Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1179
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1367275
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 72735 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1201948 original size:27 final size:27
Alignment explanation
Indices: 1201910--1202026 Score: 207
Period size: 27 Copynumber: 4.3 Consensus size: 27
1201900 ACCACTACAT
1201910 GTACATTTATATTCATTAAGCATTATA
1 GTACATTTATATTCATTAAGCATTATA
* *
1201937 GTACATTTATATTCATTAAACGTTATA
1 GTACATTTATATTCATTAAGCATTATA
1201964 GTACATTTATATTCATTAAGCATTATA
1 GTACATTTATATTCATTAAGCATTATA
1201991 GTACATTTATATTCATTAAGCATTATA
1 GTACATTTATATTCATTAAGCATTATA
1202018 GTATCATTT
1 GTA-CATTT
1202027 TTTTCTGGAC
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
27 80 0.94
28 5 0.06
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (27 bp):
GTACATTTATATTCATTAAGCATTATA
Found at i:1210384 original size:2 final size:2
Alignment explanation
Indices: 1210377--1210403 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1210367 AAAAGGAATC
1210377 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1210404 CCCCCCCCCC
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1210409 original size:1 final size:1
Alignment explanation
Indices: 1210403--1210447 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
1210393 CACACACACA
1210403 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1210448 ACACACACAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1214503 original size:2 final size:2
Alignment explanation
Indices: 1214496--1214542 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1214486 GATAAAGTAA
1214496 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1214538 CT CT C
1 CT CT C
1214543 AGGAAGATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1220093 original size:16 final size:16
Alignment explanation
Indices: 1220072--1220103 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1220062 TATACGGGAC
1220072 ATACTAAAGACCTGAA
1 ATACTAAAGACCTGAA
*
1220088 ATACTAATGACCTGAA
1 ATACTAAAGACCTGAA
1220104 TGACATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (16 bp):
ATACTAAAGACCTGAA
Found at i:1230702 original size:344 final size:341
Alignment explanation
Indices: 1229926--1231652 Score: 2261
Period size: 344 Copynumber: 5.1 Consensus size: 341
1229916 AAAGAATCAT
* *
1229926 CTGGCTTATTAGTTTCTGAGAAGAAGA-TTTTAAAGATTTACTCTATATATTCCCATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * *
1229990 TCGACCTCCCTCCCCCATCGTGGCCCCACCCTACCCTCGAGGGTCATGATTTTCACAACTTTGAA
66 TTGACC-CCC-CCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
* * * * * *
1230055 TCTACACTACCTGTGGAT-GCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGGTTCTGAGAT
129 TCTACACTACCTG-AGATATCTTCCATACAAGTTTCAGCTTTCCTGGCAGATTAGTTTCTGAGAA
** *
1230119 GAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTAACACCCCCCCCCCAAATGT
193 GAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGAC-CCCCCCCCCC-ATTGT
* * * *
1230184 GGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATACT
256 GGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCT
** *
1230249 TCCATGCAAGTTTCAGCTATC
321 TCCACACAAGTTTCAGCTTTC
* * * * *
1230270 ATGGCAGATTAGTTTCTAAGAAGAAGA-TTTTAAAGATTTCCTCTATATATTCCCATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* **
1230334 TCGACCCCCCTCCCCCATTGTGGCCCCACCCTACCCTTGGGGGTCATGATTTTCACAACTTTGAA
66 TTGA-CCCCC-CCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
* * * *
1230399 TCTACACTACCTGATATATCTTCCATGCAAGTTTCAGCTATCATGGCAGATTAGTTTCTGAGAAG
129 TCTACACTACCTGAGATATCTTCCATACAAGTTTCAGCTTTCCTGGCAGATTAGTTTCTGAGAAG
* * * *
1230464 ACGA-TTATAAAGATTTCCTCTATATATTCCCATGTAAAACTTCGACCCCCCTCCCCCATTGTGG
194 AAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCC-CCCCCATTGTGG
** *
1230528 CCCCACCCTACCCTTGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGTGGATGCTTC
258 CCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTC
1230593 CACACAAGTTTCAGCTTTC
323 CACACAAGTTTCAGCTTTC
* *
1230612 CTGGCTGATTAGGTTCTGA-AATGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAG
1 CTGGCTGATTAGTTTCTGAGAA-GAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC
* * * * *
1230676 TTTAACACCCCCCCCCAATATGTGGCCTCATCCTACCCCCAGGGATCATGATTTTCACAACTTTG
65 TTTGAC-CCCCCCCCC-AT-TGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTG
* * *
1230741 AATCTACACTACCTGAGGATA-CTTCCATGCAAGTTTCAGCTATCATGGCAGATTAGTTTCTGAG
127 AATCTACACTACCTGA-GATATCTTCCATACAAGTTTCAGCTTTCCTGGCAGATTAGTTTCTGAG
* * * *
1230805 AAGACGA-TTATAAAGATTTCCTCTATATATTCCCATGTAAAACTTCGA-----CCCCCCATTGT
191 AAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCCCCCCATTGT
* * *
1230864 GGCCCCACCCTACCCTCGGGGGTCATGATTTTCACAACTTTGAATCTACACTTCTTGAGGATGCT
256 GGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCT
1230929 TCCACACAAGTTTCAGCTTTC
321 TCCACACAAGTTTCAGCTTTC
* *
1230950 CTGGCTCATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTAATCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* *
1231015 TTGACCCCCCCCCCCATTGTGGCCCCATCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAAT
66 TTGA-CCCCCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAT
* * * * *
1231080 CTACACTACCTGAAGGT-GCTTCCATACAAGTTCCAGCTTTCCTGGCGGA-TAGTTTCTAAGAAG
130 CTACACTACCTG-AGATATCTTCCATACAAGTTTCAGCTTTCCTGGCAGATTAGTTTCTGAGAAG
* * *
1231143 AAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCCCCCCTTTGGGGC
194 AAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCCCCCCATTGTGGC
** * * *
1231208 CCC-CTCCCCCCCCCGGGGGCCTTGATTTTCACAACTTTGAATCTACACTACCTGTGGATGCTTC
259 CCCAC-CCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTC
* *
1231272 CACACAAGTTCCAGCTCTC
323 CACACAAGTTTCAGCTTTC
1231291 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * *
1231356 TCGA-----CCCCCATTGTGGCCCCACCCTACCACCGGGAGTCATGATTTTCACAACTTTTAATC
66 TTGACCCCCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATC
* * * * *
1231416 TACACTACCTGAGGAT-GCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGGTTCTGAGATGA
131 TACACTACCTGA-GATATCTTCCATACAAGTTTCAGCTTTCCTGGCAGATTAGTTTCTGAGAAGA
1231480 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGA------CCCCCATTGTGGCC
195 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCCCCCCATTGTGGCC
* * *
1231539 CCACCCTACCACCGGGAGTCATGATTTTCACAACTTTTAATCTACACTACCTGAGGATGCTTCCA
260 CCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCA
1231604 CACAAGTTTCAGCTTTC
325 CACAAGTTTCAGCTTTC
* *
1231621 CTGGCT--TTCTGGTTCTTGAGAAGAAGATTTTT
1 CTGGCTGATT-AGTTTC-TGAGAAGAAGATTTTT
1231653 GAAAATATCT
Statistics
Matches: 1242, Mismatches: 116, Indels: 64
0.87 0.08 0.05
Matches are distributed among these distances:
328 2 0.00
329 4 0.00
330 104 0.08
331 1 0.00
334 1 0.00
335 109 0.09
336 179 0.14
337 3 0.00
338 162 0.13
339 4 0.00
340 1 0.00
341 151 0.12
342 111 0.09
343 86 0.07
344 319 0.26
345 5 0.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (341 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
TTGACCCCCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATC
TACACTACCTGAGATATCTTCCATACAAGTTTCAGCTTTCCTGGCAGATTAGTTTCTGAGAAGAA
GATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCCCCCCATTGTGGCCC
CACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAC
ACAAGTTTCAGCTTTC
Found at i:1230925 original size:165 final size:167
Alignment explanation
Indices: 1229926--1231652 Score: 2176
Period size: 171 Copynumber: 10.2 Consensus size: 167
1229916 AAAGAATCAT
* *
1229926 CTGGCTTATTAGTTTCTGAGAAGAAGA-TTTTAAAGATTTACTCTATATATTCCCATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * *
1229990 TCGACCTCCCTCCCCCATCGTGGCCCCACCCTACCCTCGAGGGTCATGATTTTCACAACTTTGAA
66 TCGA----CC-CCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
*
1230055 TCTACACTACCTGTGGATGCTTCCACACAAGTTTCAGCTTTC
126 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
1230097 CTGGCTGATTAGGTTCTGAGATGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-
* * * *
1230162 TTAAC-ACCCCCCCCCCAAATGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTG
65 TT--CGA---CCCCCCC-ATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTG
* ** *
1230226 AATCTACACTACCTGAGGATACTTCCATGCAAGTTTCAGCTATC
124 AATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * * * *
1230270 ATGGCAGATTAGTTTCTAAGAAGAAGA-TTTTAAAGATTTCCTCTATATATTCCCATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
**
1230334 TCGACCCCCCTCCCCCATTGTGGCCCCACCCTACCCTTGGGGGTCATGATTTTCACAACTTTGAA
66 TCGA----CC-CCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
* * ** *
1230399 TCTACACTACCTGA-TATATCTTCCATGCAAGTTTCAGCTATC
126 TCTACACTACCTGAGGAT-GCTTCCACACAAGTTTCAGCTTTC
* * * * * *
1230441 ATGGCAGATTAGTTTCTGAGAAGACGA-TTATAAAGATTTCCTCTATATATTCCCATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
**
1230505 TCGACCCCCCTCCCCCATTGTGGCCCCACCCTACCCTTGGGGGTCATGATTTTCACAACTTTGAA
66 TCGA----CC-CCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
*
1230570 TCTACACTACCTGTGGATGCTTCCACACAAGTTTCAGCTTTC
126 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
1230612 CTGGCTGATTAGGTTCTGA-AATGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAG
1 CTGGCTGATTAGTTTCTGAGAA-GAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAA-
* * * * *
1230676 TTTAAC-ACCCCCCCCCAATATGTGGCCTCATCCTACCCCCAGGGATCATGATTTTCACAACTTT
64 CTT--CGA--CCCCCCC-AT-TGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTT
* ** *
1230740 GAATCTACACTACCTGAGGATACTTCCATGCAAGTTTCAGCTATC
123 GAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * * * * *
1230785 ATGGCAGATTAGTTTCTGAGAAGACGA-TTATAAAGATTTCCTCTATATATTCCCATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
*
1230849 TCGA-CCCCCCATTGTGGCCCCACCCTACCCTCGGGGGTCATGATTTTCACAACTTTGAATCTAC
66 TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTAC
* *
1230913 ACTTCTTGAGGATGCTTCCACACAAGTTTCAGCTTTC
131 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
1230950 CTGGCTCATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTAATCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * *
1231015 TTGACCCCCCCCCCCATTGTGGCCCCATCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAAT
66 TCGA----CCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAT
* *
1231080 CTACACTACCTGAAGG-TGCTTCCATACAAGTTCCAGCTTTC
127 CTACACTACCTG-AGGATGCTTCCACACAAGTTTCAGCTTTC
* *
1231121 CTGGCGGA-TAGTTTCTAAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * ** * *
1231185 TTGACCCCCCCCCCCTTTGGGGCCCC-CTCCCCCCCCCGGGGGCCTTGATTTTCACAACTTTGAA
66 TCGA----CCCCCCCATTGTGGCCCCAC-CCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA
* * *
1231249 TCTACACTACCTGTGGATGCTTCCACACAAGTTCCAGCTCTC
126 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1231291 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * *
1231356 TCGA--CCCCCATTGTGGCCCCACCCTACCACCGGGAGTCATGATTTTCACAACTTTTAATCTAC
66 TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTAC
1231419 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
131 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
1231456 CTGGCTGATTAGGTTCTGAGATGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * *
1231521 TCGA--CCCCCATTGTGGCCCCACCCTACCACCGGGAGTCATGATTTTCACAACTTTTAATCTAC
66 TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTAC
1231584 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
131 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
1231621 CTGGCT--TTCTGGTTCTTGAGAAGAAGATTTTT
1 CTGGCTGATT-AGTTTC-TGAGAAGAAGATTTTT
1231653 GAAAATATCT
Statistics
Matches: 1395, Mismatches: 129, Indels: 70
0.88 0.08 0.04
Matches are distributed among these distances:
163 2 0.00
164 5 0.00
165 367 0.26
166 39 0.03
167 6 0.00
169 4 0.00
170 158 0.11
171 447 0.32
172 154 0.11
173 207 0.15
174 4 0.00
175 2 0.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (167 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTAC
ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
Found at i:1231839 original size:12 final size:12
Alignment explanation
Indices: 1231822--1231890 Score: 113
Period size: 12 Copynumber: 5.8 Consensus size: 12
1231812 TGAAAAGTTT
1231822 ACGGACAGACGG
1 ACGGACAGACGG
1231834 ACGGACAGACGG
1 ACGGACAGACGG
*
1231846 ACGGACGGACGG
1 ACGGACAGACGG
1231858 ACGGACAGACGG
1 ACGGACAGACGG
*
1231870 ACGGACGGACGG
1 ACGGACAGACGG
1231882 AC-GACAGAC
1 ACGGACAGAC
1231891 AAAATGTGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
11 6 0.11
12 47 0.89
ACGTcount: A:0.32, C:0.26, G:0.42, T:0.00
Consensus pattern (12 bp):
ACGGACAGACGG
Found at i:1231891 original size:4 final size:4
Alignment explanation
Indices: 1231822--1231884 Score: 99
Period size: 4 Copynumber: 15.8 Consensus size: 4
1231812 TGAAAAGTTT
* * *
1231822 ACGG ACAG ACGG ACGG ACAG ACGG ACGG ACGG ACGG ACGG ACAG ACGG
1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG
1231870 ACGG ACGG ACGG ACG
1 ACGG ACGG ACGG ACG
1231885 ACAGACAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.30, C:0.25, G:0.44, T:0.00
Consensus pattern (4 bp):
ACGG
Found at i:1234172 original size:1 final size:1
Alignment explanation
Indices: 1234161--1234190 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
1234151 TATTCTTTTA
*
1234161 CCCCACCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1234191 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1235702 original size:12 final size:12
Alignment explanation
Indices: 1235685--1235753 Score: 113
Period size: 12 Copynumber: 5.8 Consensus size: 12
1235675 TGAAAAGTTT
1235685 ACGGACAGACGG
1 ACGGACAGACGG
1235697 ACGGACAGACGG
1 ACGGACAGACGG
*
1235709 ACGGACGGACGG
1 ACGGACAGACGG
1235721 ACGGACAGACGG
1 ACGGACAGACGG
*
1235733 ACGGACGGACGG
1 ACGGACAGACGG
1235745 AC-GACAGAC
1 ACGGACAGAC
1235754 AAAATGTGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
11 6 0.11
12 47 0.89
ACGTcount: A:0.32, C:0.26, G:0.42, T:0.00
Consensus pattern (12 bp):
ACGGACAGACGG
Found at i:1235754 original size:4 final size:4
Alignment explanation
Indices: 1235685--1235747 Score: 99
Period size: 4 Copynumber: 15.8 Consensus size: 4
1235675 TGAAAAGTTT
* * *
1235685 ACGG ACAG ACGG ACGG ACAG ACGG ACGG ACGG ACGG ACGG ACAG ACGG
1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG
1235733 ACGG ACGG ACGG ACG
1 ACGG ACGG ACGG ACG
1235748 ACAGACAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.30, C:0.25, G:0.44, T:0.00
Consensus pattern (4 bp):
ACGG
Found at i:1241866 original size:21 final size:22
Alignment explanation
Indices: 1241842--1241889 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
1241832 TATGCACATA
* *
1241842 ATTTCATT-TATACACAATTGC
1 ATTTCATTATATACAAAATTAC
*
1241863 ATTTTTATTATATACAAAATTAC
1 A-TTTCATTATATACAAAATTAC
1241886 ATTT
1 ATTT
1241890 GCTCACTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 9 0.41
23 12 0.55
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTCATTATATACAAAATTAC
Found at i:1244955 original size:4 final size:4
Alignment explanation
Indices: 1244928--1244970 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
1244918 GGAATCACCT
* * * *
1244928 TGTC CGTC TGTC CGTC TATC TGTC TGTC TGTC CGTC TGTC TGT
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
1244971 GCAATCGTGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.02, C:0.30, G:0.23, T:0.44
Consensus pattern (4 bp):
TGTC
Found at i:1245537 original size:146 final size:146
Alignment explanation
Indices: 1244975--1245517 Score: 926
Period size: 146 Copynumber: 3.7 Consensus size: 146
1244965 GTCTGTGCAA
* * * *
1244975 TCGTGTCCGGTCCATATCTTTCATATAGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTCCTTACTTCACACAAAGATTGC
* * * *
1245040 TTTTGACCTAAAGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC
66 TTATGATCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
*
1245105 AGAAAAAGTGCAAAAT
131 AGAAAAAATGCAAAAT
1245121 TCGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTCCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTCCTTACTTCACACAAAGATTGC
* *
1245186 TTATGATCTAAGGGTGTGTCATGATCTTGGCCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGATCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
1245251 AGAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
*
1245267 TTGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTCCTTACTTCACACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTCCTTACTTCACACAAAGATTGC
1245332 TTATGATCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
66 TTATGATCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
1245397 AGAAAAAATGCAAAAT
131 AGAAAAAATGCAAAAT
* * *
1245413 TCGTGTCCGGTCCATATCTTTCTTATGGGGATACATTGGAAGTTCTTACTTCTCACAAAGATTGC
1 TCGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTCCTTACTTCACACAAAGATTGC
*
1245478 TTATGAT-TAAAGGGTGTGTCATGACCTTGATCCAAGGTCA
66 TTATGATCT-AAGGGTGTGTCATGACCTTGACCCAAGGTCA
1245518 ATTGAGAAAG
Statistics
Matches: 377, Mismatches: 19, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
145 1 0.00
146 376 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (146 bp):
TCGTGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTCCTTACTTCACACAAAGATTGC
TTATGATCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC
AGAAAAAATGCAAAAT
Found at i:1255846 original size:2 final size:2
Alignment explanation
Indices: 1255839--1255867 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1255829 TTATCTGTAA
1255839 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1255868 GCACATGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1267066 original size:8 final size:8
Alignment explanation
Indices: 1267053--1267105 Score: 88
Period size: 8 Copynumber: 6.6 Consensus size: 8
1267043 TGCGTCTACA
1267053 GACAGACG
1 GACAGACG
1267061 GACAGACG
1 GACAGACG
1267069 GACAGACG
1 GACAGACG
1267077 GACAGACG
1 GACAGACG
* *
1267085 GACGGACA
1 GACAGACG
1267093 GACAGACG
1 GACAGACG
1267101 GACAG
1 GACAG
1267106 GGTGAAACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:1267067 original size:12 final size:12
Alignment explanation
Indices: 1267053--1267105 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
1267043 TGCGTCTACA
* *
1267053 GACAGACGGACA
1 GACAGACAGACG
*
1267065 GACGGACAGACG
1 GACAGACAGACG
*
1267077 GACAGACGGACG
1 GACAGACAGACG
1267089 GACAGACAGACG
1 GACAGACAGACG
1267101 GACAG
1 GACAG
1267106 GGTGAAACCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (12 bp):
GACAGACAGACG
Found at i:1272131 original size:37 final size:33
Alignment explanation
Indices: 1272050--1272121 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 33
1272040 TAAATTTTGA
1272050 TGAAAATGTAATTTGTAATTTAATTAATTACATC
1 TGAAAATGTAA-TTGTAATTTAATTAATTACATC
* *
1272084 TGCAAA-GTAATTGTAATTTAATTAATTACATT
1 TGAAAATGTAATTGTAATTTAATTAATTACATC
1272116 TGAAAA
1 TGAAAA
1272122 CTCTTGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 26 0.74
33 4 0.11
34 5 0.14
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.42
Consensus pattern (33 bp):
TGAAAATGTAATTGTAATTTAATTAATTACATC
Found at i:1281880 original size:23 final size:24
Alignment explanation
Indices: 1281840--1281887 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1281830 ATAAAGAATT
*
1281840 ATCAGTCGTACAAACGATA-TATA
1 ATCAGTCGCACAAACGATATTATA
**
1281863 ATCAGTCGCACATCCGATATTATA
1 ATCAGTCGCACAAACGATATTATA
1281887 A
1 A
1281888 ATAGCAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (24 bp):
ATCAGTCGCACAAACGATATTATA
Found at i:1288838 original size:7 final size:7
Alignment explanation
Indices: 1288828--1288859 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1288818 CTTCGTCCGT
1288828 CGTCGTG
1 CGTCGTG
1288835 CGTCTGTG
1 CGTC-GTG
1288843 CGTCGTG
1 CGTCGTG
1288850 CGTCGTG
1 CGTCGTG
1288857 CGT
1 CGT
1288860 TAACAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.00, C:0.28, G:0.41, T:0.31
Consensus pattern (7 bp):
CGTCGTG
Found at i:1288848 original size:15 final size:14
Alignment explanation
Indices: 1288828--1288859 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1288818 CTTCGTCCGT
1288828 CGTCGTGCGTCTGTG
1 CGTCGTGCGTC-GTG
1288843 CGTCGTGCGTCGTG
1 CGTCGTGCGTCGTG
1288857 CGT
1 CGT
1288860 TAACAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.00, C:0.28, G:0.41, T:0.31
Consensus pattern (14 bp):
CGTCGTGCGTCGTG
Found at i:1290042 original size:167 final size:168
Alignment explanation
Indices: 1289031--1290153 Score: 1389
Period size: 168 Copynumber: 6.7 Consensus size: 168
1289021 CAAATTTTCA
** * * * *
1289031 AAAATCTTCTTCTCTACTCCCACGCATGTGAGGAAAAAACTAAATGCATGGTTATGTTGTCCATG
1 AAAATCTTCTTCTCTACTCCCATACATATGTGCAAAAAACTAAATGCATGGTTATGATGTCCATG
* * * *
1289096 AAGCCCTCTACCAAAATTGTGAAATTTATGGCCCCTGGGTCAGGGGTTCTGACTCTAGGGTGGGG
66 AAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
* *
1289161 CCAATGTGGCCATATAGTAAAAATGTATTAAATCTTAG
131 CCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAG
* *
1289199 AAAATCTTCTTCTCTACTACCATATACAT-TG-GTC-AAAAACTAAATGCATGATTATGATGTCC
1 AAAATCTTCTTCTCTACT-CC-CATACATATGTG-CAAAAAACTAAATGCATGGTTATGATGTCC
* *
1289261 ATGAAGCCCT-TAACCTAAATTGTGAAATTTATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGT
63 ATGAAGCCCTCT-ACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGT
*
1289325 GGGGCCAATATGGCCAAATCGTAAAAATGTATTAAATCTTAG
127 GGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAG
** * * * *
1289367 AAAATCTTCTTCTCTACTATCATATATATTTGTC-AAAAACTAAATGCATGATAATGATGTCCAT
1 AAAATCTTCTTCTCTACTCCCATACATATGTG-CAAAAAACTAAATGCATGGTTATGATGTCCAT
* * *
1289431 GAAGCCCTCAACCTAAATTGTGAAATTCATAACCCCAT-GGTCAGGGGTTCAGGCTCTAGGGTGG
65 GAAGCCCTCTACCAAAATTGTGAAATTCATGACCCC-TGGGTCAGGGGTTCAGGCTCTAGGGTGG
*
1289495 GGCCAATATGGCCAAATTGTAAAAATGTATTAAATCTTAG
129 GGCCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAG
* * * ** *
1289535 AAAATCTTCTTCTCTACCCCCATATATATTTGTTAAAAACTAAATGCATGATTATGATGTCCATG
1 AAAATCTTCTTCTCTACTCCCATACATATGTGCAAAAAACTAAATGCATGGTTATGATGTCCATG
1289600 AAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
66 AAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
1289665 CCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAG
131 CCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAG
* * ** * *
1289703 AAAATCTTCTTCTCTACTCCCATATATATTTGTTAAAAATTAAATGCATTGTTATGATGTCCATG
1 AAAATCTTCTTCTCTACTCCCATACATATGTGCAAAAAACTAAATGCATGGTTATGATGTCCATG
* * *** * *
1289768 AGGCCCTCTACCAAAATTGTGAAATTCATGACCACTTTATTAGGTGTTCAGGCTCTAGGGTGGGG
66 AAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
* * * * *
1289833 CCAATATGGCCATATAGTAAAACTTTTTTAAATCTTAA
131 CCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAG
* * * * *
1289871 AAAATCTTCTTCTCTACTCCCACACATGTGAGCAAAAAACTGAATACATGGTTATGATGTCCATG
1 AAAATCTTCTTCTCTACTCCCATACATATGTGCAAAAAACTAAATGCATGGTTATGATGTCCATG
* * * ** * * *
1289936 AGGGCCTCTACTAAAATTGTGAAATTCATG-CCCCTTTGTTAGGTGTTCAGGCTCTAGGGTTGGG
66 AAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
* * *
1290000 CCAATATGGCCATATAGTAAAAATGTTTTAAATCTTAA
131 CCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAG
* * * * * * * *
1290038 AAAATCTTTTTCTCTACTCCCACACATGTGGGCAAAAAAATAAATACATGGTTATGATATCCA-C
1 AAAATCTTCTTCTCTACTCCCATACATATGTGCAAAAAACTAAATGCATGGTTATGATGTCCATG
* * * ** * *
1290102 AATCTCCTTTACCTAAATTGTGAAATTCATGGTCCTTGGGTCAAGGGTTCAG
66 AAGC-CCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAG
1290154 AACATGAAAA
Statistics
Matches: 858, Mismatches: 85, Indels: 24
0.89 0.09 0.02
Matches are distributed among these distances:
166 6 0.01
167 151 0.18
168 692 0.81
169 5 0.01
170 4 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (168 bp):
AAAATCTTCTTCTCTACTCCCATACATATGTGCAAAAAACTAAATGCATGGTTATGATGTCCATG
AAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
CCAATATGGCCAAATAGTAAAAATGTATTAAATCTTAG
Found at i:1290846 original size:16 final size:16
Alignment explanation
Indices: 1290825--1290856 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1290815 ACATGACTGT
1290825 TACATTGCAGTAACTA
1 TACATTGCAGTAACTA
1290841 TACATTGCAGTAACTA
1 TACATTGCAGTAACTA
1290857 GATAAGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
TACATTGCAGTAACTA
Found at i:1308962 original size:25 final size:24
Alignment explanation
Indices: 1308928--1308974 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1308918 GATTTTATTT
*
1308928 ATTTTTTTTTTTTTTACTATTTACA
1 ATTTTTTTTTATTTTAC-ATTTACA
1308953 ATTTTTTTTTATTTTACATTTA
1 ATTTTTTTTTATTTTACATTTA
1308975 TTTTGTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (24 bp):
ATTTTTTTTTATTTTACATTTACA
Found at i:1308973 original size:17 final size:20
Alignment explanation
Indices: 1308934--1308985 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1308924 ATTTATTTTT
1308934 TTTTTTTTTACTATTTACAA
1 TTTTTTTTTACTATTTACAA
*
1308954 TTTTTTTTTA-T-TTTACAT
1 TTTTTTTTTACTATTTACAA
1308972 TTATTTTGTTTACT
1 TT-TTTT-TTTACT
1308986 TATTGGACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.29
19 5 0.18
20 14 0.50
21 1 0.04
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTTTTTACTATTTACAA
Found at i:1311728 original size:225 final size:225
Alignment explanation
Indices: 1311337--1311837 Score: 914
Period size: 225 Copynumber: 2.2 Consensus size: 225
1311327 NNNNNNAACA
1311337 CAGCTCTCCACTACTCATCTGGAAGCTGTCTTTCTGCCTCCTCTTTTTATACAAGTAAGATAAAA
1 CAGCTCTCCACTACTCATCTGGAAGCTGTCTTTCTGCCTCCTCTTTTTATACAAGTAAGATAAAA
1311402 TATAACTCTTGCGCACATTCTCAAAAGTAATGTTAATAGATTTAGAGGGTTCAACTAATATCTTA
66 TATAACTCTTGCGCACATTCTCAAAAGTAATGTTAATAGATTTAGAGGGTTCAACTAATATCTTA
1311467 TTTTCAGAGATTTTTGTACTGAATATTAATGTTTAATTTCATTGTAATAAATATTGATATTTATT
131 TTTTCAGAGATTTTTGTACTGAATATTAATGTTTAATTTCATTGTAATAAATATTGATATTTATT
1311532 GATAGAATATCATATTAAAATGTTTTATTT
196 GATAGAATATCATATTAAAATGTTTTATTT
1311562 CAGCTCTCCACTACTCATCTGGAAGCTGTCTTTCTGCCTCCTCTTTTTATACAAGTAAGATAAAA
1 CAGCTCTCCACTACTCATCTGGAAGCTGTCTTTCTGCCTCCTCTTTTTATACAAGTAAGATAAAA
1311627 TATAACTCTTGCGCACATTCTCAAAAGTAATGTTAATAGATTTAGAGGGTTCAACTAATATCTTA
66 TATAACTCTTGCGCACATTCTCAAAAGTAATGTTAATAGATTTAGAGGGTTCAACTAATATCTTA
1311692 TTTTCAGAGATTTTTGTACTGAATATTAATGTTTAATTTCATTGTAATAAATATTGATATTTATT
131 TTTTCAGAGATTTTTGTACTGAATATTAATGTTTAATTTCATTGTAATAAATATTGATATTTATT
1311757 GATAGAATATCATATTAAAATGTTTTATTT
196 GATAGAATATCATATTAAAATGTTTTATTT
** **** * *
1311787 -AAATAAAAGAGTAGTCATCTGGAAGCTGTCTTTCTGCCTCCTCTTTTTATA
1 CAGCT-CTCCACTACTCATCTGGAAGCTGTCTTTCTGCCTCCTCTTTTTATA
1311838 TAGAATGTTG
Statistics
Matches: 267, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
224 2 0.01
225 265 0.99
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (225 bp):
CAGCTCTCCACTACTCATCTGGAAGCTGTCTTTCTGCCTCCTCTTTTTATACAAGTAAGATAAAA
TATAACTCTTGCGCACATTCTCAAAAGTAATGTTAATAGATTTAGAGGGTTCAACTAATATCTTA
TTTTCAGAGATTTTTGTACTGAATATTAATGTTTAATTTCATTGTAATAAATATTGATATTTATT
GATAGAATATCATATTAAAATGTTTTATTT
Found at i:1314984 original size:2 final size:2
Alignment explanation
Indices: 1314979--1315022 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1314969 TATAACCATG
1314979 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1315021 GA
1 GA
1315023 TTATATAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1316222 original size:396 final size:395
Alignment explanation
Indices: 1315491--1316283 Score: 1478
Period size: 396 Copynumber: 2.0 Consensus size: 395
1315481 AATATTAATT
*
1315491 TCAGTTTTTATTCATCACCCCATGCACTCAAAACCTTTGCTTCGAACTACAATTGAGAACTAATA
1 TCAGTTTTTATTCATCACCCCATGCACTCAAAACCTTTGCTTCGAACAACAATTGAGAACTAATA
*
1315556 CAATGAAAAATAATTAACATGAATCATGCTCTCTTTCAATCCGCATATAATTATTGTCGAAACGT
66 CAATGAAAAATAATTAACATGAATCATGCTCTCTTTCAATCCGCATATAATTATTGTCGAAACCT
* *
1315621 TTACAGCATTGACGAATAATCAATGAACGCAAATAAAGCTGCTGTTGGGAGTTTTATAAATATGT
131 TTACAGCATTGACGAATAATCAATGAACGCAAATAAAACTGCTGTTGGAAGTTTTATAAATATGT
1315686 ATTATACACCGAATATTGCCGAATATTCAACACAAATAGATATTAACATCAATTTATGGATATAC
196 ATTATACACCGAATATTGCCGAATATTCAACACAAATAGATATTAACATCAATTTATGGATATAC
* *
1315751 AAATTGCAAATTCGCCAAAGAGTTAATCATGCCCAAAGAAATATACCATACAAGTGAAGGTAGTT
261 AAATTGCAAATTCGCCAAAGAGTTAATCATGCCCAAAGAAATATACCATACAAGTGAAAGCAGTT
* *
1315816 TGCGCCGTAAAAACAGCAATAATCTATAGTATGGATGAAATATGAACTATCACATCCTGACAACT
326 TGCGCCGTAAAAACAGCAATAATCTATAGAATGGATGAAATATGAACTATCACATCCCGACAACT
1315881 TTGGA
391 TTGGA
*
1315886 TCAGTTTTTATTCATCACCCCATGCACTCAAAACCTTTGCTTCGAACAACATGTTGAGAACTAAT
1 TCAGTTTTTATTCATCACCCCATGCACTCAAAACCTTTGCTTCGAACAACA-ATTGAGAACTAAT
1315951 ACAATGAAAAATAATTAACATGAATCATGCTCTCTTTCAATCCGCATATAATTATTGTCGAAACC
65 ACAATGAAAAATAATTAACATGAATCATGCTCTCTTTCAATCCGCATATAATTATTGTCGAAACC
*
1316016 TTTACAGCATTGACGAATAATCAATGAACGTAAATAAAACTGCTGTTGGAAGTTTTATAAATATG
130 TTTACAGCATTGACGAATAATCAATGAACGCAAATAAAACTGCTGTTGGAAGTTTTATAAATATG
1316081 TATTATACACCGAATATTGCCGAATATTCAACACAAATAGATATTAACATCAATTTATGGATATA
195 TATTATACACCGAATATTGCCGAATATTCAACACAAATAGATATTAACATCAATTTATGGATATA
*
1316146 CAAATTGCAAATTCGCCAAAGAGTTAATCATGCCCAAAGAAATATACCATATAAGTGAAAGCAGT
260 CAAATTGCAAATTCGCCAAAGAGTTAATCATGCCCAAAGAAATATACCATACAAGTGAAAGCAGT
1316211 TTGCGCCGTAAAAACAGCAATAATCTATAGAATGGATGAAATATGAACTATCACATCCCGACAAC
325 TTGCGCCGTAAAAACAGCAATAATCTATAGAATGGATGAAATATGAACTATCACATCCCGACAAC
1316276 TTTGGA
390 TTTGGA
1316282 TC
1 TC
1316284 TAAATCGATT
Statistics
Matches: 386, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
395 50 0.13
396 336 0.87
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (395 bp):
TCAGTTTTTATTCATCACCCCATGCACTCAAAACCTTTGCTTCGAACAACAATTGAGAACTAATA
CAATGAAAAATAATTAACATGAATCATGCTCTCTTTCAATCCGCATATAATTATTGTCGAAACCT
TTACAGCATTGACGAATAATCAATGAACGCAAATAAAACTGCTGTTGGAAGTTTTATAAATATGT
ATTATACACCGAATATTGCCGAATATTCAACACAAATAGATATTAACATCAATTTATGGATATAC
AAATTGCAAATTCGCCAAAGAGTTAATCATGCCCAAAGAAATATACCATACAAGTGAAAGCAGTT
TGCGCCGTAAAAACAGCAATAATCTATAGAATGGATGAAATATGAACTATCACATCCCGACAACT
TTGGA
Found at i:1317228 original size:22 final size:21
Alignment explanation
Indices: 1317193--1317235 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1317183 GCAATGTTAA
1317193 ACAAACATAAAACAACAACAC
1 ACAAACATAAAACAACAACAC
*
1317214 ACAAACATTAAAACACCAACAC
1 ACAAACA-TAAAACAACAACAC
1317236 TCGGGCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.63, C:0.30, G:0.00, T:0.07
Consensus pattern (21 bp):
ACAAACATAAAACAACAACAC
Found at i:1323113 original size:2 final size:2
Alignment explanation
Indices: 1323106--1323135 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1323096 AGGTACCGGG
1323106 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1323136 GGGTAGGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1324064 original size:42 final size:43
Alignment explanation
Indices: 1324017--1324099 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
1324007 TCTTGACATC
1324017 TTTTAACATTT-TTTATAATTACATTTTACAAAACTTGTAATT
1 TTTTAACATTTATTTATAATTACATTTTACAAAACTTGTAATT
1324059 TTTTAACATTTATTTATAATTACATTTTACAAAACTTGTAA
1 TTTTAACATTTATTTATAATTACATTTTACAAAACTTGTAA
1324100 ACATTCATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 11 0.28
43 29 0.73
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (43 bp):
TTTTAACATTTATTTATAATTACATTTTACAAAACTTGTAATT
Found at i:1328227 original size:180 final size:180
Alignment explanation
Indices: 1327924--1328465 Score: 985
Period size: 180 Copynumber: 3.0 Consensus size: 180
1327914 ACCCTACATG
* * * **
1327924 TATATGCAACATTTTGCCAAAATATGACTAAGTTCAAAAGCTAGTATTTTTTTTTATAAATTATC
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTA-TTTTTTCAATAAATTATC
1327989 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
65 GGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAA
1328054 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
130 CTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
* *
1328105 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCAATAAAATATCA
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCAATAAATTATCG
1328170 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
*
1328235 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTTCCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
*
1328285 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCAATAAATTATCG
1328350 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
*
1328415 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
1328465 T
1 T
1328466 TTTGGCAGCC
Statistics
Matches: 348, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
180 305 0.88
181 43 0.12
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (180 bp):
TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCAATAAATTATCG
GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
Found at i:1347470 original size:27 final size:27
Alignment explanation
Indices: 1347432--1347487 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1347422 GGGAGGGTAA
1347432 CAGTTGAAATTGACACCCCGAGAAAAC
1 CAGTTGAAATTGACACCCCGAGAAAAC
1347459 CAGTTGAAATTGACACCCCGAGAAAAC
1 CAGTTGAAATTGACACCCCGAGAAAAC
1347486 CA
1 CA
1347488 TTGTCAACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14
Consensus pattern (27 bp):
CAGTTGAAATTGACACCCCGAGAAAAC
Found at i:1347837 original size:62 final size:62
Alignment explanation
Indices: 1347740--1347863 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
1347730 AGGGTAATAG
1347740 TAAATATTATTAACTGCGTCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
1 TAAATATTATTAACTGCGTCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
1347802 TAAATATTATTAACTGCGTCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
1 TAAATATTATTAACTGCGTCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
1347864 ATCGTGATAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (62 bp):
TAAATATTATTAACTGCGTCTTAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
Found at i:1348024 original size:2 final size:2
Alignment explanation
Indices: 1348017--1348056 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1348007 ATACTGTTAT
1348017 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1348057 CGGAATCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1349235 original size:1 final size:1
Alignment explanation
Indices: 1349229--1349259 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1349219 TGCCTTGGGA
1349229 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1349260 TTCTGGTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1352748 original size:2 final size:2
Alignment explanation
Indices: 1352741--1352794 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1352731 AATAGACTGA
1352741 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1352783 CT CT CT CT CT CT
1 CT CT CT CT CT CT
1352795 GTTGTTTCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1358802 original size:12 final size:12
Alignment explanation
Indices: 1358785--1358809 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1358775 AACAAAAAGG
1358785 ATCATTATACAA
1 ATCATTATACAA
1358797 ATCATTATACAA
1 ATCATTATACAA
1358809 A
1 A
1358810 GTATATTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCATTATACAA
Found at i:1361701 original size:42 final size:42
Alignment explanation
Indices: 1361642--1361724 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1361632 TTTGTTATCA
1361642 ACTGACACAAATGAATTAGCAACTGTAAACGATACACTGACT
1 ACTGACACAAATGAATTAGCAACTGTAAACGATACACTGACT
* *
1361684 ACTGACACAAATGAATTAGCTACTGTAAACGCTACACTGAC
1 ACTGACACAAATGAATTAGCAACTGTAAACGATACACTGAC
1361725 AAGACTGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (42 bp):
ACTGACACAAATGAATTAGCAACTGTAAACGATACACTGACT
Found at i:1365372 original size:32 final size:32
Alignment explanation
Indices: 1365331--1365396 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1365321 AATGGCATTT
1365331 GCGCCATCTTATTCTCCCACCTTCTTTAGATC
1 GCGCCATCTTATTCTCCCACCTTCTTTAGATC
*
1365363 GCGCCATCTTATTCTCCCATCTTCTTTAGATC
1 GCGCCATCTTATTCTCCCACCTTCTTTAGATC
1365395 GC
1 GC
1365397 ATATATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.15, C:0.36, G:0.11, T:0.38
Consensus pattern (32 bp):
GCGCCATCTTATTCTCCCACCTTCTTTAGATC
Found at i:1365582 original size:12 final size:12
Alignment explanation
Indices: 1365567--1365600 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1365557 ATTANGAGAG
1365567 AGATAGAGAAAT
1 AGATAGAGAAAT
* *
1365579 AGATAGATAGAT
1 AGATAGAGAAAT
1365591 AGATAGAGAA
1 AGATAGAGAA
1365601 TAGTAGTGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (12 bp):
AGATAGAGAAAT
Done.