Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2681
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: 141227
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:106754 original size:128 final size:128
Alignment explanation
Indices: 106417--106767 Score: 377
Period size: 128 Copynumber: 2.7 Consensus size: 128
106407 ACAAAAGTCA
* * * *
106417 GTGGCAACCTTTCTCAAAAGTCCACATAAGTTGGTGGCAACCCTTTCAACA-CCCACACAAGTCA
1 GTGGCAACCTTTTTCAAAAGCCCACACAAGTTGGTGGCAACCCTTTCAA-AGCCCACATAAGT-A
* * * * * *
106481 GTGGAAATCCCTTTCAAAGGACTACATAAGTCGGTCACAACCTTTTTTAAAGCCCACACAAGTTG
64 GTGGAAACCCCTTTCAAAAGCCCACAGAAGTCGGTCACAACCCTTTTTAAAGCCCACACAAGTTG
* * * *
106546 GTGGTAA-CTCTTTTCAAAAGCCCATACAAGTTGGTGGCAACCCTTTCAAAGCCCACATAAATTG
1 GTGGCAACCT-TTTTCAAAAGCCCACACAAGTTGGTGGCAACCCTTTCAAAGCCCACATAAGTAG
* * ** * *
106610 -GTGTAACCCCTTTCAAAAGCCCATAGAAGTCGGTGGCAACCCTTTTTAAAGGCCATACAAGTTG
65 TG-GAAACCCCTTTCAAAAGCCCACAGAAGTCGGTCACAACCCTTTTTAAAGCCCACACAAGTTG
* * * *
106674 GTGGCAACCTTTTTCGAAAGCCCACACAAGTCGATGGCAATCCTTTTCAAAGCCCACATAAGTAG
1 GTGGCAACCTTTTTCAAAAGCCCACACAAGTTGGTGGCAA-CCCTTTCAAAGCCCACATAAGTAG
* * * *
106739 TGGCAA-CCCTCTCAAAAGCCTACACAAGT
65 TGGAAACCCCTTTCAAAAGCCCACAGAAGT
106768 TGATCGCATC
Statistics
Matches: 183, Mismatches: 33, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
127 1 0.01
128 105 0.57
129 76 0.42
130 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (128 bp):
GTGGCAACCTTTTTCAAAAGCCCACACAAGTTGGTGGCAACCCTTTCAAAGCCCACATAAGTAGT
GGAAACCCCTTTCAAAAGCCCACAGAAGTCGGTCACAACCCTTTTTAAAGCCCACACAAGTTG
Found at i:106869 original size:58 final size:58
Alignment explanation
Indices: 106781--106925 Score: 195
Period size: 58 Copynumber: 2.5 Consensus size: 58
106771 TCGCATCTCC
* * *
106781 TTCT-AAGCCCAATGTCATTGGCCTTAAATCAACACATTAG-CACTTGTCAACCCTTCT
1 TTCTCAAGCCCAATGTCATTGGCCTTGAATCAACACATT-GTCACTTATCAAACCTTCT
* * * * *
106838 TTCTCAAGTCCAATGTTATTGGCCTTGAATCAATACATTGTCACTTATCAAATCTTTT
1 TTCTCAAGCCCAATGTCATTGGCCTTGAATCAACACATTGTCACTTATCAAACCTTCT
106896 TTCTCAAGCCCAATGTCATTGGCCTTGAAT
1 TTCTCAAGCCCAATGTCATTGGCCTTGAAT
106926 TAGCATATTG
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
57 5 0.07
58 71 0.93
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (58 bp):
TTCTCAAGCCCAATGTCATTGGCCTTGAATCAACACATTGTCACTTATCAAACCTTCT
Found at i:107115 original size:52 final size:52
Alignment explanation
Indices: 106953--107118 Score: 163
Period size: 52 Copynumber: 3.2 Consensus size: 52
106943 TTAAACCTTC
* * * * * *
106953 TCATTTTTAAGTCTAATGTTGCTGGCTTTAAATCAGCACATTGGCA-TTCTTC
1 TCATCTTTAAGTCCAATGTCGCTGGCTTTGAATCAGCACATTGGCACCT-TTA
* * * * * * * * *
107005 TCATCTTAAAGTCCGATATCGCTAGCTTTGAATTAGCATATTAGCACCCTTG
1 TCATCTTTAAGTCCAATGTCGCTGGCTTTGAATCAGCACATTGGCACCTTTA
* *
107057 TAATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA
1 TCATCTTTAAGTCCAATGTCGCTGGCTTTGAATCAGCACATTGGCACCTTTA
107109 TCATCTTTAA
1 TCATCTTTAA
107119 ATCTAGTGTC
Statistics
Matches: 87, Mismatches: 26, Indels: 2
0.76 0.23 0.02
Matches are distributed among these distances:
52 87 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (52 bp):
TCATCTTTAAGTCCAATGTCGCTGGCTTTGAATCAGCACATTGGCACCTTTA
Found at i:110063 original size:20 final size:20
Alignment explanation
Indices: 110038--110124 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
110028 TTTTTACCCA
110038 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
110058 AATGTATCGATACATTCTGTCTTTTTACC
1 AATGTATCGATACA-------TTTTT--C
110087 TAGATGTATCGATACATTTTTC
1 -A-ATGTATCGATACATTTTTC
110109 AATGTATCGATACATT
1 AATGTATCGATACATT
110125 ATGTCTTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 22
0.72 0.00 0.28
Matches are distributed among these distances:
20 29 0.52
21 1 0.02
22 1 0.02
24 5 0.09
27 5 0.09
29 1 0.02
30 1 0.02
31 13 0.23
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:110104 original size:51 final size:51
Alignment explanation
Indices: 110028--110158 Score: 235
Period size: 51 Copynumber: 2.6 Consensus size: 51
110018 AAAAGTCAAA
* * *
110028 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATTCTGTC
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTATGTC
110079 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTATGTC
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTATGTC
110130 TTTTTACCTAGATGTATCGATACATTTTT
1 TTTTTACCTAGATGTATCGATACATTTTT
110159 ACCCCTAGAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 77 1.00
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.46
Consensus pattern (51 bp):
TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTATGTC
Found at i:117151 original size:27 final size:27
Alignment explanation
Indices: 117081--118231 Score: 1307
Period size: 27 Copynumber: 41.9 Consensus size: 27
117071 AATGTAACCT
* * *
117081 CTTTAAAGTGCACAACTCCGTGGTAGCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
117109 CTTTTTAAGTCCACAACTCCGTGGCATC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
* * *
117137 CTTTTAAGTCTACAACTCCATGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
117164 CTTTTAAGTTCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
117191 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
117219 CTTTTAAGTCCACAGCTCCATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
117246 CTTTTAAAGTCCACAACTCCGTGGCAAC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
117274 CATTTAAGTCCACAGCTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
117301 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * * **
117328 TTTTTAAAGTCCACAACTCTGGGGCTTC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
117356 CTTTTAAAGTCCACAGCTCCATGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
117384 CTTTCAAAGTCCACAACTTCGTGGCACC
1 CTTT-TAAGTCCACAACTCCGTGGCACC
* *
117412 CTTTTAAGCCCACAACTCCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
117439 CTTTTAATTCCACAACTTTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
** *
117466 CTTTTAAGTATACAACACCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
117494 CTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
117521 CTTTTAAGTCCACAGCTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
117548 CTTTTAAGTCCACAGCTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
117575 CTTTTAAAGTCCAC-ACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
117602 CTTTTAAAGTCCATAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
117630 CTTTTAAAGTCTACAACTCGGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
117658 CTTTCAAAGTCCACAACTCCGTGGCACC
1 CTTT-TAAGTCCACAACTCCGTGGCACC
* *
117686 CTTTTAAGTCCACAACTTCGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
117713 CTTTTAAGTCCACAACTCTGTGGCAAC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
117740 CTTTTAAGTCCATAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
117767 CTTTTAAGTCCACAAATCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
117794 CTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
117820 CTTTTAAAGTCCACAACCCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
117848 CTTTTAAAGTCCACAACTCTGTGACACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* ** *
117876 CTTTTAAAGTCCACAATTTTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
117904 CTTTTAAAGTCCACAACTCTGTAGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* * *
117932 CTTTAAAGTCCACAACTTCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
117959 CTTTCAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
117986 CTTTTAAGTCCACAACTCCGTGGTAGCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
118014 CTTTTTAAGTCCACAACTCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
* *
118042 CTTTTAAGTCCATAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* ** *
118069 CTTTTAAGTCCATAACTCCACGGTAGCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
118097 CTTTTTAAGTCCACAACCCCGTGGCACC
1 C-TTTTAAGTCCACAACTCCGTGGCACC
* *
118125 CTTTTAAGTCCACAAGTCAGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * * * * *
118152 TTTTTAAAGCCCACAAGTCAGTCGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
118180 ATTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
118207 CTTTTAAGTCCACAAGTCAGTGGCA
1 CTTTTAAGTCCACAACTCCGTGGCA
118232 TCATTTCAAA
Statistics
Matches: 971, Mismatches: 136, Indels: 33
0.85 0.12 0.03
Matches are distributed among these distances:
26 6 0.01
27 574 0.59
28 328 0.34
29 63 0.06
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:117209 original size:28 final size:28
Alignment explanation
Indices: 117082--118390 Score: 1295
Period size: 27 Copynumber: 47.5 Consensus size: 28
117072 ATGTAACCTC
* *
117082 TTTAAAGTGCACAACTCCGTGGTAGCCCT
1 TTTAAAGTCCACAACTCCGTGGCA-CCCT
* *
117111 TTTTAAGTCCACAACTCCGTGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * *
117139 TTT-AAGTCTACAACTCCATGGCACTCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
117166 TTT-AAGTTCACAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
117193 TTTAAAGTCCACAACTCCGTGGTACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * *
117221 TTT-AAGTCCACAGCTCCATGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117248 TTTAAAGTCCACAACTCCGTGGCAACCA
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
117276 TTT-AAGTCCACAGCTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117303 TTT-AAGTCCACAACTCCGTGGCATCTT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * **
117330 TTTAAAGTCCACAACTCTGGGGCTTCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * *
117358 TTTAAAGTCCACAGCTCCATGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117386 TTCAAAGTCCACAACTTCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117414 TTT-AAGCCCACAACTCCGTGGCAACCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* **
117441 TTT-AATTCCACAACTTTGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
** *
117468 TTT-AAGTATACAACACCGTGGCATCCC-
1 TTTAAAGTCCACAACTCCGTGGCA-CCCT
117495 TTTAAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
117523 TTT-AAGTCCACAGCTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117550 TTT-AAGTCCACAGCTCCGTGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117577 TTTAAAGTCCAC-ACTCTGTGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * *
117604 TTTAAAGTCCATAACTCTGTGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * *
117632 TTTAAAGTCTACAACTCGGTGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
117660 TTCAAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117688 TTT-AAGTCCACAACTTCGTGGCAACCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117715 TTT-AAGTCCACAACTCTGTGGCAACCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117742 TTT-AAGTCCATAACTCCGTGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
117769 TTT-AAGTCCACAAATCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
117796 TTT-AAGTCCACAACTCCGTGGCA-CCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
117822 TTTAAAGTCCACAACCCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117850 TTTAAAGTCCACAACTCTGTGACACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* ** *
117878 TTTAAAGTCCACAATTTTGTGGCATCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * *
117906 TTTAAAGTCCACAACTCTGTAGCATCC-
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117933 TTTAAAGTCCACAACTTCGTGGTACCC-
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
117960 TTTCAAGTCCATAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
*
117988 TTT-AAGTCCACAACTCCGTGGTAGCCCT
1 TTTAAAGTCCACAACTCCGTGGCA-CCCT
*
118016 TTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* *
118044 TTT-AAGTCCATAACTCCATGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* ** *
118071 TTT-AAGTCCATAACTCCACGGTAGCCCT
1 TTTAAAGTCCACAACTCCGTGGCA-CCCT
* *
118099 TTTTAAGTCCACAACCCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * *
118127 TTT-AAGTCCACAAGTCAGTGGCACCTT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * * * * *
118154 TTTAAAGCCCACAAGTCAGTCGCATCAT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
118182 TTT-AAGTCCACAACTCCGTGGCACCCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * * *
118209 TTT-AAGTCCACAAGTCAGTGGCATCAT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * * * * *
118236 TTCAAAGCCCACAAGTCAGTGGCATCAT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * * * * * *
118264 TTCAAAGCCCACAAGTCAGTGACATCTT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * * * *
118292 TTTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTT-AAAGTCCACAACTCCGTGGCACCCT
** * * * *
118321 TCCAAAGCCCACGAGTCAGTGGCA-CCT
1 TTTAAAGTCCACAACTCCGTGGCACCCT
* * * *
118348 TTTCAAAGTCCACGAGTCAGTGGCATCCT
1 TTT-AAAGTCCACAACTCCGTGGCACCCT
* *
118377 TTCAAAGCCCACAA
1 TTTAAAGTCCACAA
118391 GTCAATGGCA
Statistics
Matches: 1108, Mismatches: 152, Indels: 41
0.85 0.12 0.03
Matches are distributed among these distances:
26 6 0.01
27 571 0.52
28 448 0.40
29 83 0.07
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (28 bp):
TTTAAAGTCCACAACTCCGTGGCACCCT
Found at i:117222 original size:82 final size:81
Alignment explanation
Indices: 117079--118231 Score: 1244
Period size: 82 Copynumber: 14.0 Consensus size: 81
117069 GTAATGTAAC
* * * *
117079 CTCTTTAAAGTGCACAACTCCGTGGTAGCCCTTTTTAAGTCCACAACTCCGTGGCATCCTTTTAA
1 CTCTTTTAAGTCCACAACTCCGTGGCA-CCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
* *
117144 GTCTACAACTCCATGGCA
64 GTCCACAACTCCGTGGCA
* *
117162 CTCTTTTAAGTTCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGTACCCTTTTAAG
1 CTCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAG
* *
117227 TCCACAGCTCCATGGCA
65 TCCACAACTCCGTGGCA
* * *
117244 -TCCTTTTAAAGTCCACAACTCCGTGGCAACCATTTAAGTCCACAGCTCCGTGGCACCCTTTTAA
1 CT-CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
117308 GTCCACAACTCCGTGGCA
64 GTCCACAACTCCGTGGCA
* * ** * * * *
117326 -TCTTTTTAAAGTCCACAACTCTGGGGCTTCCTTTTAAAGTCCACAGCTCCATGGCATCCTTTCA
1 CTC-TTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTT-T
*
117390 AAGTCCACAACTTCGTGGCA
62 AAGTCCACAACTCCGTGGCA
* * * * **
117410 CCCTTTTAAGCCCACAACTCCGTGGCAACCTTTTAATTCCACAACTTTGTGGCACCCTTTTAAGT
1 CTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
** *
117475 ATACAACACCGTGGCA
66 CCACAACTCCGTGGCA
* * *
117491 TCCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAGCTCCGTGGCACCCTTTTAAG
1 -CTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAG
*
117556 TCCACAGCTCCGTGGCA
65 TCCACAACTCCGTGGCA
* * * * *
117573 -TCCTTTTAAAGTCCAC-ACTCTGTGGCATCCTTTTAAAGTCCATAACTCTGTGGCATCCTTTTA
1 CT-CTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-
* *
117636 AAGTCTACAACTCGGTGGCA
62 AAGTCCACAACTCCGTGGCA
* * *
117656 -TCCTTTCAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCGTGGCAACCTTTTAA
1 CT-CTTT-TAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
*
117720 GTCCACAACTCTGTGGCAA
64 GTCCACAACTCCGTGGC-A
* * *
117739 C-CTTTTAAGTCCATAACTCCGTGGCATCCTTTTAAGTCCACAAATCCGTGGCACCCTTTTAAGT
1 CTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
117803 CCACAACTCCGTGGCA
66 CCACAACTCCGTGGCA
* * *
117819 C-CTTTTAAAGTCCACAACCCCGTGGCACCCTTTTAAAGTCCACAACTCTGTGACACCCTTTTAA
1 CTCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-A
* **
117883 AGTCCACAATTTTGTGGCA
63 AGTCCACAACTCCGTGGCA
* * * * * * *
117902 -TCCTTTTAAAGTCCACAACTCTGTAGCATCCTTTAAAGTCCACAACTTCGTGGTACCCTTTCAA
1 CT-CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
*
117966 GTCCATAACTCCGTGGCA
64 GTCCACAACTCCGTGGCA
* *
117984 CCCTTTTAAGTCCACAACTCCGTGGTAGCCCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
1 CTCTTTTAAGTCCACAACTCCGTGGCA-CCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
* *
118049 GTCCATAACTCCATGGCA
64 GTCCACAACTCCGTGGCA
* * ** * *
118067 CCCTTTTAAGTCCATAACTCCACGGTAGCCCTTTTTAAGTCCACAACCCCGTGGCACCCTTTTAA
1 CTCTTTTAAGTCCACAACTCCGTGGCA-CCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
* *
118132 GTCCACAAGTCAGTGGCA
64 GTCCACAACTCCGTGGCA
* * * * * *
118150 C-CTTTTTAAAGCCCACAAGTCAGTCGCATCATTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
1 CTC-TTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAA
* *
118214 GTCCACAAGTCAGTGGCA
64 GTCCACAACTCCGTGGCA
118232 TCATTTCAAA
Statistics
Matches: 914, Mismatches: 130, Indels: 53
0.83 0.12 0.05
Matches are distributed among these distances:
80 7 0.01
81 150 0.16
82 362 0.40
83 315 0.34
84 79 0.09
85 1 0.00
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (81 bp):
CTCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
CCACAACTCCGTGGCA
Found at i:117437 original size:165 final size:164
Alignment explanation
Indices: 117082--118261 Score: 1379
Period size: 165 Copynumber: 7.2 Consensus size: 164
117072 ATGTAACCTC
* * * *
117082 TTTAAAGTGCACAACTCCGTGGTAGCCCTTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTC
1 TTTAAAGTCCACAACTCCGTGGCA-TCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* * *
117147 TACAACTCCATGGCA-CTCTTTT-AAGTTCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTC
64 CACAACTCCGTGGCATC-CTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTC
* * *
117210 CGTGGTACCCTTTTAAGTCCACAGCTCCATGGCATCCT
127 CGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCT
* * *
117248 TTTAAAGTCCACAACTCCGTGGCAACCATTTAAGTCCACAGCTCCGTGGCACCCTTTTAAGTCCA
1 TTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* * * ** * *
117313 CAACTCCGTGGCATCTTTTTAAAGTCCACAACTCTGGGGCTTCCTTTTAAAGTCCACAGCTCCAT
66 CAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGT
* * * *
117378 GGCATCCTTTCAAAGTCCACAACTTCGTGGCACCCT
130 GGCACCCTTT-TAAGTCCACAACTCCGTGGCATCCT
* * * ** **
117414 TTT-AAGCCCACAACTCCGTGGCAACCTTTTAATTCCACAACTTTGTGGCACCCTTTTAAGTATA
1 TTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* * *
117478 CAACACCGTGGCATCCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAGCTCCGTG
66 CAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
*
117543 GCACCCTTTTAAGTCCACAGCTCCGTGGCATCCT
131 GCACCCTTTTAAGTCCACAACTCCGTGGCATCCT
* * * *
117577 TTTAAAGTCCAC-ACTCTGTGGCATCCTTTTAAAGTCCATAACTCTGTGGCATCCTTTTAAAGTC
1 TTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
* * * *
117641 TACAACTCGGTGGCATCCTTTCAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTTCG
64 CACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCG
* * *
117706 TGGCAACCTTTTAAGTCCACAACTCTGTGGCAACCT
129 TGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCT
* *
117742 TTT-AAGTCCATAACTCCGTGGCATCCTTTTAAGTCCACAAATCCGTGGCACCCTTTTAAGTCCA
1 TTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* *
117806 CAACTCCGTGGCA-CCTTTTAAAGTCCACAACCCCGTGGCACCCTTTTAAAGTCCACAACTCTGT
66 CAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGT
* * **
117870 GACACCCTTTTAAAGTCCACAATTTTGTGGCATCCT
130 GGCACCCTTTT-AAGTCCACAACTCCGTGGCATCCT
* * * * * *
117906 TTTAAAGTCCACAACTCTGTAGCATCCTTTAAAGTCCACAACTTCGTGGTACCCTTTCAAGTCCA
1 TTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* * *
117971 TAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGTAGCCCTTTTTAAGTCCACAACTCCG
66 CAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCA-CCC-TTTTAAGTCCACAACTCCG
* * *
118035 TGGCACCCTTTTAAGTCCATAACTCCATGGCACCCT
129 TGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCT
* ** * * *
118071 TTT-AAGTCCATAACTCCACGGTAGCCCTTTTTAAGTCCACAACCCCGTGGCACCCTTTTAAGTC
1 TTTAAAGTCCACAACTCCGTGGCA-TCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* * * * * * * *
118135 CACAAGTCAGTGGCA-CCTTTTTAAAGCCCACAAGTCAGTCGCATCATTTTAAGTCCACAACTCC
64 CACAACTCCGTGGCATCC-TTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCC
* * *
118199 GTGGCACCCTTTTAAGTCCACAAGTCAGTGGCATCAT
128 GTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCT
* * * *
118236 TTCAAAGCCCACAAGTCAGTGGCATC
1 TTTAAAGTCCACAACTCCGTGGCATC
118262 ATTTCAAAGC
Statistics
Matches: 861, Mismatches: 135, Indels: 37
0.83 0.13 0.04
Matches are distributed among these distances:
162 32 0.04
163 81 0.09
164 172 0.20
165 417 0.48
166 140 0.16
167 19 0.02
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.29
Consensus pattern (164 bp):
TTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
CAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTG
GCACCCTTTTAAGTCCACAACTCCGTGGCATCCT
Found at i:118393 original size:28 final size:28
Alignment explanation
Indices: 117115--118641 Score: 749
Period size: 28 Copynumber: 55.3 Consensus size: 28
117105 AGCCCTTTTT
* * *
117115 AAGTCCACAACTCCGTGGCATCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
117142 AAGTCTACAACTCCA-TGGCA-CTCTTT-T
1 AAGTCCACAAGT-CAGTGGCATC-CTTTCA
* * * * *
117169 AAGTTCACAACTCCGTGGCACCCTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * * *
117197 AAGTCCACAACTCCGTGGTACCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
*
117224 AAGTCCAC-AGCTCCA-TGGCATCCTTTTA
1 AAGTCCACAAG-T-CAGTGGCATCCTTTCA
* * *
117252 AAGTCCACAACTCCGTGGCAACCATTT--
1 AAGTCCACAAGTCAGTGGCATCC-TTTCA
* * *
117279 AAGTCCAC-AGCTCCGTGGCACCCTTT-T
1 AAGTCCACAAG-TCAGTGGCATCCTTTCA
* * * *
117306 AAGTCCACAACTCCGTGGCATCTTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * * *
117334 AAGTCCACAACTCTGGGGCTTCCTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
117362 AAGTCCAC-AGCTCCA-TGGCATCCTTTCA
1 AAGTCCACAAG-T-CAGTGGCATCCTTTCA
* * *
117390 AAGTCCACAACTTC-GTGGCACCCTTT-T
1 AAGTCCACAA-GTCAGTGGCATCCTTTCA
* * * * *
117417 AAGCCCACAACTCCGTGGCAACCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * ** * *
117444 AATTCCACAACTTTGTGGCACCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
** ** *
117471 AAGTATACAACACCGTGGCATCCCTTT-A
1 AAGTCCACAAGTCAGTGGCAT-CCTTTCA
* * * *
117499 AAGTCCACAACTCCGTGGCACCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
117526 AAGTCCAC-AGCTCCGTGGCACCCTTT-T
1 AAGTCCACAAG-TCAGTGGCATCCTTTCA
* *
117553 AAGTCCAC-AGCTCCGTGGCATCCTTTTA
1 AAGTCCACAAG-TCAGTGGCATCCTTTCA
* * *
117581 AAGTCCAC-ACTCTGTGGCATCCTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * *
117608 AAGTCCATAACTCTGTGGCATCCTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
117636 AAGTCTACAACTCGGTGGCATCCTTTCA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * *
117664 AAGTCCACAACTCCGTGGCACCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
117691 AAGTCCACAACTTC-GTGGCAACCTTT-T
1 AAGTCCACAA-GTCAGTGGCATCCTTTCA
* * * *
117718 AAGTCCACAACTCTGTGGCAACCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * *
117745 AAGTCCATAACTCCGTGGCATCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * *
117772 AAGTCCACAAATCCGTGGCACCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
117799 AAGTCCACAACTCCGTGGCA-CCTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
** * * *
117826 AAGTCCACAACCCCGTGGCACCCTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * * *
117854 AAGTCCACAACTCTGTGACACCCTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* ** *
117882 AAGTCCACAATTTTGTGGCATCCTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
117910 AAGTCCACAACTCTGTAGCATCCTTT-A
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
117937 AAGTCCACAACTTC-GTGGTACCCTTTC-
1 AAGTCCACAA-GTCAGTGGCATCCTTTCA
* * * * *
117964 AAGTCCATAACTCCGTGGCACCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * * **
117991 AAGTCCACAACTCCGTGGTAGCCCTTTTT
1 AAGTCCACAAGTCAGTGGCA-TCCTTTCA
* * * *
118020 AAGTCCACAACTCCGTGGCACCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * *
118047 AAGTCCATAACTCCA-TGGCACCCTTT-T
1 AAGTCCACAAGT-CAGTGGCATCCTTTCA
* * * **
118074 AAGTCCATAACTCCACGGTAGC--CCTTTTT
1 AAGTCCACAAGT-CA--GTGGCATCCTTTCA
** * * *
118103 AAGTCCACAACCCCGTGGCACCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
*
118130 AAGTCCACAAGTCAGTGGCA-CCTTTTTA
1 AAGTCCACAAGTCAGTGGCATCC-TTTCA
* * * *
118158 AAGCCCACAAGTCAGTCGCATCATTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * *
118185 AAGTCCACAACTCCGTGGCACCCTTT-T
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
*
118212 AAGTCCACAAGTCAGTGGCATCATTTCA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* *
118240 AAGCCCACAAGTCAGTGGCATCATTTCA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
118268 AAGCCCACAAGTCAGTGACATCTTTTTCA
1 AAGTCCACAAGTCAGTGGCATC-CTTTCA
* * *
118297 AAGCCCATAAGTCAGTGGCATCCTTCCA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* *
118325 AAGCCCACGAGTCAGTGGCA-CCTTTTCA
1 AAGTCCACAAGTCAGTGGCATCC-TTTCA
*
118353 AAGTCCACGAGTCAGTGGCATCCTTTCA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
118381 AAGCCCACAAGTCAATGGCAT-ATCTTCA
1 AAGTCCACAAGTCAGTGGCATCCT-TTCA
* *
118409 AAGCCCATAAGTCAGTGGCATCC-TTCTA
1 AAGTCCACAAGTCAGTGGCATCCTTTC-A
* * *
118437 AAGCCCACAGGTCAATGGCAT-CTCTTCA
1 AAGTCCACAAGTCAGTGGCATCCT-TTCA
* * * * *
118465 AAGCCCACAAGTTAGTGGTATTCTTCCA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * * * *
118493 AAGCCCACGAGTTAGTGGCATCATTCCA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
* * *
118521 AAGCCCACGAGTTAGTGGCATCCTTTCA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
*
118549 AAGCCCACAAGTCAGTGGCAT-CTCTTCA
1 AAGTCCACAAGTCAGTGGCATCCT-TTCA
* *
118577 AAGCCCACAAGTCAGAGGCA-CCTTCTCA
1 AAGTCCACAAGTCAGTGGCATCCTT-TCA
** * *
118605 AAACCCACAAGTTAGTGGCATCCTTTTA
1 AAGTCCACAAGTCAGTGGCATCCTTTCA
*
118633 AAGCCCACA
1 AAGTCCACA
118642 CAAGTCGATG
Statistics
Matches: 1273, Mismatches: 168, Indels: 117
0.82 0.11 0.08
Matches are distributed among these distances:
26 25 0.02
27 536 0.42
28 634 0.50
29 75 0.06
30 3 0.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (28 bp):
AAGTCCACAAGTCAGTGGCATCCTTTCA
Found at i:118759 original size:49 final size:49
Alignment explanation
Indices: 118698--119047 Score: 196
Period size: 52 Copynumber: 6.7 Consensus size: 49
118688 CCCTTCTAAA
* *
118698 CCCAATACCGCTGGCCTTGAATCAACACATTAGCACCTTCATCTTTAAG
1 CCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAG
*
118747 CCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCCTTCTTATCTTTAAG
1 CCCAATATCGCTGGCCTTGAATCAGC--A----CA---TTAGCA-CCTTC--ATCTTTAAG
* * * * *
118808 TCTAATGTCGCTGGTCTTGAATCAGCACATTGGCACCTTCATCTTTAAG
1 CCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAG
* ** * * * **
118857 TCTGATATCGCTGGCCTTGAACCAGCATATTAGCATCTTCGACATCCCTAAG
1 CCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTT---CATCTTTAAG
* * * * * * * *
118909 CCCGATATCGTTGGCCTTGAATTAGCATATTGGCATCTTTAACATTCCTAAG
1 CCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCATC-TT--TAAG
* ** *
118961 CCCAATGTCATTGGCCTTGAATCAGCACATTAGCATTCTTCTCATCTTTAAG
1 CCCAATATCGCTGGCCTTGAATCAGCACATTAGCA--CCT-TCATCTTTAAG
* * * * * * *
119013 TCCAGTGTTGCAGGCCTTGAATCTGCACACTAGCA
1 CCCAATATCGCTGGCCTTGAATCAGCACATTAGCA
119048 AATTGCAAAA
Statistics
Matches: 234, Mismatches: 46, Indels: 39
0.73 0.14 0.12
Matches are distributed among these distances:
49 67 0.29
51 6 0.03
52 109 0.47
54 3 0.01
55 7 0.03
58 5 0.02
59 6 0.03
61 31 0.13
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (49 bp):
CCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAG
Found at i:123620 original size:96 final size:97
Alignment explanation
Indices: 123407--123624 Score: 275
Period size: 96 Copynumber: 2.3 Consensus size: 97
123397 AAAATTTTAT
* * *
123407 TTATCGGGGATACTCCAACCCCATTCTTCCAAAGAGATACTCCAACCCCAGTTTTAAACTATTAA
1 TTATCGAGGATACTCTAACCCCATTCTTCCAAAGAGAAACTCCAACCCCAGTTTTAAACTATTAA
*
123472 AGGTTTAAATCTTGTTTTTGCCTAAATTGTCA
66 AGATTTAAATCTTGTTTTTGCCTAAATTGTCA
* * * **
123504 TCATCGAAGATACT-TCAACCCTATTCTT-CTGAGAGGAAACTCC-ACCCTCAGTTTT-AACT-T
1 TTATCGAGGATACTCT-AACCCCATTCTTCCAAAGA-GAAACTCCAACCC-CAGTTTTAAACTAT
*
123564 GTCAAGATTTAAATCTTGTTTTTGCCTAAATTGTCA
63 -TAAAGATTTAAATCTTGTTTTTGCCTAAATTGTCA
123600 TTATCGAGGATACTCTAACCCCATT
1 TTATCGAGGATACTCTAACCCCATT
123625 TTTTCGAGGA
Statistics
Matches: 103, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
95 1 0.01
96 65 0.63
97 37 0.36
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (97 bp):
TTATCGAGGATACTCTAACCCCATTCTTCCAAAGAGAAACTCCAACCCCAGTTTTAAACTATTAA
AGATTTAAATCTTGTTTTTGCCTAAATTGTCA
Found at i:123655 original size:96 final size:97
Alignment explanation
Indices: 123415--123692 Score: 237
Period size: 96 Copynumber: 2.9 Consensus size: 97
123405 ATTTATCGGG
* * * * * * * *
123415 GATACTCCAACCCCATTCTTC-CAAAGAGATACTCCAACCCCAGTTTTAAACTATTA--AAGGTT
1 GATACTTCAACCCCATTCTTCTGAGAG-GAAACTACAAACTCAGTTTTAAA--ATTATCAAGATT
123477 TAAATCTTGTTTTTGCCTAAATTGTCATCATCGAA
63 TAAATCTTGTTTTTGCCTAAATTGTCATCATCGAA
* * ** * *
123512 GATACTTCAACCCTATTCTTCTGAGAGGAAACTCCACCCTCAGTTTT-AACTTGTCAAGATTTAA
1 GATACTTCAACCCCATTCTTCTGAGAGGAAACTACAAACTCAGTTTTAAAATTATCAAGATTTAA
* *
123576 ATCTTGTTTTTGCCTAAATTGTCATTATCGAG
66 ATCTTGTTTTTGCCTAAATTGTCATCATCGAA
* * * * *
123608 GATAC-TCTAACCCCATT-TTTTCGAG-GAGATACTAGAAACTCATTTTTAAAATTATCAAGCTT
1 GATACTTC-AACCCCATTCTTCT-GAGAG-GAAACTACAAACTCAGTTTTAAAATTATCAAGATT
* * *
123670 TTAATTTTATTTTTGCCTAAATT
63 TAAATCTTGTTTTTGCCTAAATT
123693 ATTATCGTTA
Statistics
Matches: 148, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
94 2 0.01
95 6 0.04
96 70 0.47
97 67 0.45
98 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (97 bp):
GATACTTCAACCCCATTCTTCTGAGAGGAAACTACAAACTCAGTTTTAAAATTATCAAGATTTAA
ATCTTGTTTTTGCCTAAATTGTCATCATCGAA
Found at i:123814 original size:30 final size:30
Alignment explanation
Indices: 123766--123835 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
123756 CAAAAATTAA
*
123766 ATCT-TTTTTTCTCTCGAATTTTGAGTC-T
1 ATCTATTTTTTCTCCCGAATTTTGAGTCAT
123794 ATCTATTTTTCTCTCCCGAATTTTGAGTCAT
1 ATCTATTTTT-TCTCCCGAATTTTGAGTCAT
*
123825 ATCAATTTTTT
1 ATCTATTTTTT
123836 TTACTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 4 0.11
29 5 0.14
30 18 0.49
31 10 0.27
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.54
Consensus pattern (30 bp):
ATCTATTTTTTCTCCCGAATTTTGAGTCAT
Found at i:129053 original size:13 final size:13
Alignment explanation
Indices: 129035--129059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
129025 ACCAAGATCA
129035 TGTATCGATACAG
1 TGTATCGATACAG
129048 TGTATCGATACA
1 TGTATCGATACA
129060 AAGCAATATT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:129709 original size:20 final size:20
Alignment explanation
Indices: 129681--129744 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
129671 CCCCCTTTAA
*
129681 TTAAAAAAAATTTTCTCCCC
1 TTAATAAAAATTTTCTCCCC
*
129701 TTAATAAAATTTTTTTCTCCCCC
1 TTAATAAAA--ATTTTCT-CCCC
*
129724 TTAAT-AAAATTTTCTTCCC
1 TTAATAAAAATTTTCTCCCC
129743 TT
1 TT
129745 TTAAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.14
20 14 0.38
22 9 0.24
23 9 0.24
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATAAAAATTTTCTCCCC
Found at i:129716 original size:22 final size:23
Alignment explanation
Indices: 129691--129736 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
129681 TTAAAAAAAA
129691 TTTTCT-CCCCTTAATAAAATTT
1 TTTTCTCCCCCTTAATAAAATTT
129713 TTTTCTCCCCCTTAATAAAATTT
1 TTTTCTCCCCCTTAATAAAATTT
129736 T
1 T
129737 CTTCCCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTCTCCCCCTTAATAAAATTT
Found at i:129752 original size:20 final size:20
Alignment explanation
Indices: 129687--129742 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 20
129677 TTAATTAAAA
129687 AAAATTTTC-TCCCCTTAAT
1 AAAATTTTCTTCCCCTTAAT
*
129706 AAAATTTTTTTCTCCCCCTTAAT
1 AAAA---TTTTCTTCCCCTTAAT
129729 AAAATTTTCTTCCC
1 AAAATTTTCTTCCC
129743 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 4 0.13
20 9 0.29
22 5 0.16
23 13 0.42
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTTTCTTCCCCTTAAT
Found at i:129753 original size:21 final size:20
Alignment explanation
Indices: 129684--129754 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
129674 CCTTTAATTA
129684 AAAAAAATTTTC-TCCCCTT
1 AAAAAAATTTTCTTCCCCTT
* *
129703 AATAAAATTTTTTTCTCCCCCTT
1 AA-AAAA--ATTTTCTTCCCCTT
* *
129726 AATAAAATTTTCTTCCCTTTT
1 AAAAAAATTTTCTTCCC-CTT
129747 AAAAAAAT
1 AAAAAAAT
129755 ATCTCTCCCT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 9 0.22
22 8 0.20
23 8 0.20
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAAAATTTTCTTCCCCTT
Found at i:133258 original size:784 final size:784
Alignment explanation
Indices: 131749--133308 Score: 2295
Period size: 784 Copynumber: 2.0 Consensus size: 784
131739 AGTTAAATTA
131749 AAAAACAAATCATCATGATTAAACATCAAAACCAACAAATAACACAATCATCAAAAATCACAAAA
1 AAAAACAAATCATCATGATTAAACATCAAAACCAACAAATAACACAATCATCAAAAATCACAAAA
*
131814 GCTCAAAATCATACAAACAAATTATAAAAAGTGCAACATAACATATCATGTGACCATAGACATGC
66 GCTCAAAATCATACAAACAAATTATAAAAAGTGCAACATAACATATCATGTGACCATAAACATGC
*
131879 ATATTAGCATTATGAACATATTTTGGTCATTCAATATGATTTAAAAAACATTAAAAACACAATTA
131 ATATTAGCATTATGAACATATTTTGGTCATTCAATATGATTTAAAAAACATTAAAAACACAAGTA
131944 AAGGAGATATCAAATAGGGTACATAAACTTGGAATTAAATAAAACAAATCAAGGTGGATTCATAA
196 AAGGAGATATCAAATAGGGTACATAAACTTGGAATTAAATAAAACAAATCAAGGTGGATTCATAA
132009 GACCAAGTTCTCTCCTAATAGTGCAAAATCTACTTTATCAAGAGGTTTAGTAAAAATATCTACTA
261 GACCAAGTTCTCTCCTAATAGTGCAAAATCTACTTTATCAAGAGGTTTAGTAAAAATATCTACTA
* * *
132074 CTTAGTTCAAGGTATTTACAAATTCATTACAACTCCTTTTTGCACATGATCTCTAATAAAGTGGA
326 ATTAGGTCAAGGTATCTACAAATTCATTACAACTCCTTTTTGCACATGATCTCTAATAAAGTGGA
* * *
132139 TGTCCTAGTTTTATGTGCTTAGTCCTAGAGTATTGTATAGGAGTTTTGGTGAGACAAATGGCACT
391 TGTCCTAGTTCTATGTGCTAAGTCCTAGAGTATTGTACAGGAGTTTTGGTGAGACAAATGGCACT
* * *
132204 AGCGTTGCCACATTTAATGGGAATATGATCCATGGTAATACTAAAATCCTCCAATTGTTGTTTAT
456 AGCGTTACCACATTTAATGGGAATATGATCCATGGTAATACTAAAATCCTACAATTATTGTTTAT
*
132269 CCACAATACCTGTGCACAACAACTTCCCACGGATATATAACTCCACCTCAGTTGTGGATAACGCA
521 CCACAATACCTGTGCACAACAACTTCCCACGGATATATAACTCCACCTCAGGTGTGGATAACGCA
*
132334 ACACTATTTTGTTTCTTCTTGGAAAACCATGATATAGGCATATTACCAGAAATTGGACATGTACT
586 ACACTATTTTGTTTCTTCTTGAAAAACCATGATATAGGCATATTACCAGAAATTGGACATGTACT
* * *
132399 GGAAGTGCCTCTTTCTATCTATTTTACAAAACCATAAAAGTCCGCATTCGAGTATACATGTAAGG
651 CGAAGTGCCTCTTTCTATCTATTTTAC-AAACCACAAAAGTCCGCATCCGAGTATACATGTAAGG
* * **
132464 CTAGGGAGGTTTCTTTAGGGTACCAACAATCCTAGGTTTTGGGTATCTTGTAAATATTTAAAATT
715 CTAGGGAGGTTTCTTTAAGGTACC-AC-ATCCTAGGTTTGGGGTATCTCATAAATATTTAAAATT
132529 ATACATT
778 ATACATT
*
132536 AAAAACAAATCATC-TGATT-AACATCAAAATCAACAAATAACACAATCATCAAAAATCACAAAA
1 AAAAACAAATCATCATGATTAAACATCAAAACCAACAAATAACACAATCATCAAAAATCACAAAA
* **
132599 -CTTAAAATCATACAAACAAATTATCGAAAGTGCAACATAACATATCATGTGACCATAAACATGC
66 GCTCAAAATCATACAAACAAATTATAAAAAGTGCAACATAACATATCATGTGACCATAAACATGC
* *
132663 ATATTTGGCATTGTGAACATA-TTTGGTCATTCAATATGATTTAAAAAAAAACATTAAAAACACA
131 ATA-TTAGCATTATGAACATATTTTGGTCATTCAATATGATTT---AAAAAACATTAAAAACACA
* *
132727 AGTAAAGGAGATATCAAAATA-GGTACATAACCTTGGCATT-AA-AAAA-AAATCAAGGTGGATT
192 AGTAAAGGAGATATC-AAATAGGGTACATAAACTTGGAATTAAATAAAACAAATCAAGGTGGATT
* *
132788 CATAAGACCAAGTTCTCTCCTAATGGTGCAAAATCTACTTTTGTCAAGAGGTTTAGTAAAAAATA
256 CATAAGACCAAGTTCTCTCCTAATAGTGCAAAATCTAC-TTTATCAAGAGGTTTAGT-AAAAATA
* *
132853 TC-AGCTAATTAGGTCAAGGTATCTACAAATTCAATTACAACATCTCCTTTTTGCATATGATGTC
319 TCTA-CTAATTAGGTCAAGGTATCTACAAATTC-ATTAC-A-A-CTCCTTTTTGCACATGATCTC
* * *
132917 TAAT-AAGTTGATGTCTTAGTTCTATGTGCTAAGTCCTAGAGTGTTGTACAGGA-TTTTGGGGTG
379 TAATAAAGTGGATGTCCTAGTTCTATGTGCTAAGTCCTAGAGTATTGTACAGGAGTTTT--GGTG
* *
132980 AGACAAATGGCACTAGCGTTATCACATTTAATGGGAATATGATCCATGGTAATAC-CAAATCCAT
442 AGACAAATGGCACTAGCGTTACCACATTTAATGGGAATATGATCCATGGTAATACTAAAATCC-T
* ** * * ** *
133044 ATAATTATTGTTTTATCCGTAATACCTGTGCACAATAATTTTTCACGGATATAT-ACTCCACTTC
506 ACAATTATTG-TTTATCCACAATACCTGTGCACAACAACTTCCCACGGATATATAACTCCACCTC
* * *
133108 -GGTGTGGATAATGCAAACCCTA-TTTG-TT-TTCTTGAAAAATCATGATAT-GAGCATATTACC
570 AGGTGTGGATAACGC-AACACTATTTTGTTTCTTCTTGAAAAACCATGATATAG-GCATATTACC
133168 AAGAAATT-GACATGTAC-CGAAGTG-CTCTTTCTATCTATGTTTAC-AACCACCAAAA-TCCGC
633 -AGAAATTGGACATGTACTCGAAGTGCCTCTTTCTATCTAT-TTTACAAACCA-CAAAAGTCCGC
133228 ATCCGAGTA-AGCATGTAAGGCTAGGGAGGTTTCTTTAAGGTACCACATCCTAGGTTTGGGGTAT
695 ATCCGAGTATA-CATGTAAGGCTAGGGAGGTTTCTTTAAGGTACCACATCCTAGGTTTGGGGTAT
133292 CTCATAAATATTTAAAA
759 CTCATAAATATTTAAAA
133309 ATTCTTTTTA
Statistics
Matches: 703, Mismatches: 48, Indels: 49
0.88 0.06 0.06
Matches are distributed among these distances:
782 32 0.05
783 3 0.00
784 186 0.26
785 98 0.14
786 53 0.08
787 106 0.15
788 19 0.03
789 66 0.09
790 103 0.15
791 37 0.05
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (784 bp):
AAAAACAAATCATCATGATTAAACATCAAAACCAACAAATAACACAATCATCAAAAATCACAAAA
GCTCAAAATCATACAAACAAATTATAAAAAGTGCAACATAACATATCATGTGACCATAAACATGC
ATATTAGCATTATGAACATATTTTGGTCATTCAATATGATTTAAAAAACATTAAAAACACAAGTA
AAGGAGATATCAAATAGGGTACATAAACTTGGAATTAAATAAAACAAATCAAGGTGGATTCATAA
GACCAAGTTCTCTCCTAATAGTGCAAAATCTACTTTATCAAGAGGTTTAGTAAAAATATCTACTA
ATTAGGTCAAGGTATCTACAAATTCATTACAACTCCTTTTTGCACATGATCTCTAATAAAGTGGA
TGTCCTAGTTCTATGTGCTAAGTCCTAGAGTATTGTACAGGAGTTTTGGTGAGACAAATGGCACT
AGCGTTACCACATTTAATGGGAATATGATCCATGGTAATACTAAAATCCTACAATTATTGTTTAT
CCACAATACCTGTGCACAACAACTTCCCACGGATATATAACTCCACCTCAGGTGTGGATAACGCA
ACACTATTTTGTTTCTTCTTGAAAAACCATGATATAGGCATATTACCAGAAATTGGACATGTACT
CGAAGTGCCTCTTTCTATCTATTTTACAAACCACAAAAGTCCGCATCCGAGTATACATGTAAGGC
TAGGGAGGTTTCTTTAAGGTACCACATCCTAGGTTTGGGGTATCTCATAAATATTTAAAATTATA
CATT
Found at i:136736 original size:21 final size:21
Alignment explanation
Indices: 136710--136760 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
136700 CATCATAGCC
136710 TTCTTCTTCGGCTTATTTAAA
1 TTCTTCTTCGGCTTATTTAAA
*
136731 TTCTTCTTTGGCTTATTTAAA
1 TTCTTCTTCGGCTTATTTAAA
136752 TTCTTCTTC
1 TTCTTCTTC
136761 TTCAATTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.57
Consensus pattern (21 bp):
TTCTTCTTCGGCTTATTTAAA
Found at i:140407 original size:21 final size:22
Alignment explanation
Indices: 140372--140413 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
140362 AGGTTTGGCT
140372 AGCTTATAATGAAATAATCTTA
1 AGCTTATAATGAAATAATCTTA
* *
140394 AGCTTA-ATTGAAATATTCTT
1 AGCTTATAATGAAATAATCTT
140414 TCATAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
AGCTTATAATGAAATAATCTTA
Done.