Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003479.1 Hibiscus syriacus cultivar Beakdansim tig00007353_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: 77526
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5938 original size:30 final size:30
Alignment explanation
Indices: 5899--5964 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
5889 TTGATTGATT
*
5899 TTTGTCTATAAATTAATTATCAAATTGTTA
1 TTTGCCTATAAATTAATTATCAAATTGTTA
**
5929 TTTGCCTATAAATTGCTTATCAAATTGTTA
1 TTTGCCTATAAATTAATTATCAAATTGTTA
5959 TTTGCC
1 TTTGCC
5965 ATGGACTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (30 bp):
TTTGCCTATAAATTAATTATCAAATTGTTA
Found at i:8344 original size:21 final size:23
Alignment explanation
Indices: 8302--8349 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
8292 ATTTATCTTT
8302 TAAATTTTATAAAAAAATATATA
1 TAAATTTTATAAAAAAATATATA
*
8325 TAAATTTTATTAAAAAATATATA
1 TAAATTTTATAAAAAAATATATA
8348 TA
1 TA
8350 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATTTTATAAAAAAATATATA
Found at i:8924 original size:2 final size:2
Alignment explanation
Indices: 8917--8942 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8907 CTTTAGTTTA
8917 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8943 TAATAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9410 original size:61 final size:61
Alignment explanation
Indices: 9330--9471 Score: 178
Period size: 61 Copynumber: 2.3 Consensus size: 61
9320 ATGTTCTTAT
* * * *
9330 TTAATTAAATCAATTAATAATTGATCCTAATAAGTTTAACTTA-TTCTAATTAGATCTTTAA
1 TTAATTAAATTAATTAATAATTGAGCCTAATAAATTTAACTTATTTC-AATTAGATCATTAA
* * ** * *
9391 TTAGTTTAATTAATTAATAATTGAGCCTAATAAATTTAGTTTCTTTCAATTAGATCATTAT
1 TTAATTAAATTAATTAATAATTGAGCCTAATAAATTTAACTTATTTCAATTAGATCATTAA
9452 TTAATTAAATTAATTAATAA
1 TTAATTAAATTAATTAATAA
9472 GTTTAGCTTC
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
61 65 0.96
62 3 0.04
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (61 bp):
TTAATTAAATTAATTAATAATTGAGCCTAATAAATTTAACTTATTTCAATTAGATCATTAA
Found at i:9470 original size:109 final size:108
Alignment explanation
Indices: 9357--9574 Score: 267
Period size: 109 Copynumber: 2.0 Consensus size: 108
9347 TAATTGATCC
** * *
9357 TAATAAGTTTAACTTATTCTAATTAGATCTTTAATTAGTTTAATTAATTAATAATTGAGCCTAAT
1 TAATAAGTTTAACTTATTCTAATTAGATCCCTAATTAGTTAAATTAAATAATAATTGAG-CTAAT
**
9422 AAATTTAGTTTCTTTCAATTAGATCATT-ATTTAATTAAATTAAT
65 AAATTTAACTTCTTTCAATTAGATCATTGA-TTAATTAAATTAAT
* * * * * *
9466 TAATAAGTTTAGCTTCTTTTAGTTAGGTCCCTAATTAGTTAAATTAAATATTAATTGAGCTAATA
1 TAATAAGTTTAACTTATTCTAATTAGATCCCTAATTAGTTAAATTAAATAATAATTGAGCTAATA
* * * *
9531 AGTTTAACTTCTTTCAATTAGGTCCTTGATTAGTTAAATTAAT
66 AATTTAACTTCTTTCAATTAGATCATTGATTAATTAAATTAAT
9574 T
1 T
9575 GATAGTTGAG
Statistics
Matches: 92, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
108 42 0.46
109 50 0.54
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (108 bp):
TAATAAGTTTAACTTATTCTAATTAGATCCCTAATTAGTTAAATTAAATAATAATTGAGCTAATA
AATTTAACTTCTTTCAATTAGATCATTGATTAATTAAATTAAT
Found at i:9614 original size:61 final size:60
Alignment explanation
Indices: 9466--9683 Score: 244
Period size: 61 Copynumber: 3.6 Consensus size: 60
9456 TTAAATTAAT
* * * *
9466 TAATAAGTTTAGCTTCTTT-TAGTTAGGTCCCTAATTAGTTAAATTAAAT-ATTAATTGAG-C
1 TAATAAGTTTAACTTCTTTCGA-TTAGGTCCTTAATTAGTTAAATTAATTGA-T-ATTGAGCC
* *
9526 TAATAAGTTTAACTTCTTTCAATTAGGTCCTTGATTAGTTAAATTAATTGATAGTTGAGCC
1 TAATAAGTTTAACTTCTTTCGATTAGGTCCTTAATTAGTTAAATTAATTGATA-TTGAGCC
** * * *
9587 TAATAAGTTTAACTTCTTTCGATTAGGTTTTTAATTAATTAAATTAATCGATATTCGAGCA
1 TAATAAGTTTAACTTCTTTCGATTAGGTCCTTAATTAGTTAAATTAATTGATATT-GAGCC
* * *
9648 TAATAAGTTTACCTTCTTTCGATTAGGCCCTAAATT
1 TAATAAGTTTAACTTCTTTCGATTAGGTCCTTAATT
9684 TAAGCATGTT
Statistics
Matches: 136, Mismatches: 17, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
59 1 0.01
60 50 0.37
61 85 0.62
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (60 bp):
TAATAAGTTTAACTTCTTTCGATTAGGTCCTTAATTAGTTAAATTAATTGATATTGAGCC
Found at i:12423 original size:20 final size:20
Alignment explanation
Indices: 12398--12452 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
12388 GGCCATTCGA
12398 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
12418 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
12438 CCGAGGCCATTCGAA
1 CCGAGGCCATCCGAA
12453 CGAGCTATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.35, G:0.27, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:12442 original size:10 final size:10
Alignment explanation
Indices: 12405--12442 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
12395 CGACCGAGGC
*
12405 CATCCGAAAG
1 CATCCGAGAG
12415 CATCCGAG-G
1 CATCCGAGAG
12424 CCATCCGAGAG
1 -CATCCGAGAG
12435 CATCCGAG
1 CATCCGAG
12443 GCCATTCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 1 0.04
10 23 0.92
11 1 0.04
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (10 bp):
CATCCGAGAG
Found at i:12583 original size:29 final size:30
Alignment explanation
Indices: 12534--12602 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
12524 CGGAGTGCAT
*
12534 GGCGACCTACGTAGGTCGCCATGTACTCCG
1 GGCGACCTACGTAGGTCGCCATGCACTCCG
*
12564 GGCGACCT-TGTAGGTCGCCATGCACTCCG
1 GGCGACCTACGTAGGTCGCCATGCACTCCG
12593 GGCGACCTAC
1 GGCGACCTAC
12603 CCTCGCTCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 27 0.77
30 8 0.23
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.19
Consensus pattern (30 bp):
GGCGACCTACGTAGGTCGCCATGCACTCCG
Found at i:12645 original size:33 final size:33
Alignment explanation
Indices: 12604--12692 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
12594 GCGACCTACC
* * *
12604 CTCGCTCGGTTGCCCTTGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
12637 CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
* * *
12670 CTCGTTCGGATGGCCTCGGATGC
1 CTCGCTCGGTTGCCCTCGGATGC
12693 TCTCGGATGG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.10, C:0.36, G:0.27, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCACATAG
Found at i:14707 original size:20 final size:19
Alignment explanation
Indices: 14684--14731 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
14674 ATCCAATTTC
14684 GCAACACAATTTCCGAATTA
1 GCAACACAATTT-CGAATTA
* * *
14704 GCAACTCAAATTTGGAATTC
1 GCAACAC-AATTTCGAATTA
14724 GCAACACA
1 GCAACACA
14732 GAAGTTGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.74
21 5 0.22
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (19 bp):
GCAACACAATTTCGAATTA
Found at i:14791 original size:22 final size:22
Alignment explanation
Indices: 14763--14821 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 22
14753 ACATGGAAAT
14763 TTTCGCAACTCGAATTC-CACAA
1 TTTCGCAACTCGAATTCGC-CAA
14785 TTTCGCAACTCGAATTCGCCAA
1 TTTCGCAACTCGAATTCGCCAA
14807 TTTCGCAACTC-AATT
1 TTTCGCAACTCGAATT
14822 ACCGATATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.11
22 31 0.86
23 1 0.03
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (22 bp):
TTTCGCAACTCGAATTCGCCAA
Found at i:15032 original size:120 final size:118
Alignment explanation
Indices: 14795--15036 Score: 358
Period size: 120 Copynumber: 2.0 Consensus size: 118
14785 TTTCGCAACT
* *
14795 CGAATTCGCCAATTTCGCAACTCAATTACCGATATAGGTAAACACAGTAAAAAAATCTGGTAAAA
1 CGAATTCGCCAATTTCGCAACTCAATTACCGATATAGGTAAACACAGTAAAAAAATCCGATAAAA
* *
14860 ATCTAAATTCGCCAATTTGAAAACTGAGTTGCGAATTTGACAAATTCATGTTG
66 ATCCAAATTCGCCAATTTAAAAACTGAGTTGCGAATTTGACAAATTCATGTTG
* * * *
14913 CGAATTTGACCAATTTCGCAACTCAATTACCGATATAGGTAAACACGGTAGAACAATCCGATAAA
1 CGAATTCG-CCAATTTCGCAACTCAATTACCGATATAGGTAAACACAGTAAAAAAATCCGAT-AA
* * * *
14978 AAATCCGAATTCGCCAATTTAAAAATTGAGTTGCGAATTTGGCAAATTCGTGTTG
64 AAATCCAAATTCGCCAATTTAAAAACTGAGTTGCGAATTTGACAAATTCATGTTG
15033 CGAA
1 CGAA
15037 ATGTAAAATC
Statistics
Matches: 110, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
118 7 0.06
119 48 0.44
120 55 0.50
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (118 bp):
CGAATTCGCCAATTTCGCAACTCAATTACCGATATAGGTAAACACAGTAAAAAAATCCGATAAAA
ATCCAAATTCGCCAATTTAAAAACTGAGTTGCGAATTTGACAAATTCATGTTG
Found at i:17333 original size:25 final size:25
Alignment explanation
Indices: 17299--17347 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
17289 TTCAAGATTG
17299 AGTTGTAATACTCAAAGACCTTATC
1 AGTTGTAATACTCAAAGACCTTATC
17324 AGTTGTAATACTCAAAGACCTTAT
1 AGTTGTAATACTCAAAGACCTTAT
17348 TCAAGATTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (25 bp):
AGTTGTAATACTCAAAGACCTTATC
Found at i:18236 original size:20 final size:20
Alignment explanation
Indices: 18161--18232 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
18151 TGGTTCACGA
*
18161 AATATAAGATTACCAGTGGG
1 AATAAAAGATTACCAGTGGG
18181 AATAAAAGATTACCAGTGGG
1 AATAAAAGATTACCAGTGGG
* *
18201 AATAAAAGATTATCAGTGAG
1 AATAAAAGATTACCAGTGGG
18221 AATAAAAGATTA
1 AATAAAAGATTA
18233 TCAGGGAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.24
Consensus pattern (20 bp):
AATAAAAGATTACCAGTGGG
Found at i:23149 original size:22 final size:22
Alignment explanation
Indices: 23124--23488 Score: 563
Period size: 22 Copynumber: 16.6 Consensus size: 22
23114 ATAATAAATT
*
23124 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
23146 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
23168 TTTTAAAATAAATCAAT-CATA
1 TTTTAAAATAAATCAATCCATA
23189 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
23211 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
23233 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
23255 TTTTAAAATAATTCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
23277 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
23299 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
* *
23321 TTTTAAAATAAATCAATCTATTT
1 TTTTAAAATAAATCAATCCA-TA
23344 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
23366 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
23388 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
23410 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
23432 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *
23454 TTTTAAGATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
23476 TTTTAAAATAAAT
1 TTTTAAAATAAAT
23489 TCTAAAATAG
Statistics
Matches: 315, Mismatches: 24, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
21 25 0.08
22 267 0.85
23 23 0.07
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:25979 original size:2 final size:2
Alignment explanation
Indices: 25974--25999 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25964 TAAAATTTTA
25974 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
26000 TTAAATTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30188 original size:17 final size:18
Alignment explanation
Indices: 30162--30204 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30152 TATTATTGTA
*
30162 TAATTGAAT-ATAAAATT
1 TAATTGAATAAAAAAATT
*
30179 TAATTTAATAAAAAAATT
1 TAATTGAATAAAAAAATT
*
30197 TATTTGAA
1 TAATTGAA
30205 GACATGAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TAATTGAATAAAAAAATT
Found at i:30977 original size:2 final size:2
Alignment explanation
Indices: 30970--31010 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30960 TTCCATTTTA
30970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31011 AGATCTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31401 original size:190 final size:189
Alignment explanation
Indices: 31168--31509 Score: 612
Period size: 190 Copynumber: 1.8 Consensus size: 189
31158 TTTAACGGTT
* **
31168 CTAAATATGTGTAAAATTAAAAACTTTTACATTATATAAGTGGATCATAACCGTAAAAAAACTCT
1 CTAAATATGTGTAAAACTAAAAAAATTTACATTATATAAGTGGATCATAACCGTAAAAAAACTCT
*
31233 TAGCTTTACACATATTTAAAATCATTAGATGAGTGAAAATAGATGACTGAGATTAAAAATAAGAA
66 TAGCTTTACACATATTTAAAATCATTAGATGAGTAAAAATAGATGACTGAGATTAAAAATAAGAA
31298 TTATGAATATATTTACTGAAAAAAACGAAAGTTTAGATGACTAGACATCTATTTTCACTC
131 TTATGAATATATTTACT-AAAAAAACGAAAGTTTAGATGACTAGACATCTATTTTCACTC
* *
31358 CTAAATATGTGTAAAACTAAAAAAATTTACATTGTATAAGTGGATCGTAACCGTAAAAAAACTCT
1 CTAAATATGTGTAAAACTAAAAAAATTTACATTATATAAGTGGATCATAACCGTAAAAAAACTCT
*
31423 TAGCTTTACACATATTTAAAATCATTAGATGAGTAAAAATAGATTACTGAGATTAAAAATAAGAA
66 TAGCTTTACACATATTTAAAATCATTAGATGAGTAAAAATAGATGACTGAGATTAAAAATAAGAA
31488 TTATGAATATATTTACTAAAAA
131 TTATGAATATATTTACTAAAAA
31510 CAGATGATTA
Statistics
Matches: 145, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
189 5 0.03
190 140 0.97
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (189 bp):
CTAAATATGTGTAAAACTAAAAAAATTTACATTATATAAGTGGATCATAACCGTAAAAAAACTCT
TAGCTTTACACATATTTAAAATCATTAGATGAGTAAAAATAGATGACTGAGATTAAAAATAAGAA
TTATGAATATATTTACTAAAAAAACGAAAGTTTAGATGACTAGACATCTATTTTCACTC
Found at i:31568 original size:22 final size:23
Alignment explanation
Indices: 31543--31589 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
31533 TTGATAGTTT
* *
31543 ATATATTCAGTAAATA-AGATGA
1 ATATATTCACTAAAAACAGATGA
*
31565 ATATATTTACTAAAAACAGATGA
1 ATATATTCACTAAAAACAGATGA
31588 AT
1 AT
31590 GAGTAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (23 bp):
ATATATTCACTAAAAACAGATGA
Found at i:32302 original size:2 final size:2
Alignment explanation
Indices: 32297--32338 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
32287 ACACACACAC
32297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32339 GAGATCATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33186 original size:5 final size:5
Alignment explanation
Indices: 33172--33225 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
33162 GTCCGTCCGT
* * * *
33172 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
33222 CTCG
1 CTCG
33226 AGGTCGAGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:33234 original size:6 final size:6
Alignment explanation
Indices: 33227--33295 Score: 120
Period size: 6 Copynumber: 11.5 Consensus size: 6
33217 CTCGGCTCGA
* *
33227 GGTCGA GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
33275 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
33296 AATACGTGTC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.03, C:0.16, G:0.51, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:38538 original size:5 final size:5
Alignment explanation
Indices: 38524--38567 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
38514 GTCCGTCCGT
* * * *
38524 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
38568 AGGTCGAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:38616 original size:18 final size:18
Alignment explanation
Indices: 38565--38619 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
38555 TCGGCTCGGC
*
38565 TCGAGGTCGAGGTCGAGG
1 TCGAGGTCGAGGTCGTGG
38583 TCGAGGTCGAGGTCGTGG
1 TCGAGGTCGAGGTCGTGG
* *
38601 TCGTGGTCGTGGTCGTGG
1 TCGAGGTCGAGGTCGTGG
38619 T
1 T
38620 AATACGTGTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.09, C:0.16, G:0.49, T:0.25
Consensus pattern (18 bp):
TCGAGGTCGAGGTCGTGG
Found at i:38619 original size:6 final size:6
Alignment explanation
Indices: 38565--38615 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
38555 TCGGCTCGGC
* * *
38565 TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG
38613 TCG
1 TCG
38616 TGGTAATACG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.10, C:0.18, G:0.49, T:0.24
Consensus pattern (6 bp):
TCGAGG
Found at i:38919 original size:22 final size:22
Alignment explanation
Indices: 38894--38948 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
38884 TCAGGAGTTA
* *
38894 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
38916 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
38938 CGGGAGTTATA
1 CAGGAGTTATA
38949 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:48173 original size:43 final size:43
Alignment explanation
Indices: 48103--48365 Score: 271
Period size: 43 Copynumber: 6.1 Consensus size: 43
48093 TGAGAACAAA
* * ** * *
48103 AAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTCTAGAAAA
1 AAACGCCGCAAAAGGTCA-GACCTATAGCGGCGTTTTTAGAAAC
* * *
48147 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGAAAC
* * *
48190 AAACGCCGCAAAAGATAAGACCTATA-CTGGCATTTTTAG-AAC
1 AAACGCCGCAAAAGGTCAGACCTATAGC-GGCGTTTTTAGAAAC
* * * *
48232 AAACGCCGTAAAAGGTCAGACCTATAGTGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGAAAC
* * *
48275 AAATGCCGCAAAATGTCAGACCTATAACGGCGTTTTT-GAACAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGAA-AC
* * * *
48318 AAACGCCGCAAAAAGTCAGACATATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGAAAC
48361 AAACG
1 AAACG
48366 ACGCTAATTA
Statistics
Matches: 183, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
42 37 0.20
43 128 0.70
44 18 0.10
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGAAAC
Found at i:48245 original size:85 final size:85
Alignment explanation
Indices: 48147--48365 Score: 284
Period size: 85 Copynumber: 2.6 Consensus size: 85
48137 TTCTAGAAAA
*
48147 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAA-GATAAGAC
1 AAACGCCGCAAAAGGTCAGA-CTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATG-TAAGAC
48211 CTAT-ACTGGCATTTTT-AGA-AC
64 CTATAAC-GGCATTTTTGA-ACAC
* * * * *
48232 AAACGCCGTAAAAGGTCAGACCTATAGTGGCGTTTTTGGACACAAATGCCGCAAAATGTCAGACC
1 AAACGCCGCAAAAGGTCAGA-CTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATGTAAGACC
*
48297 TATAACGGCGTTTTTGAACAC
65 TATAACGGCATTTTTGAACAC
*
48318 AAACGCCGCAAAAAGTCAGACATATAGCGGCGTTTTTGGATACAAACG
1 AAACGCCGCAAAAGGTCAGAC-TATAGCGGCGTTTTTGGATACAAACG
48366 ACGCTAATTA
Statistics
Matches: 116, Mismatches: 13, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
85 69 0.59
86 47 0.41
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (85 bp):
AAACGCCGCAAAAGGTCAGACTATAGCGGCGTTTTTGGATACAAACGCCGCAAAATGTAAGACCT
ATAACGGCATTTTTGAACAC
Found at i:51121 original size:142 final size:142
Alignment explanation
Indices: 50858--51125 Score: 335
Period size: 142 Copynumber: 1.9 Consensus size: 142
50848 GATCTATGAT
*
50858 TGTCAAAAGGTAGAATCACCAACCATTCATGCTTAAAAAACATGCTTTTTTATCTAAGACAAATC
1 TGTCAAAAGGTAGAATCACCAACCATTCATGCTTAAAAAACATGCTTTTTTATCCAAGACAAATC
* * ** *
50923 GATATATGTTCATTTATATGTCCATCACTACAACAAAATAAAAAATTGTGGTGACCATATCAGAT
66 AATATATATTCATTTATAAATCCATCACTACAACAAAATAAAAAATTGAGGTGACCATATCAGAT
50988 TATTTTTCTCCA
131 TATTTTTCTCCA
* * * * * * *
51000 TGTCAAAAGGTAGCATTATCAACCATTCTTGCTTAAAACACATG-TTTTTTCTCCAAGGCAAATC
1 TGTCAAAAGGTAGAATCACCAACCATTCATGCTTAAAAAACATGCTTTTTTATCCAAGACAAATC
* ***
51064 AATATCATATT-GTTTATAAATCCATCACTAACAACAAAATTGGAAATTGCAGG-GACCATATC
66 AATAT-ATATTCATTTATAAATCCATCACT-ACAACAAAATAAAAAATTG-AGGTGACCATATC
51126 GAGTATAGAA
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
141 36 0.34
142 68 0.64
143 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (142 bp):
TGTCAAAAGGTAGAATCACCAACCATTCATGCTTAAAAAACATGCTTTTTTATCCAAGACAAATC
AATATATATTCATTTATAAATCCATCACTACAACAAAATAAAAAATTGAGGTGACCATATCAGAT
TATTTTTCTCCA
Found at i:51932 original size:41 final size:41
Alignment explanation
Indices: 51858--52215 Score: 371
Period size: 41 Copynumber: 8.6 Consensus size: 41
51848 TTGTAAACTT
* * * * * *
51858 GCGGCGTTTGTAAACACAAATGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
*
51901 GCGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
51942 GCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * *
51983 GCTGTGTTTGTATAAAAATGCCACTAAATTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
52024 GCGGCGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGA-GTCTTTA
* * * *
52067 ACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
52108 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
52149 GCAGCG-TTGTATAAAAACGCCACTAAAGTACTACTCTTTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
52189 GCGGCGTTTGT-TGAAAAAACGCCACTA
1 GCGGCGTTTGTAT--AAAAACGCCACTA
52216 TCGATGAACC
Statistics
Matches: 264, Mismatches: 44, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
40 35 0.13
41 169 0.64
42 18 0.07
43 42 0.16
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:52095 original size:125 final size:123
Alignment explanation
Indices: 51858--52179 Score: 380
Period size: 125 Copynumber: 2.6 Consensus size: 123
51848 TTGTAAACTT
* * * * * *
51858 GCGGCGTTTGTAAACACAAATGCCACTATAGTACAAGTGTATAGCGGCGTTTG-AATAAAAACGC
1 GCGGCGTTTGTATA-A-AAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAA-AAAAACGC
* * * * * *
51922 CACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTA
63 CACTAAAGTACGAGTCTATAACGGCGTTTGTATAAAAACGCCAATAAAGTACAAGTCTATA
* * *
51983 GCTGTGTTTGTATAAAAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCC
1 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAA-A-AAACGCC
* * * *
52048 ACTATAGTAC-ATGTGTATAACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATA
64 ACTAAAGTACGA-GTCTATAACGGCGTTTGTATAAAAACGCCAATAAAGTACAAGTCTATA
* *
52108 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCAGCG-TTGTATAAAAACGCCAC
1 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAAAAAACGCCAC
52172 TAAAGTAC
66 TAAAGTAC
52180 TACTCTTTTG
Statistics
Matches: 168, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
122 16 0.10
123 32 0.19
124 11 0.07
125 109 0.65
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (123 bp):
GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTAAAAAAACGCCAC
TAAAGTACGAGTCTATAACGGCGTTTGTATAAAAACGCCAATAAAGTACAAGTCTATA
Found at i:52143 original size:166 final size:165
Alignment explanation
Indices: 51858--52216 Score: 517
Period size: 166 Copynumber: 2.2 Consensus size: 165
51848 TTGTAAACTT
* *
51858 GCGGCGTTTGTAAACACAAATGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCC
* * * * *
51923 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTAGCTGT
66 ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATGCCAATAAAGTACGAGTCTTTAGCAGC
* * *
51988 GTTTGTATAAAAATGCCACTAAATTA-TGAGTCTTTA
131 G-TTGTATAAAAACGCCACTAAAGTACT-ACTCTTTA
* *
52024 GCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGGCGTTTGTATAAAAACGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCC
* * *
52089 ACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCAGC
66 ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATGCCAATAAAGTACGAGTCTTTAGCAGC
*
52154 GTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
131 GTTGTATAAAAACGCCACTAAAGTACTACTCTTTA
*
52189 GCGGCGTTTGTTGAA-A-AAACGCCACTAT
1 GCGGCGTTTG-TAAACACAAACGCCACTAT
52217 CGATGAACCT
Statistics
Matches: 174, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
164 12 0.07
165 39 0.22
166 123 0.71
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (165 bp):
GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAACGCC
ACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAATGCCAATAAAGTACGAGTCTTTAGCAGC
GTTGTATAAAAACGCCACTAAAGTACTACTCTTTA
Found at i:52237 original size:81 final size:81
Alignment explanation
Indices: 51899--52259 Score: 250
Period size: 82 Copynumber: 4.4 Consensus size: 81
51889 TACAAGTGTA
* * * * * *
51899 TAGCGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTC
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCC
* * **
51964 AATAAAGTACGAGTCTT
66 ACTAATG-ACGAACCTT
* * * * ** * * *
51981 TAGCTGTGTTTGTATAAAAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACG
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATA-A-AAACG
**
52046 CCACT-AT-A-GTACATGTGT
64 CCACTAATGACG-A-ACCT-T
* * *
52064 ATAACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGC
1 -TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGC
* **
52129 CACTAAATTACGAGTCTT
65 CACT-AATGACGAACCTT
* * * *
52147 TAGCAGCG-TTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAACG
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTAT--AAAAACG
*
52210 CCACT-ATCGATGAACCTAT
64 CCACTAAT-GACGAACCT-T
* **
52229 T-GCGGCGTTTTTATAAAAACGCTGCTAAAGT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGT
52260 TACCATTTTG
Statistics
Matches: 223, Mismatches: 41, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
80 4 0.02
81 53 0.24
82 100 0.45
83 5 0.02
84 58 0.26
85 2 0.01
86 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (81 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAACTCTATAGCGGCGTTTGTATAAAAACGCC
ACTAATGACGAACCTT
Found at i:53351 original size:20 final size:22
Alignment explanation
Indices: 53307--53351 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
53297 TATATAATTA
*
53307 ATATTTTAGTAGTTTAATCATC
1 ATATTTTAGTAGTTTAATAATC
*
53329 ATATTTTA-TA-TTTTATAATC
1 ATATTTTAGTAGTTTAATAATC
53349 ATA
1 ATA
53352 GGTTATGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 2 0.10
22 8 0.38
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (22 bp):
ATATTTTAGTAGTTTAATAATC
Found at i:56792 original size:21 final size:21
Alignment explanation
Indices: 56768--56828 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
56758 AACTTTGAAA
56768 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
56789 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
56803 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
56824 AAATG
1 AAATG
56829 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:56875 original size:36 final size:36
Alignment explanation
Indices: 56760--56868 Score: 184
Period size: 35 Copynumber: 3.0 Consensus size: 36
56750 TGGCAACCAA
56760 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
56797 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
56832 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
56869 GTTGAAATAT
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
35 35 0.51
36 7 0.10
37 27 0.39
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:58091 original size:15 final size:15
Alignment explanation
Indices: 58067--58098 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
58057 AGGCAGATCG
*
58067 AAATCTAGAACGGGA
1 AAATCAAGAACGGGA
58082 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
58097 AA
1 AA
58099 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.25, T:0.09
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:61426 original size:21 final size:20
Alignment explanation
Indices: 61402--61462 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
61392 AACTTTGAAA
61402 AAATGGCTTTCAAAGTTTGGT
1 AAATGG-TTTCAAAGTTTGGT
*
61423 AAAT-GTTTC----TTT-GA
1 AAATGGTTTCAAAGTTTGGT
61437 AAATGGTTTTCAAAGTTTGGT
1 AAATGG-TTTCAAAGTTTGGT
61458 AAATG
1 AAATG
61463 TTTATTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (20 bp):
AAATGGTTTCAAAGTTTGGT
Found at i:61509 original size:36 final size:36
Alignment explanation
Indices: 61395--61502 Score: 164
Period size: 35 Copynumber: 3.0 Consensus size: 36
61385 GGCAACCAAC
* *
61395 TTTGAAAAAATGGCTTTCAAAGTTTGGTAAATGTTTC
1 TTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
61432 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTA
1 TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
*
61467 TTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 TTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
61503 GTTGAAATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
35 33 0.50
36 7 0.11
37 26 0.39
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTA
Found at i:64429 original size:21 final size:21
Alignment explanation
Indices: 64405--64445 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
64395 AGTTTAATTT
64405 TAAACTTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
64426 TAAACTTTGTTTCAATTATC
1 TAAACTTTGTTTCAATTATC
64446 AAACTTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (21 bp):
TAAACTTTGTTTCAATTATCG
Found at i:64484 original size:33 final size:33
Alignment explanation
Indices: 64435--64507 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
64425 GTAAACTTTG
*
64435 TTTCAA-TTATCAAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCAAACTTGGAAGTATTTAAGTA
* *
64467 TTTGAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCAAACTTGGAAGTATTTAAGTA
64500 TTTCAATT
1 TTTCAATT
64508 ATTGTAAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 5 0.14
33 31 0.86
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (33 bp):
TTTCAATTTATCAAACTTGGAAGTATTTAAGTA
Found at i:65367 original size:2 final size:2
Alignment explanation
Indices: 65350--65403 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
65340 CTAACATAAC
* *
65350 AT AT TT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65392 AT AT AT AT AT AT
1 AT AT AT AT AT AT
65404 TGTTTATTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66024 original size:45 final size:43
Alignment explanation
Indices: 65953--66036 Score: 132
Period size: 45 Copynumber: 1.9 Consensus size: 43
65943 GAAGCCCGTT
*
65953 GGTCACCATTTTTTGAAGGTACAGTTTGGAAAGTGAAGACGAC
1 GGTCACCATTTTTTGAAGCTACAGTTTGGAAAGTGAAGACGAC
*
65996 GGTCACTATTTTTTTCGAAGCTACAGTTTGGAAAGTGAAGA
1 GGTCACCA-TTTTTT-GAAGCTACAGTTTGGAAAGTGAAGA
66037 GCCCCGGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 7 0.19
44 6 0.16
45 24 0.65
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (43 bp):
GGTCACCATTTTTTGAAGCTACAGTTTGGAAAGTGAAGACGAC
Found at i:66575 original size:28 final size:28
Alignment explanation
Indices: 66521--66575 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
66511 AACATTTCTT
* * ***
66521 CATTTTTATTTTTATTTTTTTTCTTTAA
1 CATTTTTATTGTTATTTTATCAATTTAA
66549 CATTTTTATTGTTATTTTATCAATTTA
1 CATTTTTATTGTTATTTTATCAATTTA
66576 TTTATTTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (28 bp):
CATTTTTATTGTTATTTTATCAATTTAA
Found at i:72243 original size:212 final size:214
Alignment explanation
Indices: 71942--72512 Score: 780
Period size: 211 Copynumber: 2.7 Consensus size: 214
71932 GCTTCCCAGT
* * * * *
71942 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATACTGGACTCAATAC-ACA-AGCTCATCTTCAC
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAGCTCAACTTCAC
* * * * *
72005 AACGAAGGGGCGACTGGTTGTCAACAAACAACTTCCCAGTTTAAGAGCCAATTTCAACTTCACAA
66 AGCGAAGGGGCGGCTGATTATCAACAAACAACTTCCCAGTTTCAGAGCCAATTTCAACTTCACAA
* *
72070 CGAAGAATATTGGACTCA-ACAGCACAAGCTCAACTTCACAGCGGAGGGGCGGCTGACTGACAAC
131 CGAAG-ATATTGGACTCAGACAACACAAGCTCAACTTCACAGCAGAGGGGCGGCTGACTGACAA-
72134 AA-ACAACTTCTTCAGTTTCA
194 AACACAACTTCTTCAGTTTCA
*
72154 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAGCTCAACTTCAC
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAGCTCAACTTCAC
* * *
72219 AGCG-A-TGGCGGCTGATTATCAAC-AA-AACTTTCCAGTTTCAGAGCCAATTTCAACTTCACAG
66 AGCGAAGGGGCGGCTGATTATCAACAAACAACTTCCCAGTTTCAGAGCCAATTTCAACTTCACAA
* * *
72280 CGAATGATATTGGACTAAGATAACACAAGCTCAACTTCACAGCAGAGGGGCGGCTGACTGTCAAA
131 CGAA-GATATTGGACTCAGACAACACAAGCTCAACTTCACAGCAGAGGGGCGGCTGACTGACAAA
72345 ACACAACTTCTTCAGTTTCA
195 ACACAACTTCTTCAGTTTCA
*
72365 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACAC-AGCTCAACTTCA
* * * * * * * *
72430 CAGCGAAGGGGCGGTTGACTATCAACAAGCAATTTCTCAGTTCCAGAACCAATTTCAACTTCACG
65 CAGCGAAGGGGCGGCTGATTATCAACAAACAACTTCCCAGTTTCAGAGCCAATTTCAACTTCACA
*
72495 ACGGAGTATATTGGACTC
130 ACGAAG-ATATTGGACTC
72513 GGAGCAATAC
Statistics
Matches: 314, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
210 50 0.16
211 112 0.36
212 73 0.23
213 5 0.02
214 30 0.10
215 2 0.01
216 42 0.13
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (214 bp):
TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAACACAGCTCAACTTCAC
AGCGAAGGGGCGGCTGATTATCAACAAACAACTTCCCAGTTTCAGAGCCAATTTCAACTTCACAA
CGAAGATATTGGACTCAGACAACACAAGCTCAACTTCACAGCAGAGGGGCGGCTGACTGACAAAA
CACAACTTCTTCAGTTTCA
Found at i:72470 original size:110 final size:108
Alignment explanation
Indices: 71942--72512 Score: 610
Period size: 110 Copynumber: 5.4 Consensus size: 108
71932 GCTTCCCAGT
* * *
71942 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATACTGGACTCA-A-TACACAAGCTCATCTTCAC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAGACAACACAAGCTCAACTTCAC
* * ** * *
72005 AACGAAGGGGCGACTGGTTGTCAACAAACAACTTCCCAGTTTA
66 AGCGAAGGGGCGGCTGACTATCAACAAACAACTTCTCAGTTTA
* * *
72048 ---AGAGCCAATTTCAACTTCACAACGAAGAATATTGGACTCA-ACAGCACAAGCTCAACTTCAC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAGACAACACAAGCTCAACTTCAC
*
72109 AGCGGAGGGGCGGCTGACTGA-CAACAAACAACTTCTTCAGTTTCA
66 AGCGAAGGGGCGGCTGACT-ATCAACAAACAACTTC-TCAGTTT-A
* *
72154 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACAC-AGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC-AGACAACACAAGCTCAACTTCA
* *
72218 CAGCG-A-TGGCGGCTGATTATCAAC-AA-AACTT-TCCAG--T-
65 CAGCGAAGGGGCGGCTGACTATCAACAAACAACTTCT-CAGTTTA
* * *
72255 TTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTAAGATAACACAAGCTCAACTTCAC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAGACAACACAAGCTCAACTTCAC
*
72320 AGC-AGAGGGGCGGCTGACTGTCAA-AACACAACTTCTTCAGTTTCA
66 AGCGA-AGGGGCGGCTGACTATCAACAA-ACAACTTC-TCAGTTT-A
* * *
72365 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC-AGACAACACAAGCTCAACTTCA
* * *
72430 CAGCGAAGGGGCGGTTGACTATCAACAAGCAATTTCTCAG--T-
65 CAGCGAAGGGGCGGCTGACTATCAACAAACAACTTCTCAGTTTA
* * * *
72471 TCCAGAACCAATTTCAACTTCAC-GACGGAGTATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
72513 GGAGCAATAC
Statistics
Matches: 393, Mismatches: 44, Indels: 56
0.80 0.09 0.11
Matches are distributed among these distances:
100 8 0.02
101 54 0.14
102 1 0.00
103 54 0.14
104 46 0.12
105 15 0.04
106 43 0.11
107 4 0.01
108 16 0.04
109 36 0.09
110 60 0.15
111 53 0.13
112 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (108 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAGACAACACAAGCTCAACTTCAC
AGCGAAGGGGCGGCTGACTATCAACAAACAACTTCTCAGTTTA
Found at i:72928 original size:36 final size:36
Alignment explanation
Indices: 72882--72961 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 36
72872 ATTGACCCAA
72882 CTTG-AACAATTTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAATTTTTGTCTCTCTTGAGACAGTTTCC
72917 CTTGAAACAATTTTTGTCTCTCTTGAGACAGTTTCC
1 CTTGAAACAATTTTTGTCTCTCTTGAGACAGTTTCC
72953 CTTGAAACA
1 CTTGAAACA
72962 TAACATTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 4 0.09
36 40 0.91
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (36 bp):
CTTGAAACAATTTTTGTCTCTCTTGAGACAGTTTCC
Found at i:73030 original size:36 final size:36
Alignment explanation
Indices: 72990--73063 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
72980 ACTTGAAATG
72990 AATTTTGTCTCTCTTGAAACAGTTTCCCTTAAAACA
1 AATTTTGTCTCTCTTGAAACAGTTTCCCTTAAAACA
* * * *
73026 AATTTTGTTTCTCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCTTGAAACAGTTTCCCTTAAAACA
73062 AA
1 AA
73064 ATCTTTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (36 bp):
AATTTTGTCTCTCTTGAAACAGTTTCCCTTAAAACA
Found at i:73132 original size:33 final size:33
Alignment explanation
Indices: 73090--73157 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
73080 TCCTTTAAAC
73090 AAATTTTGTCTCTC-TCGAGACAATTTCTCTTGA
1 AAATTTTGTCTC-CATCGAGACAATTTCTCTTGA
* *
73123 AAATTTTGTCTCCATTGAGACAGTTTCTCTTGA
1 AAATTTTGTCTCCATCGAGACAATTTCTCTTGA
73156 AA
1 AA
73158 CACAAATCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (33 bp):
AAATTTTGTCTCCATCGAGACAATTTCTCTTGA
Found at i:73710 original size:2 final size:2
Alignment explanation
Indices: 73703--73799 Score: 185
Period size: 2 Copynumber: 48.5 Consensus size: 2
73693 TAACATAAAC
73703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
73745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73787 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
73800 GTTTATTAGA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.