTGACACTTT
1 TCATCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
15834 TACCACCTCTTAAGTCCAATGTTGCTGGTCTTAAATCAGCACATTGGCA-C--
1 T--CA--TCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * * *
15884 T--T-TTGAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCACCTTT
1 TCATCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TT
* * * **
15931 GTCATATTTAAGTCTAATGTCGCTGACCTTGAATCAGCACATTAACA-C--
1 -TCAT-CTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * * *
15979 -C-T-TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGACACCTT
1 TCATCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
16025 TACCACCTTTTTAAGTCTAATGTTGCTGGCCTTGAATCAGCACATTGGCACC-T
1 T--CA---TCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
16078 TCATCATAAAGTCCAATGTTGCTGGCCTTGAATTAGCACATTGGCA----
1 TCATC-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
16124 TC-T-TTAAGTCCAATATCGCTAGCCTTGAATCAGCACATTGACACC-T
1 TCATCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
*
16170 TCACCTTTAAGTCCAAT
1 TCATC-TTAAGTCCAAT
16187 ATCACTGCTT
Statistics
Matches: 568, Mismatches: 98, Indels: 135
0.71 0.12 0.17
Matches are distributed among these distances:
43 227 0.40
44 10 0.02
45 10 0.02
46 10 0.02
47 1 0.00
48 3 0.01
49 54 0.10
50 9 0.02
51 5 0.01
52 125 0.22
53 78 0.14
54 36 0.06
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (49 bp):
TCATCTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:15584 original size:95 final size:95
Alignment explanation
Indices: 15407--16129 Score: 754
Period size: 95 Copynumber: 7.5 Consensus size: 95
15397 TTTTTCTCAT
* * ** * * * * * *
15407 CTTTAAGCCCAATGTCATTGGCCTTAAATCAGCACATTGGCATCTTTTTC-TTTCTTAAGTCCAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCT-TTAAGTTCAA
15471 TGTTGCTGGCCTTGAATCAGCACATTGGCAC
65 TGTTGCTGGCCTTGAATCAGCACATTGGCAC
15502 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGTTCAAT
* * * * *
15567 GTCGCTAGACTTAAATCAGCACATTAGCAC
66 GTTGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
15597 ATTTAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCACCTCTTAA-TTCCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCT-TTAAGTT-CA
15661 ATGTTGCTGGCCTTGAATCAGCACATTGGCAC
64 ATGTTGCTGGCCTTGAATCAGCACATTGGCAC
* ** * * ** * *
15693 CTTTAAGTCTAATATTACTAGCCTTGAATCAACATATTGGCGTCTTTGTCATTTTTAAG-TCTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGTTC-AA
* * *
15757 TGTCGTTAGCCTTGAATCAGCACATTGGCAC
65 TGTTGCTGGCCTTGAATCAGCACATTGGCAC
* * * * * * *
15788 CTTTAAGTCCAATATCGTTAGCCTTGAATCAGCATATTGACACTTTTACCACCTCTTAAGTCCAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCT-TTAAGTTCAA
* *
15853 TGTTGCTGGTCTTAAATCAGCACATTGGCAC
65 TGTTGCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
15884 TTTTGAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCACCTTTGTCATATTTAAG-TCTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGTTC-AA
* * **
15948 TGTCGCTGACCTTGAATCAGCACATTAACAC
65 TGTTGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
15979 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGACACCTTTACCACCTTTTTAAG-TCT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCA--TCTTTAAGTTC-
16043 AATGTTGCTGGCCTTGAATCAGCACATTGGCAC
63 AATGTTGCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
16076 CTTCATCATAAAGTCCAATGTTGCTGGCCTTGAATTAGCACATTGGCATCTTTA
1 C-T--T--T-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
16130 AGTCCAATAT
Statistics
Matches: 516, Mismatches: 96, Indels: 24
0.81 0.15 0.04
Matches are distributed among these distances:
94 2 0.00
95 281 0.54
96 152 0.29
97 41 0.08
98 1 0.00
100 1 0.00
102 1 0.00
103 37 0.07
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (95 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGTTCAAT
GTTGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:15752 original size:191 final size:191
Alignment explanation
Indices: 15459--16128 Score: 939
Period size: 191 Copynumber: 3.5 Consensus size: 191
15449 TCTTTTTCTT
15459 TCTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
1 TCTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
* * *
15524 CTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGT-TCAATGTCGCTAGACTTAAATCAGCA
66 CTTGAATCAGCATATTGGCACCTTTGTCATATTTAAGTCT-AATGTCGCTAGACTTGAATCAGCA
* * * *
15588 CATTAGCACATTTAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCACC
130 CATTAGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGACACCTTTACCACC
* * ** *
15650 TCTTAATTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCTAATATTACTAGC
1 TCTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
* ** * * *
15715 CTTGAATCAACATATTGGCGTCTTTGTCATTTTTAAGTCTAATGTCGTTAGCCTTGAATCAGCAC
66 CTTGAATCAGCATATTGGCACCTTTGTCATATTTAAGTCTAATGTCGCTAGACTTGAATCAGCAC
* * *
15780 ATTGGCACCTTTAAGTCCAATATCGTTAGCCTTGAATCAGCATATTGACACTTTTACCACC
131 ATTAGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGACACCTTTACCACC
* * * *
15841 TCTTAAGTCCAATGTTGCTGGTCTTAAATCAGCACATTGGCACTTTTGAGTCCAATATCGCTGGC
1 TCTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
*
15906 TTTGAATCAGCATATTGGCACCTTTGTCATATTTAAGTCTAATGTCGCT-GACCTTGAATCAGCA
66 CTTGAATCAGCATATTGGCACCTTTGTCATATTTAAGTCTAATGTCGCTAGA-CTTGAATCAGCA
*
15970 CATTAACACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGACACCTTTACCACC
130 CATTAGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGACACCTTTACCACC
* * *
16032 TTTTTAAGTCTAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCATAAAGTCCAATGT
1 -TCTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACC-T--T--T-AAGTCCAATAT
* * * *
16097 TGCTGGCCTTGAATTAGCACATTGGCATCTTT
59 CGCTGGCCTTGAATCAGCATATTGGCACCTTT
16129 AAGTCCAATA
Statistics
Matches: 418, Mismatches: 52, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
190 1 0.00
191 338 0.81
192 40 0.10
193 1 0.00
195 1 0.00
197 1 0.00
198 36 0.09
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (191 bp):
TCTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
CTTGAATCAGCATATTGGCACCTTTGTCATATTTAAGTCTAATGTCGCTAGACTTGAATCAGCAC
ATTAGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGACACCTTTACCACC
Found at i:16167 original size:146 final size:147
Alignment explanation
Indices: 15900--16170 Score: 409
Period size: 146 Copynumber: 1.8 Consensus size: 147
15890 GTCCAATATC
* * ** *
15900 GCTGGCTTTGAATCAGCATATTGGCACCTTTGTCATATTTAAGTCTAATGTCGCTGACCTTGAAT
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCATA--TAAGTCCAATGTCGCTGACCTTGAAT
*
15965 CAGCACATTAACACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGACACCTTTACCA
64 CAGCACATTAACACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCACATTGACACCTTTACCA
16030 CCTTTTTAAGTCTAATGTT
129 CCTTTTTAAGTCTAATGTT
* * *
16049 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCATA-AAGTCCAATGTTGCTGGCCTTGAATTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCATATAAGTCCAATGTCGCTGACCTTGAATCA
** *
16113 GCACATTGGCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCACATTGACACCTT
66 GCACATTAACACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCACATTGACACCTT
16171 CACCTTTAAG
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
146 77 0.70
149 33 0.30
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (147 bp):
GCTGGCCTTGAATCAGCACATTGGCACCTTCATCATATAAGTCCAATGTCGCTGACCTTGAATCA
GCACATTAACACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCACATTGACACCTTTACCACC
TTTTTAAGTCTAATGTT
Found at i:16286 original size:11 final size:11
Alignment explanation
Indices: 16270--16300 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
16260 ACTGATCATA
16270 CCTTCCAAATC
1 CCTTCCAAATC
16281 CCTTCCAAATC
1 CCTTCCAAATC
*
16292 CTTTCCAAA
1 CCTTCCAAA
16301 ATTTATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (11 bp):
CCTTCCAAATC
Found at i:24393 original size:130 final size:129
Alignment explanation
Indices: 24143--24386 Score: 332
Period size: 130 Copynumber: 1.9 Consensus size: 129
24133 CCCATTAATT
* * *
24143 TAAACAAATATTAATCGTTTTTAATCTTTTATATTCCTATAGGTATCTGTAGGGATATTAAAAGA
1 TAAACAAATATTAATCATTGTTAATCTTTTATATTCCTATAGGTATCCGTAGGGATATTAAAAGA
** * * *
24208 TTTTAAAAACTTTTCATATCTTTTCGGGTTTCCATTAAGGTATGAAATGATTTTTTTTCAAAAAA
66 TTTTAAAAACTTTTCA-ATCTTGGCGGGTTTCCATCAAGGTACGAAATGACTTTTTTTCAAAAAA
*
24273 TAAATAAATATTAATCATTGTTAATCTTTTATATTCCTATAGGTATCCGTAAGGG-TATTAAAAG
1 TAAACAAATATTAATCATTGTTAATCTTTTATATTCCTATAGGTATCCGT-AGGGATATTAAAAG
* **
24337 A-TTTCAAATTTTTTGC-ATCTTGGCGGGTTTCCATCAAGGTACGAAATGAC
65 ATTTTAAAAACTTTT-CAATCTTGGCGGGTTTCCATCAAGGTACGAAATGAC
24387 ACTTTTTGAG
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
128 29 0.29
129 10 0.10
130 57 0.57
131 4 0.04
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (129 bp):
TAAACAAATATTAATCATTGTTAATCTTTTATATTCCTATAGGTATCCGTAGGGATATTAAAAGA
TTTTAAAAACTTTTCAATCTTGGCGGGTTTCCATCAAGGTACGAAATGACTTTTTTTCAAAAAA
Found at i:29978 original size:20 final size:20
Alignment explanation
Indices: 29953--30004 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
29943 TACAAGCCAA
**
29953 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
29973 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
29992 TGTATCGATACAA
1 TGTATCGATACAA
30005 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:32090 original size:21 final size:20
Alignment explanation
Indices: 32061--32103 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
32051 GACTAGTGTG
*
32061 GGGACTGCCCGGTTATGACCT
1 GGGACTG-CCGGTCATGACCT
* *
32082 GGGAGTGCCGGTCGTGACCT
1 GGGACTGCCGGTCATGACCT
32102 GG
1 GG
32104 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.26, G:0.42, T:0.21
Consensus pattern (20 bp):
GGGACTGCCGGTCATGACCT
Found at i:32551 original size:13 final size:13
Alignment explanation
Indices: 32533--32570 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
32523 ATAATCCCCC
32533 TGTATCGATACAG
1 TGTATCGATACAG
*
32546 TGTATCGATACAT
1 TGTATCGATACAG
32559 TGTATCGATACA
1 TGTATCGATACA
32571 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:38705 original size:20 final size:20
Alignment explanation
Indices: 38680--38731 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
38670 TACAAGCCAA
**
38680 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
38700 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
38719 TGTATCGATACAA
1 TGTATCGATACAA
38732 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:43003 original size:2 final size:2
Alignment explanation
Indices: 42996--43022 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42986 TTAAAGGCAT
42996 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
43023 TCTAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50096 original size:79 final size:79
Alignment explanation
Indices: 49991--50198 Score: 231
Period size: 80 Copynumber: 2.6 Consensus size: 79
49981 GAGATAATAA
* * * * * *
49991 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTAGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-
*
50055 A-TTAGAAAAAAAAAT
64 ATTTAGAAAAAAAAAC
* *
50070 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * * *
50135 TTTGGGAAATAAAGC
65 TTTAGAAAAAAAAAC
* * *
50150 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
50199 GAAATAACGA
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
78 7 0.06
79 48 0.44
80 53 0.49
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:50190 original size:28 final size:28
Alignment explanation
Indices: 50150--50221 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
50140 GAAATAAAGC
** *
50150 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
50178 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
50206 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
50222 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:50214 original size:108 final size:107
Alignment explanation
Indices: 50070--50432 Score: 264
Period size: 108 Copynumber: 3.4 Consensus size: 107
50060 AAAAAAAAAT
* *
50070 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGATTGGAGTATCCC-TCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* *
50135 TTTGGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAA
65 TTTGGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
* * * * ***
50178 CGGGGTTGGAGTATCCC-CGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTA
1 CGGGATTGGAGTATCCCTCGA--AAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATA
* * *
50242 TTTTTGGAAATAAAATCGGAGTTGGAGTAT-CCC-C-G-ATTAA
64 TTTTGGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
* * * * * * *
50282 AGGAAAATTGGCGT-T---TTGAAAATAAAACCAGGATTGGAGTATCCCCAATTGTGGAAAAATT
1 CGG--GATTGGAGTATCCCTCGAAAAT--AACGAGG-TTGGAGTATCCCCAATTAT-GAAAAATC
* * * * * *
50343 AGTGTTTTAGCG--ATAAAACCGGAGTTGGAGCATCCCCTCGAAAATAA
60 AATATTTT-GGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
* * * *
50390 TGGGGTTGGAGTATCCC-CGATAATTAACGGGGTTGGAGTATCC
1 CGGGATTGGAGTATCCCTCGA-AAATAACGAGGTTGGAGTATCC
50433 TCGATTGTGA
Statistics
Matches: 198, Mismatches: 38, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
101 4 0.02
103 8 0.04
104 42 0.21
105 19 0.10
106 18 0.09
107 15 0.08
108 87 0.44
109 2 0.01
110 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (107 bp):
CGGGATTGGAGTATCCCTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATATT
TTGGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAA
Found at i:50279 original size:52 final size:52
Alignment explanation
Indices: 50210--50547 Score: 158
Period size: 52 Copynumber: 6.4 Consensus size: 52
50200 AAATAACGAG
*
50210 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
50262 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * * *
50315 -TTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* * * * **** * *
50366 GTTGGAGCATCCCC--TCG-AAAATAATGGGGTTGGAGTATCCCCGATAAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AAT-TGG-T--A-T-TTTTGGA-AATAAAATCGGA
* *
50421 GTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGA
* * * * *
50476 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* * *
50527 GTTAGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
50548 GAGAATTGAT
Statistics
Matches: 210, Mismatches: 50, Indels: 52
0.67 0.16 0.17
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 3 0.01
51 39 0.19
52 77 0.37
53 19 0.09
54 13 0.06
55 38 0.18
56 2 0.01
57 4 0.02
58 7 0.03
59 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:50398 original size:28 final size:28
Alignment explanation
Indices: 50353--50432 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 28
50343 AGTGTTTTAG
* * *
50353 CGATAAA-ACCGGAGTTGGAGCATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
*
50380 TCGA-AAATAATGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
*
50407 CGATAATTAACGGGGTTGGAGTATCC
1 CGATAAATAACGGGGTTGGAGTATCC
50433 TCGATTGTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.07
27 24 0.56
28 16 0.37
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:52922 original size:13 final size:13
Alignment explanation
Indices: 52904--52929 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52894 ACAAAGATCC
52904 ATGTATCGATACA
1 ATGTATCGATACA
52917 ATGTATCGATACA
1 ATGTATCGATACA
52930 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:52925 original size:33 final size:33
Alignment explanation
Indices: 52883--52949 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
52873 AAAATTTCCA
***
52883 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
52916 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
52949 A
1 A
52950 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:53751 original size:55 final size:55
Alignment explanation
Indices: 53667--55222 Score: 2397
Period size: 55 Copynumber: 28.3 Consensus size: 55
53657 ATAAACTGTA
* * * * *
53667 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
53722 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
**
53777 TCCTGCTCTTTGAATACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
53831 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
53886 TCCTGCTCTTTGGGGACT--AAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAA--TGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
53941 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
53996 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
54051 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
54106 TCCTGCTCCTTGAGGACTGGAAAATGCCACCAACTTGTGTAGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
54161 TCCTGCTCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
54216 TCCAGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
54271 TCCAGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
54326 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
**
54381 TCCTGCTCTTTGAATACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
54435 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
54490 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
54545 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTATGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
54600 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
54655 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
54710 TCCTGCTCCTTGAGGACTGGAAAATGCCACCAACTTGTGTAGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
54765 TCCTGCTCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
54820 TCCAGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
54875 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
54930 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
54985 TCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
55040 TCCTGCTCTTTGAGGACTGGAAGACGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
55095 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
55150 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
55205 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
55223 AAAAAAGCGG
Statistics
Matches: 1418, Mismatches: 56, Indels: 54
0.93 0.04 0.04
Matches are distributed among these distances:
53 8 0.01
54 118 0.08
55 1264 0.89
56 24 0.02
57 4 0.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:54018 original size:27 final size:27
Alignment explanation
Indices: 53988--54073 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
53978 TATGGGCTTT
53988 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
54015 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
54043 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
54070 GAAA
1 GAAA
54074 ATGCCACCAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:54229 original size:26 final size:26
Alignment explanation
Indices: 54200--54282 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 26
54190 CCAACTTGTG
54200 TGGGCTTTGAAAGGTGTCCAGCTCTT
1 TGGGCTTTGAAAGGTGTCCAGCTCTT
*** * *
54226 TGGGGACTGAAAGGTG-CCACCAACTTGT
1 TGGGCTTTGAAAGGTGTCCAGC-TC-T-T
54254 GTGGGCTTT-AAGAGGTGTCCAGCTCTT
1 -TGGGCTTTGAA-AGGTGTCCAGCTCTT
54281 TG
1 TG
54283 AGGACTGGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
25 4 0.10
26 16 0.39
27 2 0.05
28 4 0.10
29 11 0.27
30 4 0.10
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (26 bp):
TGGGCTTTGAAAGGTGTCCAGCTCTT
Found at i:54622 original size:27 final size:27
Alignment explanation
Indices: 54592--54677 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
54582 TATGGGCTTT
54592 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
54619 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
54647 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
54674 GAAA
1 GAAA
54678 ATGCCACCAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:54840 original size:26 final size:26
Alignment explanation
Indices: 54811--54900 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
54801 GTGTGGGCTT
54811 TGAAAGGTGTCCAGCTCTTTGGGGAC
1 TGAAAGGTGTCCAGCTCTTTGGGGAC
* *
54837 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCAGC-TCTT-TG-GGGAC
* * *
54864 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCAGCTCTTTGGGGAC
54892 TGAAAGGTG
1 TGAAAGGTG
54901 CCACCAACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
25 4 0.08
26 17 0.35
27 8 0.16
28 9 0.18
29 8 0.16
30 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCAGCTCTTTGGGGAC
Found at i:55119 original size:26 final size:26
Alignment explanation
Indices: 55090--55175 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
55080 GGGCTTTAAG
55090 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
55116 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
55144 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
55171 AGGTG
1 AGGTG
55176 CCACCAACTT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.29
27 9 0.20
28 9 0.20
29 8 0.18
30 3 0.07
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:56247 original size:23 final size:24
Alignment explanation
Indices: 56190--56248 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
56180 CTTAAGTAGG
56190 TTTTTT-CTTTTCTCTCTTTTTCTT
1 TTTTTTGCTTTT-TCTCTTTTTCTT
* *
56214 TGTTTTG-TTTTTCTGTTTTT-TT
1 TTTTTTGCTTTTTCTCTTTTTCTT
56236 TTTTTTGCTTTTT
1 TTTTTTGCTTTTT
56249 TTTTTTGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 8 0.27
23 13 0.43
24 9 0.30
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (24 bp):
TTTTTTGCTTTTTCTCTTTTTCTT
Found at i:56253 original size:15 final size:15
Alignment explanation
Indices: 56206--56254 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
56196 CTTTTCTCTC
56206 TTTTT-CTTTGTTTTGT
1 TTTTTGCTTT-TTTT-T
56222 TTTTCTG-TTTTTTTT
1 TTTT-TGCTTTTTTTT
56237 TTTTTGCTTTTTTTT
1 TTTTTGCTTTTTTTT
56252 TTT
1 TTT
56255 GAAGAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.07
15 16 0.53
16 8 0.27
17 4 0.13
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.86
Consensus pattern (15 bp):
TTTTTGCTTTTTTTT
Found at i:56254 original size:13 final size:13
Alignment explanation
Indices: 56231--56255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56221 TTTTTCTGTT
56231 TTTTTTTTTTTGC
1 TTTTTTTTTTTGC
56244 TTTTTTTTTTTG
1 TTTTTTTTTTTG
56256 AAGAAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.04, G:0.08, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTGC
Found at i:69086 original size:26 final size:25
Alignment explanation
Indices: 69030--69086 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
69020 AATAAAGCCG
*
69030 GGGTTGGAGTATCCCTCGAAGTAAC
1 GGGTTGGAGTATCCCTCGAAATAAC
69055 GCGGTTGGAGTATCCC-CATGAAATAAC
1 G-GGTTGGAGTATCCCTC--GAAATAAC
69082 GGGTT
1 GGGTT
69087 TTGATATCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 2 0.07
26 18 0.64
27 8 0.29
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (25 bp):
GGGTTGGAGTATCCCTCGAAATAAC
Done.