Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004494.1 Hibiscus syriacus cultivar Beakdansim tig00009909_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: 79668
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6436 original size:6 final size:6
Alignment explanation
Indices: 6230--6429 Score: 377
Period size: 6 Copynumber: 33.5 Consensus size: 6
6220 ATTTTAAAAA
6230 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
6278 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATA--
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
6324 TATATG TATATG TATATG TTATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG -TATATG TATATG TATATG TATATG TATATG
6373 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
6421 TATATG TAT
1 TATATG TAT
6430 GTATATGAGA
Statistics
Matches: 191, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.02
6 181 0.95
7 6 0.03
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:7414 original size:15 final size:15
Alignment explanation
Indices: 7369--7398 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7359 GGTAAAAAAA
7369 AACATTTTCGATATT
1 AACATTTTCGATATT
*
7384 AATATTTTCGATATT
1 AACATTTTCGATATT
7399 TTCGATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (15 bp):
AACATTTTCGATATT
Found at i:8845 original size:21 final size:21
Alignment explanation
Indices: 8819--8863 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8809 GATTTCTGGG
* *
8819 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
8840 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
8861 CAA
1 CAA
8864 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:10528 original size:149 final size:149
Alignment explanation
Indices: 10258--10572 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
10248 GAGTCGAGGG
10258 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
10323 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
10388 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
10407 TCTACGCGGTCCTTCGGGATATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
**
10472 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTTTTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
10537 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
10556 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
10573 TGCAATTATA
Statistics
Matches: 162, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 161 0.99
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:10573 original size:23 final size:23
Alignment explanation
Indices: 10540--10584 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
10530 ATTTTTATAT
*
10540 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
10563 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
10585 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:11667 original size:30 final size:31
Alignment explanation
Indices: 11633--11694 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
11623 ACCTATCTAG
* *
11633 AGGTCATAAAGAACCTTGG-AAACTATCCAT
1 AGGTCACAAAGAACCTAGGTAAACTATCCAT
* * *
11663 AGGTCCCGAAGAACCTAGGTAAACTGTCCAT
1 AGGTCACAAAGAACCTAGGTAAACTATCCAT
11694 A
1 A
11695 TGTTCCTTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (31 bp):
AGGTCACAAAGAACCTAGGTAAACTATCCAT
Found at i:12490 original size:30 final size:30
Alignment explanation
Indices: 12375--12473 Score: 155
Period size: 30 Copynumber: 3.3 Consensus size: 30
12365 GAAGGACCTA
* * *
12375 TCCAGATGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
12404 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
12434 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
12464 TCCATAGGTC
1 TCCAGAGGTC
12474 CCGAAGAACC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 15 0.23
30 50 0.77
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:12490 original size:60 final size:60
Alignment explanation
Indices: 12375--12498 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 60
12365 GAAGGACCTA
* * * *
12375 TCCAGATGTCACAAAGACCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGT-AACTG
1 TCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAAACTG
* * * * *
12434 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGA-CCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAAACTG
12495 TCCA
1 TCCA
12499 TATGTCTCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 15 0.28
60 30 0.56
61 9 0.17
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGACCCCGGTAACTGTCCAGAGGTCACAAAGAACCTAGGTAAACTG
Found at i:20607 original size:77 final size:78
Alignment explanation
Indices: 20521--20666 Score: 179
Period size: 78 Copynumber: 1.9 Consensus size: 78
20511 AAGGTTCCGC
** * * * *
20521 CCAAAAATGTCAT-GATTCACTAAGAAA-TAGGTTGTGATATGTATTGTTAATATTTTTATTAAT
1 CCAAAAATGTCATAG-TTCACTAAGAAAGTAGGTTGCAATATGAAATCTTAATATTTTTAATAAT
20584 AAAATAGGTTGTGT
65 AAAATAGGTTGTGT
* * * *
20598 CCAAGAATGTCATAGTTCACTATGAAAGTATGTTGCAATCTGAAATCTTAATATTTTTAATAATA
1 CCAAAAATGTCATAGTTCACTAAGAAAGTAGGTTGCAATATGAAATCTTAATATTTTTAATAATA
20663 AAAT
66 AAAT
20667 GTTATCAGAG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
77 23 0.40
78 34 0.60
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (78 bp):
CCAAAAATGTCATAGTTCACTAAGAAAGTAGGTTGCAATATGAAATCTTAATATTTTTAATAATA
AAATAGGTTGTGT
Found at i:23750 original size:264 final size:257
Alignment explanation
Indices: 23242--23792 Score: 704
Period size: 264 Copynumber: 2.1 Consensus size: 257
23232 TATTATTATT
* * * *
23242 TCGGGTCGGATTTATAATTTATATATTCCGGTCGGGTCGGTGAAACTTTATTTAGATCGGGTCTG
1 TCGGGT-GGATTTCTAATTCATATATTCCGGTCGGGTAGGTGAAACTTTATTTAGATCGGGTCGG
* * *
23307 GTTGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATATCCGA
65 GTGGGTTTTTTTAAGTGTGATATTCGGGTC-GG-CGAGTTCGGGTTTAGGGAGAAAAATAACCGA
*
23372 CCTGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATA
128 CCTGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATA
23437 TATTTTTTTCAATTAAGTCACAATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCG-G
193 TATTTTTTTCAATTAAGTCACAATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGTG
* * * * *
23501 ATCAGGTTGGATTTCTAATTCATATATTCGGGTCAGGTTAGGTGAAACTTTATTTTGTTCGGGTC
1 -TC-GGGTGGATTTCTAATTCATATATTCCGGTC-GGGTAGGTGAAACTTTATTTAGATCGGGTC
23566 GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC-G-G-GTTCGGGTTTAGGGAGAAAAA-AACCG
63 GGGT-GGGTTTTTTTAAGTGTGATATTCGGGTCGGCGAGTTCGGGTTTAGGGAGAAAAATAACC-
* *
23627 GACCGGCTTGAAAAATATATATATAATTTTACCTTATATATTTAGGGATAATTGCAATAATA-CC
126 GA-C--C-TG--AAA-ATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCC
*
23691 CTATATATATAATTTTTTTCAATTAAGTCA-ATATTTTT-TTGAATAAAAATAATTTTTTTATTA
184 CTATATATAT-ATTTTTTTCAATTAAGTCACA-ATTTTTATTAAATAAAAATAA-TTTTTTATTA
* *
23754 TTTTGTGTCGTG
246 TTTCGGGTCGTG
*
23766 TCGGGTCGAGTTTCTAATTCATATATT
1 TCGGGTGGA-TTTCTAATTCATATATT
23793 GAATAAAAAT
Statistics
Matches: 255, Mismatches: 20, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
256 3 0.01
257 22 0.09
258 2 0.01
260 27 0.11
261 34 0.13
262 27 0.11
263 33 0.13
264 106 0.42
265 1 0.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.41
Consensus pattern (257 bp):
TCGGGTGGATTTCTAATTCATATATTCCGGTCGGGTAGGTGAAACTTTATTTAGATCGGGTCGGG
TGGGTTTTTTTAAGTGTGATATTCGGGTCGGCGAGTTCGGGTTTAGGGAGAAAAATAACCGACCT
GAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTATATATATAT
TTTTTTCAATTAAGTCACAATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGTG
Found at i:32483 original size:20 final size:20
Alignment explanation
Indices: 32460--32511 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
32450 AACGCGATCC
32460 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
32480 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
32500 CCAAAATCGCAA
1 CCAGAATCGCAA
32512 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:32592 original size:20 final size:20
Alignment explanation
Indices: 32567--32760 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
32557 GATTTTCCAT
* *
32567 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
32587 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
32607 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
32627 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
32647 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
32667 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
32687 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
32707 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
32728 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
32748 AATCGCAACGCGA
1 AATCGCAACGCGA
32761 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:32612 original size:40 final size:39
Alignment explanation
Indices: 32563--32760 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
32553 TTGCGATTTT
* ** *
32563 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
32601 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
32642 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
32682 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
32721 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
32761 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:32650 original size:60 final size:60
Alignment explanation
Indices: 32567--32759 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
32557 GATTTTCCAT
* ** * *
32567 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
32627 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
32687 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
32748 AATCGCAACGCG
1 AATCGCAACGCG
32760 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:32930 original size:22 final size:22
Alignment explanation
Indices: 32905--32959 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
32895 CTCTCTACGG
*
32905 CGAAGAAATCTGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
32927 CGAAGATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
32949 CGGCGAAATCC
1 CGAAGAAATCC
32960 CTCACAACCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:33180 original size:33 final size:33
Alignment explanation
Indices: 33141--33211 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
33131 TTCACTTAGA
*
33141 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
33174 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
33207 TTTCA
1 TTTCA
33212 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:33351 original size:14 final size:14
Alignment explanation
Indices: 33332--33386 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
33322 AGAATGACTG
33332 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
33346 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
33365 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
33379 TCGCAACG
1 TCGCAACG
33387 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:33399 original size:33 final size:33
Alignment explanation
Indices: 33332--33402 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
33322 AGAATGACTG
***
33332 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
33365 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
33398 TCGCA
1 TCGCA
33403 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:33439 original size:14 final size:14
Alignment explanation
Indices: 33420--33509 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
33410 TTTCATTTCG
33420 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
33434 CGTTGCGATTTCTATTTCG
1 CGTTGCGA-TTC----TCT
33453 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
33467 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
33484 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
33500 CGTTGCGATT
1 CGTTGCGATT
33510 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 4 0.06
16 5 0.08
17 5 0.08
18 4 0.06
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:33451 original size:33 final size:33
Alignment explanation
Indices: 33403--33510 Score: 175
Period size: 33 Copynumber: 3.3 Consensus size: 33
33393 CAAAATCGCA
33403 TTGCGATTT-TCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTCT-ATTTCGCGTTGCGATTCTCTCG
33436 TTGCGATTTCTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTCTATTTCGCGTTGCGATTCTCTCG
*
33469 TTGCGATTGTC-ATCTCGCGTTGCGATTCTCTCG
1 TTGCGATT-TCTATTTCGCGTTGCGATTCTCTCG
33502 TTGCGATTT
1 TTGCGATTT
33511 TCATTTCAAC
Statistics
Matches: 72, Mismatches: 1, Indels: 5
0.92 0.01 0.06
Matches are distributed among these distances:
32 1 0.01
33 68 0.94
34 3 0.04
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTTCTATTTCGCGTTGCGATTCTCTCG
Found at i:33489 original size:19 final size:18
Alignment explanation
Indices: 33398--33510 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
33388 GAAACCAAAA
* *
33398 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
33417 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
*
33433 T--CGTTGCGATTTCTATT
1 TCGCGTTGCGATTTC-ATC
33450 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
33466 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
33483 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
33499 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
33511 TCATTTCAAC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
15 6 0.08
16 9 0.11
17 10 0.13
18 4 0.05
19 26 0.33
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:35443 original size:185 final size:186
Alignment explanation
Indices: 35214--35593 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
35204 TAGATTGCTT
35214 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35279 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
35344 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
35399 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35464 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
35529 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
35585 AGTAAATTT
1 AGTAAATTT
35594 ATCCATTCAA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:35528 original size:93 final size:93
Alignment explanation
Indices: 35214--35593 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
35204 TAGATTGCTT
35214 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35279 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
35307 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35371 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
35399 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35464 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
35492 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35557 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
35585 AGTAAATTT
1 AGTAAATTT
35594 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:35677 original size:19 final size:19
Alignment explanation
Indices: 35637--35765 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
35627 TAGTTTGCTT
* *
35637 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
35657 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
35676 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
35695 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
35709 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
35728 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
35742 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
35761 TCGCA
1 TCGCA
35766 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:35716 original size:33 final size:32
Alignment explanation
Indices: 35673--35765 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
35663 CGCGAAACCA
**
35673 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
35705 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
35738 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
35766 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:35763 original size:52 final size:52
Alignment explanation
Indices: 35637--35765 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
35627 TAGTTTGCTT
**
35637 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
35689 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
35742 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
35766 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:35783 original size:19 final size:19
Alignment explanation
Indices: 35761--35895 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
35751 GAAACCAAAA
*
35761 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
35780 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
35796 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
35813 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
35829 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
35846 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
35865 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
35885 TCGTGTTGCGA
1 TCGCGTTGCGA
35896 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:35802 original size:14 final size:14
Alignment explanation
Indices: 35783--35839 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35773 TTTCATTTCG
35783 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
35797 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
35814 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
35830 CGTTGCGATT
1 CGTTGCGATT
35840 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:35808 original size:33 final size:33
Alignment explanation
Indices: 35766--35858 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
35756 CAAAATCGCA
*
35766 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
35799 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
35832 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
35859 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:37753 original size:38 final size:38
Alignment explanation
Indices: 37710--37782 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
37700 AATTGATTGT
*
37710 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
37748 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
37783 GTAAAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:37769 original size:19 final size:19
Alignment explanation
Indices: 37705--37769 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
37695 AGTTTAATTG
*
37705 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
37724 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
37742 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
37762 ATTGATTT
1 ATTGATTT
37770 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:37798 original size:14 final size:14
Alignment explanation
Indices: 37763--37798 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
37753 GATTGTTTAA
37763 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
37777 ATGA-TTGTAAAAG
1 TTGATTTGTAAAAG
37790 TTGATTTGT
1 TTGATTTGT
37799 GTAATTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:37991 original size:20 final size:19
Alignment explanation
Indices: 37905--38005 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
37895 AAAAATGACT
37905 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
37923 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37942 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
37956 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
37975 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
37995 ATCGCAATGCG
1 ATCGCAATGCG
38006 TTTATAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 17 0.23
19 23 0.31
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:38054 original size:33 final size:33
Alignment explanation
Indices: 38012--38341 Score: 212
Period size: 33 Copynumber: 9.5 Consensus size: 33
38002 TGCGTTTATA
38012 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
38045 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCT-CG--TTGCGATTTTC
*
38082 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
38117 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
38155 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
38188 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
38228 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
38259 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
38292 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
38326 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
38342 GTATTTTCCG
Statistics
Matches: 251, Mismatches: 20, Indels: 52
0.78 0.06 0.16
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 82 0.33
34 46 0.18
35 15 0.06
36 20 0.08
37 9 0.04
38 47 0.19
39 9 0.04
40 9 0.04
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:38058 original size:19 final size:19
Alignment explanation
Indices: 38034--38341 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
38024 GATTATCTCG
38034 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
38053 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
38073 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
38087 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
38106 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
38125 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
38144 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
38163 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
38178 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
38196 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
38215 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
38229 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
38248 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
38267 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
38281 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
38301 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
38315 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
38334 TTGCGATT
1 TTGCGATT
38342 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 13, Indels: 54
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 28 0.11
17 28 0.11
18 8 0.03
19 129 0.52
20 22 0.09
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:38211 original size:52 final size:52
Alignment explanation
Indices: 38034--38313 Score: 338
Period size: 52 Copynumber: 5.2 Consensus size: 52
38024 GATTATCTCG
*
38034 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TT-ATCT-CG--TTGCGATTTTCATTTCGCA
* *
38087 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCA
* *
38144 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTC-GTTGCGATTTTCATTTCGCA
*
38196 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCA
*
38248 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCA
38301 TTGCGATTTTCAT
1 TTGCGATTTTCAT
38314 GTTGGGATTT
Statistics
Matches: 213, Mismatches: 6, Indels: 16
0.91 0.03 0.07
Matches are distributed among these distances:
51 3 0.01
52 118 0.55
53 53 0.25
54 7 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCA
Found at i:40662 original size:12 final size:12
Alignment explanation
Indices: 40645--40669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40635 TCTTCGGGGA
40645 CTTTTTCTTCTT
1 CTTTTTCTTCTT
40657 CTTTTTCTTCTT
1 CTTTTTCTTCTT
40669 C
1 C
40670 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:40878 original size:24 final size:24
Alignment explanation
Indices: 40844--40890 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40834 CTGAAACATC
40844 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
40868 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
40891 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:41592 original size:20 final size:20
Alignment explanation
Indices: 41564--41932 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
41554 AAATTTCAGT
* * * *
41564 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
41584 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
41604 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
41624 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
41644 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
41664 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
41684 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
41704 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
41724 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
41744 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
41764 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
41784 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
41804 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
41824 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
41844 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
41864 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
41884 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
41904 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
41924 GTTGCGATT
1 GTTGCGATT
41933 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:48102 original size:41 final size:41
Alignment explanation
Indices: 48047--48134 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
48037 AAGCAGTCCA
*
48047 AGAA-CCGTACGCCATCCCTGATGTCACATCTCCATCCACC
1 AGAAGCCGTACGCCATCCCTGATATCACATCTCCATCCACC
* *
48087 AGAAGCCGTGCGCCATCCCTGATATCACATCTTCATCCACC
1 AGAAGCCGTACGCCATCCCTGATATCACATCTCCATCCACC
48128 AGAAGCC
1 AGAAGCC
48135 CCATGTGTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.26, C:0.40, G:0.15, T:0.19
Consensus pattern (41 bp):
AGAAGCCGTACGCCATCCCTGATATCACATCTCCATCCACC
Found at i:50152 original size:14 final size:15
Alignment explanation
Indices: 50104--50156 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
50094 TTCGAATTCT
50104 ATGAATTACTGAAAA
1 ATGAATTACTGAAAA
*
50119 ATGAATTACTGAAAT
1 ATGAATTACTGAAAA
*
50134 TTGAATT-CTGAAAA
1 ATGAATTACTGAAAA
50148 ATGAATTAC
1 ATGAATTAC
50157 ATTTCTGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 12 0.36
15 21 0.64
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (15 bp):
ATGAATTACTGAAAA
Found at i:50517 original size:91 final size:87
Alignment explanation
Indices: 50365--50534 Score: 209
Period size: 89 Copynumber: 1.9 Consensus size: 87
50355 TTATTATTTT
* * * *
50365 AAAATATTAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTATTAATAAAAATATTA
1 AAAATATTAAAATAATTTAATTATTATTAAATAATATTGTTATAATTATATTAATAAAAATATT-
*
50430 ATATTGGTATATTTTAGTGAAATA
65 A-ATTAGTATATTTTAGTGAAATA
* *
50454 AAAATATTATAAATTATATTAATTATTTATTAAAGTAATATTGTTAT-ATTATATT-TTAAAAAT
1 AAAATATTA-AAATAAT-TTAATTA-TTATTAAA-TAATATTGTTATAATTATATTAATAAAAAT
50517 ATTAATTAGTATATTTTA
62 ATTAATTAGTATATTTTA
50535 AATATTTGTA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
89 22 0.31
90 7 0.10
91 16 0.23
92 15 0.21
93 10 0.14
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (87 bp):
AAAATATTAAAATAATTTAATTATTATTAAATAATATTGTTATAATTATATTAATAAAAATATTA
ATTAGTATATTTTAGTGAAATA
Found at i:50616 original size:22 final size:21
Alignment explanation
Indices: 50549--50616 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
50539 TTTGTATTAA
*
50549 AATATTATTAGATTATTATAT-T
1 AATATTATT--ATTATTAAATAT
50571 AATATTA-TATATATATATAA-AT
1 AATATTATTAT-TAT-TA-AATAT
50593 AATATTATTCATTATTAAATAT
1 AATATTATT-ATTATTAAATAT
50615 AA
1 AA
50617 AAAAAATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 5 0.13
22 22 0.58
23 4 0.11
24 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (21 bp):
AATATTATTATTATTAAATAT
Found at i:50634 original size:26 final size:26
Alignment explanation
Indices: 50573--50634 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
50563 ATTATATTAA
* * *
50573 TATTATATA-TATATATAAATAATAT
1 TATTATATATTAAATATAAAAAAAAT
50598 TATTCAT-TATTAAATATAAAAAAAAT
1 TATT-ATATATTAAATATAAAAAAAAT
50624 TATTATATATT
1 TATTATATATT
50635 TATTAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTATATATTAAATATAAAAAAAAT
Found at i:50638 original size:30 final size:30
Alignment explanation
Indices: 50603--50676 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
50593 AATATTATTC
*
50603 ATTATTAAATATAAAAAAA-ATTAT-TATAT
1 ATTATTAAATATAAAAAAATAATATGT-TAT
50632 ATTTATTAAA-ATAAAAAAATAATATGTTAT
1 A-TTATTAAATATAAAAAAATAATATGTTAT
50662 ATTATTATAATATAA
1 ATTATTA-AATATAA
50677 TTGATTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 16 0.41
30 18 0.46
31 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
ATTATTAAATATAAAAAAATAATATGTTAT
Found at i:50666 original size:29 final size:28
Alignment explanation
Indices: 50593--50673 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
50583 ATATATAAAT
50593 AATATTAT-TCATTATTAAATATAAAAAAA
1 AATATTATAT-ATTATTAAA-ATAAAAAAA
*
50622 ATTATTATATATTTATTAAAATAAAAAAA
1 AATATTATATA-TTATTAAAATAAAAAAA
*
50651 TAATATGT-TATATTATTATAATA
1 -AATAT-TATATATTATTAAAATA
50674 TAATTGATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
29 27 0.60
30 17 0.38
31 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (28 bp):
AATATTATATATTATTAAAATAAAAAAA
Found at i:50676 original size:23 final size:23
Alignment explanation
Indices: 50650--50697 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
50640 AAATAAAAAA
50650 ATAATATG-TTATATTATTATAAT
1 ATAAT-TGATTATATTATTATAAT
*
50673 ATAATTGATTATTTTATTATAAT
1 ATAATTGATTATATTATTATAAT
50696 AT
1 AT
50698 TAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
ATAATTGATTATATTATTATAAT
Found at i:50715 original size:22 final size:22
Alignment explanation
Indices: 50687--50729 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
50677 TTGATTATTT
50687 TATTATAATATTAAAAATATAA
1 TATTATAATATTAAAAATATAA
* *
50709 TATTATATTATTATAAATATA
1 TATTATAATATTAAAAATATA
50730 TTATAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTATAATATTAAAAATATAA
Found at i:50748 original size:53 final size:53
Alignment explanation
Indices: 50643--50748 Score: 126
Period size: 55 Copynumber: 2.0 Consensus size: 53
50633 TTTATTAAAA
* *
50643 TAAAAAAATAATATGTTATATTATTATAATATAATTGATTATTTTATTATAATAT
1 TAAAAAAATAATA-GTTATATTATTATAATATAATTAAATATTTTA-TATAATAT
* *
50698 TAAAAATATAATA-TTATATTATTATAAATATATTATAAATATTTTA-ATAAT
1 TAAAAAAATAATAGTTATATTATTAT-AATATAAT-TAAATATTTTATATAAT
50749 TAATATTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
53 17 0.38
54 7 0.16
55 21 0.47
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (53 bp):
TAAAAAAATAATAGTTATATTATTATAATATAATTAAATATTTTATATAATAT
Found at i:51008 original size:42 final size:42
Alignment explanation
Indices: 50952--51046 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
50942 TTCCTCTAAC
* * *
50952 CAAACACTGGAAAACATTTTTCGGAAAACGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
50994 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
1 CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
51036 CAAACACGGGA
1 CAAACACGGGA
51047 TTTCGGGGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.17
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAAA
Found at i:51535 original size:20 final size:19
Alignment explanation
Indices: 51489--51536 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
51479 AGTGTGACTA
* *
51489 TATATTAAATATCAAATCT
1 TATATTAAAAATCAAATAT
*
51508 TATGATTAAGAAATGAAATAT
1 TAT-ATTAA-AAATCAAATAT
51529 TATATTAA
1 TATATTAA
51537 TATTATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (19 bp):
TATATTAAAAATCAAATAT
Found at i:53148 original size:30 final size:31
Alignment explanation
Indices: 53089--53154 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
53079 GTTAATTTCT
* ** *
53089 AATTTAATTCTTAAATTTTCAATAAAATATC
1 AATTTAATTCTTAAATGTGAAATAAAATATA
*
53120 AATTTAA-TCTTAAATGTGAAATATAATATA
1 AATTTAATTCTTAAATGTGAAATAAAATATA
53150 AATTT
1 AATTT
53155 GATCCCATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (31 bp):
AATTTAATTCTTAAATGTGAAATAAAATATA
Found at i:53504 original size:21 final size:21
Alignment explanation
Indices: 53480--53519 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53470 GCAATACAGG
53480 TTCCAAATTCGCAACGCGATT
1 TTCCAAATTCGCAACGCGATT
*
53501 TTCCAAATTTGCAACGCGA
1 TTCCAAATTCGCAACGCGA
53520 ATATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCCAAATTCGCAACGCGATT
Found at i:53668 original size:22 final size:23
Alignment explanation
Indices: 53643--53693 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
53633 TCACTCTCTA
* * *
53643 CGGCGACATTC-GTCCCCATCTC
1 CGGCGACAATCAGTCCACATATC
53665 CGGCGA-AATCAGTCCACATATC
1 CGGCGACAATCAGTCCACATATC
53687 CGGCGAC
1 CGGCGAC
53694 CCACTCTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.22, C:0.39, G:0.22, T:0.18
Consensus pattern (23 bp):
CGGCGACAATCAGTCCACATATC
Found at i:54095 original size:23 final size:20
Alignment explanation
Indices: 54034--54101 Score: 91
Period size: 20 Copynumber: 3.2 Consensus size: 20
54024 TTTGAAACTT
*
54034 AAATTCGCAACACGAAAATG
1 AAATTCGCAACGCGAAAATG
*
54054 AAAATCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
54074 AAATTCGCAACGTTGCGAAAATG
1 AAATTCGCAAC---GCGAAAATG
54097 AAATT
1 AAATT
54102 TGCGTTGCGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.67
23 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:54109 original size:20 final size:21
Alignment explanation
Indices: 54065--54111 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
54055 AAATCGCAAC
54065 GCGAAAATGAAATTCGCAACGTT
1 GCGAAAATGAAATTCG--ACGTT
*
54088 GCGAAAATGAAATTTG-CGTT
1 GCGAAAATGAAATTCGACGTT
54108 GCGA
1 GCGA
54112 TTTTCATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
23 15 0.65
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (21 bp):
GCGAAAATGAAATTCGACGTT
Found at i:55768 original size:21 final size:21
Alignment explanation
Indices: 55741--55790 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
55731 GTTAGGGGAG
*
55741 TTACGTGATGAGGTCAATACT
1 TTACGTGAGGAGGTCAATACT
* *
55762 TTGCGTGAGGAGGTCAGTACT
1 TTACGTGAGGAGGTCAATACT
55783 TTACGTGA
1 TTACGTGA
55791 CGACAATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:55831 original size:21 final size:23
Alignment explanation
Indices: 55807--55904 Score: 77
Period size: 21 Copynumber: 4.6 Consensus size: 23
55797 TGGTGCATGG
55807 CGTGATGAGGTA-CGGT-CTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* *
55828 CGTGGTGAGGTAGAGGT--TTTA
1 CGTGATGAGGTAGCGGTACTTTA
* **
55849 CGCGATGA--TAATGGTACTTTA
1 CGTGATGAGGTAGCGGTACTTTA
* *
55870 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTAGCGGTACTTTA
55891 CGTGATGAGGTAGC
1 CGTGATGAGGTAGC
55905 CACTCTACGT
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.08
21 50 0.83
22 3 0.05
23 2 0.03
ACGTcount: A:0.21, C:0.12, G:0.34, T:0.33
Consensus pattern (23 bp):
CGTGATGAGGTAGCGGTACTTTA
Found at i:55913 original size:21 final size:21
Alignment explanation
Indices: 55868--55916 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
55858 AATGGTACTT
* * * *
55868 TACGTGGTGAGGTATCTACTT
1 TACGTGATGAGGTAGCCACTC
55889 TACGTGATGAGGTAGCCACTC
1 TACGTGATGAGGTAGCCACTC
55910 TACGTGA
1 TACGTGA
55917 GATTATTGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (21 bp):
TACGTGATGAGGTAGCCACTC
Found at i:56230 original size:21 final size:21
Alignment explanation
Indices: 56198--56298 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
56188 AATTCACCTG
* *
56198 TCATCATTCAAGAGGTCTCTA
1 TCATCGTTCAAGAGGTCCCTA
56219 -CTATCGTTCAAGAGG-CCCTTA
1 TC-ATCGTTCAAGAGGTCCC-TA
* * *
56240 TCATCCTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGTCCCTA
* * *
56261 CCACCGTTCAAAAGGTCCCTA
1 TCATCGTTCAAGAGGTCCCTA
56282 TCATCGTTCAAGAGGTC
1 TCATCGTTCAAGAGGTC
56299 ACTCCCACTG
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.05
21 56 0.89
22 4 0.06
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.27
Consensus pattern (21 bp):
TCATCGTTCAAGAGGTCCCTA
Found at i:56244 original size:42 final size:42
Alignment explanation
Indices: 56198--56313 Score: 117
Period size: 42 Copynumber: 2.8 Consensus size: 42
56188 AATTCACCTG
* * * *
56198 TCATCATTCAAGAGGTCTCTACTATCGTTCAAGAGG-CCCTTA
1 TCATCATTCAAGAGGTCCCTACCACCGTTCAAAAGGTCCC-TA
* * *
56240 TCATCCTTCAAGAGGCCCCTCCCACCGTTCAAAAGGTCCCTA
1 TCATCATTCAAGAGGTCCCTACCACCGTTCAAAAGGTCCCTA
* * * *
56282 TCATCGTTCAAGAGGTCACTCCCACTGTTCAA
1 TCATCATTCAAGAGGTCCCTACCACCGTTCAA
56314 GAGCCCGATT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
42 59 0.95
43 3 0.05
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.27
Consensus pattern (42 bp):
TCATCATTCAAGAGGTCCCTACCACCGTTCAAAAGGTCCCTA
Found at i:56311 original size:21 final size:21
Alignment explanation
Indices: 56246--56316 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
56236 CTTATCATCC
* *
56246 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGTCCCTCCCACTG
* **
56267 TTCAAAAGGTCCCTATCA-TCG
1 TTCAAGAGGTCCCTCCCACT-G
*
56288 TTCAAGAGGTCACTCCCACTG
1 TTCAAGAGGTCCCTCCCACTG
56309 TTCAAGAG
1 TTCAAGAG
56317 CCCGATTCAC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGTCCCTCCCACTG
Found at i:58224 original size:15 final size:15
Alignment explanation
Indices: 58204--58252 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
58194 CCGACCCGAC
58204 CCGTTGACCTGTTGA
1 CCGTTGACCTGTTGA
**
58219 CCGTTGACCCATTGA
1 CCGTTGACCTGTTGA
58234 CCGTTGACCGGTGTTGA
1 CCGTTGACC--TGTTGA
58251 CC
1 CC
58253 ACTGTTGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 22 0.79
17 6 0.21
ACGTcount: A:0.14, C:0.31, G:0.27, T:0.29
Consensus pattern (15 bp):
CCGTTGACCTGTTGA
Found at i:58226 original size:7 final size:7
Alignment explanation
Indices: 58204--58243 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
58194 CCGACCCGAC
58204 CCGTTGA
1 CCGTTGA
58211 CCTGTTGA
1 CC-GTTGA
58219 CCGTTGA
1 CCGTTGA
*
58226 CCCATTGA
1 -CCGTTGA
58234 CCGTTGA
1 CCGTTGA
58241 CCG
1 CCG
58244 GTGTTGACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.15, C:0.33, G:0.25, T:0.28
Consensus pattern (7 bp):
CCGTTGA
Found at i:60781 original size:12 final size:12
Alignment explanation
Indices: 60744--60806 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
60734 ATCTGATACT
60744 TGACATGGATTC
1 TGACATGGATTC
60756 TGATC-T-GATATC
1 TGA-CATGGAT-TC
60768 TGACATGGATTC
1 TGACATGGATTC
* *
60780 TGATAT-GATAC
1 TGACATGGATTC
*
60791 TTGACTTGGATTC
1 -TGACATGGATTC
60804 TGA
1 TGA
60807 TATGTTACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
11 8 0.20
12 24 0.60
13 8 0.20
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:60850 original size:24 final size:24
Alignment explanation
Indices: 60732--60843 Score: 147
Period size: 24 Copynumber: 4.7 Consensus size: 24
60722 ATTTGAATTA
*
60732 TGATCTGATACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTC
*
60756 TGATCTGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTC
*
60780 TGATATGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTC
* *
60804 TGATATGTTACTTGACCT-GATTTC
1 TGATATGATACTTGACATGGA-TTC
60828 TGATATGATACTTGAC
1 TGATATGATACTTGAC
60844 CTGATTTATA
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
23 3 0.04
24 76 0.95
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:61033 original size:2 final size:2
Alignment explanation
Indices: 61026--61050 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61016 GGGATGGGGG
61026 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
61051 GTTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62014 original size:20 final size:20
Alignment explanation
Indices: 61991--62040 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
61981 GAAAGTCAAA
*
61991 TTCGCGTTGCGATTTTGACT
1 TTCGCGTTACGATTTTGACT
*
62011 TTCGTGTTACGATTTTGACT
1 TTCGCGTTACGATTTTGACT
62031 TTCGCGTTAC
1 TTCGCGTTAC
62041 AAATTTGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (20 bp):
TTCGCGTTACGATTTTGACT
Found at i:62047 original size:20 final size:20
Alignment explanation
Indices: 62004--62052 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
61994 GCGTTGCGAT
* * *
62004 TTTGACTTTCGTGTTACGAT
1 TTTGACTTTCGCGTTACAAA
62024 TTTGACTTTCGCGTTACAAA
1 TTTGACTTTCGCGTTACAAA
*
62044 TTTGTCTTT
1 TTTGACTTT
62053 TGCAACAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (20 bp):
TTTGACTTTCGCGTTACAAA
Found at i:62180 original size:16 final size:15
Alignment explanation
Indices: 62150--62184 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
62140 TGTAAATAAG
*
62150 AATTGTTTTTTGTTT
1 AATTGTTTGTTGTTT
62165 AATTGATTTGTTGTTT
1 AATTG-TTTGTTGTTT
62181 AATT
1 AATT
62185 TCACTCTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (15 bp):
AATTGTTTGTTGTTT
Found at i:62256 original size:20 final size:20
Alignment explanation
Indices: 62231--62325 Score: 118
Period size: 20 Copynumber: 4.8 Consensus size: 20
62221 AGGTACACTT
*
62231 TCGCAACGCGGAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
62251 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* * * *
62271 TTGCAACACGAAAGTCTACA
1 TCGCAACGCGAAAGTCAAAA
*
62291 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAA
* *
62311 TCGTAATGCGAAAGT
1 TCGCAACGCGAAAGT
62326 TAAATTCGAG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:62371 original size:20 final size:20
Alignment explanation
Indices: 62343--62475 Score: 176
Period size: 20 Copynumber: 6.7 Consensus size: 20
62333 GAGTTGCGAT
*
62343 TTTCGCGTTGTGATTTTGAC
1 TTTCGCGTTGCGATTTTGAC
* * *
62363 TTTCACGTTACGAATTTGAC
1 TTTCGCGTTGCGATTTTGAC
* * *
62383 TTTCGCATAGCGAATTTGAC
1 TTTCGCGTTGCGATTTTGAC
*
62403 TTTCGCGTTGCGGTTTTGAC
1 TTTCGCGTTGCGATTTTGAC
*
62423 TTTCGCGTTGCGGTTTTGAC
1 TTTCGCGTTGCGATTTTGAC
*
62443 TTTCGCATTGCGATTTTGAC
1 TTTCGCGTTGCGATTTTGAC
62463 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
62476 AAGTGTACCT
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 98 1.00
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTGAC
Found at i:62441 original size:60 final size:60
Alignment explanation
Indices: 62343--62475 Score: 194
Period size: 60 Copynumber: 2.2 Consensus size: 60
62333 GAGTTGCGAT
*
62343 TTTCGCGTTGTGATTTTGACTTTCACGTTACGAATTTGACTTTCGCATAGCGAATTTGAC
1 TTTCGCGTTGCGATTTTGACTTTCACGTTACGAATTTGACTTTCGCATAGCGAATTTGAC
* * * ** * *
62403 TTTCGCGTTGCGGTTTTGACTTTCGCGTTGCGGTTTTGACTTTCGCATTGCGATTTTGAC
1 TTTCGCGTTGCGATTTTGACTTTCACGTTACGAATTTGACTTTCGCATAGCGAATTTGAC
62463 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
62476 AAGTGTACCT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.43
Consensus pattern (60 bp):
TTTCGCGTTGCGATTTTGACTTTCACGTTACGAATTTGACTTTCGCATAGCGAATTTGAC
Found at i:62803 original size:18 final size:18
Alignment explanation
Indices: 62780--62815 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
62770 AAGTCGGTTG
*
62780 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
62798 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
62816 CCTTTTGCTT
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:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:65113 original size:24 final size:24
Alignment explanation
Indices: 65079--65132 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
65069 CTGAAACATC
65079 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
65103 ATCAAAGTCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
65127 ATCAAA
1 ATCAAA
65133 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:65146 original size:24 final size:24
Alignment explanation
Indices: 65079--65148 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
65069 CTGAAACATC
* * *
65079 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* * *
65103 ATCAAAGTCCGAGTATTGACCAAT
1 ATCAAAGTCCGAATACTGACCAAG
* *
65127 ATCAAATTTCGAATACTGACCA
1 ATCAAAGTCCGAATACTGACCA
65149 GTACTCACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:65906 original size:16 final size:16
Alignment explanation
Indices: 65884--65923 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
65874 GAAATCATTG
*
65884 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
65900 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
65916 AAAAATTA
1 AAAAATTA
65924 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:66224 original size:20 final size:20
Alignment explanation
Indices: 66176--66311 Score: 109
Period size: 20 Copynumber: 6.8 Consensus size: 20
66166 TGAAAAATAA
** *
66176 ATTCGCGTTGCGATTTTGAA
1 ATTCGCGTTGCGATTTACAT
* *
66196 AATCACGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACAT
** *
66216 ATTATCGTTGCGATTTACCT
1 ATTCGCGTTGCGATTTACAT
66236 ATTCGCGTTGCGATTTTGAC-T
1 ATTCGCGTTGCGA-TTT-ACAT
*
66257 -TTCGCGTTGCGATTTAGAT
1 ATTCGCGTTGCGATTTACAT
**
66276 ATTATCGTTGTC-ATTTA-ACT
1 ATTCGCGTTG-CGATTTACA-T
66296 ATTCGCGTTGCGATTT
1 ATTCGCGTTGCGATTT
66312 TGGAACCTGT
Statistics
Matches: 93, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.01
19 6 0.06
20 79 0.85
21 5 0.05
22 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.43
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACAT
Found at i:66240 original size:60 final size:60
Alignment explanation
Indices: 66176--66313 Score: 206
Period size: 60 Copynumber: 2.3 Consensus size: 60
66166 TGAAAAATAA
*
66176 ATTCGCGTTGCGATTTTGAAAATCACGTTGCGATTTACATATTATCGTTG-CGATTTACCT
1 ATTCGCGTTGCGATTTTGAAAATCACGTTGCGATTTACATATTATCGTTGTC-ATTTAACT
*** * *
66236 ATTCGCGTTGCGATTTTGACTTTCGCGTTGCGATTTAGATATTATCGTTGTCATTTAACT
1 ATTCGCGTTGCGATTTTGAAAATCACGTTGCGATTTACATATTATCGTTGTCATTTAACT
66296 ATTCGCGTTGCGATTTTG
1 ATTCGCGTTGCGATTTTG
66314 GAACCTGTGT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
60 70 0.99
61 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (60 bp):
ATTCGCGTTGCGATTTTGAAAATCACGTTGCGATTTACATATTATCGTTGTCATTTAACT
Done.