Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004441.1 Hibiscus syriacus cultivar Beakdansim tig00009741_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: 39720
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:583 original size:280 final size:285
Alignment explanation
Indices: 49--618 Score: 985
Period size: 280 Copynumber: 2.0 Consensus size: 285
39 GAAAAGATGA
49 CATCTTCATCAATCAAGCTAAGTACATCAAAGATATGCTCAAGAAGTTTGGACTATAAAATGGGA
1 CATCTTCATCAATCAAGCTAAGTACATCAAAGATATGCTCAAGAAGTTTGGAC-ATAAAATGGGA
*
114 AACCTCATGACACTCCAATGAGCTCATCAACAAAGCTTGACATAGATGAATGAGGTAAATGTGTG
65 AACCTCATGACACTCCAATGAGCTCATCAACAAAGCTTGACATAGATGAAGGAGGTAAATGTGTG
179 GATGTTAAATTATATAGGTCAATGATTGGTTCTTTACTTTATCTAACTGCAAGTAGATCAGACAT
130 GATGTTAAATTATATAGGTCAATGATTGGTTCTTTACTTTATCTAACTGCAAGTAGATCAGACAT
244 TATGTTTAGTGTTGCTTATGCTATATTTCAATCATGCCCTAAGGAATCAAATATACTAGC-AA-A
195 TATGTTTAGTGTTGCTTATGCTATATTTCAATCATGCCCTAAGGAATCAAATATACTAGCTAAGA
307 GAA-CTTTAGAT-CCTTAAGGACACT
260 GAATCTTTAGATACCTTAAGGACACT
*
331 CATCTTCATCAATCAAGCTAAGTACATCAAATATATGCTCAAGAAGTTTGGAC-TAAAATGGGAA
1 CATCTTCATCAATCAAGCTAAGTACATCAAAGATATGCTCAAGAAGTTTGGACATAAAATGGGAA
395 ACCTCATGACACTCCAATGAGCTCATC-ACAAAGCTTGACATAGATGAAGGAGGTAAATGTGTGG
66 ACCTCATGACACTCCAATGAGCTCATCAACAAAGCTTGACATAGATGAAGGAGGTAAATGTGTGG
459 ATGTTAAATTATATAGGTCAATGATTGGTTCTTTAC-TTATCT-ACTGCAAGTAGATCAGACATT
131 ATGTTAAATTATATAGGTCAATGATTGGTTCTTTACTTTATCTAACTGCAAGTAGATCAGACATT
* *
522 ATGTTTAGTGTTTGCTTATGTGCTATATTTCAATCATGCCCTAAGGAATCACATTTACTAGCTAT
196 ATGTTTAGTG-TTGCTTA--TGCTATATTTCAATCATGCCCTAAGGAATCAAATATACTAGC---
587 TAAGAGAATCTTTAGATACCTTAAGGACACT
255 TAAGAGAATCTTTAGATACCTTAAGGACACT
618 C
1 C
619 CTAGTTTAGG
Statistics
Matches: 274, Mismatches: 4, Indels: 15
0.94 0.01 0.05
Matches are distributed among these distances:
277 31 0.11
278 13 0.05
279 72 0.26
280 78 0.28
282 52 0.19
284 2 0.01
285 4 0.01
286 8 0.03
287 14 0.05
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (285 bp):
CATCTTCATCAATCAAGCTAAGTACATCAAAGATATGCTCAAGAAGTTTGGACATAAAATGGGAA
ACCTCATGACACTCCAATGAGCTCATCAACAAAGCTTGACATAGATGAAGGAGGTAAATGTGTGG
ATGTTAAATTATATAGGTCAATGATTGGTTCTTTACTTTATCTAACTGCAAGTAGATCAGACATT
ATGTTTAGTGTTGCTTATGCTATATTTCAATCATGCCCTAAGGAATCAAATATACTAGCTAAGAG
AATCTTTAGATACCTTAAGGACACT
Found at i:1408 original size:20 final size:21
Alignment explanation
Indices: 1383--1477 Score: 70
Period size: 23 Copynumber: 4.4 Consensus size: 21
1373 TTTTGCTTCA
1383 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-AG
* *
1403 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAAAG
* *
1425 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAAAG
* *
1446 TGCACCGATGCACGCCTTGAATA-
1 TGCATCGAT--ACACCTTGAA-AG
1469 TGCATCGAT
1 TGCATCGAT
1478 GCACAAGGCC
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
20 11 0.19
21 17 0.29
22 13 0.22
23 18 0.31
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAAAG
Found at i:1448 original size:21 final size:20
Alignment explanation
Indices: 1383--1454 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
1373 TTTTGCTTCA
1383 TGCATCGATACACCT-AACAG
1 TGCATCGATACACCTGAA-AG
* *
1403 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CC-TGAAAG
*
1425 TGCATCGATACACCATGAAGG
1 TGCATCGATACACC-TGAAAG
*
1446 TGCACCGAT
1 TGCATCGAT
1455 GCACGCCTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 11 0.26
21 17 0.40
22 13 0.30
23 2 0.05
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (20 bp):
TGCATCGATACACCTGAAAG
Found at i:1474 original size:44 final size:42
Alignment explanation
Indices: 1382--1477 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 42
1372 TTTTTGCTTC
* *
1382 ATGCATCGATACACCTAACAGTGCATCGATGCATCCTTGAAT
1 ATGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAAT
* *
1424 GTGCATCGATACACCATGAA-GGTGCACCGATGCACGCCTTGAAT
1 ATGCATCGATACACC-T-AACAGTGCACCGATGCA-GCCTTGAAT
1468 ATGCATCGAT
1 ATGCATCGAT
1478 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 19 0.41
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (42 bp):
ATGCATCGATACACCTAACAGTGCACCGATGCAGCCTTGAAT
Found at i:1498 original size:43 final size:42
Alignment explanation
Indices: 1401--1500 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 42
1391 TACACCTAAC
* * * *
1401 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCAGCCTTGAATATGCATCGATACACAAGGA
* * *
1443 AGGTGCACCGATGCACGCCTTGAATATGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-GCCTTGAATATGCATCGATACACAAGG-A
1488 A-TGCATCGATGCA
1 AGTGCATCGATGCA
1501 TCCGTCGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.49
44 22 0.47
45 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATATGCATCGATACACAAGGA
Found at i:3034 original size:21 final size:21
Alignment explanation
Indices: 2992--3035 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2982 ACTCCGGGAG
* *
2992 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
3013 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
3034 CT
1 CT
3036 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:3392 original size:14 final size:15
Alignment explanation
Indices: 3367--3395 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3357 ATTGTTTTGA
3367 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
3382 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
3396 AGATGCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:14146 original size:12 final size:12
Alignment explanation
Indices: 14112--14161 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
14102 TCTCAAACCC
*
14112 TAAACCCAAATCA
1 TAAACCCTAA-CA
14125 TAAA-CCTAACA
1 TAAACCCTAACA
14136 TAAACCCTAACA
1 TAAACCCTAACA
*
14148 GAAAACCC-AACA
1 -TAAACCCTAACA
14160 TA
1 TA
14162 TAAGCAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 7 0.22
12 15 0.47
13 10 0.31
ACGTcount: A:0.54, C:0.30, G:0.02, T:0.14
Consensus pattern (12 bp):
TAAACCCTAACA
Found at i:17176 original size:26 final size:27
Alignment explanation
Indices: 17141--17202 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
17131 AGGGGAAAGA
* *
17141 CACAAGGTGATCCGAGG-AGGGGGAGT
1 CACATGGTGATCCGAGGAAGGAGGAGT
* * *
17167 CGCATGGTGATCTGGGGAAGGAGGAGT
1 CACATGGTGATCCGAGGAAGGAGGAGT
17194 CACATGGTG
1 CACATGGTG
17203 TTCCATGCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.24, C:0.15, G:0.45, T:0.16
Consensus pattern (27 bp):
CACATGGTGATCCGAGGAAGGAGGAGT
Found at i:18970 original size:14 final size:15
Alignment explanation
Indices: 18951--18983 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
18941 TAATAATAAT
18951 AATTAAACATATT-A
1 AATTAAACATATTGA
18965 AATTAAACATATTGA
1 AATTAAACATATTGA
18980 AATT
1 AATT
18984 TAAAGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (15 bp):
AATTAAACATATTGA
Found at i:20208 original size:16 final size:16
Alignment explanation
Indices: 20187--20226 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
20177 CATAGAAGCA
20187 TTGGGCCTTCTCGAGT
1 TTGGGCCTTCTCGAGT
20203 TTGGGCCTTCTCGAGT
1 TTGGGCCTTCTCGAGT
20219 TTGGGCCT
1 TTGGGCCT
20227 ATATCAAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.25, G:0.33, T:0.38
Consensus pattern (16 bp):
TTGGGCCTTCTCGAGT
Found at i:20317 original size:3 final size:3
Alignment explanation
Indices: 20309--20400 Score: 90
Period size: 3 Copynumber: 32.0 Consensus size: 3
20299 GATCTGTTTG
*
20309 TAA TAA TAA TAA TAT TAA TAAA TAA TAA TAA TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
*
20354 TAA TAG TAA TAAA TAAA TAA -AA TAA TAA -AA -AA TAA -AA -AA TAA
1 TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20396 -AA TAA
1 TAA TAA
20401 AATGAAAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
2 14 0.18
3 54 0.69
4 10 0.13
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:20356 original size:36 final size:38
Alignment explanation
Indices: 20309--20388 Score: 121
Period size: 36 Copynumber: 2.2 Consensus size: 38
20299 GATCTGTTTG
*
20309 TAATAATAATAATATTAATAAAT-AAT-AATAATAAAA
1 TAATAATAATAATAGTAATAAATAAATAAATAATAAAA
20345 TAATAATAATAATAGTAATAAATAAATAAAATAATAAAA
1 TAATAATAATAATAGTAATAAATAAAT-AAATAATAAAA
20384 -AATAA
1 TAATAA
20389 AAAATAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 22 0.55
37 3 0.08
38 5 0.12
39 10 0.25
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (38 bp):
TAATAATAATAATAGTAATAAATAAATAAATAATAAAA
Found at i:20397 original size:7 final size:7
Alignment explanation
Indices: 20361--20397 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
20351 TAATAATAGT
20361 AATAAATA
1 AATAAA-A
20369 AATAAAA
1 AATAAAA
20376 TAATAAAA
1 -AATAAAA
20384 AATAAAA
1 AATAAAA
20391 AATAAAA
1 AATAAAA
20398 TAAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
AATAAAA
Found at i:20402 original size:17 final size:18
Alignment explanation
Indices: 20313--20410 Score: 83
Period size: 19 Copynumber: 5.1 Consensus size: 18
20303 TGTTTGTAAT
* *
20313 AATAATAATATTAATAAAT
1 AATAATAATA-AAATAAAA
20332 AATAATAATAAAATAATAA
1 AATAATAATAAAATAA-AA
*
20351 TAATAATAGTAATAAATAAATAA
1 -AATAATAAT-A-AAAT-AA-AA
20374 AATAATAA-AAAATAAAA
1 AATAATAATAAAATAAAA
20391 AATAA-AATAAAATGAAAA
1 AATAATAATAAAAT-AAAA
20409 AA
1 AA
20411 ACTAGTGTCT
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
16 2 0.03
17 12 0.18
18 13 0.19
19 15 0.22
20 9 0.13
21 1 0.01
22 11 0.16
23 5 0.07
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AATAATAATAAAATAAAA
Found at i:20408 original size:6 final size:5
Alignment explanation
Indices: 20332--20408 Score: 52
Period size: 6 Copynumber: 14.4 Consensus size: 5
20322 ATTAATAAAT
*
20332 AATAA TAATAA AATAA TAATAA TAATAGT AAT-A AAT-A AATAA AATAA
1 AATAA -AATAA AATAA -AATAA -AATA-A AATAA AATAA AATAA AATAA
20379 TAA-AA AATAAAA AATAA AATAA AATGAA AA
1 -AATAA AAT--AA AATAA AATAA AAT-AA AA
20409 AAACTAGTGT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
4 9 0.15
5 23 0.38
6 24 0.39
7 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:20884 original size:123 final size:123
Alignment explanation
Indices: 20753--21332 Score: 975
Period size: 123 Copynumber: 4.7 Consensus size: 123
20743 GAATTAAGGC
20753 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
20818 GAAC-TCCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
66 GAACTTCC-TCTGGAAACGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
* *
20876 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
20941 GAACTTCCTCTGGAAACGTTGATGCTGATCTATCTCCTTCTGTGATAAAGTCGAGCAA
66 GAACTTCCTCTGGAAACGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
* * * * *
20999 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTATTCAAATGAGTTCTTTTAATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
21064 GAACTTCCTCTAGAAACGTTGATGCTGATCTATCTCCTTCTATGATAGAGTCAAGCAA
66 GAACTTCCTCTGGAAACGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
*
21122 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
21187 GAACTTCCTCTGGAAACGTTGATGCTAATCTATCTCCTTCTGTGATAGAGTCGAGCAA
66 GAACTTCCTCTGGAAACGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
*
21245 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
21310 GAACTCTAC-CTGGAAACGTTGAT
66 GAACT-TCCTCTGGAAACGTTGAT
21333 CCATCGAGTT
Statistics
Matches: 428, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
123 423 0.99
124 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTTCCTCTGGAAACGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGAGCAA
Found at i:21411 original size:36 final size:35
Alignment explanation
Indices: 21371--21570 Score: 105
Period size: 36 Copynumber: 5.5 Consensus size: 35
21361 AGTGAATCTG
*
21371 TCTCAAGCGAGACGAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAAT-TTGTTTTAAGAAAAACAA
* * ** ** ***
21407 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAATTG
1 TCTCAAGCGAGACAAA-T-TTGTTTTAAGAAAAACAA
* *
21444 TATCAAACGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAA-TTTGTTTTAAGAAAAACAA
* * ** ** **
21480 TCTCAAGTGAGATAAATTGATGTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAATT--TGTTTTAAGAAAAACAA
* *
21517 TCTCAAGCGAGACGCAGA-TTGTGTTAAGAAAAACAA
1 TCTCAAGCGAGA--CAAATTTGTTTTAAGAAAAACAA
* *
21553 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGACAAATT
21571 ACTATTTGAA
Statistics
Matches: 113, Mismatches: 45, Indels: 13
0.66 0.26 0.08
Matches are distributed among these distances:
34 2 0.02
35 3 0.03
36 57 0.50
37 48 0.42
38 1 0.01
39 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (35 bp):
TCTCAAGCGAGACAAATTTGTTTTAAGAAAAACAA
Found at i:21473 original size:73 final size:73
Alignment explanation
Indices: 21353--21570 Score: 321
Period size: 73 Copynumber: 3.0 Consensus size: 73
21343 ATGGAAACTT
* *
21353 ATGTTTCTAGTG-AATCTGTCTCAAGCGAGACGAATCTTGTTTTAAGAAAAACAATCTCAAGTGA
1 ATGTTTCGAGTGAAAT-TGTCTCAAGCGAGACGAATATTGTTTTAAGAAAAACAATCTCAAGTGA
21417 GATAAATTG
65 GATAAATTG
* * * * *
21426 TTGTTTCGAGTGAAATTGTATCAAACGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
1 ATGTTTCGAGTGAAATTGTCTCAAGCGAGACGAATATTGTTTTAAGAAAAACAATCTCAAGTGAG
21491 ATAAATTG
66 ATAAATTG
* * * *
21499 ATGTTTCGAGTGAAACTGTCTCAAGCGAGACGCAGATTGTGTTAAGAAAAACAATCTCAAGTGAG
1 ATGTTTCGAGTGAAATTGTCTCAAGCGAGACGAATATTGTTTTAAGAAAAACAATCTCAAGTGAG
21564 ATAAATT
66 ATAAATT
21571 ACTATTTGAA
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
73 126 0.98
74 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (73 bp):
ATGTTTCGAGTGAAATTGTCTCAAGCGAGACGAATATTGTTTTAAGAAAAACAATCTCAAGTGAG
ATAAATTG
Found at i:21504 original size:37 final size:37
Alignment explanation
Indices: 21389--21570 Score: 129
Period size: 37 Copynumber: 5.0 Consensus size: 37
21379 GAGACGAATC
21389 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
** ** *** * ** *
21426 TTGTTTCGAGTGAAATTGTATCAAACGAGACAAATT-
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
21462 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
* ** ** ** * * *
21499 ATGTTTCGAGTGAAACTGTCTCAAGCGAGACGCAGATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGA--TAAATTG
21538 -TG--TTAAGAAAAACAATCTCAAGTGAGATAAATT
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATT
21571 ACTATTTGAA
Statistics
Matches: 101, Mismatches: 41, Indels: 9
0.67 0.27 0.06
Matches are distributed among these distances:
34 4 0.04
36 43 0.43
37 47 0.47
38 2 0.02
39 5 0.05
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (37 bp):
TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
Found at i:22336 original size:22 final size:22
Alignment explanation
Indices: 22308--22362 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
22298 AATAAAGTTT
22308 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
22330 TCATCTTTGAATAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
22352 TCATCTTTGAA
1 TCATCTTTGAA
22363 GAATGTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:28252 original size:15 final size:15
Alignment explanation
Indices: 28232--28283 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
28222 TACAAACGTA
*
28232 AAAATGCAAAGATGC
1 AAAATGCAAAGATGT
28247 AAAATGC-AA-AT-T
1 AAAATGCAAAGATGT
*
28259 AACATGCAAAGATGT
1 AAAATGCAAAGATGT
28274 AAAATGCAAA
1 AAAATGCAAA
28284 TGCATGTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 6 0.19
13 4 0.13
14 4 0.13
15 17 0.55
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (15 bp):
AAAATGCAAAGATGT
Found at i:30525 original size:18 final size:18
Alignment explanation
Indices: 30502--30536 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30492 TCCTTTTCTT
30502 AATATTAA-AAAATAAATA
1 AATATTAATAAAA-AAATA
30520 AATATTAATAAAAAAAT
1 AATATTAATAAAAAAAT
30537 TCTCTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATTAATAAAAAAATA
Found at i:32361 original size:19 final size:18
Alignment explanation
Indices: 32339--32379 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
32329 ATAAACAAAT
*
32339 AAAATAAAAATGAAAAAA
1 AAAAAAAAAATGAAAAAA
*
32357 AAAAACAAAATGAAAAAA
1 AAAAAAAAAATGAAAAAA
32375 AAAAA
1 AAAAA
32380 CTAGTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.85, C:0.02, G:0.05, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAATGAAAAAA
Found at i:32366 original size:18 final size:18
Alignment explanation
Indices: 32345--32380 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
32335 AAATAAAATA
32345 AAAATGAAAAAAAAAAAC
1 AAAATGAAAAAAAAAAAC
32363 AAAATGAAAAAAAAAAAC
1 AAAATGAAAAAAAAAAAC
32381 TAGTGTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.83, C:0.06, G:0.06, T:0.06
Consensus pattern (18 bp):
AAAATGAAAAAAAAAAAC
Found at i:34423 original size:20 final size:20
Alignment explanation
Indices: 34394--34434 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
34384 AGTAAAATTT
*
34394 TTTTTTTTAATAT-TTTTATG
1 TTTTTCTTAAT-TGTTTTATG
34414 TTTTTCTTAATTGTTTTATG
1 TTTTTCTTAATTGTTTTATG
34434 T
1 T
34435 AATAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.73
Consensus pattern (20 bp):
TTTTTCTTAATTGTTTTATG
Found at i:35950 original size:18 final size:17
Alignment explanation
Indices: 35906--35952 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
35896 TATGGAATTG
*
35906 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
35923 GATTCTAATTCCTTCACA
1 GATTCCAATTCC-TCACA
*
35941 TATTCCAATTCC
1 GATTCCAATTCC
35953 CTCATAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Done.