Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001637.1 Hibiscus syriacus cultivar Beakdansim tig00003276_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 136541
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3180 original size:11 final size:11
Alignment explanation
Indices: 3164--3205 Score: 61
Period size: 10 Copynumber: 4.0 Consensus size: 11
3154 TAAATAATTA
3164 ATTATTTTATT
1 ATTATTTTATT
3175 ATTATTTTATT
1 ATTATTTTATT
*
3186 -TTATTTTAGT
1 ATTATTTTATT
3196 ATT-TTTTATT
1 ATTATTTTATT
3206 TTTTATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 15 0.54
11 13 0.46
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:3184 original size:5 final size:5
Alignment explanation
Indices: 3165--3207 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
3155 AAATAATTAA
*
3165 TTATT TTATT ATTATT TTATT TTATT TTAGTA TT-TT TTATT TT
1 TTATT TTATT -TTATT TTATT TTATT TTA-TT TTATT TTATT TT
3208 TTATTGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 22 0.67
6 8 0.24
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:3208 original size:21 final size:21
Alignment explanation
Indices: 3165--3207 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3155 AAATAATTAA
*
3165 TTATTTTATTATTATTTTATT
1 TTATTTTAGTATTATTTTATT
3186 TTATTTTAGTATT-TTTTATT
1 TTATTTTAGTATTATTTTATT
3206 TT
1 TT
3208 TTATTGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (21 bp):
TTATTTTAGTATTATTTTATT
Found at i:3219 original size:21 final size:20
Alignment explanation
Indices: 3165--3220 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
3155 AAATAATTAA
3165 TTATTTTATTATTATTTTATT
1 TTATTTTATTATT-TTTTATT
*
3186 TTATTTTAGTATTTTTTATT
1 TTATTTTATTATTTTTTATT
3206 TT-TTATTGATTATTT
1 TTATT-TT-ATTATTT
3221 AATTATAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 11 0.35
21 18 0.58
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (20 bp):
TTATTTTATTATTTTTTATT
Found at i:4026 original size:17 final size:17
Alignment explanation
Indices: 4006--4040 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3996 AAGTAGCCGA
4006 CACATTGAGTTGGGGGT
1 CACATTGAGTTGGGGGT
4023 CACATTGAGTTGGGGGT
1 CACATTGAGTTGGGGGT
4040 C
1 C
4041 TGCAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29
Consensus pattern (17 bp):
CACATTGAGTTGGGGGT
Found at i:6354 original size:32 final size:32
Alignment explanation
Indices: 6318--6378 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
6308 GAAAAGTCTT
*
6318 TTTTAGGTGTGTGTGCATGCTTTTATTTACTA
1 TTTTAGGTGTATGTGCATGCTTTTATTTACTA
* *
6350 TTTTAGGTGTATGTGTATGTTTTTATTTA
1 TTTTAGGTGTATGTGCATGCTTTTATTTA
6379 TTGTTTAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.57
Consensus pattern (32 bp):
TTTTAGGTGTATGTGCATGCTTTTATTTACTA
Found at i:7459 original size:83 final size:83
Alignment explanation
Indices: 7365--7850 Score: 571
Period size: 83 Copynumber: 5.9 Consensus size: 83
7355 ATGTCATAGT
* * * *
7365 GTTTTCCATTATTATTCAGAGAATATCTGCCATGTAATAGTGTTTCATCCCATTCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
* * *
7430 GCACATTCCAGATGAAAC
66 ACACATTCTAGAGGAAAC
* * *
7448 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAATGTTTCATCCCATCCAAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
* * * *
7513 ACGCGTTCCATAGGAAAC
66 ACACATTCTAGAGGAAAC
7531 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
*** *
7596 GTGCATTCTA-AGGGAAGC
66 ACACATTCTAGA-GGAAAC
* *** * * * *
7614 ATTTTCCATTATTATTCAGAGAATCTCTATGATGTCATAGTATTTCATCCTATCCTAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
* * * *
7679 ACGCGTTCTAGGGGAATC
66 ACACATTCTAGAGGAAAC
* * * * * *
7697 ATTTTTCATTATTATTCAGAGAATCTCTACCATGTCATTGTGTTCCATCTCTTCCGAAATGAAAT
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAA-
* *
7762 G-CACATTCTACAGGAAGC
65 GACACATTCTAGAGGAAAC
* * *
7780 GTTTTCTATTATTATTCAAAGAATCTTTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
7845 ACACAT
66 ACACAT
7851 GTTCCATTAT
Statistics
Matches: 344, Mismatches: 55, Indels: 8
0.85 0.14 0.02
Matches are distributed among these distances:
82 2 0.01
83 341 0.99
84 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (83 bp):
GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
ACACATTCTAGAGGAAAC
Found at i:7639 original size:166 final size:166
Alignment explanation
Indices: 7365--7846 Score: 635
Period size: 166 Copynumber: 2.9 Consensus size: 166
7355 ATGTCATAGT
* * * *
7365 GTTTTCCATTATTATTCAGAGAATATCTGCCATGTAATAGTGTTTCATCCCATTCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
* * * *
7430 GCACATTC-CAGATGAAACGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAATGTTTC
66 GCACATTCTAAG-GGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTC
*
7494 ATCCCATCCAAAATGAAAGACGCGTTCCATAGGAAAC
130 ATCCCATCCAAAATGAAAGACGCGTTCCAGAGGAAAC
7531 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
** * *** *
7596 GTGCATTCTAAGGGAAGCATTTTCCATTATTATTCAGAGAATCTCTATGATGTCATAGTATTTCA
66 GCACATTCTAAGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCA
* * * * *
7661 TCCTATCCTAAATGAAAGACGCGTTCTAGGGGAATC
131 TCCCATCCAAAATGAAAGACGCGTTCCAGAGGAAAC
* * * * * * *
7697 ATTTTTCATTATTATTCAGAGAATCTCTACCATGTCATTGTGTTCCATCTCTTCCGAAATGAAAT
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
* * * *
7762 GCACATTCTACA-GGAAGCGTTTTCTATTATTATTCAAAGAATCTTTGCCATGTCATAGTGTTCC
66 GCACATTCTA-AGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTC
*
7826 ATCCCATCCGAAATGAAAGAC
130 ATCCCATCCAAAATGAAAGAC
7847 ACATGTTCCA
Statistics
Matches: 273, Mismatches: 41, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
166 270 0.99
167 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (166 bp):
GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
GCACATTCTAAGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTTCA
TCCCATCCAAAATGAAAGACGCGTTCCAGAGGAAAC
Found at i:7805 original size:249 final size:249
Alignment explanation
Indices: 7366--7844 Score: 645
Period size: 249 Copynumber: 1.9 Consensus size: 249
7356 TGTCATAGTG
* * * *
7366 TTTTCCATTATTATTCAGAGAATATCTGCCATGTAATAGTGTTTCATCCCATTCGAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATATCTACCATGTAATAGTATTTCATCCCATCCGAAATGAAAGA
* * * *
7431 CACATTCCAGATGAAACGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAATGTTTCAT
66 CACATTCCAGAGGAAACATTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAATGTTCCAT
* * * *
7496 CCCATCCAAAATGAAAGACGCGTTCCATAGGAAACGTTTTCCATTATTATTCAGAGAATCTCTGC
131 CCCATCCAAAATGAAAGACACATTCCACAGGAAACGTTTTCCATTATTATTCAAAGAATCTCTGC
7561 CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGTGCATTCTAAGGGAAGCA
196 CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGTGCATTCTAAGGGAAGCA
* ** * * *
7615 TTTTCCATTATTATTCAGAGAATCTCTATGATGTCATAGTATTTCATCCTATCCTAAATGAAAGA
1 TTTTCCATTATTATTCAGAGAATATCTACCATGTAATAGTATTTCATCCCATCCGAAATGAAAGA
* * * * * * **
7680 CGCGTTCTAGGGGAATCATTTTTCATTATTATTCAGAGAATCTCTACCATGTCATTGTGTTCCAT
66 CACATTCCAGAGGAAACATTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAATGTTCCAT
* * * * * * *
7745 CTCTTCCGAAATGAAATG-CACATTCTACAGGAAGCGTTTTCTATTATTATTCAAAGAATCTTTG
131 CCCATCCAAAATGAAA-GACACATTCCACAGGAAACGTTTTCCATTATTATTCAAAGAATCTCTG
7809 CCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
195 CCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
7845 ACACATGTTC
Statistics
Matches: 196, Mismatches: 33, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
249 195 0.99
250 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (249 bp):
TTTTCCATTATTATTCAGAGAATATCTACCATGTAATAGTATTTCATCCCATCCGAAATGAAAGA
CACATTCCAGAGGAAACATTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAATGTTCCAT
CCCATCCAAAATGAAAGACACATTCCACAGGAAACGTTTTCCATTATTATTCAAAGAATCTCTGC
CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGTGCATTCTAAGGGAAGCA
Found at i:12683 original size:43 final size:43
Alignment explanation
Indices: 12622--12703 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
12612 TCTTTCACCT
12622 TGCAACATGAATAAGTTGCCCATCTGGCTGTAAACTGTCGAAA
1 TGCAACATGAATAAGTTGCCCATCTGGCTGTAAACTGTCGAAA
*
12665 TGCAACGTGAATAAGTTGCCCATCTGGCTGTAAACTGTC
1 TGCAACATGAATAAGTTGCCCATCTGGCTGTAAACTGTC
12704 AAAAAGATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (43 bp):
TGCAACATGAATAAGTTGCCCATCTGGCTGTAAACTGTCGAAA
Found at i:18899 original size:279 final size:279
Alignment explanation
Indices: 18387--19440 Score: 1189
Period size: 279 Copynumber: 3.8 Consensus size: 279
18377 TTAGGACCCA
* * * * * * * *
18387 TTCCTGACTGTCCTTGAAAGCTATTACTAGACAGATAATTCCTATTATCAAGCACACAATCATTT
1 TTCCTGACTGTTCTTGAAAGCTATCACTCGATAGACAATTCATATTATCAAGCGCACGATCATTT
* * * *
18452 TCCGTCTCGACATTGGAGGAACTCCCTCCATTTTCCATG-CTATTCCTCCCTTTCTCATCGAAGA
66 TCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGTC-ATTCCTCCCTTCCTCGTCGAAGA
** * * * *
18516 CTTC--CTTCGGGCTTTCATCCAAGAAATTAGGATTATTAAACAAACTAGAAAGACCATAAGGAC
130 --TCGACTTCGGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCATAAGGAC
* * * *
18579 TTCTAGGAGAAAATAATTTCATTTCCTCGCGAAACAAATTAGCAATACCATAAGGTGTTCTAGGA
193 TTCTAGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTCTAGGA
18644 GAAAACCTGTCCATTTCCTCCC
258 GAAAACCTGTCCATTTCCTCCC
* * *
18666 TTTCC-GACTGTTCTTGAAATCTATCACTCGATAGACAATTCGTATTATCAAGCGCACGGTCATT
1 -TTCCTGACTGTTCTTGAAAGCTATCACTCGATAGACAATTCATATTATCAAGCGCACGATCATT
* *
18730 TTCCGACTCGATATTGGAGGAACTCCCTCCATGTTCCATGTCATTCCTCCCTTCCTCGTCAAAGA
65 TTCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGTCATTCCTCCCTTCCTCGTCGAAGA
* * *
18795 TCGACTTCGGATTTTCATCAAAGAAATTACGATCACTAAACAATCTAGCAAGACCGTAAGGACTT
130 TCGACTTCGGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCATAAGGACTT
* *
18860 CTTGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTCTAGGTGA
195 CTAGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTCTAGGAGA
* *
18925 GAACTTGTCCATTTCCTCCC
260 AAACCTGTCCATTTCCTCCC
* * * * * ** * * *
18945 ATCCTGTCTGTTCTTGAAAGTTATCACTCAATCGTGAATTCAT-TTCAGCAAGTGCTCGATCATT
1 TTCCTGACTGTTCTTGAAAGCTATCACTCGATAGACAATTCATATT-ATCAAGCGCACGATCATT
* *
19009 TGCAGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGTCATTCCTCCCTTCCTCGTCGAAGA
65 TTCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGTCATTCCTCCCTTCCTCGTCGAAGA
* * * * * *
19074 TTGACTTTGAATTTTCATCCGAGAAATTACTATCACTAAACAAACGAGCAAGACCATAAGGACTT
130 TCGACTTCGGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCATAAGGACTT
*
19139 CTGGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTCTAGGAGA
195 CTAGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTCTAGGAGA
* *
19204 AAACCTGTTCGTTTCCTCCC
260 AAACCTGTCCATTTCCTCCC
* ** ** ** * * ** * *
19224 TTCCT-ATCTGTTGTTGAAAGCTATCACTAAACCGTGACTTCCTA-CCTCGAAGTGCTCGATCAT
1 TTCCTGA-CTGTTCTTGAAAGCTATCACTCGATAGACAATTCATATTATC-AAGCGCACGATCAT
** ** ** * *
19287 TTTTTGTCTTAATATTAAAGGAACTCCCTCCATGTTCCATG-CTATTCCTTCCTTTCTCGTCGAA
64 TTTCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGTC-ATTCCTCCCTTCCTCGTCGAA
* * * * *
19351 TACCGAC-TCTGGATTTTCATCCAAG---TTAGGATCACTAAACAAACTAGCAAGTCCATAGGGA
128 GATCGACTTC-GGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCATAAGGA
*
19412 CTTCTAGGAGAAAATC-TGTTCATTTCCTC
192 CTTCTAGGAGAAAA-CATTTTCATTTCCTC
19441 CCTTCCTGAC
Statistics
Matches: 665, Mismatches: 98, Indels: 26
0.84 0.12 0.03
Matches are distributed among these distances:
276 56 0.08
277 3 0.00
278 8 0.01
279 593 0.89
280 5 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (279 bp):
TTCCTGACTGTTCTTGAAAGCTATCACTCGATAGACAATTCATATTATCAAGCGCACGATCATTT
TCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGTCATTCCTCCCTTCCTCGTCGAAGAT
CGACTTCGGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCATAAGGACTTC
TAGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTCTAGGAGAA
AACCTGTCCATTTCCTCCC
Found at i:19187 original size:57 final size:57
Alignment explanation
Indices: 19106--19221 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 57
19096 GAAATTACTA
* * *
19106 TCACTAAACAAACGAGCAAGACCATAAGGACTTCTGGGAGAAAACATTTTCATTTCC
1 TCACGAAACAAACGAGCAAGACCATAAGGACTTCTAGGAGAAAACATGTTCATTTCC
** * * * *
19163 TCACGAAACAAATTAGCAATACCATAAGGAGTTCTAGGAGAAAACCTGTTCGTTTCC
1 TCACGAAACAAACGAGCAAGACCATAAGGACTTCTAGGAGAAAACATGTTCATTTCC
19220 TC
1 TC
19222 CCTTCCTATC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (57 bp):
TCACGAAACAAACGAGCAAGACCATAAGGACTTCTAGGAGAAAACATGTTCATTTCC
Found at i:19704 original size:222 final size:221
Alignment explanation
Indices: 19163--19881 Score: 917
Period size: 219 Copynumber: 3.3 Consensus size: 221
19153 TTTCATTTCC
* * * * * * *
19163 TCACGAAACAAATTAGCAATACCATAAGGAGTTCTAGGAGAAAACCTGTTCGTTTCCTCCCTTCC
1 TCACTAAACAAACTAGCAAGACCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTCC
*
19228 T-ATCTGTTGTTGAAAGCTATCACTAAACCGTGACTTCCTACC-TCGAAGTGCTCGATCATTTTT
66 TGA-CTGTTGTTGAAAGCTATCACTAAACCGCGACTT-CTACCAT-GAAGTGCTCGATCATTTTT
* *
19291 TGTCTTAATATTAAAGGAACTCCCTCC-ATGTTCCATGCTATTCCTTCCTTTCTCGTCGAATACC
128 TGTCTTAATATTGAAGGAACTCCCTCCTATGTTCCATGCTATTCCTCCCTTTCTCGTCGAATACC
* * *
19355 GACTCTGGATTTTCATCC--AAGTTAGGA
193 GACTCCGGATTTTCGTCCAGAAATTAGGA
*
19382 TCACTAAACAAACTAGCAAGTCCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTCC
1 TCACTAAACAAACTAGCAAGACCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTCC
* *
19447 TGACTGTTGTTGAAAGCTATTACTAAACCGCGACTTCGTACCATGAAGTGCTTGATCATTTTTT-
66 TGACTGTTGTTGAAAGCTATCACTAAACCGCGACTTC-TACCATGAAGTGCTCGATCATTTTTTG
* * *
19511 TCCTTAATATTGAAGGAACTCCC-CCTATGTTCCATGCTATTACTCCCTTTCTCGGCAAATACCG
130 T-CTTAATATTGAAGGAACTCCCTCCTATGTTCCATGCTATTCCTCCCTTTCTCGTCGAATACCG
*
19575 ACTCCGAATTTTCGTCCGAGAAATTAGGA
194 ACTCCGGATTTTCGTCC-AGAAATTAGGA
* * *
19604 ACACTAAACAAACTA-CGATGACCGTAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTC
1 TCACTAAACAAACTAGC-AAGACCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTC
* * * ** * *
19668 CTGACTGTCGTTGGAAGCTATCACTCAATTGCGAC-T-T---AGGAAGTGCCCGATCATTTTTTG
65 CTGACTGTTGTTGAAAGCTATCACTAAACCGCGACTTCTACCATGAAGTGCTCGATCATTTTTTG
* *
19728 TCTTAATATTGAAGGAACTCCCTCCTCCATGTTCCATGCTATTCCTCCCTTTGTCGTCGAAGACC
130 TCTTAATATTGAAGGAACTCCCTCCT--ATGTTCCATGCTATTCCTCCCTTTCTCGTCGAATACC
19793 GACTCCGGATTTTCGTCCAAGAAATTAGGA
193 GACTCCGGATTTTCGTCC-AGAAATTAGGA
* * * *
19823 TCATTAAACAAACTAGCAGGACCATAAGGACTTCTAGGAGAAAA-CATTTTCATTTCCTC
1 TCACTAAACAAACTAGCAAGACCATAGGGACTTCTAGGAGAAAATC-TGTTCATTTCCTC
19882 ACGAAACAAG
Statistics
Matches: 439, Mismatches: 46, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
216 40 0.09
217 4 0.01
218 5 0.01
219 290 0.66
220 3 0.01
221 2 0.00
222 95 0.22
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (221 bp):
TCACTAAACAAACTAGCAAGACCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTCC
TGACTGTTGTTGAAAGCTATCACTAAACCGCGACTTCTACCATGAAGTGCTCGATCATTTTTTGT
CTTAATATTGAAGGAACTCCCTCCTATGTTCCATGCTATTCCTCCCTTTCTCGTCGAATACCGAC
TCCGGATTTTCGTCCAGAAATTAGGA
Found at i:19937 original size:57 final size:57
Alignment explanation
Indices: 19828--19940 Score: 140
Period size: 57 Copynumber: 2.0 Consensus size: 57
19818 TAGGATCATT
* * *
19828 AAACAAACTAGCAGGACCATAAGGACTTCTAGGAGAAAACATTTTCATTTCCTCACG
1 AAACAAACTAGCAAGACCATAAGGACTTCTAGGAGAAAACATGTTCAATTCCTCACG
* * *
19885 AAACAAGCTAGCAATACCATAAGGACTTGC-AGGAGAAATGC-TGTTCAATTCCTCAC
1 AAACAAACTAGCAAGACCATAAGGACTT-CTAGGAGAAA-ACATGTTCAATTCCTCAC
19941 TATCTTTTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
57 46 0.96
58 2 0.04
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (57 bp):
AAACAAACTAGCAAGACCATAAGGACTTCTAGGAGAAAACATGTTCAATTCCTCACG
Found at i:21066 original size:21 final size:21
Alignment explanation
Indices: 21027--21067 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
21017 GTTGCAACAC
21027 TTTCCTTCTTCTCATCCTCCCT
1 TTTCCTTCTTCTCA-CCTCCCT
21049 TTTCCTCTCTTCTC-CCTCC
1 TTTCCT-TCTTCTCACCTCC
21068 GCAAAGCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTCCTTCTTCTCACCTCCCT
Found at i:21803 original size:3 final size:3
Alignment explanation
Indices: 21795--21834 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
21785 AACCGAGGAT
*
21795 GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
21835 GTGCTGAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:26865 original size:23 final size:23
Alignment explanation
Indices: 26839--26899 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
26829 CTCATATAAA
*
26839 TGCACTGAAGTGCCACATAGAAT
1 TGCACTGTAGTGCCACATAGAAT
* *
26862 TGCA-TCGTAGTGCCGCGTAGAAT
1 TGCACT-GTAGTGCCACATAGAAT
*
26885 TGCACCGTAGTGCCA
1 TGCACTGTAGTGCCA
26900 TATAATAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCACTGTAGTGCCACATAGAAT
Found at i:27033 original size:18 final size:18
Alignment explanation
Indices: 27010--27045 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27000 GAATACATAT
27010 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
27028 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
27046 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:27120 original size:121 final size:121
Alignment explanation
Indices: 26906--27148 Score: 441
Period size: 121 Copynumber: 2.0 Consensus size: 121
26896 GCCATATAAT
*
26906 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
1 AATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
*
26971 GTCTCACCAGACTTCACACACGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACACGTTCCAAAGAATACATATATGTCCCAAAGGACCAC
* *
27027 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 AATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
*
27092 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCAAAGGACCAC
66 GTCTCACCAGACTTCACACACGTTCCAAAGAATACATATATGTCCCAAAGGACCAC
27148 A
1 A
27149 TAGACCCTCG
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 117 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (121 bp):
AATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
GTCTCACCAGACTTCACACACGTTCCAAAGAATACATATATGTCCCAAAGGACCAC
Found at i:28452 original size:21 final size:21
Alignment explanation
Indices: 28426--28469 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28416 ATTTTATTCG
* *
28426 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
28447 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
28468 CT
1 CT
28470 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:29786 original size:2 final size:2
Alignment explanation
Indices: 29779--29804 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29769 TCTCATATGC
29779 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29805 TAGCTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47104 original size:24 final size:24
Alignment explanation
Indices: 47077--47183 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
47067 AAACGGAGAT
*
47077 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
47101 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
47125 CTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
47149 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
47173 ATCAGAAATCA
1 ATCAGAAATCA
47184 GATAAAATAT
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:47183 original size:48 final size:48
Alignment explanation
Indices: 47077--47185 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
47067 AAACGGAGAT
* * * *
47077 ATCAGAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
47125 CTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
47173 ATCAGAAATCAGA
1 ATCAGAAATCAGA
47186 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:49665 original size:7 final size:7
Alignment explanation
Indices: 49653--49690 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
49643 GGTCAACGCG
49653 GGTCAAC
1 GGTCAAC
49660 GGTCAAC
1 GGTCAAC
49667 GGTCAAC
1 GGTCAAC
49674 GGTCAAC
1 GGTCAAC
49681 AGGTCAAC
1 -GGTCAAC
49689 GG
1 GG
49691 GTCGGGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.29, C:0.26, G:0.32, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:49698 original size:5 final size:5
Alignment explanation
Indices: 49688--49753 Score: 51
Period size: 5 Copynumber: 11.4 Consensus size: 5
49678 AACAGGTCAA
49688 CGGGT CGGGT CGGGT CAACGGGT CGGGT AAACGGGT CGGGT CGGGT AAACGGGT
1 CGGGT CGGGT CGGGT ---CGGGT CGGGT ---CGGGT CGGGT CGGGT ---CGGGT
49742 CGGGT CGGGT CG
1 CGGGT CGGGT CG
49754 TGACCGGTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
5 37 0.71
8 15 0.29
ACGTcount: A:0.12, C:0.20, G:0.52, T:0.17
Consensus pattern (5 bp):
CGGGT
Found at i:49705 original size:18 final size:18
Alignment explanation
Indices: 49682--49752 Score: 89
Period size: 18 Copynumber: 4.2 Consensus size: 18
49672 ACGGTCAACA
49682 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
49700 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
*
49713 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
49731 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
49749 GGTC
1 GGTC
49753 GTGACCGGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
13 12 0.26
18 34 0.74
ACGTcount: A:0.14, C:0.20, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:49709 original size:13 final size:13
Alignment explanation
Indices: 49693--49729 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
49683 GTCAACGGGT
49693 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
49706 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
49719 CGGGTCGGGTC
1 CGGGTCGGGTC
49730 GGGTAAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:49724 original size:31 final size:31
Alignment explanation
Indices: 49686--49746 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
49676 TCAACAGGTC
*
49686 AACGGGTCGGGTCGGGTCAACGGGTCGGGTA
1 AACGGGTCGGGTCGGGTAAACGGGTCGGGTA
49717 AACGGGTCGGGTCGGGTAAACGGGTCGGGT
1 AACGGGTCGGGTCGGGTAAACGGGTCGGGT
49747 CGGGTCGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.16, C:0.18, G:0.49, T:0.16
Consensus pattern (31 bp):
AACGGGTCGGGTCGGGTAAACGGGTCGGGTA
Found at i:51847 original size:24 final size:24
Alignment explanation
Indices: 51820--51925 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
51810 AAACGGAGAT
51820 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACATAATTCAG
* * * *
51844 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACATAATTCAG
* * * * *
51868 CTTAGGAATCAGAACA-GATTCAG
1 ATCAGAAATCAAAACATAATTCAG
** *
51891 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACATAATTCAG
51915 ATCAGAAATCA
1 ATCAGAAATCA
51926 GATAAAATAT
Statistics
Matches: 60, Mismatches: 21, Indels: 2
0.72 0.25 0.02
Matches are distributed among these distances:
23 15 0.25
24 45 0.75
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACATAATTCAG
Found at i:51925 original size:47 final size:48
Alignment explanation
Indices: 51820--51927 Score: 119
Period size: 47 Copynumber: 2.3 Consensus size: 48
51810 AAACGGAGAT
* * *
51820 ATCAGAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
51868 CTTAGGAATCAGAACA-GATTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
51915 ATCAGAAATCAGA
1 ATCAGAAATCAGA
51928 TAAAATATTC
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
47 35 0.74
48 12 0.26
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:54404 original size:7 final size:7
Alignment explanation
Indices: 54392--54430 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
54382 GGTCAACGCG
54392 GGTCAAC
1 GGTCAAC
54399 GGTCAAC
1 GGTCAAC
54406 GGGTCAAC
1 -GGTCAAC
54414 GGTCAAC
1 GGTCAAC
54421 AGGTCAAC
1 -GGTCAAC
54429 GG
1 GG
54431 GTCGGGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.28, C:0.26, G:0.33, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:54410 original size:15 final size:15
Alignment explanation
Indices: 54390--54430 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
54380 GTGGTCAACG
54390 CGGGTCAACGGTCAA
1 CGGGTCAACGGTCAA
54405 CGGGTCAACGGTCAA
1 CGGGTCAACGGTCAA
*
54420 CAGGTCAACGG
1 CGGGTCAACGG
54431 GTCGGGTCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.34, T:0.12
Consensus pattern (15 bp):
CGGGTCAACGGTCAA
Found at i:54438 original size:5 final size:5
Alignment explanation
Indices: 54428--54493 Score: 51
Period size: 5 Copynumber: 11.4 Consensus size: 5
54418 AACAGGTCAA
54428 CGGGT CGGGT CGGGT CAACGGGT CGGGT AAACGGGT CGGGT CGGGT AAACGGGT
1 CGGGT CGGGT CGGGT ---CGGGT CGGGT ---CGGGT CGGGT CGGGT ---CGGGT
54482 CGGGT CGGGT CG
1 CGGGT CGGGT CG
54494 TGACCGGTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
5 37 0.71
8 15 0.29
ACGTcount: A:0.12, C:0.20, G:0.52, T:0.17
Consensus pattern (5 bp):
CGGGT
Found at i:54445 original size:18 final size:18
Alignment explanation
Indices: 54422--54492 Score: 89
Period size: 18 Copynumber: 4.2 Consensus size: 18
54412 ACGGTCAACA
54422 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
54440 GGTCAA-----CGGGTCG
1 GGTCAACGGGTCGGGTCG
*
54453 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
54471 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
54489 GGTC
1 GGTC
54493 GTGACCGGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
13 12 0.26
18 34 0.74
ACGTcount: A:0.14, C:0.20, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:54449 original size:13 final size:13
Alignment explanation
Indices: 54433--54469 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
54423 GTCAACGGGT
54433 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
54446 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
54459 CGGGTCGGGTC
1 CGGGTCGGGTC
54470 GGGTAAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:54451 original size:8 final size:8
Alignment explanation
Indices: 54390--54433 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
54380 GTGGTCAACG
54390 CGGGTCAA
1 CGGGTCAA
54398 C-GGTCAA
1 CGGGTCAA
54405 CGGGTCAA
1 CGGGTCAA
54413 C-GGTCAA
1 CGGGTCAA
*
54420 CAGGTCAA
1 CGGGTCAA
54428 CGGGTC
1 CGGGTC
54434 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (8 bp):
CGGGTCAA
Found at i:54464 original size:31 final size:31
Alignment explanation
Indices: 54426--54486 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
54416 TCAACAGGTC
*
54426 AACGGGTCGGGTCGGGTCAACGGGTCGGGTA
1 AACGGGTCGGGTCGGGTAAACGGGTCGGGTA
54457 AACGGGTCGGGTCGGGTAAACGGGTCGGGT
1 AACGGGTCGGGTCGGGTAAACGGGTCGGGT
54487 CGGGTCGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.16, C:0.18, G:0.49, T:0.16
Consensus pattern (31 bp):
AACGGGTCGGGTCGGGTAAACGGGTCGGGTA
Found at i:59973 original size:22 final size:22
Alignment explanation
Indices: 59945--59990 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
59935 AAGACACTAG
59945 TTTTTTTCATTTTCATTT-TTTA
1 TTTTTTTCATTTT-ATTTGTTTA
*
59967 TTTTTTTTATTTTATTTGTTTA
1 TTTTTTTCATTTTATTTGTTTA
59989 TT
1 TT
59991 ATTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTTTTCATTTTATTTGTTTA
Found at i:59992 original size:3 final size:3
Alignment explanation
Indices: 59986--60039 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
59976 TTTTATTTGT
59986 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
60031 TTA TTA TTA
1 TTA TTA TTA
60040 AATAAATATT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:60050 original size:33 final size:33
Alignment explanation
Indices: 59985--60050 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
59975 ATTTTATTTG
* * *
59985 TTTATTATTATTATTATATTATTATTATTATTA
1 TTTATTATTATTATTATATTATAATAAATATTA
60018 TTTATTATTATTATTATTATTA-AATAAATATTA
1 TTTATTATTATTATTA-TATTATAATAAATATTA
60051 CAGGCCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TTTATTATTATTATTATATTATAATAAATATTA
Found at i:63173 original size:20 final size:19
Alignment explanation
Indices: 63144--63223 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 19
63134 AGAACCCCAT
*
63144 GGGGGTATCGATTCCCTACA
1 GGGGGAATCGATTCCCT-CA
*
63164 GGGGGAATCGGTTCCCATTCAA
1 GGGGGAATCGATTCCC--TC-A
* *
63186 AGGGGAATCGGTTCCCTCA
1 GGGGGAATCGATTCCCTCA
* *
63205 TGGGGGTATCGATTACCTC
1 -GGGGGAATCGATTCCCTC
63224 TGTACCAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.02
20 30 0.61
21 1 0.02
22 17 0.35
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (19 bp):
GGGGGAATCGATTCCCTCA
Found at i:69579 original size:22 final size:21
Alignment explanation
Indices: 69537--69576 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
69527 GAGTTTATTT
*
69537 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
69558 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
69577 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:71720 original size:19 final size:19
Alignment explanation
Indices: 71696--71733 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
71686 TTTTAAAAGA
71696 TTTGGAGTAATATTTTGAT
1 TTTGGAGTAATATTTTGAT
71715 TTTGGAGTAATATTTTGAT
1 TTTGGAGTAATATTTTGAT
71734 ATTCGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (19 bp):
TTTGGAGTAATATTTTGAT
Found at i:71744 original size:19 final size:19
Alignment explanation
Indices: 71703--71744 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
71693 AGATTTGGAG
* * *
71703 TAATATTTTGATTTTGGAG
1 TAATATTTTGATATTCGAA
71722 TAATATTTTGATATTCGAA
1 TAATATTTTGATATTCGAA
71741 TAAT
1 TAAT
71745 TATATCGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.50
Consensus pattern (19 bp):
TAATATTTTGATATTCGAA
Found at i:72484 original size:21 final size:21
Alignment explanation
Indices: 72447--72486 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
72437 ATTTTTTAAT
*
72447 TTTTAATCTTTATATTTTATA
1 TTTTAATCTATATATTTTATA
72468 TTTTAATCCTATA-ATTTTA
1 TTTTAAT-CTATATATTTTA
72487 GTTTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAATCTATATATTTTATA
Found at i:72616 original size:19 final size:17
Alignment explanation
Indices: 72592--72640 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
72582 ATCAATACTT
72592 TAAATATTATTTTAACGTA
1 TAAATATTATTTTAA--TA
*
72611 TAAATA-TATATTTAATT
1 TAAATATTAT-TTTAATA
72628 TAAATATTATTTT
1 TAAATATTATTTT
72641 TTAAGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 10 0.37
18 6 0.22
19 11 0.41
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TAAATATTATTTTAATA
Found at i:72985 original size:18 final size:18
Alignment explanation
Indices: 72962--72997 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
72952 GAAAATTATT
72962 ATTATTT-TATTATTAATA
1 ATTATTTAT-TTATTAATA
72980 ATTATTTATTTATTAATA
1 ATTATTTATTTATTAATA
72998 TTAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTATTTATTTATTAATA
Found at i:78471 original size:18 final size:18
Alignment explanation
Indices: 78448--78487 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
78438 AAACTTTTAC
78448 ATTTACTTGCTTTATCTT
1 ATTTACTTGCTTTATCTT
** *
78466 ATTTACTTTTTTTATTTT
1 ATTTACTTGCTTTATCTT
78484 ATTT
1 ATTT
78488 TTTTAGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.70
Consensus pattern (18 bp):
ATTTACTTGCTTTATCTT
Found at i:78497 original size:22 final size:23
Alignment explanation
Indices: 78458--78535 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 23
78448 ATTTACTTGC
78458 TTTATCTTATTTACTTTTTTTAT
1 TTTATCTTATTTACTTTTTTTAT
* * *
78481 TTTAT-TTTTTTAGTTTTTTTAC
1 TTTATCTTATTTACTTTTTTTAT
** *
78503 TCAATCTTA-TTATCTTTATTTA-
1 TTTATCTTATTTA-CTTTTTTTAT
*
78525 TTTATTTTATT
1 TTTATCTTATT
78536 ATTGTTATTA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
22 26 0.63
23 15 0.37
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.72
Consensus pattern (23 bp):
TTTATCTTATTTACTTTTTTTAT
Found at i:84265 original size:103 final size:103
Alignment explanation
Indices: 84086--84406 Score: 543
Period size: 103 Copynumber: 3.1 Consensus size: 103
84076 AGTCGAGGTC
* *
84086 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
84151 TTGATCTTTGGCATATATATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
84189 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
84254 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
84292 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
84357 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
84395 TTTGTGGTCCTT
1 TATGTGGTCCTT
84407 ATGGACATTA
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:84456 original size:23 final size:23
Alignment explanation
Indices: 84422--84508 Score: 165
Period size: 23 Copynumber: 3.8 Consensus size: 23
84412 CATTATTATA
*
84422 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
84445 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
84468 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
84491 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
84509 ATATGAGCTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:86654 original size:179 final size:177
Alignment explanation
Indices: 86347--86703 Score: 696
Period size: 179 Copynumber: 2.0 Consensus size: 177
86337 TTTAGCACCA
86347 TCAAAGAAAGGTAGAGATTCTGGTTCAACTTTAAACTAGACATGAATTAGTTGTATTCTCCGTCA
1 TCAAAGAAAGGTAGAGATTCTGGTTCAACTTTAAACTAGACATGAATTAGTTGTATTCTCCGTCA
86412 GAGAATCAAATCAGATGAGAGTTCGACAGACTCCAACAGTAAGTTTGATCTTGAAAGATTAAACA
66 GAGAATCAAATCAGATGAGAGTTCGACAGACTCCAACAGTAAGTTTGATCTTGAAAGATTAAACA
86477 AAGAGTTAATTGAGGATAAGTCAGGGTTAAAGACAACCCTTGTGAAT
131 AAGAGTTAATTGAGGATAAGTCAGGGTTAAAGACAACCCTTGTGAAT
86524 TCAAAGAAGAAGGTAGAGATTCTGGTTCAACTTTAAACTAGACATGAATTAGTTGTATTCTCCGT
1 TCAAAG-A-AAGGTAGAGATTCTGGTTCAACTTTAAACTAGACATGAATTAGTTGTATTCTCCGT
86589 CAGAGAATCAAATCAGATGAGAGTTCGACAGACTCCAACAGTAAGTTTGATCTTGAAAGATTAAA
64 CAGAGAATCAAATCAGATGAGAGTTCGACAGACTCCAACAGTAAGTTTGATCTTGAAAGATTAAA
86654 CAAAGAGTTAATTGAGGATAAGTCAGGGTTAAAGACAACCCTTGTGAAT
129 CAAAGAGTTAATTGAGGATAAGTCAGGGTTAAAGACAACCCTTGTGAAT
86703 T
1 T
86704 AGGTTAAAAG
Statistics
Matches: 178, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
177 6 0.03
178 1 0.01
179 171 0.96
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (177 bp):
TCAAAGAAAGGTAGAGATTCTGGTTCAACTTTAAACTAGACATGAATTAGTTGTATTCTCCGTCA
GAGAATCAAATCAGATGAGAGTTCGACAGACTCCAACAGTAAGTTTGATCTTGAAAGATTAAACA
AAGAGTTAATTGAGGATAAGTCAGGGTTAAAGACAACCCTTGTGAAT
Found at i:89419 original size:19 final size:19
Alignment explanation
Indices: 89395--89446 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
89385 AATGCAATTC
89395 GTGCATCGATGCATAAGTA
1 GTGCATCGATGCATAAGTA
89414 GTGCATCGATGCATAAGTA
1 GTGCATCGATGCATAAGTA
89433 GTGCATCGATGCAT
1 GTGCATCGATGCAT
89447 CCCAGTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATAAGTA
Found at i:90397 original size:103 final size:103
Alignment explanation
Indices: 90163--90582 Score: 731
Period size: 103 Copynumber: 4.1 Consensus size: 103
90153 GAGTCGGGTC
90163 TATGTGGTCCTTCGGG--ATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
90226 TTGATCCTTGG--TATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
90262 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
90327 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
90365 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
90430 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * * * *
90468 TATGTGATCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAATTTTGGTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
90533 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
90571 TTTGTGGTCCTT
1 TATGTGGTCCTT
90583 ATGGACATTA
Statistics
Matches: 307, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
99 16 0.05
101 58 0.19
103 233 0.76
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:90633 original size:23 final size:23
Alignment explanation
Indices: 90598--90661 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
90588 CATTATTATA
90598 TGGCACTAC-GGTGCAATTCTACG
1 TGGCACT-CTGGTGCAATTCTACG
90621 TGGCACTCTGGTGCAATTCTACG
1 TGGCACTCTGGTGCAATTCTACG
90644 TGGCACT-TCGGTGCAATT
1 TGGCACTCT-GGTGCAATT
90662 ATATGAGCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.05
23 37 0.95
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGCACTCTGGTGCAATTCTACG
Found at i:92179 original size:120 final size:120
Alignment explanation
Indices: 91996--92216 Score: 295
Period size: 120 Copynumber: 1.8 Consensus size: 120
91986 TTCGAGAGTA
* * *
91996 GATTTTAACTTCACGACGAAGGATATCTAACTCGAAGCTAAACTTCACAACAAAGGGGTCATCCA
1 GATTTCAACTTCACGACGAAGGATATCTAACTCGAAGCTAAACTTCACAACAAAGGCGCCATCCA
* *
92061 CGGTTTCAACTTCACGACGAAGAGA-ATCGTGCCCACCCGCAACATACAATACTTG
66 CGATTTCAACTCCACGACGAAG-GATATCGTGCCCACCCGCAACATACAATACTTG
* * * *
92116 GATTTCAACTTCACGACGAAGGATAT-TCAAGTC-AAGGCTCAACTTCACGACGAAGGCGCCATC
1 GATTTCAACTTCACGACGAAGGATATCT-AACTCGAA-GCTAAACTTCACAACAAAGGCGCCATC
* *
92179 CATGATTTCAACTCCACGACGGAGGATATCGTGCCCAC
64 CACGATTTCAACTCCACGACGAAGGATATCGTGCCCAC
92217 AAACCCACGA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
119 5 0.06
120 82 0.94
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (120 bp):
GATTTCAACTTCACGACGAAGGATATCTAACTCGAAGCTAAACTTCACAACAAAGGCGCCATCCA
CGATTTCAACTCCACGACGAAGGATATCGTGCCCACCCGCAACATACAATACTTG
Found at i:92814 original size:83 final size:82
Alignment explanation
Indices: 92575--92863 Score: 298
Period size: 84 Copynumber: 3.5 Consensus size: 82
92565 TTATCTGCCA
* *
92575 ACCAAAGACCTTCGAGTTCGACCA-AGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAG
1 ACCAAAGACCTTCGAGTTCGACTACA-CTCAACTCAAAGGCACATCATTTGCAGCATAGCTTAAG
*
92639 TCGAGAAGGG--CTATCC
65 TCGAGAAGGGTTATATCC
* * * * ** * *
92655 ACCAAAGACCCTCGAGTTCGATTACACTCAGCTTC-AAGGACACATCATTTACAAAATAACTCAA
1 ACCAAAGACCTTCGAGTTCGACTACACTCAAC-TCAAAGG-CACATCATTTGCAGCATAGCTTAA
* * *
92719 GGCTAGAAGGGTTATATATC
64 GTCGAGAAGGGTTATAT-CC
* * *
92739 ACCAAAGACCTTCGAGTTCAACTACGCTCAACTCAAAGGCACATCATTTGTAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACACTCAACTCAAAGGCACATCATTTGCAGCATAGCTTAAGT
*
92804 CGAGAAGGGTTATCTGCC
66 CGAGAAGGGTTATAT-CC
* * * *
92822 AACCGAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGCA
1 -ACCAAAGACCTTCGAGTTCGACTACACTCAACTCAAAGGCA
92864 AACCAAATTT
Statistics
Matches: 166, Mismatches: 35, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
80 30 0.18
81 31 0.19
83 38 0.23
84 67 0.40
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (82 bp):
ACCAAAGACCTTCGAGTTCGACTACACTCAACTCAAAGGCACATCATTTGCAGCATAGCTTAAGT
CGAGAAGGGTTATATCC
Found at i:93931 original size:29 final size:29
Alignment explanation
Indices: 93888--93970 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
93878 CTCACCTAAC
*
93888 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
93918 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
93947 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
93971 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:100133 original size:13 final size:14
Alignment explanation
Indices: 100115--100143 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
100105 TCTGAATATG
100115 TTCCTCTGAAC-GT
1 TTCCTCTGAACTGT
100128 TTCCTCTGAACTGT
1 TTCCTCTGAACTGT
100142 TT
1 TT
100144 TGTCATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (14 bp):
TTCCTCTGAACTGT
Found at i:102346 original size:35 final size:35
Alignment explanation
Indices: 102307--102377 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
102297 AAAAAATAAG
* *
102307 TTTATGGGC-CTTGCTTCTAATTTAGTTTATTAATA
1 TTTATGGGCTC-TGCTTCTAATTTAATATATTAATA
* *
102342 TTTATGGGTTCTGCTTTTAATTTAATATATTAATA
1 TTTATGGGCTCTGCTTCTAATTTAATATATTAATA
102377 T
1 T
102378 AATTTTTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (35 bp):
TTTATGGGCTCTGCTTCTAATTTAATATATTAATA
Found at i:102475 original size:125 final size:116
Alignment explanation
Indices: 102254--102499 Score: 280
Period size: 116 Copynumber: 2.0 Consensus size: 116
102244 TGACATTATG
* * * *
102254 ATTAATTTAGTTTTTAACGTTATGATGAGAACAATAAGTCAATAAAAAATAAGTTTATGGGCCTT
1 ATTAATATAATTTTTAACGTTATGATGAGAAAAATAAATCAATAAAAAATAAGTTTATGGGCCTT
* *
102319 GCTTCTAATTTAGTTTATTAATATTTATGGGT-TCTGCTTTTAATTTAATAT
66 GCATCTAATTAAGTTTATTAATATTTATGGGTCT-TGCTTTTAATTTAATAT
* * *
102370 ATTAATATAATTTTTAACGTTGTGATGAGAAAAATAAATCAATAAGAACTAAGTTTATGGGCCCT
1 ATTAATATAATTTTTAACGTTATGATGAGAAAAATAAATCAATAAAAAATAAGTTTATGGG--C-
* *
102435 CTTGCAT-TAATTAAGAAAATAATATATTAATATTTATGGGTCTTGTTTTTAATTTAATTT
63 CTTGCATCTAATTAAG----T--T-TATTAATATTTATGGGTCTTGCTTTTAATTTAATAT
102495 ATTAA
1 ATTAA
102500 AATATAATAA
Statistics
Matches: 108, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
116 54 0.50
118 8 0.07
119 6 0.06
122 1 0.01
124 1 0.01
125 37 0.34
126 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (116 bp):
ATTAATATAATTTTTAACGTTATGATGAGAAAAATAAATCAATAAAAAATAAGTTTATGGGCCTT
GCATCTAATTAAGTTTATTAATATTTATGGGTCTTGCTTTTAATTTAATAT
Found at i:112985 original size:21 final size:21
Alignment explanation
Indices: 112956--113011 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
112946 ACCGTGATTG
*
112956 CGGCTGTCGCGGGCGCTATTA
1 CGGCCGTCGCGGGCGCTATTA
* *
112977 CGGTCGTCG-GGGACGCTATTG
1 CGGCCGTCGCGGG-CGCTATTA
112998 CGGCCGTCGCGGGC
1 CGGCCGTCGCGGGC
113012 AACTCGGACG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.10
21 23 0.79
22 3 0.10
ACGTcount: A:0.07, C:0.30, G:0.43, T:0.20
Consensus pattern (21 bp):
CGGCCGTCGCGGGCGCTATTA
Found at i:130206 original size:42 final size:43
Alignment explanation
Indices: 130005--130206 Score: 193
Period size: 42 Copynumber: 4.8 Consensus size: 43
129995 TTAATTTTAT
* *
130005 TTTTTATCTTTATAATTGAGGCCCTTAA-TTTTTCAATCCCAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCCCAC
* * * * *
130047 TTTGTACTTTTATAATTGA-GCTCCTAAGTTTTTCAA-CCTTAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCC-CAC
* * *
130089 TTTCTACCTTTATAATTGAGGCCCCAAATTTTTT-AATCTCAC
1 TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCCCAC
* **
130131 TTTTTACCTTTATAGTTG-CCCCCCTAATTTTTTTCAATCCCA-
1 TTTTTACCTTTATAATTGAGGCCCCTAA-TTTTTTCAATCCCAC
* *
130173 TTTTTA-CTTATATAATTTAGGTCCCTAATTTTTT
1 TTTTTACCTT-TATAATTGAGGCCCCTAATTTTTT
130207 TTATTCTTAC
Statistics
Matches: 128, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
41 17 0.13
42 87 0.68
43 24 0.19
ACGTcount: A:0.23, C:0.21, G:0.07, T:0.49
Consensus pattern (43 bp):
TTTTTACCTTTATAATTGAGGCCCCTAATTTTTTCAATCCCAC
Found at i:130250 original size:127 final size:127
Alignment explanation
Indices: 130033--130263 Score: 286
Period size: 127 Copynumber: 1.8 Consensus size: 127
130023 AGGCCCTTAA
*
130033 TTTTTCAATCCCACTTTGTACTTTTATAATTGAGCTCCTAAGTTTTTCAACCTTACTTTCTACCT
1 TTTTTCAATCCCACTTTGTACTTATATAATTGAGCTCCTAAGTTTTTCAACCTTACTTTCTACCT
* *
130098 TTATAATTGAGGCCCCAAATTTTTTAATCTCACTTTTTACCTTTATAGTTGCCCCCCTAATT
66 TTAAAATTAAGGCCCCAAATTTTTTAATCTCACTTTTTACCTTTATAGTTGCCCCCCTAATT
* * * * * ** *
130160 TTTTTCAATCCCA-TTTTTACTTATATAATTTAGGTCCCTAATTTTTTTTATTCTTACTTT-TAG
1 TTTTTCAATCCCACTTTGTACTTATATAATTGAGCT-CCTAA-GTTTTTCAACCTTACTTTCTAC
* ** * *
130223 CTTTAAAATTAAGGCCCTATTTTTTTTAATTTGACTTTTTA
64 CTTTAAAATTAAGGCCCCAAATTTTTTAATCTCACTTTTTA
130264 ATTTATAATT
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
126 18 0.21
127 54 0.63
128 14 0.16
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.50
Consensus pattern (127 bp):
TTTTTCAATCCCACTTTGTACTTATATAATTGAGCTCCTAAGTTTTTCAACCTTACTTTCTACCT
TTAAAATTAAGGCCCCAAATTTTTTAATCTCACTTTTTACCTTTATAGTTGCCCCCCTAATT
Found at i:130263 original size:42 final size:44
Alignment explanation
Indices: 130173--130280 Score: 102
Period size: 41 Copynumber: 2.5 Consensus size: 44
130163 TTCAATCCCA
* * *
130173 TTTTTACTTATATAATTTAGGTCCCTAATTTTTTTTATTCTTAC
1 TTTTTACTTATAAAATTAAGGTCCCTAATTTTTTTTATTCTGAC
130217 -TTTTAGCTT-TAAAATTAAGG-CCCT-ATTTTTTTTAATT-TGAC
1 TTTTTA-CTTATAAAATTAAGGTCCCTAATTTTTTTT-ATTCTGAC
* * *
130258 TTTTTAATT-TATAATTGAGGTCC
1 TTTTTACTTATAAAATTAAGGTCC
130281 TCAATCATAC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
41 23 0.43
42 14 0.26
43 14 0.26
44 3 0.06
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (44 bp):
TTTTTACTTATAAAATTAAGGTCCCTAATTTTTTTTATTCTGAC
Found at i:136440 original size:3 final size:3
Alignment explanation
Indices: 136432--136517 Score: 140
Period size: 3 Copynumber: 28.7 Consensus size: 3
136422 ATACATTGAT
136432 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
136479 ATA ATA ATA ATA ATAA ATA A-A ATA ATA ATA ATA AGTA AT
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A-TA AT
136518 GCAATGCAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.05
3 69 0.87
4 6 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Done.