Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008966.1 Hibiscus syriacus cultivar Beakdansim tig00112308_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: 265444
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:195275 original size:19 final size:20
Alignment explanation
Indices: 195251--195301 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
195241 CGGCCAAGAG
* *
195251 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
195270 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
195290 CATGTATTTTCA
1 CATGTATTTTCA
195302 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:203300 original size:11 final size:11
Alignment explanation
Indices: 203284--203321 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
203274 TTTTTTTTTC
203284 AAAAAAACAAA
1 AAAAAAACAAA
203295 AAAAAAACAAA
1 AAAAAAACAAA
*
203306 AAAAAAGGCAAA
1 AAAAAA-ACAAA
203318 AAAA
1 AAAA
203322 TAAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:203334 original size:23 final size:22
Alignment explanation
Indices: 203284--203343 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
203274 TTTTTTTTTC
203284 AAAAAAA-CAAAAAAAAAACAA
1 AAAAAAAGCAAAAAAAAAACAA
*
203305 AAAAAAAGGCAAAAAAATAAA-AT
1 AAAAAAA-GCAAAAAAA-AAACAA
* *
203328 AATAAAAGCTAAAAAA
1 AAAAAAAGCAAAAAAA
203344 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 7 0.21
22 8 0.24
23 15 0.45
24 3 0.09
ACGTcount: A:0.82, C:0.07, G:0.05, T:0.07
Consensus pattern (22 bp):
AAAAAAAGCAAAAAAAAAACAA
Found at i:211917 original size:16 final size:16
Alignment explanation
Indices: 211896--211927 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
211886 GTGCACTTCA
211896 TGTGACATCAAATTGG
1 TGTGACATCAAATTGG
211912 TGTGACATCAAATTGG
1 TGTGACATCAAATTGG
211928 CGCCCAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
TGTGACATCAAATTGG
Found at i:213495 original size:35 final size:35
Alignment explanation
Indices: 213436--213553 Score: 150
Period size: 35 Copynumber: 3.4 Consensus size: 35
213426 ACTATCTGTT
213436 CATCACCATTTTCACGCCTATATCATCACCATCTTC
1 CATCACCA-TTTCACGCCTATATCATCACCATCTTC
* *
213472 CATCACCATTGCATGCCTATATCATCACCATCTTC
1 CATCACCATTTCACGCCTATATCATCACCATCTTC
* * *
213507 TATCACTATTTCACACCTATATCATCACCA--TTC
1 CATCACCATTTCACGCCTATATCATCACCATCTTC
*
213540 CATTACCATCTTCA
1 CATCACCAT-TTCA
213554 TCTTTTCACC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
33 9 0.13
34 4 0.06
35 50 0.70
36 8 0.11
ACGTcount: A:0.27, C:0.36, G:0.03, T:0.34
Consensus pattern (35 bp):
CATCACCATTTCACGCCTATATCATCACCATCTTC
Found at i:217364 original size:19 final size:20
Alignment explanation
Indices: 217340--217379 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
217330 TATCATTTCC
217340 TTATTTCATATCATT-CTTA
1 TTATTTCATATCATTACTTA
* *
217359 TTATTTCTTTTCATTACTTA
1 TTATTTCATATCATTACTTA
217379 T
1 T
217380 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATATCATTACTTA
Found at i:217681 original size:13 final size:13
Alignment explanation
Indices: 217665--217702 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
217655 GAAAAAAATC
217665 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
*
217678 AGAAGAAAAGAAA
1 AGAAAAAAAGAAA
*
217691 AGAAAAAGAGAA
1 AGAAAAAAAGAA
217703 GTTCAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:217681 original size:27 final size:26
Alignment explanation
Indices: 217648--217702 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
217638 TTGGAGTGCA
217648 AAAAGAAGAAAA-AAATCAGAAAAAAAG
1 AAAAGAAGAAAAGAAA--AGAAAAAAAG
*
217675 AAAAGAAGAAAAGAAAAGAAAAAGAG
1 AAAAGAAGAAAAGAAAAGAAAAAAAG
217701 AA
1 AA
217703 GTTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.42
27 12 0.46
28 3 0.12
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (26 bp):
AAAAGAAGAAAAGAAAAGAAAAAAAG
Found at i:221917 original size:19 final size:20
Alignment explanation
Indices: 221893--221932 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
221883 TATCATTTCC
221893 TTATTTCATATCATT-CTTA
1 TTATTTCATATCATTACTTA
* *
221912 TTATTTCTTTTCATTACTTA
1 TTATTTCATATCATTACTTA
221932 T
1 T
221933 ATTATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTCATATCATTACTTA
Found at i:223166 original size:36 final size:35
Alignment explanation
Indices: 223073--223183 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
223063 TTGGTGGTTA
* * *
223073 TATAGGCGTGAAATGGTGATAGAAGATGGTAATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
223108 TATAGGCGTGCAATGGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
*
223143 TATAGGCATGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
223179 T-TAGG
1 TATAGG
223184 TAGTATCTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 43 0.64
36 24 0.36
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:227842 original size:16 final size:16
Alignment explanation
Indices: 227802--227834 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
227792 ATCTCACACG
*
227802 CTCAAGTCTCTTTCAT
1 CTCAATTCTCTTTCAT
227818 CTCAATTCTCTTT-AT
1 CTCAATTCTCTTTCAT
227833 CT
1 CT
227835 TAAGTTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.18, C:0.30, G:0.03, T:0.48
Consensus pattern (16 bp):
CTCAATTCTCTTTCAT
Found at i:228123 original size:25 final size:26
Alignment explanation
Indices: 228095--228143 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
228085 CTTTCTTTTC
* *
228095 TTTTTTT-TTTTTTTTGAGTGCTTGA
1 TTTTTTTCTTCTTTTGGAGTGCTTGA
228120 TTTTTTTCTTCTTTTGGAGTGCTT
1 TTTTTTTCTTCTTTTGGAGTGCTT
228144 CAATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.06, C:0.08, G:0.16, T:0.69
Consensus pattern (26 bp):
TTTTTTTCTTCTTTTGGAGTGCTTGA
Found at i:228414 original size:26 final size:26
Alignment explanation
Indices: 228353--228414 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
228343 ATGTCAAGGT
* *
228353 GAAATGGTTGGCTATTTATGGTATGA
1 GAAATGGTAGGCTATTTATGATATGA
*
228379 GACATGGTAGGCTATTTATGATATGA
1 GAAATGGTAGGCTATTTATGATATGA
*
228405 GAAATAGTAG
1 GAAATGGTAG
228415 TGGAATATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (26 bp):
GAAATGGTAGGCTATTTATGATATGA
Found at i:229151 original size:20 final size:22
Alignment explanation
Indices: 229113--229152 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
229103 TCCCAGCTAC
229113 TTTCAGCTACATTTAGTCCACT
1 TTTCAGCTACATTTAGTCCACT
*
229135 TTTCAG-TA-ATTTGGTCCA
1 TTTCAGCTACATTTAGTCCA
229153 AAGCTCTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (22 bp):
TTTCAGCTACATTTAGTCCACT
Found at i:229252 original size:62 final size:62
Alignment explanation
Indices: 229158--229302 Score: 229
Period size: 62 Copynumber: 2.4 Consensus size: 62
229148 GTCCAAAGCT
* * * * *
229158 CTCCTCCAACTTAGTT-CAGCTAGATACTAGCTCCTCTAGCTAAGTTGAAGCTGGATGCTAG
1 CTCCTCCAGCTAAGTTGAAGCTAGATACTAGCTCCTCCAGCTAAGTTGAAGCTAGATGCTAG
*
229219 CTCCTCCAGCTAAGTTGAAGCTAGATGCTAGCTCCTCCAGCTAAGTTGAAGCTAGATGCTAG
1 CTCCTCCAGCTAAGTTGAAGCTAGATACTAGCTCCTCCAGCTAAGTTGAAGCTAGATGCTAG
229281 CTCCTCCAGCTAAGTTGAAGCT
1 CTCCTCCAGCTAAGTTGAAGCT
229303 CCTTAAGTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
61 14 0.18
62 63 0.82
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (62 bp):
CTCCTCCAGCTAAGTTGAAGCTAGATACTAGCTCCTCCAGCTAAGTTGAAGCTAGATGCTAG
Found at i:231916 original size:23 final size:19
Alignment explanation
Indices: 231864--231922 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
231854 GTGCTACAAC
* *
231864 AAAAAGCAACAAGAAAGAA
1 AAAAACCAAAAAGAAAGAA
231883 AAAAACCAAAAAGAAAGAA
1 AAAAACCAAAAAGAAAGAA
*
231902 AAAAACCAAAAAAAAAGAA
1 AAAAACCAAAAAGAAAGAA
231921 AA
1 AA
231923 GTCTCCTACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAACCAAAAAGAAAGAA
Found at i:233709 original size:30 final size:31
Alignment explanation
Indices: 233657--233716 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
233647 CTTAGCTTTA
**
233657 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
233687 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
233717 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:234648 original size:19 final size:21
Alignment explanation
Indices: 234624--234675 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
234614 CGGCCAAGAG
*
234624 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTCAAAAT
234643 CATGTATTTTCATTTCAAAAT
1 CATGTATTTTCATTTCAAAAT
234664 CATGTATTTTCA
1 CATGTATTTTCA
234676 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTCAAAAT
Found at i:235936 original size:19 final size:20
Alignment explanation
Indices: 235912--235962 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
235902 CGGCCAAGAG
* *
235912 CATGTATCTTCCT-TAAAAT
1 CATGTATCTTCATCAAAAAT
*
235931 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
*
235951 CATGTATTTTCA
1 CATGTATCTTCA
235963 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:236742 original size:35 final size:38
Alignment explanation
Indices: 236677--236759 Score: 102
Period size: 35 Copynumber: 2.3 Consensus size: 38
236667 ATTGGAGTAC
* *
236677 AAAAAGAAAGAAAAGACAAAAAGAAGAAGAAAATTC-AG
1 AAAAAGAAAGAAAAGACAAAAAGAAAAAG-AAATTCAAA
*
236715 AAAAAGAAA-AAAA-A-GAAAAGAAAAAGAAATTCAAA
1 AAAAAGAAAGAAAAGACAAAAAGAAAAAGAAATTCAAA
236750 AAAAAGAAAG
1 AAAAAGAAAG
236760 CAAGCCAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 6 0.15
35 20 0.50
36 1 0.03
37 4 0.10
38 9 0.22
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.05
Consensus pattern (38 bp):
AAAAAGAAAGAAAAGACAAAAAGAAAAAGAAATTCAAA
Found at i:238292 original size:17 final size:17
Alignment explanation
Indices: 238270--238304 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
238260 AGGTCATTCG
238270 AGAATGCCTATGGATGA
1 AGAATGCCTATGGATGA
238287 AGAATGCCTATGGATGA
1 AGAATGCCTATGGATGA
238304 A
1 A
238305 ACGAAAGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (17 bp):
AGAATGCCTATGGATGA
Found at i:239206 original size:30 final size:31
Alignment explanation
Indices: 239154--239213 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
239144 CTTAGCTTTA
**
239154 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
239184 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
239214 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:240142 original size:19 final size:20
Alignment explanation
Indices: 240118--240165 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
240108 CGGCCAAGAG
240118 CATGTATCTTCA-TT-AAAAT
1 CATGTAT-TTCATTTAAAAAT
240137 CATGTATTTCATTTAAAAAT
1 CATGTATTTCATTTAAAAAT
240157 CATGTATTT
1 CATGTATTT
240166 TCAAAGGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.15
19 9 0.33
20 14 0.52
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.46
Consensus pattern (20 bp):
CATGTATTTCATTTAAAAAT
Found at i:245627 original size:19 final size:18
Alignment explanation
Indices: 245590--245630 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
245580 GGGTAATAAT
245590 ATAAGCAATGAAAAAATA
1 ATAAGCAATGAAAAAATA
245608 ATAAG-AATGAAATGAAATA
1 ATAAGCAATGAAA--AAATA
245627 ATAA
1 ATAA
245631 AATATAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 5 0.24
19 9 0.43
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (18 bp):
ATAAGCAATGAAAAAATA
Found at i:247840 original size:34 final size:33
Alignment explanation
Indices: 247797--247860 Score: 119
Period size: 34 Copynumber: 1.9 Consensus size: 33
247787 CACATGCCAT
247797 ACACATGAGAGCCTTTGGCGCCAAGCATGAAGAG
1 ACACATGAGAGCCTTTGGCGCCAAG-ATGAAGAG
247831 ACACATGAGAGCCTTTGGCGCCAAGATGAA
1 ACACATGAGAGCCTTTGGCGCCAAGATGAA
247861 CCAACATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.16
Consensus pattern (33 bp):
ACACATGAGAGCCTTTGGCGCCAAGATGAAGAG
Found at i:250403 original size:19 final size:20
Alignment explanation
Indices: 250368--250415 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
250358 TAATAAGGGT
250368 AATAATATAGTAATGAAAAT-A
1 AATAATA-AGTAATG-AAATGA
250389 AATAATAAG-AATGAAATGA
1 AATAATAAGTAATGAAATGA
250408 AATAATAA
1 AATAATAA
250416 AAGATAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 2 0.08
21 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
AATAATAAGTAATGAAATGA
Found at i:250868 original size:19 final size:21
Alignment explanation
Indices: 250825--250876 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
250815 GAAACCCCTT
250825 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
250846 TGAAAATATATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
250865 TGAAGATACATG
1 TGAAAATACATG
250877 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:251820 original size:30 final size:31
Alignment explanation
Indices: 251780--251839 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
251770 ACATGCTGCC
**
251780 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
251811 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
251840 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:255067 original size:19 final size:21
Alignment explanation
Indices: 255024--255075 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
255014 GAAACCCCTT
255024 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
255045 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
255064 TGAAGATACATG
1 TGAAAATACATG
255076 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:256014 original size:30 final size:31
Alignment explanation
Indices: 255973--256032 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
255963 ACATGCTGCC
**
255973 ATGATATCTAAAGGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
256004 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
256033 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:258582 original size:28 final size:27
Alignment explanation
Indices: 258522--258582 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
258512 CTTGGCTTGC
258522 TTTTC-TCTTTTTGAAATATTTTTCTT
1 TTTTCTTCTTTTTGAAATATTTTTCTT
258548 TTTTCTTCTTTTATG-AAT-TTTCTTCTT
1 TTTTCTTCTTTT-TGAAATATTT-TTCTT
258575 TTTGTCTT
1 TTT-TCTT
258583 TTATTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 17 0.55
28 6 0.19
ACGTcount: A:0.11, C:0.13, G:0.05, T:0.70
Consensus pattern (27 bp):
TTTTCTTCTTTTTGAAATATTTTTCTT
Found at i:262165 original size:15 final size:14
Alignment explanation
Indices: 262140--262177 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
262130 TTTTTTCAAA
262140 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
262155 AACAAAAAAAAAGGC
1 AA-AAAAAAAAAGGC
262170 AAAAAAAA
1 AAAAAAAA
262178 CAAAAAGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 14 0.64
16 2 0.09
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Done.