Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001428.1 Hibiscus syriacus cultivar Beakdansim tig00002773_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: 85273
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1515 original size:22 final size:22
Alignment explanation
Indices: 1489--1570 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 22
1479 ATAGGGCAGA
1489 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
*
1511 GGGAA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATACCCCC-TTGAAG
* * *
1534 GGGAACCGATTCTCCCC-TGTAG
1 GGGAATCGATAC-CCCCTTGAAG
1556 GGGAATCGATACCCC
1 GGGAATCGATACCCC
1571 TGGGGTTCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
21 4 0.08
22 27 0.52
23 16 0.31
24 5 0.10
ACGTcount: A:0.23, C:0.29, G:0.27, T:0.21
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:1531 original size:23 final size:23
Alignment explanation
Indices: 1489--1551 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
1479 ATAGGGCAGA
* *
1489 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
1511 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
1534 GGGAACCGATTCTCCCCT
1 GGGAACCGATTC-CCCCT
1552 GTAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 13 0.37
23 17 0.49
24 5 0.14
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.22
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:6235 original size:21 final size:22
Alignment explanation
Indices: 6193--6249 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
6183 CTTCGATGAG
*
6193 CTTTTTAAAATTTATGTGTTTT-
1 CTTTTTAAAA-ATATGTGTTTTA
* *
6215 CTTTTTAAAAATATTTTTTTTA
1 CTTTTTAAAAATATGTGTTTTA
*
6237 ATTTTATAAAAAT
1 CTTTT-TAAAAAT
6250 TTTAAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 8 0.28
22 14 0.48
23 7 0.24
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (22 bp):
CTTTTTAAAAATATGTGTTTTA
Found at i:24160 original size:2 final size:2
Alignment explanation
Indices: 24153--24201 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
24143 TTGGTTTCTT
24153 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24195 TA TA TA T
1 TA TA TA T
24202 CAATCATCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28851 original size:41 final size:42
Alignment explanation
Indices: 28774--28866 Score: 125
Period size: 41 Copynumber: 2.2 Consensus size: 42
28764 GAGGTATAGA
*
28774 ACTTTCGATTCTCATCTAAAGTAGAACAGAAGGAAGCATCGC
1 ACTTTCGATTCTCATCTAAAGTAGAACAGAAGGAAGCATCAC
* * ** *
28816 ACTTTCGATTCTCGTCT-ATGTAGAATGGAATGAAGCATCAC
1 ACTTTCGATTCTCATCTAAAGTAGAACAGAAGGAAGCATCAC
28857 ACTTTCGATT
1 ACTTTCGATT
28867 GCATCATACT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 29 0.64
42 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (42 bp):
ACTTTCGATTCTCATCTAAAGTAGAACAGAAGGAAGCATCAC
Found at i:28872 original size:17 final size:17
Alignment explanation
Indices: 28850--28883 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28840 ATGGAATGAA
28850 GCATCACACTTTCGATT
1 GCATCACACTTTCGATT
*
28867 GCATCATACTTTCGATT
1 GCATCACACTTTCGATT
28884 CATACGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (17 bp):
GCATCACACTTTCGATT
Found at i:32853 original size:51 final size:52
Alignment explanation
Indices: 32740--32855 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 52
32730 GTAATTATTG
* * * * * * *
32740 AATAAAATAATAATAAATTGAAGATAATATTTTTGATTCTATCCTAATTCTT
1 AATAAAATAATAATAAACTAAAAATAATAGTTTTAACTCTATCCTAATTCCT
* *
32792 AATAAAATAATAATAAACTAAAAATAAT-GTTTTAACTCTATCTTACTTCCT
1 AATAAAATAATAATAAACTAAAAATAATAGTTTTAACTCTATCCTAATTCCT
32843 AATAAAATAATAA
1 AATAAAATAATAA
32856 ATCTAATATT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
51 30 0.55
52 25 0.45
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (52 bp):
AATAAAATAATAATAAACTAAAAATAATAGTTTTAACTCTATCCTAATTCCT
Found at i:35724 original size:29 final size:28
Alignment explanation
Indices: 35689--35750 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
35679 TTAATGTATG
*
35689 TATTTCGTTTTAGTTTAGTGTTTAACG-TT
1 TATTTCGTTTTAATTTAGTG--TAACGTTT
35718 TATTTCGTTTTAATTTAGTGTAACGTTT
1 TATTTCGTTTTAATTTAGTGTAACGTTT
35746 TATTT
1 TATTT
35751 TATTGCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 5 0.16
28 7 0.23
29 19 0.61
ACGTcount: A:0.19, C:0.06, G:0.15, T:0.60
Consensus pattern (28 bp):
TATTTCGTTTTAATTTAGTGTAACGTTT
Found at i:36413 original size:17 final size:18
Alignment explanation
Indices: 36380--36413 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36370 CCGTTATTAG
36380 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
36398 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
36414 AACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:41524 original size:43 final size:43
Alignment explanation
Indices: 41463--41547 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
41453 AAAATTTACC
41463 AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACAAACAG
1 AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACAAACAG
*
41506 AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACTAACA
1 AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACAAACA
41548 TGAACAACAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (43 bp):
AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACAAACAG
Found at i:44398 original size:24 final size:22
Alignment explanation
Indices: 44371--44432 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
44361 CCGCTGGGAA
44371 TTAATTTTTTTAAATAATAAATTT
1 TTAATTTTTTTAAATAATAAA--T
* *
44395 TTAATATTTTTGAAGATGATAAAT
1 TTAAT-TTTTTTAA-ATAATAAAT
*
44419 TAAATTTTTTTAAA
1 TTAATTTTTTTAAA
44433 AAATTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.03
23 7 0.22
24 10 0.31
25 7 0.22
26 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TTAATTTTTTTAAATAATAAAT
Found at i:45191 original size:20 final size:21
Alignment explanation
Indices: 45150--45202 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
45140 AAAAACGTGC
45150 CATAAAGACAGAGATAAACATAT
1 CATAAAGAC--AGATAAACATAT
45173 CATAAAGACAGAT-AACATAT
1 CATAAAGACAGATAAACATAT
*
45193 CACAAAGACA
1 CATAAAGACA
45203 TAAATAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 16 0.55
21 4 0.14
23 9 0.31
ACGTcount: A:0.57, C:0.17, G:0.11, T:0.15
Consensus pattern (21 bp):
CATAAAGACAGATAAACATAT
Found at i:49454 original size:15 final size:15
Alignment explanation
Indices: 49431--49460 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49421 CTAAATCATT
49431 TTCCCTCTCTTCCCC
1 TTCCCTCTCTTCCCC
*
49446 TTCCTTCTCTTCCCC
1 TTCCCTCTCTTCCCC
49461 GTCAGTTTCT
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:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (15 bp):
TTCCCTCTCTTCCCC
Found at i:60489 original size:191 final size:192
Alignment explanation
Indices: 60148--60523 Score: 551
Period size: 191 Copynumber: 2.0 Consensus size: 192
60138 TTATCGCCAT
* * * *
60148 TGAATTTTAATAAACGGCACAGAATCGGTTTCGAGTATTTTTAATAAACAGCATAGAAACATCAT
1 TGAATTTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATAAACAGCACAGAAACATCAC
* * * *
60213 TCATGATGTTGTTGCAGAGAATTATATTCCATGGATGTATGTCACCACTTGTGTGTCCTTTGGCA
66 GCATGATGTTGTAGCACAGAATTATATTCCATAGATGTATGTCACCACTTGTGTGTCCTTTGGCA
* * *
60278 TCTACTCTGCAATTACTTTGTTTCACTTAACTGAAAGATTTGCCTGTATTTGTTCTTTTAAG
131 TCTACTCTACAATCACTTTGTTTCACTTAACTGAAAGATTTGACTGTATTTGTTCTTTTAAG
*
60340 TGAATTTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATCAAC-GCACAGAAACATCAC
1 TGAATTTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATAAACAGCACAGAAACATCAC
* *
60404 GCATGATGTTGTAGCACAGAATTTTATGT-CATAGATGTATGTCTCCACTTGTGTGTCCTTTGGC
66 GCATGATGTTGTAGCACAGAATTATAT-TCCATAGATGTATGTCACCACTTGTGTGTCCTTTGGC
* * * *
60468 ATCTAAGT-TACAATCACTTTGTTTCACTTAGCTGGAAGATTTGATTGTATTTGTTC
130 ATCT-ACTCTACAATCACTTTGTTTCACTTAACTGAAAGATTTGACTGTATTTGTTC
60524 ATTTCAAGAA
Statistics
Matches: 164, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
191 115 0.70
192 49 0.30
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (192 bp):
TGAATTTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATAAACAGCACAGAAACATCAC
GCATGATGTTGTAGCACAGAATTATATTCCATAGATGTATGTCACCACTTGTGTGTCCTTTGGCA
TCTACTCTACAATCACTTTGTTTCACTTAACTGAAAGATTTGACTGTATTTGTTCTTTTAAG
Found at i:60734 original size:213 final size:215
Alignment explanation
Indices: 60340--60776 Score: 621
Period size: 213 Copynumber: 2.0 Consensus size: 215
60330 TTCTTTTAAG
* * *
60340 TGAATTTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATCAACGCACAGAAACATCACG
1 TGAATTTTAATAAACGGCACAGAATCAGTTTCAACTATTTATAATAAACGCACAGAAACATCACG
*
60405 CATGATGTTGTAGCACAGAATTTTATGTCATAGATGTATGTCTCCACTTGTGTGTCCTTTGGCAT
66 CATGACGTTGTAGCACAGAATTTTATGTCATAGATGTATGTCTCCACTTGTGTGTCCTTTGGCAT
* * * * *
60470 CTAAGTTACAATCACTTTGTTTCACTTAGCTGGAAGATTTGATTGTATTTGTTCATTTCAAGAAC
131 CTAAGTTACAATCACTTTGTTTCACTAAGCCGAAAGATCTGATTATATTTGTTCATTTCAAGAAC
* *
60535 TTTTGGCTCTTTATTTCTGT
196 TTTTGGCTCTTCATTCCTGT
* * * *
60555 TGAATTTTAATAAA-GGACACAGAATCAGTTTCAAGTATTTTTAATAAATGGTACAGAAACATCA
1 TGAATTTTAATAAACGG-CACAGAATCAGTTTCAACTATTTATAATAAA-CGCACAGAAACATCA
* * * *
60619 TGCATGACG-T-T-GCAGAGAATTTTATGTCATAGATGTATGTCTCCACTTGTTTTTCCTTTGGC
64 CGCATGACGTTGTAGCACAGAATTTTATGTCATAGATGTATGTCTCCACTTGTGTGTCCTTTGGC
* * * *
60681 ATCTAAGTTGCATTCACTTTGTTTCCCTAAGCCGAAAGATCTGCTTATATTTGTTCATTTCAAGA
129 ATCTAAGTTACAATCACTTTGTTTCACTAAGCCGAAAGATCTGATTATATTTGTTCATTTCAAGA
60746 ACTTTTGGCTCTTCATTCCTGT
194 ACTTTTGGCTCTTCATTCCTGT
60768 TGAATTTTA
1 TGAATTTTA
60777 GCTAGTTCGG
Statistics
Matches: 197, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
213 133 0.68
214 3 0.02
215 41 0.21
216 20 0.10
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (215 bp):
TGAATTTTAATAAACGGCACAGAATCAGTTTCAACTATTTATAATAAACGCACAGAAACATCACG
CATGACGTTGTAGCACAGAATTTTATGTCATAGATGTATGTCTCCACTTGTGTGTCCTTTGGCAT
CTAAGTTACAATCACTTTGTTTCACTAAGCCGAAAGATCTGATTATATTTGTTCATTTCAAGAAC
TTTTGGCTCTTCATTCCTGT
Found at i:62280 original size:51 final size:51
Alignment explanation
Indices: 62203--62430 Score: 279
Period size: 51 Copynumber: 4.6 Consensus size: 51
62193 CTAGTCAACA
* * *
62203 ATGAAACTCTGGTCGAAGTACTCAAGGAGAGCAAACACCATACCATTGGTG
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
* * * *
62254 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGC-AA-GC-AT---ATCGACA
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
* * *
62299 ATGAAACTCTGGTTGAAGTACCCAAGGACAGCAAACACAATACCATTGGTG
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
* *
62350 ATGAAAATCCGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
* **
62401 ATGAAACACCAGTCGAAGTACCCAAGGAGA
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGA
62431 TCAAGCATAT
Statistics
Matches: 150, Mismatches: 21, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
45 33 0.22
46 2 0.01
47 1 0.01
48 4 0.03
49 1 0.01
50 2 0.01
51 107 0.71
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (51 bp):
ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
Found at i:62364 original size:96 final size:96
Alignment explanation
Indices: 62200--62383 Score: 314
Period size: 96 Copynumber: 1.9 Consensus size: 96
62190 TCGCTAGTCA
* * * * *
62200 ACAATGAAACTCTGGTCGAAGTACTCAAGGAGAGCAAACACCATACCATTGGTGATGAAACTCTG
1 ACAATGAAACTCTGGTCGAAGTACCCAAGGACAGCAAACACAATACCATTGGTGATGAAAATCCG
62265 GTCGAAGTACCCAAGGAGAGCAAGCATATCG
66 GTCGAAGTACCCAAGGAGAGCAAGCATATCG
*
62296 ACAATGAAACTCTGGTTGAAGTACCCAAGGACAGCAAACACAATACCATTGGTGATGAAAATCCG
1 ACAATGAAACTCTGGTCGAAGTACCCAAGGACAGCAAACACAATACCATTGGTGATGAAAATCCG
62361 GTCGAAGTACCCAAGGAGAGCAA
66 GTCGAAGTACCCAAGGAGAGCAA
62384 ACACAATACC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (96 bp):
ACAATGAAACTCTGGTCGAAGTACCCAAGGACAGCAAACACAATACCATTGGTGATGAAAATCCG
GTCGAAGTACCCAAGGAGAGCAAGCATATCG
Found at i:64202 original size:32 final size:32
Alignment explanation
Indices: 64145--64207 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
64135 TATCAATATC
*
64145 GGGTCGGGTTAATACCATATAGGTTGATTTTT
1 GGGTCGGGTTAATACCAGATAGGTTGATTTTT
* * *
64177 GGGTCGGGTTAATATCGGATCGGTTGATTTT
1 GGGTCGGGTTAATACCAGATAGGTTGATTTT
64208 CGGTTTAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.19, C:0.10, G:0.32, T:0.40
Consensus pattern (32 bp):
GGGTCGGGTTAATACCAGATAGGTTGATTTTT
Found at i:64479 original size:25 final size:25
Alignment explanation
Indices: 64445--64497 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
64435 ATACGTGTTA
64445 GATTTTGTTATCAAAATTTTATATT
1 GATTTTGTTATCAAAATTTTATATT
64470 GATTTTGTTATCAAAATTTTATATT
1 GATTTTGTTATCAAAATTTTATATT
64495 GAT
1 GAT
64498 CTCGTACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (25 bp):
GATTTTGTTATCAAAATTTTATATT
Found at i:64847 original size:19 final size:19
Alignment explanation
Indices: 64820--64879 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
64810 TCTTAAACTT
*
64820 TATATTATTTTATTATAAA
1 TATAATATTTTATTATAAA
*
64839 TATAATATTTT-TAATAAA
1 TATAATATTTTATTATAAA
*
64857 TTATCA-ATTTTATT-TAAA
1 -TATAATATTTTATTATAAA
64875 T-TAAT
1 TATAAT
64880 TTATTATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 15 0.45
19 15 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TATAATATTTTATTATAAA
Found at i:64979 original size:16 final size:15
Alignment explanation
Indices: 64960--65003 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
64950 TCGGATTAAA
64960 TTCGGTTCAGGTTGCT
1 TTCGGTTC-GGTTGCT
**
64976 TTCGGATGGGGTTGCT
1 TTCGG-TTCGGTTGCT
64992 TTCGGTTCGGTT
1 TTCGGTTCGGTT
65004 TAATTTCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.22
16 17 0.74
17 1 0.04
ACGTcount: A:0.05, C:0.16, G:0.36, T:0.43
Consensus pattern (15 bp):
TTCGGTTCGGTTGCT
Found at i:66476 original size:20 final size:20
Alignment explanation
Indices: 66451--66497 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
66441 TTTAGTTGTT
66451 TGTTCTGGGTAATTTTTCTA
1 TGTTCTGGGTAATTTTTCTA
66471 TGTTCTGGGTAATTTTTCTA
1 TGTTCTGGGTAATTTTTCTA
*
66491 GGTTCTG
1 TGTTCTG
66498 AAGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (20 bp):
TGTTCTGGGTAATTTTTCTA
Found at i:71797 original size:12 final size:12
Alignment explanation
Indices: 71766--71790 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71756 TCTATTATTA
71766 AAAATTAAAAAT
1 AAAATTAAAAAT
71778 AAAATTAAAAAT
1 AAAATTAAAAAT
71790 A
1 A
71791 TATTTAATTT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTAAAAAT
Found at i:73438 original size:3 final size:3
Alignment explanation
Indices: 73432--73530 Score: 108
Period size: 3 Copynumber: 33.0 Consensus size: 3
73422 TATATGTATT
* * *
73432 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
73480 TTA TAG TAA TTA TAA TAA TAA TAA TTA TAA TTA TAA TTA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
73528 TAA
1 TAA
73531 ATCAATATGG
Statistics
Matches: 76, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:73463 original size:24 final size:24
Alignment explanation
Indices: 73428--73524 Score: 140
Period size: 24 Copynumber: 4.0 Consensus size: 24
73418 TATTTATATG
73428 TATTTAATAATAATAATAATAATAA
1 TATTT-ATAATAATAATAATAATAA
73453 TATTTATAATAATAATAATAATAA
1 TATTTATAATAATAATAATAATAA
* *
73477 TATTTATAGTAATTATAATAATAA
1 TATTTATAATAATAATAATAATAA
* * *
73501 TAATTATAATTATAATTATAATAA
1 TATTTATAATAATAATAATAATAA
73525 AAATAAATCA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
24 60 0.92
25 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
TATTTATAATAATAATAATAATAA
Found at i:73566 original size:2 final size:2
Alignment explanation
Indices: 73561--73680 Score: 204
Period size: 2 Copynumber: 60.0 Consensus size: 2
73551 AGTATCTTCA
* * * *
73561 AT AT AT AT AT AT AT AC AC AC AC 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
73603 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
73645 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
73681 TCCTTCTTAT
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 116 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:76575 original size:29 final size:29
Alignment explanation
Indices: 76533--76590 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
76523 CTCACGAGGC
76533 GCCCTGAAAATGAACGATGACCAGGACGG
1 GCCCTGAAAATGAACGATGACCAGGACGG
76562 GCCCTGAAAATGAACGATGACCAGGACGG
1 GCCCTGAAAATGAACGATGACCAGGACGG
76591 AGCCGTTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.31, T:0.10
Consensus pattern (29 bp):
GCCCTGAAAATGAACGATGACCAGGACGG
Found at i:77085 original size:30 final size:29
Alignment explanation
Indices: 77051--77114 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
77041 AATAAATATT
* *
77051 TAAAACATATTTATGTTTAAAATAGGTACC
1 TAAAACAT-TTTATGGTCAAAATAGGTACC
* * *
77081 TAAAATATTTTTTGGTCAAAATAGGTACT
1 TAAAACATTTTATGGTCAAAATAGGTACC
77110 TAAAA
1 TAAAA
77115 TATTCAATGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (29 bp):
TAAAACATTTTATGGTCAAAATAGGTACC
Found at i:78002 original size:20 final size:20
Alignment explanation
Indices: 77977--78032 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
77967 CATATTCCCT
77977 GGTAATCTTACATTCCCACC
1 GGTAATCTTACATTCCCACC
*
77997 GGTAATCTTACATTCCCACT
1 GGTAATCTTACATTCCCACC
78017 GGTAATCTTACATTCC
1 GGTAATCTTACATTCC
78033 GTAAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (20 bp):
GGTAATCTTACATTCCCACC
Found at i:78298 original size:12 final size:12
Alignment explanation
Indices: 78281--78305 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
78271 ATCAATAAGT
78281 ACTAGTAGGTGA
1 ACTAGTAGGTGA
78293 ACTAGTAGGTGA
1 ACTAGTAGGTGA
78305 A
1 A
78306 GTTAGATGGA
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:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
ACTAGTAGGTGA
Found at i:85114 original size:22 final size:24
Alignment explanation
Indices: 85081--85133 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
85071 ACTATAACAT
85081 TTAA-ATTCTATTTAATT-A-TTG
1 TTAATATTCTATTTAATTAATTTG
* *
85102 TTAATATTTTATTTATTTAATTTG
1 TTAATATTCTATTTAATTAATTTG
85126 TTAATATT
1 TTAATATT
85134 AATTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 4 0.15
22 11 0.41
23 1 0.04
24 11 0.41
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (24 bp):
TTAATATTCTATTTAATTAATTTG
Found at i:85138 original size:19 final size:20
Alignment explanation
Indices: 85111--85160 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
85101 GTTAATATTT
* *
85111 TATTTATTTAATTTGT-TAA
1 TATTAATTTAATTTCTATAA
85130 TATTAATTTATAATTTCTATAA
1 TATTAA-TT-TAATTTCTATAA
85152 TATTAATTT
1 TATTAATTT
85161 TTTATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 3 0.12
21 9 0.35
22 9 0.35
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTAATTTAATTTCTATAA
Found at i:85155 original size:22 final size:21
Alignment explanation
Indices: 85119--85160 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
85109 TTTATTTATT
*
85119 TAATTTGTTAATATTAATTTA
1 TAATTTCTTAATATTAATTTA
85140 TAATTTCTATAATATTAATTT
1 TAATTTCT-TAATATTAATTT
85161 TTTATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TAATTTCTTAATATTAATTTA
Done.