Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002830.1 Hibiscus syriacus cultivar Beakdansim tig00005821_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: 90650
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:9330 original size:22 final size:22
Alignment explanation
Indices: 9287--9330 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
9277 TTCCATTCAA
* *
9287 CATCAACACCATCAACATCTTC
1 CATCAACACCACCAACAACTTC
* *
9309 CATCAAGACCACCATCAACTTC
1 CATCAACACCACCAACAACTTC
9331 ATAATTCCGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.41, G:0.02, T:0.20
Consensus pattern (22 bp):
CATCAACACCACCAACAACTTC
Found at i:9686 original size:8 final size:9
Alignment explanation
Indices: 9671--9699 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
9661 CAAAGACAAA
9671 AAGAAAAAG
1 AAGAAAAAG
9680 AAGAAAAAG
1 AAGAAAAAG
9689 AAGAAAAAG
1 AAGAAAAAG
9698 AA
1 AA
9700 TTTCAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:9710 original size:18 final size:17
Alignment explanation
Indices: 9663--9713 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
9653 AAGGAGTTCA
9663 AAGACAAAAAGAAAAAG
1 AAGACAAAAAGAAAAAG
*
9680 AAGAAAAAGAAGAAAAAG
1 AAGACAAA-AAGAAAAAG
**
9698 AATTTCAAAAAGAAAA
1 AA-GACAAAAAGAAAA
9714 GCAAGGCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 7 0.25
18 18 0.64
19 3 0.11
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.06
Consensus pattern (17 bp):
AAGACAAAAAGAAAAAG
Found at i:22869 original size:20 final size:22
Alignment explanation
Indices: 22831--22870 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
22821 GTTTTGCAGA
22831 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
22853 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
22871 AGATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:23486 original size:20 final size:21
Alignment explanation
Indices: 23449--23488 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23439 AAACAATTGG
23449 AAACAATTGGTATCCTTTTGA
1 AAACAATTGGTATCCTTTTGA
* *
23470 AAACTATTGGTATCTTTTT
1 AAACAATTGGTATCCTTTT
23489 TATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (21 bp):
AAACAATTGGTATCCTTTTGA
Found at i:25843 original size:45 final size:45
Alignment explanation
Indices: 25761--25949 Score: 245
Period size: 45 Copynumber: 4.2 Consensus size: 45
25751 ATTTTATTTG
* * *
25761 CTTATCCAATAT-TTTACCATTTATTAACCATAAGCTCGTAAGTTTAT
1 CTTA-CCAATATACTTACCATTTA-T-CCCATAAGCTCGTAAGCTTAT
* *
25808 TTTACCAAAATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
1 CTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
* * * * *
25853 CTTACCATTATACTTACCATTTGTTCCATAAGCTCATAATCTTAT
1 CTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
*
25898 TTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
1 CTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
25943 CTTACCA
1 CTTACCA
25950 TTTGTTCCAT
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
45 102 0.84
46 7 0.06
47 13 0.11
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (45 bp):
CTTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAT
Found at i:25898 original size:90 final size:91
Alignment explanation
Indices: 25774--25951 Score: 297
Period size: 90 Copynumber: 2.0 Consensus size: 91
25764 ATCCAATATT
*
25774 TTACCATTTATTAACCATAAGCTCGTAAGTTTATTTTACCAAAATACTTACCATTTATCCCATAA
1 TTACCATTTATT-ACCATAAGCTCATAAGTTTATTTTACCAAAATACTTACCATTTATCCCATAA
25839 GCTCGTAAGCTTATCTTACCATTATAC
65 GCTCGTAAGCTTATCTTACCATTATAC
* *
25866 TTACCATTTGTT-CCATAAGCTCATAA-TCTTATTTTACCAATATACTTACCATTTATCCCATAA
1 TTACCATTTATTACCATAAGCTCATAAGT-TTATTTTACCAAAATACTTACCATTTATCCCATAA
25929 GCTCGTAAGCTTATCTTACCATT
65 GCTCGTAAGCTTATCTTACCATT
25952 TGTTCCATAA
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
89 1 0.01
90 70 0.85
92 11 0.13
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (91 bp):
TTACCATTTATTACCATAAGCTCATAAGTTTATTTTACCAAAATACTTACCATTTATCCCATAAG
CTCGTAAGCTTATCTTACCATTATAC
Found at i:25947 original size:33 final size:33
Alignment explanation
Indices: 25910--26015 Score: 167
Period size: 33 Copynumber: 3.2 Consensus size: 33
25900 TACCAATATA
* *
25910 CTTACCATTTATCCCATAAGCTCGTAAGCTTAT
1 CTTACCATTTGTTCCATAAGCTCGTAAGCTTAT
25943 CTTACCATTTGTTCCATAAGCTCGTAAGCTTAT
1 CTTACCATTTGTTCCATAAGCTCGTAAGCTTAT
* *
25976 CTTACCATTTGTTCCATAAGCTCATAAGCTCAT
1 CTTACCATTTGTTCCATAAGCTCGTAAGCTTAT
*
26009 TTTACCA
1 CTTACCA
26016 ATATACTTGC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.38
Consensus pattern (33 bp):
CTTACCATTTGTTCCATAAGCTCGTAAGCTTAT
Found at i:27602 original size:29 final size:28
Alignment explanation
Indices: 27536--27603 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
27526 AGGTTCTTCA
* *
27536 TCAATTTTCCAAAATTTACGAATTGATC
1 TCAATTTTTCAAAATTTACGAAATGATC
* * *
27564 TCCAACTTTTCAAAATTTATGAAATGGTCC
1 T-CAATTTTTCAAAATTTACGAAATGAT-C
27594 TCAATTTTTC
1 TCAATTTTTC
27604 TAAGGCTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 1 0.03
29 29 0.91
30 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.41
Consensus pattern (28 bp):
TCAATTTTTCAAAATTTACGAAATGATC
Found at i:30352 original size:23 final size:22
Alignment explanation
Indices: 30305--30394 Score: 68
Period size: 21 Copynumber: 4.3 Consensus size: 22
30295 TCTCTCATCA
*
30305 TTTTTTT-TTC-TTCTTTCTA-
1 TTTTTTTCTTCTTTCTTTTTAT
*
30324 TCTTTTTCTTCTTTCTTTTTAT
1 TTTTTTTCTTCTTTCTTTTTAT
*
30346 TTCTTTTTCTAT-TTT-TTTCTA-
1 TT-TTTTTCT-TCTTTCTTTTTAT
* *
30367 TTTTTTTCATC-TTCTTTTTCT
1 TTTTTTTCTTCTTTCTTTTTAT
30388 TTTTTTT
1 TTTTTTT
30395 AGCTTTTATG
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
19 9 0.16
20 13 0.23
21 17 0.30
22 6 0.11
23 10 0.18
24 1 0.02
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTTTCTTCTTTCTTTTTAT
Found at i:30355 original size:33 final size:31
Alignment explanation
Indices: 30305--30387 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 31
30295 TCTCTCATCA
*
30305 TTTTTT-TTTCTTCTTTCTATCTTTTTCTTCTT
1 TTTTTTATTTCTT-TTTCTATCTTTTTC-TATT
*
30337 TCTTTTTATTTCTTTTTCTATTTTTTTCTATT
1 T-TTTTTATTTCTTTTTCTATCTTTTTCTATT
*
30369 TTTTTCATCTTCTTTTTCT
1 TTTTTTAT-TTCTTTTTCT
30388 TTTTTTTAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 6 0.13
32 15 0.33
33 18 0.40
34 6 0.13
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTTTTATTTCTTTTTCTATCTTTTTCTATT
Found at i:30361 original size:9 final size:10
Alignment explanation
Indices: 30318--30394 Score: 59
Period size: 10 Copynumber: 7.3 Consensus size: 10
30308 TTTTTTCTTC
*
30318 TTTCTATCTT
1 TTTCTATTTT
30328 TTTCT-TCTTT
1 TTTCTAT-TTT
*
30338 CTTTTTATTTCTT
1 -TTTCTA-TT-TT
30351 TTTCTATTTT
1 TTTCTATTTT
30361 TTTCTATTTT
1 TTTCTATTTT
*
30371 TTTCATCTTCTT
1 TTTC-TATT-TT
30383 TTTCT-TTTT
1 TTTCTATTTT
30392 TTT
1 TTT
30395 AGCTTTTATG
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
9 6 0.11
10 25 0.45
11 10 0.18
12 12 0.21
13 3 0.05
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTATTTT
Found at i:30370 original size:17 final size:17
Alignment explanation
Indices: 30307--30365 Score: 86
Period size: 17 Copynumber: 3.5 Consensus size: 17
30297 TCTCATCATT
30307 TTTTTTTCTTCTTTCTA
1 TTTTTTTCTTCTTTCTA
*
30324 TCTTTTTCTTCTTTCT-
1 TTTTTTTCTTCTTTCTA
30340 TTTTATTTCTT-TTTCTA
1 TTTT-TTTCTTCTTTCTA
30357 TTTTTTTCT
1 TTTTTTTCT
30366 ATTTTTTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
16 13 0.34
17 25 0.66
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTCTTCTTTCTA
Found at i:30381 original size:26 final size:25
Alignment explanation
Indices: 30305--30395 Score: 64
Period size: 26 Copynumber: 3.6 Consensus size: 25
30295 TCTCTCATCA
* *
30305 TTTTTTT-TTCTTCTTTCTATCTT-T
1 TTTTTTTCTTTTTATTTC-ATCTTCT
* *
30329 TTCTTCTTTCTTTTTATTTCTTTTTCT
1 TT-TT-TTTCTTTTTATTTCATCTTCT
30356 ATTTTTTTCTATTTT-TTTCATCTTCT
1 -TTTTTTTCT-TTTTATTTCATCTTCT
30382 TTTTCTTT-TTTTTA
1 TTTT-TTTCTTTTTA
30396 GCTTTTATGC
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
24 6 0.11
25 7 0.13
26 23 0.43
27 15 0.28
28 2 0.04
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTTTCTTTTTATTTCATCTTCT
Found at i:33072 original size:45 final size:45
Alignment explanation
Indices: 32980--33235 Score: 318
Period size: 45 Copynumber: 5.7 Consensus size: 45
32970 ATTTGCATAT
* * *
32980 CCAATAT-TTTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTA-T-CCCATAAGCTCATAAGCTTATTTTA
* * * *
33026 CCAAAATACTTACCATTTATCCCACAAGGTCATAAGCTTATCTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
* * *
33071 CCATTATACTTACCATTTGTTCCATAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
* *
33116 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATCTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
* * *
33161 CCATTATACTTACCATTTGTTCCATAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
* * *
33206 CCAATATACTT-GCAATTATTCCATAAGCTC
1 CCAATATACTTACCATTTATCCCATAAGCTC
33236 GTAATATTAT
Statistics
Matches: 181, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.09
45 148 0.82
46 7 0.04
47 10 0.06
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
Found at i:33155 original size:90 final size:90
Alignment explanation
Indices: 32988--33239 Score: 398
Period size: 90 Copynumber: 2.8 Consensus size: 90
32978 ATCCAATATT
* * * *
32988 TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTATCCCACAA
1 TTACCATTTGTT--CCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAA
* *
33053 GGTCATAAGCTTATCTTACCATTATAC
64 GCTCGTAAGCTTATCTTACCATTATAC
33080 TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
1 TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
33145 TCGTAAGCTTATCTTACCATTATAC
66 TCGTAAGCTTATCTTACCATTATAC
* * *
33170 TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTT-GCAATTATTCCATAAGC
1 TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
33234 TCGTAA
66 TCGTAA
33240 TATTATTTTC
Statistics
Matches: 151, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
89 20 0.13
90 120 0.79
92 11 0.07
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (90 bp):
TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
TCGTAAGCTTATCTTACCATTATAC
Found at i:33478 original size:61 final size:61
Alignment explanation
Indices: 33357--33478 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
33347 GTAGTGCTAA
* * * *
33357 ACCTGCACTAAGCTTACGCCATAATGCTAATCCGGACAATACACAGAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACGACATAATGCTAATCCGGACAATACACAGAAGGTAGTACCCACC
* * * * * *
33418 ACCTACACTAAGCTTATGATATAGTGCTAATCCGGAC-ATGATACATAAGGTAGTATCCACC
1 ACCTACACTAAGCTTACGACATAATGCTAATCCGGACAAT-ACACAGAAGGTAGTACCCACC
33479 TTTCCCTCAC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 2 0.04
61 48 0.96
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGACATAATGCTAATCCGGACAATACACAGAAGGTAGTACCCACC
Found at i:35232 original size:17 final size:18
Alignment explanation
Indices: 35199--35233 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35189 ACCAAATATT
*
35199 TTAATACTTATTAATTCC
1 TTAATACTTAATAATTCC
35217 TTAATAC-TAATAATTCC
1 TTAATACTTAATAATTCC
35234 AACATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAATACTTAATAATTCC
Found at i:35935 original size:29 final size:28
Alignment explanation
Indices: 35865--35935 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 28
35855 CCTAGGTTCT
*
35865 TCATCAATTTTCCAAAATTTATGAATTGA
1 TCATCAATTTT-CAAAATTTATGAAATGA
*
35894 TC-TGCAACTTTTCAAAATTTATGAAATGG
1 TCAT-CAA-TTTTCAAAATTTATGAAATGA
35923 TCATCAATGTTTC
1 TCATCAAT-TTTC
35936 TAAGGCTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
28 2 0.06
29 29 0.81
30 5 0.14
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (28 bp):
TCATCAATTTTCAAAATTTATGAAATGA
Found at i:37198 original size:3 final size:3
Alignment explanation
Indices: 37190--37251 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
37180 TTTTTACCCA
*
37190 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
37238 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
37252 AATATATATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:38710 original size:19 final size:20
Alignment explanation
Indices: 38678--38715 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
38668 ATTTTATTTG
**
38678 TTTATATTTTTAAA-ATATT
1 TTTATATTCATAAATATATT
38697 TTTATATTCATAAATATAT
1 TTTATATTCATAAATATAT
38716 ATATAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTATATTCATAAATATATT
Found at i:39429 original size:18 final size:17
Alignment explanation
Indices: 39406--39456 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
39396 TTCTTGTCAA
39406 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
39423 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
39441 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
39457 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 17 0.63
19 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:49125 original size:12 final size:11
Alignment explanation
Indices: 49105--49134 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
49095 ATTATGCTTG
49105 AAGAAAAAAAA
1 AAGAAAAAAAA
49116 AAGAAAAAAAA
1 AAGAAAAAAAA
49127 AAGAAAAA
1 AAGAAAAA
49135 GGGGGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:50406 original size:83 final size:83
Alignment explanation
Indices: 50282--50905 Score: 1079
Period size: 83 Copynumber: 7.5 Consensus size: 83
50272 GAATTTGCCA
* *
50282 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGACAGAA-CACATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCA-ATCATTGAAT
50346 TTGGAAGATGAATGTGTTC
65 TTGGAAGATGAATGTGTTC
50365 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
*
50430 TGGAAGATGAATGTGCTC
66 TGGAAGATGAATGTGTTC
*
50448 ATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
50513 TGGAAGATGAATGTGTTC
66 TGGAAGATGAATGTGTTC
* *
50531 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
50596 TGGAAGATGAATGTGTTC
66 TGGAAGATGAATGTGTTC
* *
50614 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGACAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
50679 TGGAAGATGAATGTGTTC
66 TGGAAGATGAATGTGTTC
* * * *
50697 ATAGCATCTCCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGACAGAACAAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
* *
50762 TAGAAAATGAATGTGTTC
66 TGGAAGATGAATGTGTTC
*
50780 ATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
50845 TGGAAGATGAATGTGTTC
66 TGGAAGATGAATGTGTTC
* *
50863 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATTTGGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
50906 TGGTAAGAAC
Statistics
Matches: 514, Mismatches: 26, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
83 512 1.00
84 2 0.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATT
TGGAAGATGAATGTGTTC
Found at i:51966 original size:113 final size:113
Alignment explanation
Indices: 51663--52178 Score: 885
Period size: 113 Copynumber: 4.6 Consensus size: 113
51653 TGACATTTCT
51663 AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
51728 TTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTA-TTTTGCC
66 TTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCC
51775 AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
51840 TTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCC
66 TTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCC
*
51888 AGAGAAGGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
51953 TTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCC
66 TTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCC
*
52001 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* * * * **
52066 TTGTTCAACCTTTT-TGCTCAAATCTATTACTTGATGGGTTATTTTTTTC
66 TTGTTCAACCTTTTGT-CTGAATTC-ATCACTTGATGGATTATTTTTGCC
* * *
52115 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAG-AGAAAGTTCATTATGAGAAGAA
1 AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
52179 CTCATCAAAA
Statistics
Matches: 389, Mismatches: 11, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
112 106 0.27
113 204 0.52
114 79 0.20
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (113 bp):
AGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
TTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCC
Found at i:52438 original size:3 final size:3
Alignment explanation
Indices: 52430--52488 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
52420 TTTTTACCCA
* *
52430 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52478 TAT TAT TAT TA
1 TAT TAT TAT TA
52489 AATATATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:55647 original size:10 final size:9
Alignment explanation
Indices: 55625--55717 Score: 57
Period size: 10 Copynumber: 9.8 Consensus size: 9
55615 TCTCTCATCA
55625 TTTTTTTTC
1 TTTTTTTTC
55634 --TTTTTTC
1 TTTTTTTTC
55641 TATTTTTTTC
1 T-TTTTTTTC
*
55651 TTCTTTCTTC
1 TT-TTTTTTC
*
55661 TTTCTTTTTA
1 TTT-TTTTTC
*
55671 TTTATTTTC
1 TTTTTTTTC
55680 -TTTTTTTC
1 TTTTTTTTC
55688 TAGTTTGTTTCATC
1 T--TTT-TTT--TC
*
55702 TTCTTTTTC
1 TTTTTTTTC
55711 TTTTTTT
1 TTTTTTT
55718 AGTTCTTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
7 7 0.11
8 7 0.11
9 14 0.22
10 23 0.35
11 6 0.09
12 5 0.08
14 3 0.05
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.78
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:55648 original size:17 final size:17
Alignment explanation
Indices: 55626--55658 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55616 CTCTCATCAT
*
55626 TTTTTTTCTTTTTTCTA
1 TTTTTTTCTTCTTTCTA
55643 TTTTTTTCTTCTTTCT
1 TTTTTTTCTTCTTTCT
55659 TCTTTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTCTTTCTA
Found at i:55716 original size:47 final size:46
Alignment explanation
Indices: 55624--55715 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
55614 ATCTCTCATC
* * *
55624 ATTTTTTTTCTTTTTTCTATTTTTTTCTTCTTTCTTCTTTCTTTTT
1 ATTTATTTTCTTTTTTCTATTTGTTTCATCTTTCTTCTTTCTTTTT
55670 ATTTATTTTCTTTTTTTCTAGTTTGTTTCATC-TTCTT-TTTCTTTTT
1 ATTTATTTTC-TTTTTTCTA-TTTGTTTCATCTTTCTTCTTTCTTTTT
55716 TTAGTTCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
46 18 0.44
47 14 0.34
48 9 0.22
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (46 bp):
ATTTATTTTCTTTTTTCTATTTGTTTCATCTTTCTTCTTTCTTTTT
Found at i:58385 original size:45 final size:45
Alignment explanation
Indices: 58303--58526 Score: 290
Period size: 45 Copynumber: 5.0 Consensus size: 45
58293 ATTTGCATAT
* * *
58303 CCAATAT-TTTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTA-T-CCCATAAGCTCATAAGCTTATTTTA
* * *
58349 CCAAAATACTTACCATTTATCCCATAAGCTTATAAGCTTATCTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
* * * *
58394 CCATTATACTTACCATTTGTTCCAAAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
*
58439 CCAATATACTTACCATTTATCTCATAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
* * *
58484 CCAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTT
58527 CCAGTTTAAC
Statistics
Matches: 155, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
44 25 0.16
45 113 0.73
46 7 0.05
47 10 0.06
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.39
Consensus pattern (45 bp):
CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
Found at i:58434 original size:90 final size:90
Alignment explanation
Indices: 58303--58526 Score: 326
Period size: 90 Copynumber: 2.5 Consensus size: 90
58293 ATTTGCATAT
*
58303 CCAATAT-TTTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTT
1 CCAATATACTTACCATTTATT--CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTT
*
58367 ATCCCATAAGCTTATAAGCTTATCTTA
64 ATCCCATAAGCTCATAAGCTTATCTTA
* * * * *
58394 CCATTATACTTACCATTTGTTCCAAAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTAT
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAT
* *
58459 CTCATAAGCTCATAAGCTTATTTTA
66 CCCATAAGCTCATAAGCTTATCTTA
*
58484 CCAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
58527 CCAGTTTAAC
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
89 25 0.21
90 76 0.64
91 6 0.05
92 11 0.09
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.39
Consensus pattern (90 bp):
CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAT
CCCATAAGCTCATAAGCTTATCTTA
Found at i:58756 original size:61 final size:61
Alignment explanation
Indices: 58635--58756 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
58625 TTAGTGCTAA
* * * * *
58635 ACCTGCACTAAGCTTACGCCATAGTGCTAATCCGGACATTACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTAGTACCCACC
* * * *
58696 ACCTACACTAAGCTTATGCTATAGTGCTAATCCAGACATGATACATAAGGTAGTATCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTAGTACCCACC
58757 TTTCCCACAC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTAGTACCCACC
Found at i:60018 original size:29 final size:28
Alignment explanation
Indices: 59952--60019 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
59942 AGGTTCTTCA
* *
59952 TCAATTTTCCAAAATTTACGAATTGATC
1 TCAATTTTTCAAAATTTACGAAATGATC
* *
59980 TCCAACTTTTCAAAATTTACGAAATGGTCC
1 T-CAATTTTTCAAAATTTACGAAATGAT-C
60010 TCAATTTTTC
1 TCAATTTTTC
60020 TAAGGCTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 1 0.03
29 30 0.91
30 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (28 bp):
TCAATTTTTCAAAATTTACGAAATGATC
Found at i:62765 original size:17 final size:16
Alignment explanation
Indices: 62743--62797 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
62733 CTCATCATTA
62743 TTTTTTCATCTTTCTAT
1 TTTTTTC-TCTTTCTAT
62760 TTTTTTCTTCTTTCT-T
1 TTTTTTC-TCTTTCTAT
* *
62776 ATTATTTCTTTTTCTAT
1 -TTTTTTCTCTTTCTAT
62793 TTTTT
1 TTTTT
62798 CACCTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCTCTTTCTAT
Found at i:65382 original size:40 final size:40
Alignment explanation
Indices: 65327--65448 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
65317 TACAGGTTTA
65327 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
65367 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
65407 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
65447 TA
1 TA
65449 GCACTACGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:65653 original size:47 final size:45
Alignment explanation
Indices: 65553--65678 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 45
65543 GTAAGCATAC
* **
65553 AAATAAGCTTACGAGCTTTTGGAAT-AATGACAAGTATATATGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATATGAA
* *
65597 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAT-TTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAT-GAA
*
65644 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
65679 AGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
44 23 0.32
45 11 0.15
46 3 0.04
47 35 0.49
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATATGAA
Found at i:68586 original size:45 final size:45
Alignment explanation
Indices: 68505--68863 Score: 479
Period size: 45 Copynumber: 8.0 Consensus size: 45
68495 ATTTGCATAT
* *
68505 CCAATAT-TTTACCATTTATTAACCATAAGCTTGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATT--CCATAAGCTCGTAAGCTTATTTTA
* * *
68551 CCAAAATACTTACCATTTATCCCATAAGCTCGTAAGCTTATCTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
* * *
68596 CCATTATACTTACCATTTGTTCCATAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
* * *
68641 CCAATATACTTACCATTTATCCCATAAGCTCGTCAGCTTATCTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
* * *
68686 CCATTATACTTACCATTTGTTCCATAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
* ** *
68731 CCAATATACTTACCATTTATCCCATAAGCTCGCCAGCTTATCTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
* * * *
68776 CCATTATACTTACCATTTGTTCCATAAGCTCATAAGCATATTTTA
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
*
68821 CCAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
68864 CCAGTTTAAC
Statistics
Matches: 269, Mismatches: 43, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
44 25 0.09
45 227 0.84
46 6 0.02
47 11 0.04
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (45 bp):
CCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA
Found at i:68633 original size:90 final size:90
Alignment explanation
Indices: 68513--68860 Score: 581
Period size: 90 Copynumber: 3.9 Consensus size: 90
68503 ATCCAATATT
* ** *
68513 TTACCATTTATTAACCATAAGCTTGTAAGCTTATTTTACCAAAATACTTACCATTTATCCCATAA
1 TTACCATTTGTT--CCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAA
68578 GCTCGTAAGCTTATCTTACCATTATAC
64 GCTCGTAAGCTTATCTTACCATTATAC
68605 TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
1 TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
*
68670 TCGTCAGCTTATCTTACCATTATAC
66 TCGTAAGCTTATCTTACCATTATAC
68695 TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
1 TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
**
68760 TCGCCAGCTTATCTTACCATTATAC
66 TCGTAAGCTTATCTTACCATTATAC
* * *
68785 TTACCATTTGTTCCATAAGCTCATAAGCATATTTTACCAATATACTTGCCA-TTATTCCATAAGC
1 TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
68849 TCGTAAGCTTAT
66 TCGTAAGCTTAT
68861 TTTCCAGTTT
Statistics
Matches: 245, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
89 22 0.09
90 212 0.87
92 11 0.04
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.38
Consensus pattern (90 bp):
TTACCATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTATCCCATAAGC
TCGTAAGCTTATCTTACCATTATAC
Found at i:69093 original size:61 final size:61
Alignment explanation
Indices: 68977--69093 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
68967 GTTAAACCTG
* *
68977 CACTAAGCTTATGCCATAGTGCTAATCCAGACAATACACATAAGGTCGTGCCCACCACTTA
1 CACTAAGCTTATGCCATAGTGCTAATCCAGACAATACACATAAGGTAGTACCCACCACTTA
* * * *
69038 CACTAAGCTTACT-CTATAGTGCTAATCCGGAC-ATGATACATAAGGTAGTATCCACC
1 CACTAAGCTTA-TGCCATAGTGCTAATCCAGACAAT-ACACATAAGGTAGTACCCACC
69094 TTTCCCGCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 2 0.04
61 45 0.94
62 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (61 bp):
CACTAAGCTTATGCCATAGTGCTAATCCAGACAATACACATAAGGTAGTACCCACCACTTA
Found at i:75040 original size:38 final size:38
Alignment explanation
Indices: 74955--75028 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
74945 TTTTGTTTGG
* *
74955 GTCGGGTC-GGGTTTTTTATGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGGCGA
74992 GTCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGGCG
1 GTCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGGCG
75029 GATTGGGTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 8 0.24
38 26 0.76
ACGTcount: A:0.11, C:0.11, G:0.41, T:0.38
Consensus pattern (38 bp):
GTCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGGCGA
Found at i:75155 original size:270 final size:268
Alignment explanation
Indices: 74721--75318 Score: 888
Period size: 270 Copynumber: 2.2 Consensus size: 268
74711 ACTTTATTTT
* * * *
74721 GGTCGAGTCGGATCGGGTTTTTTTAAGTGTGATATT---TG-GG-TCGGGTCGGGTTGGGTTCGG
1 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGGCGGATCGGGTCGGGTCGGGTTTGG
74781 GTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATAGAATTCAGGTCGGGTCAGATTAAGT
66 GTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATAGAATTCAGGTCGGGTCAGATTAAGT
* * *
74846 CACTATTTTTTATTAAATAAAAATTATTTTTTATTATTTCGGGTCGGGTCGGGTTGGATTTCTAA
131 CACTAGTTTTTATTAAAT--AAATTATTTTTTATTATTTCGGGTCAGGTCGGGTCGGATTTCTAA
* * *
74911 TTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTTGGGTCGGGTCGGGTTTTTTATGT
194 TTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTATTCGGGTCGGGTCGGGTTTTTTAAGT
*
74976 GTGATATTCG
259 GTGACATTCG
* *
74986 GGTCGAGTCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGGCGGATTGGGTCGGGTCGGGTTTGG
1 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGGCGGATCGGGTCGGGTCGGGTTTGG
* * * *
75051 GTTTAGGGTGAAAAAAACCGGACCGACTCGAAAATATATATAATTCGGGTCGGGTAGGGTCGGAT
66 GTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATAGAATTCAGGTC-----GGGTCAGAT
75116 TAAGTCACT-GTTTTTATTAAAT-AATT-TTTTTTATTATTTCGGGTCAGGTCGGGTCGGATTTC
126 TAAGTCACTAGTTTTTATTAAATAAATTATTTTTTATTATTTCGGGTCAGGTCGGGTCGGATTTC
*
75178 TAATTTATATATTCGGGTCGGGTCGGATGAAACTTTATTTTATTCGGGTCGGGTCGGGTTTTTTA
191 TAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTATTCGGGTCGGGTCGGGTTTTTTA
75243 AGTGTGACATTCG
256 AGTGTGACATTCG
* * *
75256 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGATCGGGTCGGGTCAGGTTT
1 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGGCGGATCGGGTCGGGTCGGGTTT
75319 TTTTAAGTGT
Statistics
Matches: 300, Mismatches: 23, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
265 34 0.11
268 1 0.00
269 2 0.01
270 230 0.77
271 4 0.01
274 12 0.04
275 17 0.06
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.37
Consensus pattern (268 bp):
GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGGCGGATCGGGTCGGGTCGGGTTTGG
GTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATAGAATTCAGGTCGGGTCAGATTAAGT
CACTAGTTTTTATTAAATAAATTATTTTTTATTATTTCGGGTCAGGTCGGGTCGGATTTCTAATT
CATATATTCGGGTCGGGTCGGATGAAACTTTATTTTATTCGGGTCGGGTCGGGTTTTTTAAGTGT
GACATTCG
Found at i:75318 original size:43 final size:41
Alignment explanation
Indices: 75221--75341 Score: 169
Period size: 43 Copynumber: 3.0 Consensus size: 41
75211 TTTATTTTAT
* *
75221 TCGGGTCGGGTCGGGTTTTTTAAGTGTGACATTCGGGTCGA
1 TCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGA
75262 ----GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGA
1 TCGGGTCGGGTC-GGTTTTTTTAAGTGTGATATTCGGGTC-GA
75301 TCGGGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCG
1 TCGGGTCGGGTC-GGTTTTTTTAAGTGTGATATTCGGGTCG
75342 GGTTCGGGTT
Statistics
Matches: 71, Mismatches: 3, Indels: 11
0.84 0.04 0.13
Matches are distributed among these distances:
37 8 0.11
38 25 0.35
39 2 0.03
42 1 0.01
43 35 0.49
ACGTcount: A:0.13, C:0.12, G:0.37, T:0.37
Consensus pattern (41 bp):
TCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:75916 original size:44 final size:44
Alignment explanation
Indices: 75853--75936 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
75843 ATCTGACATG
*
75853 TCTGCGAACCAAACAGAATATGGAATTGGATTCCAATTCCATTT
1 TCTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCCATTT
75897 TCTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCC
1 TCTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCC
75937 TTCACAGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (44 bp):
TCTGCCAACCAAACAGAATATGGAATTGGATTCCAATTCCATTT
Found at i:86689 original size:18 final size:18
Alignment explanation
Indices: 86666--86701 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
86656 TTAAAGAAGC
*
86666 CGGCCCATGTTTTATTAA
1 CGGCCCAGGTTTTATTAA
86684 CGGCCCAGGTTTTATTAA
1 CGGCCCAGGTTTTATTAA
86702 TAGCCCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (18 bp):
CGGCCCAGGTTTTATTAA
Found at i:86707 original size:18 final size:18
Alignment explanation
Indices: 86668--86708 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
86658 AAAGAAGCCG
* *
86668 GCCCATGTTTTATTAACG
1 GCCCAGGTTTTATTAACA
*
86686 GCCCAGGTTTTATTAATA
1 GCCCAGGTTTTATTAACA
86704 GCCCA
1 GCCCA
86709 ACAAAGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (18 bp):
GCCCAGGTTTTATTAACA
Found at i:89839 original size:153 final size:152
Alignment explanation
Indices: 89477--89842 Score: 483
Period size: 153 Copynumber: 2.4 Consensus size: 152
89467 CAATTACTCC
* * *
89477 ATTTTAAGTTCA-TTTTTGTACCAAATTTGAATCACATGCTCTTAAACCATAGTAGAATACATGT
1 ATTTTAAG-TCACTTTTTTTACCAAATTTGAACCACATGCTCATAAACCATAGTAGAATACATGT
*
89541 GTACTTTCAATTCCTCTCTTTGATAACAATTTTTACTTTTCAATTTAGTCCTTCAATTTTTCATA
65 GTACTTTCAATTCCTCTCTTTGAT-A-AATTTTTACTTTTCAATTTAGTCCATCAATTTTTCATA
*
89606 ATCTCCTATTTCTTCAATTTTATTT
128 ATATCCTATTTCTTCAATTTTATTT
* * * * *
89631 ATTTTAACTC-CCTTTTTTACCAAATTTGAGCCACATACTCCTAAACCATAGTAGAATACATGTG
1 ATTTTAAGTCACTTTTTTTACCAAATTTGAACCACATGCTCATAAACCATAGTAGAATACATGTG
*
89695 TACTTTCAATTCCTCT-TTTGAT-AATTTTTATTTTTCAA-TTAGTCCATCAATTTTTCATAATA
66 TACTTTCAATTCCTCTCTTTGATAAATTTTTACTTTTCAATTTAGTCCATCAATTTTTCATAATA
89757 TCCT-TATTCTTTCAATTTGTGATTT
131 TCCTAT-TTC-TTCAATTT-T-ATTT
* * * *
89782 ATTTTAAGTCACTTTTTTTTACCAAATTTGAACCACATGCTGATATACCACAATAGAATAC
1 ATTTTAAGTCAC-TTTTTTTACCAAATTTGAACCACATGCTCATAAACCATAGTAGAATAC
89843 CTATGTAACT
Statistics
Matches: 186, Mismatches: 19, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
147 1 0.01
148 29 0.16
149 23 0.12
150 1 0.01
151 13 0.07
152 7 0.04
153 105 0.56
154 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (152 bp):
ATTTTAAGTCACTTTTTTTACCAAATTTGAACCACATGCTCATAAACCATAGTAGAATACATGTG
TACTTTCAATTCCTCTCTTTGATAAATTTTTACTTTTCAATTTAGTCCATCAATTTTTCATAATA
TCCTATTTCTTCAATTTTATTT
Done.