Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009323.1 Hibiscus syriacus cultivar Beakdansim tig00113084_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: 233993
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:143792 original size:189 final size:189
Alignment explanation
Indices: 143414--143797 Score: 504
Period size: 189 Copynumber: 2.0 Consensus size: 189
143404 AAACTATCTA
143414 AAGGGAGACAAAATTTTGTTCCAAGGGAAACTATCTCAAGAGAGATAAAATTAATTTCAAAGGAA
1 AAGGGAGACAAAATTTTGTTCCAAGGGAAACTATCTCAAGAGAGATAAAATTAATTTCAAAGGAA
* * * * * **
143479 ATGTTTTCAGTGTTTATGTTTCAAGAGAAACTGTCTCAAGGGGGACAAAGTTTTGTTTCAAGGGA
66 ATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGA
* * * * * *
143544 AACTACCCCAAGCGAGATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATGTTTC
131 AAATACCCCAAGCGAGACAAAATTTATTTCAAGGGAAAAGATTTAAATATTTATGTTTC
* ** * *
143603 AAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGGAA
1 AAGGGAGACAAAATTTTGTTCCAAGGGAAACTATCTCAAGAGAGATAAAATTAATTTCAAAGGAA
143668 ATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGA
66 ATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGA
** * * * *
143733 AAATGTCTCAAGGGAGACGAAA-TTAGTTTCAA-TGAAACCAGATTTAAATATTT-TGTTTC
131 AAATACCCCAAGCGAGACAAAATTTA-TTTCAAGGGAAA--AGATTTAAATATTTATGTTTC
143792 AAGGGA
1 AAGGGA
143798 AACTTGGAAA
Statistics
Matches: 168, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
188 7 0.04
189 151 0.90
190 10 0.06
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (189 bp):
AAGGGAGACAAAATTTTGTTCCAAGGGAAACTATCTCAAGAGAGATAAAATTAATTTCAAAGGAA
ATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGA
AAATACCCCAAGCGAGACAAAATTTATTTCAAGGGAAAAGATTTAAATATTTATGTTTC
Found at i:144176 original size:98 final size:98
Alignment explanation
Indices: 144022--144207 Score: 320
Period size: 98 Copynumber: 1.9 Consensus size: 98
144012 CAGCCAGCCG
144022 TCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAA
1 TCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAA
144087 TTGGCTCCGAAATTGGGAAATTGCAACCAACCA
66 TTGGCTCCGAAATTGGGAAATTGCAACCAACCA
* * *
144120 TCCCTTCGTTGTGAAGTTG-GACTTGTGTTTTCTCGAGTCCAATATCTTTCGCTGTGAAGTTGAA
1 TCCCTTCGTTGTGAAGTTGAG-CTTGTGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAA
*
144184 ATTGGCTCTGAAATTGGGAAATTG
65 ATTGGCTCCGAAATTGGGAAATTG
144208 TTTGTTGACA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
97 1 0.01
98 82 0.99
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (98 bp):
TCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAA
TTGGCTCCGAAATTGGGAAATTGCAACCAACCA
Found at i:145950 original size:67 final size:69
Alignment explanation
Indices: 145816--145951 Score: 179
Period size: 69 Copynumber: 2.0 Consensus size: 69
145806 TGTCTCTCTC
*
145816 TTGATGCTCCATGATATTCGAGTAGAGTGGTGCACTAATTCAGAAATGATTGTGATTGATCAATC
1 TTGATGATCCATGATATTCGAGTAGAGTGGTGCACTAATTCAGAAATGATTGTGATTGATCAATC
145881 TCAT
66 TCAT
* * * * * *
145885 TTGATGATCTATGATCTTCGAGT-GAAGTGGTTCAGT-ATTC-GAAATGATTGTGCTTGATTAAT
1 TTGATGATCCATGATATTCGAGTAG-AGTGGTGCACTAATTCAGAAATGATTGTGATTGATCAAT
145947 CTCAT
65 CTCAT
145952 AGTTTAAATC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
67 25 0.42
68 5 0.08
69 29 0.49
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGATCCATGATATTCGAGTAGAGTGGTGCACTAATTCAGAAATGATTGTGATTGATCAATC
TCAT
Found at i:146039 original size:27 final size:26
Alignment explanation
Indices: 146009--146074 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
145999 GCATCTTGTC
146009 TTCTTTTTTCTTCAAT-TTTCCTTTTTT
1 TTCTTTTTTCTTC--TCTTTCCTTTTTT
* *
146036 TTCTTTTTTATTCTCTTTGCTTTTTT
1 TTCTTTTTTCTTCTCTTTCCTTTTTT
146062 TCTCTTTTTTCTT
1 T-TCTTTTTTCTT
146075 TTTGTTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.03
26 11 0.32
27 22 0.65
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.76
Consensus pattern (26 bp):
TTCTTTTTTCTTCTCTTTCCTTTTTT
Found at i:146044 original size:17 final size:16
Alignment explanation
Indices: 146032--146077 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
146022 AATTTTCCTT
146032 TTTTTTCTTTTTTATTC
1 TTTTTTCTTTTTT-TTC
* *
146049 TCTTTGCTTTTTTTCTC
1 TTTTTTCTTTTTTT-TC
146066 TTTTTTCTTTTT
1 TTTTTTCTTTTT
146078 GTTTTGATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTC
Found at i:146073 original size:24 final size:24
Alignment explanation
Indices: 146031--146082 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
146021 CAATTTTCCT
*
146031 TTTTTTTCTTTTTTATTCTCTTTG
1 TTTTTTTCTCTTTTATTCTCTTTG
*
146055 CTTTTTTTCTCTTTT-TTCTTTTTG
1 -TTTTTTTCTCTTTTATTCTCTTTG
146079 TTTT
1 TTTT
146083 GATTGAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 8 0.32
25 13 0.52
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (24 bp):
TTTTTTTCTCTTTTATTCTCTTTG
Found at i:149175 original size:31 final size:31
Alignment explanation
Indices: 149109--149181 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
149099 ATAAAAAGGT
* * *
149109 AAGAAATAAATAAATAAATAAAATTAAAATG
1 AAGAAATAAACAAATAAATAAAAATAAAATA
* *
149140 AAGAAA-AAACAAATTAATAAAAGATAAGATA
1 AAGAAATAAACAAATAAATAAAA-ATAAAATA
149171 AAGAAAGTAAA
1 AAGAAA-TAAA
149182 GATAAAATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 14 0.41
31 17 0.50
33 3 0.09
ACGTcount: A:0.71, C:0.01, G:0.10, T:0.18
Consensus pattern (31 bp):
AAGAAATAAACAAATAAATAAAAATAAAATA
Found at i:149268 original size:9 final size:9
Alignment explanation
Indices: 149198--149313 Score: 66
Period size: 9 Copynumber: 12.9 Consensus size: 9
149188 ATAGTACGTA
149198 AAATAAATAT
1 AAATAAA-AT
149208 AAA-AAAAT
1 AAATAAAAT
*
149216 AAA-GAAAT
1 AAATAAAAT
*
149224 AAAGAAAA-
1 AAATAAAAT
*
149232 AGAAGAAAA-
1 A-AATAAAAT
149241 AAATATAAAT
1 AAATA-AAAT
149251 AAA-ACAAAT
1 AAATA-AAAT
149260 AAATAAAAT
1 AAATAAAAT
149269 -AATAAAA-
1 AAATAAAAT
*
149276 AAGTAAAAAT
1 AAAT-AAAAT
*
149286 AATATATATAT
1 AA-ATA-AAAT
*
149297 ATATAAAAT
1 AAATAAAAT
149306 AAATAAAA
1 AAATAAAA
149314 AATAAAAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 21
0.74 0.09 0.18
Matches are distributed among these distances:
8 25 0.29
9 43 0.50
10 13 0.15
11 5 0.06
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:149307 original size:42 final size:41
Alignment explanation
Indices: 149258--149412 Score: 133
Period size: 38 Copynumber: 3.8 Consensus size: 41
149248 AATAAAACAA
149258 ATAAATAAAATAATAAAAAAGTAAAAATAATATATATATAT
1 ATAAATAAAATAATAAAAAAGTAAAAATAATATATATATAT
* * *
149299 AT-AA-AATA-AATAAAAAA-TAAAAAATAGTAAATATATAT
1 ATAAATAAAATAATAAAAAAGT-AAAAATAATATATATATAT
* * **
149337 ATATATAAATTAATAAAACTGATAATAAAATAATATATATATAT
1 ATAAATAAAATAATAAAAAAG-T-A-AAAATAATATATATATAT
* * * *
149381 ATACATATAAT-CTAAAAAAATAAAAAT-ATATA
1 ATAAATAAAATAATAAAAAAGTAAAAATAATATA
149413 CTAAAGTAAA
Statistics
Matches: 90, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
37 1 0.01
38 28 0.31
39 9 0.10
40 9 0.10
41 10 0.11
42 1 0.01
43 8 0.09
44 24 0.27
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (41 bp):
ATAAATAAAATAATAAAAAAGTAAAAATAATATATATATAT
Found at i:149310 original size:46 final size:44
Alignment explanation
Indices: 149256--149403 Score: 160
Period size: 46 Copynumber: 3.3 Consensus size: 44
149246 TAAATAAAAC
*
149256 AAATAAATAAAATAATAAAAAAGTAAAAATAATATATATATATATA
1 AAATAAATAAAATAATAAAAAA-T-AATATAATATATATATATATA
*
149302 AAATAAATAAAA-AATAAAAAATAGTA-AATATATATATATAT-
1 AAATAAATAAAATAATAAAAAATAATATAATATATATATATATA
* * *
149343 AAATTAATAAAACTGATAATAAAATAATATATATATATATACATATA
1 AAATAAATAAAA-TAATAA-AAAATAATATA-ATATATATATATATA
**
149390 ATCTAAA-AAAATAA
1 AAATAAATAAAATAA
149404 AAATATATAC
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
41 11 0.13
42 15 0.17
43 6 0.07
44 9 0.10
45 12 0.14
46 29 0.34
47 4 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (44 bp):
AAATAAATAAAATAATAAAAAATAATATAATATATATATATATA
Found at i:149322 original size:38 final size:39
Alignment explanation
Indices: 149265--149406 Score: 137
Period size: 42 Copynumber: 3.5 Consensus size: 39
149255 CAAATAAATA
149265 AAAT-AATAAAAAAGT-AAAAATAATATATATATATATA-
1 AAATAAATAAAAAA-TAAAAAATAATATATATATATATAC
* *
149302 AAATAAATAAAAAATAAAAAATAGTAAATATATATATATAT
1 AAATAAATAAAAAATAAAAAATA--ATATATATATATATAC
* *
149343 AAATTAATAAAACTGATAATAAAATAATATATATATATATAC
1 AAATAAATAAAA--AATAA-AAAATAATATATATATATATAC
* *
149385 ATATAATCTAAAAAAATAAAAA
1 AAATAA-AT-AAAAAATAAAAA
149407 TATATACTAA
Statistics
Matches: 86, Mismatches: 9, Indels: 16
0.77 0.08 0.14
Matches are distributed among these distances:
37 5 0.06
38 16 0.19
40 14 0.16
41 14 0.16
42 22 0.26
43 5 0.06
44 10 0.12
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (39 bp):
AAATAAATAAAAAATAAAAAATAATATATATATATATAC
Found at i:150208 original size:2 final size:2
Alignment explanation
Indices: 150196--150268 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
150186 TTTCCTAATC
150196 AT AT A- 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
150237 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
150269 GCATGTATGT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:150442 original size:2 final size:2
Alignment explanation
Indices: 150435--150460 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
150425 TCTAATCATA
150435 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
150461 TATTTTTTGT
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:155767 original size:25 final size:26
Alignment explanation
Indices: 155709--155767 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 26
155699 ATGCTCGTTT
*
155709 TTCCAGTTTAGTGTCTAATGTTTTTTTCG
1 TTCCAGTTTAGTGTCTAATG---TTTTCA
*
155738 TTCCAGTTTGGTGTCTAATG-TTTCA
1 TTCCAGTTTAGTGTCTAATGTTTTCA
155763 TTCCA
1 TTCCA
155768 TTACTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.32
29 19 0.68
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (26 bp):
TTCCAGTTTAGTGTCTAATGTTTTCA
Found at i:156937 original size:12 final size:12
Alignment explanation
Indices: 156919--156951 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
156909 ATTTTATAAT
156919 CCCATGTATTAG
1 CCCATGTATTAG
*
156931 TCCATGTATTAG
1 CCCATGTATTAG
156943 CCCATGTAT
1 CCCATGTAT
156952 AGTACTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (12 bp):
CCCATGTATTAG
Found at i:158210 original size:9 final size:9
Alignment explanation
Indices: 158193--158261 Score: 75
Period size: 9 Copynumber: 7.7 Consensus size: 9
158183 CTTAAATTTT
*
158193 AAATACTAG
1 AAATTCTAG
158202 AAATTCTAG
1 AAATTCTAG
* *
158211 TAATTCCAG
1 AAATTCTAG
*
158220 AAATTATAG
1 AAATTCTAG
*
158229 AAATTCCAG
1 AAATTCTAG
*
158238 AAATTCTAT
1 AAATTCTAG
*
158247 AAATTCAAG
1 AAATTCTAG
158256 AAATTC
1 AAATTC
158262 CAGTAATGGA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (9 bp):
AAATTCTAG
Found at i:158223 original size:18 final size:18
Alignment explanation
Indices: 158200--158268 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
158190 TTTAAATACT
158200 AGAAATTCTAGTAATTCC
1 AGAAATTCTAGTAATTCC
* *
158218 AGAAATTATAGAAATTCC
1 AGAAATTCTAGTAATTCC
*
158236 AGAAATTCTA-TAAATTCA
1 AGAAATTCTAGT-AATTCC
*
158254 AGAAATTCCAGTAAT
1 AGAAATTCTAGTAAT
158269 GGAATTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 42 0.98
19 1 0.02
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.30
Consensus pattern (18 bp):
AGAAATTCTAGTAATTCC
Found at i:159511 original size:30 final size:29
Alignment explanation
Indices: 159449--159539 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 29
159439 ACCCATTTGT
* * * *
159449 AACTTTTTAAAATTACATTTTGGTCCCTA
1 AACTTTTTAAATTTATAATTTGGTCACTA
* *
159478 AACTTTTTAAAGTTTATACTTTAGTCACTA
1 AACTTTTTAAA-TTTATAATTTGGTCACTA
**
159508 AACTTTACCAAATTTATAATTTGGTCACTA
1 AACTTT-TTAAATTTATAATTTGGTCACTA
159538 AA
1 AA
159540 TAAATCTATT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 11 0.22
30 37 0.73
31 3 0.06
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (29 bp):
AACTTTTTAAATTTATAATTTGGTCACTA
Found at i:161466 original size:104 final size:104
Alignment explanation
Indices: 161268--161467 Score: 233
Period size: 104 Copynumber: 1.9 Consensus size: 104
161258 ATAAGATTGC
* * ** * *
161268 TCTTGAAGAGGAAATTATTGGAATTGAAGTTGTAAACACTGTGGACACTGGTATTGAAGAGAAAA
1 TCTTGAAGAGGAAAATAATAAAATTGAAGTTGTAAACACTGTAGAAACTGGTATTGAAGAGAAAA
** *
161333 TTATTGAAATTGAAGCTGTAAAGACTGTGGACACACTGA
66 TTATTGAAATTGAAGCCCTAAACACTGTGGACACACTGA
* * * * *
161372 TCTTGAAGAGGAAAATAATAAAATTGAAGTTTTAAATAGTGTAGAAATTGGTTTTGAAGAGGAAA
1 TCTTGAAGAGGAAAATAATAAAATTGAAGTTGTAAACACTGTAGAAACTGGTATTGAAGA-GAAA
*
161437 A-TATT-AGAATTGAAGCCCTAAACATTGTGGA
65 ATTATTGA-AATTGAAGCCCTAAACACTGTGGA
161468 AATTGGTATT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
103 1 0.01
104 73 0.92
105 5 0.06
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.29
Consensus pattern (104 bp):
TCTTGAAGAGGAAAATAATAAAATTGAAGTTGTAAACACTGTAGAAACTGGTATTGAAGAGAAAA
TTATTGAAATTGAAGCCCTAAACACTGTGGACACACTGA
Found at i:161489 original size:51 final size:51
Alignment explanation
Indices: 161270--161489 Score: 201
Period size: 51 Copynumber: 4.3 Consensus size: 51
161260 AAGATTGCTC
* * * *
161270 TTGAAGAGGAAATTATTGGAATTGAAGTTGTAAACACTGTGGACACTGGTA
1 TTGAAGAGGAAAATATTAGAATTGAAGCTGTAAACACTGTGGAAACTGGTA
* * *
161321 TTGAAGA-GAAAATTATT-GAAATTGAAGCTGTAAAGACTGTGGACACACTGATC
1 TTGAAGAGGAAAA-TATTAG-AATTGAAGCTGTAAACACTGTGGA-A-ACTGGTA
* * * * * * * * *
161374 TTGAAGAGGAAAATAATAAAATTGAAGTTTTAAATAGTGTAGAAATTGGTT
1 TTGAAGAGGAAAATATTAGAATTGAAGCTGTAAACACTGTGGAAACTGGTA
** * *
161425 TTGAAGAGGAAAATATTAGAATTGAAGCCCTAAACATTGTGGAAATTGGTA
1 TTGAAGAGGAAAATATTAGAATTGAAGCTGTAAACACTGTGGAAACTGGTA
*
161476 TTGAAGAGAAAAAT
1 TTGAAGAGGAAAAT
161490 GTTGGGAATG
Statistics
Matches: 137, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
50 5 0.04
51 92 0.67
52 1 0.01
53 34 0.25
54 5 0.04
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (51 bp):
TTGAAGAGGAAAATATTAGAATTGAAGCTGTAAACACTGTGGAAACTGGTA
Found at i:163753 original size:21 final size:21
Alignment explanation
Indices: 163727--163769 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
163717 TTTCTGGGCT
* *
163727 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
163748 AGGGGAATCGATACCCACTCA
1 AGGGGAATCGATACCCACTCA
163769 A
1 A
163770 CGAATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:163865 original size:14 final size:14
Alignment explanation
Indices: 163840--163879 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
163830 CCCCATATAA
163840 AAAAAAAG-AGAAG
1 AAAAAAAGAAGAAG
*
163853 AAAAGAAGAAGAAG
1 AAAAAAAGAAGAAG
163867 AAAAAAAGAAGAA
1 AAAAAAAGAAGAA
163880 AGACTAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAGAAG
Found at i:170582 original size:21 final size:21
Alignment explanation
Indices: 170540--170582 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
170530 TTTCTGGGCT
* *
170540 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
170561 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
170582 A
1 A
170583 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:170634 original size:20 final size:20
Alignment explanation
Indices: 170609--170646 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
170599 GAATGCTAGA
*
170609 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
170629 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
170647 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:170678 original size:17 final size:17
Alignment explanation
Indices: 170650--170699 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
170640 TCCCCCATAT
*
170650 AAAAAAAAAAGAAAGAG
1 AAAAAAAGAAGAAAGAG
*
170667 AAGAAAAGAAG-AAGAAG
1 AAAAAAAGAAGAAAG-AG
170684 AAAAAAAGAAGAAAGA
1 AAAAAAAGAAGAAAGA
170700 CTAAACTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.11
17 22 0.79
18 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAGAAAGAG
Found at i:170693 original size:14 final size:14
Alignment explanation
Indices: 170656--170696 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
170646 ATATAAAAAA
170656 AAAAGAAAG-AGAAG
1 AAAA-AAAGAAGAAG
*
170670 AAAAGAAGAAGAAG
1 AAAAAAAGAAGAAG
170684 AAAAAAAGAAGAA
1 AAAAAAAGAAGAA
170697 AGACTAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 3 0.12
14 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAGAAG
Found at i:174397 original size:27 final size:27
Alignment explanation
Indices: 174367--174434 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
174357 TTCACTCTTA
*
174367 GACCTCTAGACGACGAGTTACTCCGAC
1 GACCTCCAGACGACGAGTTACTCCGAC
* * *
174394 GACCTCCAGAAGATGAGTTACTCCTAC
1 GACCTCCAGACGACGAGTTACTCCGAC
174421 GACCTCCAGACGAC
1 GACCTCCAGACGAC
174435 AAGCACAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.18
Consensus pattern (27 bp):
GACCTCCAGACGACGAGTTACTCCGAC
Found at i:175247 original size:21 final size:21
Alignment explanation
Indices: 175223--175270 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
175213 TTTTAAGCTC
175223 GAGTCTTGAGATTGCATAAAT
1 GAGTCTTGAGATTGCATAAAT
175244 GAGTCTTGAGATTGCATAAAT
1 GAGTCTTGAGATTGCATAAAT
175265 GAGTCT
1 GAGTCT
175271 AAAGACTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.33
Consensus pattern (21 bp):
GAGTCTTGAGATTGCATAAAT
Found at i:177413 original size:22 final size:20
Alignment explanation
Indices: 177388--177427 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
177378 GTTTTGGTAT
177388 ATATAGTTTTCTATTCTTTTTA
1 ATATAGTTTTC-ATT-TTTTTA
*
177410 ATATATTTTTCATTTTTT
1 ATATAGTTTTCATTTTTT
177428 CTAAACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (20 bp):
ATATAGTTTTCATTTTTTTA
Found at i:177714 original size:20 final size:21
Alignment explanation
Indices: 177676--177719 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
177666 ACATGATCCG
177676 AAATAATATTTTTTATTAA-A
1 AAATAATATTTTTTATTAATA
*
177696 AAATATTA-TTTTTATTTAATA
1 AAATAATATTTTTTA-TTAATA
177717 AAA
1 AAA
177720 ATATGAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATAATATTTTTTATTAATA
Found at i:184513 original size:27 final size:27
Alignment explanation
Indices: 184483--184550 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
184473 TTCACTCTTA
* *
184483 GACCTCTAGACGATGAGTTACTCCGAC
1 GACCTCAAGACGACGAGTTACTCCGAC
* * *
184510 GACCTCCAGAAGACGAGTTACTCCTAC
1 GACCTCAAGACGACGAGTTACTCCGAC
184537 GACCTCAAGACGAC
1 GACCTCAAGACGAC
184551 AAGCACAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.18
Consensus pattern (27 bp):
GACCTCAAGACGACGAGTTACTCCGAC
Found at i:185364 original size:21 final size:21
Alignment explanation
Indices: 185340--185387 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
185330 TTTTAAGCTC
185340 GAGTCTTGAGATTGCATAAAT
1 GAGTCTTGAGATTGCATAAAT
185361 GAGTCTTGAGATTGCATAAAT
1 GAGTCTTGAGATTGCATAAAT
185382 GAGTCT
1 GAGTCT
185388 CAAGACTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.33
Consensus pattern (21 bp):
GAGTCTTGAGATTGCATAAAT
Found at i:187526 original size:22 final size:20
Alignment explanation
Indices: 187501--187540 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
187491 GTTTTGGTAT
187501 ATATAGTTTTCTATTCTTTTTA
1 ATATAGTTTTC-ATT-TTTTTA
*
187523 ATATATTTTTCATTTTTT
1 ATATAGTTTTCATTTTTT
187541 CTAAACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (20 bp):
ATATAGTTTTCATTTTTTTA
Found at i:188438 original size:20 final size:19
Alignment explanation
Indices: 188401--188454 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
188391 AAGCGTATAT
188401 AAACAATATTATATATAAG
1 AAACAATATTATATATAAG
188420 AAACATATATTA-ATAATAA-
1 AAACA-ATATTATAT-ATAAG
*
188439 AAGATAATATTATATA
1 AA-ACAATATTATATA
188455 GTCGCATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (19 bp):
AAACAATATTATATATAAG
Found at i:199557 original size:7 final size:7
Alignment explanation
Indices: 199545--199569 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
199535 GCATCAACTG
199545 CAAAGAC
1 CAAAGAC
199552 CAAAGAC
1 CAAAGAC
199559 CAAAGAC
1 CAAAGAC
199566 CAAA
1 CAAA
199570 ACTTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.12, T:0.00
Consensus pattern (7 bp):
CAAAGAC
Found at i:200256 original size:23 final size:23
Alignment explanation
Indices: 200192--200279 Score: 68
Period size: 23 Copynumber: 3.8 Consensus size: 23
200182 TTTTATTCTT
* * *
200192 AACAAACATGTTCGCAAACACTA
1 AACAAACATGTTCACGAACGCTA
* * * **
200215 AACGAATATATTCGTGAACGCTA
1 AACAAACATGTTCACGAACGCTA
*
200238 AACAAACATGTTCACGAACGTTA
1 AACAAACATGTTCACGAACGCTA
** *
200261 AATGAATATGTTCACGAAC
1 AACAAACATGTTCACGAAC
200280 ATTTAAATGA
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (23 bp):
AACAAACATGTTCACGAACGCTA
Found at i:200290 original size:24 final size:23
Alignment explanation
Indices: 200242--200303 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
200232 ACGCTAAACA
200242 AACATGTTCACGAACGTTAAATG
1 AACATGTTCACGAACGTTAAATG
* *
200265 AATATGTTCACGAACATTTAAATG
1 AACATGTTCACGAAC-GTTAAATG
*
200289 AACATATTCAC-AACG
1 AACATGTTCACGAACG
200304 AATACGTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (23 bp):
AACATGTTCACGAACGTTAAATG
Found at i:201374 original size:29 final size:29
Alignment explanation
Indices: 201332--201393 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
201322 TTCTACAGCA
*
201332 ACCTTGGAGGTCGCCATGGCATCCGGGCG
1 ACCTTGGAGGTCGCCATGGCATCCGAGCG
201361 ACCTTGGAGGTCGCCATGGCATCCGAGCG
1 ACCTTGGAGGTCGCCATGGCATCCGAGCG
201390 ACCT
1 ACCT
201394 GTGTGGTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (29 bp):
ACCTTGGAGGTCGCCATGGCATCCGAGCG
Found at i:201478 original size:20 final size:20
Alignment explanation
Indices: 201453--201525 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
201443 GTATTGGAGC
201453 ATGCATGGGGGAGTTGTGGG
1 ATGCATGGGGGAGTTGTGGG
**
201473 ATGCATGTTGTGCATGG-GACGTGGG
1 ATGCATG--G-G---GGAGTTGTGGG
201498 AATGCATGGGGGAGTTGTGGG
1 -ATGCATGGGGGAGTTGTGGG
201519 ATGCATG
1 ATGCATG
201526 CTGTGCATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
20 16 0.39
21 6 0.15
22 1 0.02
23 2 0.05
24 1 0.02
25 6 0.15
26 9 0.22
ACGTcount: A:0.18, C:0.08, G:0.48, T:0.26
Consensus pattern (20 bp):
ATGCATGGGGGAGTTGTGGG
Found at i:201506 original size:46 final size:46
Alignment explanation
Indices: 201453--201545 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
201443 GTATTGGAGC
*
201453 ATGCATGGGGGAGTTGTGGGATGCATGTTGTGCATGGGACGTGGGA
1 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
*
201499 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTTGGA
1 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
201545 A
1 A
201546 CTGTGCATGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.18, C:0.10, G:0.46, T:0.26
Consensus pattern (46 bp):
ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
Found at i:202116 original size:21 final size:21
Alignment explanation
Indices: 202091--202134 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
202081 AATCTAGTTA
202091 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
202112 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
202133 AT
1 AT
202135 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:202144 original size:28 final size:28
Alignment explanation
Indices: 202111--202164 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
202101 TAGTATAAAT
*
202111 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAGTTTATTAGTTTAAGTTATATTA
202139 TATTAGTTTATTAGTTTAAGTTATAT
1 TATTAGTTTATTAGTTTAAGTTATAT
202165 ATTATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAGTTTATTAGTTTAAGTTATATTA
Found at i:202724 original size:20 final size:21
Alignment explanation
Indices: 202680--202724 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
202670 AAATATTGTG
**
202680 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
202701 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
202721 TTTA
1 TTTA
202725 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:203013 original size:26 final size:25
Alignment explanation
Indices: 202984--203042 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
202974 AAATCATCTT
*
202984 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
203010 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
203036 ATTATTA
1 ATTATTA
203043 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:205955 original size:26 final size:26
Alignment explanation
Indices: 205928--206268 Score: 255
Period size: 26 Copynumber: 13.6 Consensus size: 26
205918 GATGATTTAG
* *
205928 TAATGATTTGATAATAATCATTACAG
1 TAATGATTTGATAATAATCATTATAA
205954 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
205980 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
206006 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
206029 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
206052 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
206078 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
206104 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * * *
206130 AAATGATTTAATAAT-GT-TTTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
206153 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
206176 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* * *
206202 TAATGATTTTATAATAATTATT-TAG
1 TAATGATTTGATAATAATCATTATAA
* * *
206227 TAATTATTT-ATAATAATGATTTAATAC
1 TAATGATTTGATAATAATCA-TT-ATAA
*
206254 TAATGATTTAATAAT
1 TAATGATTTGATAAT
206269 TATTACTAAT
Statistics
Matches: 251, Mismatches: 44, Indels: 38
0.75 0.13 0.11
Matches are distributed among these distances:
21 5 0.02
22 7 0.03
23 24 0.10
24 23 0.09
25 27 0.11
26 148 0.59
27 12 0.05
28 5 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:206090 original size:124 final size:124
Alignment explanation
Indices: 205870--206268 Score: 678
Period size: 124 Copynumber: 3.2 Consensus size: 124
205860 ATGTATTTAT
205870 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
205935 TTGATAATAATCATTACAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
205994 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
206059 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
206118 TAATCATTATAAAAATGATTTAATAATGTTTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * *
206183 TTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTAATTATTTA-TAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
206240 TAATGATT-TAATACTAATGATTTAATAAT
1 TAATCATTATAA-A--AATGATTTAATAAT
206269 TATTACTAAT
Statistics
Matches: 264, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
121 3 0.01
122 11 0.04
123 11 0.04
124 239 0.91
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:206240 original size:38 final size:37
Alignment explanation
Indices: 205965--206281 Score: 156
Period size: 38 Copynumber: 8.5 Consensus size: 37
205955 AATGATTTGA
* * *
205965 TAATAATCATTATAATAATGATTTAGTAATAATCATT
1 TAATAATTATTATAATAATGATTTAATAATAATGATT
* * *
206002 ATAAAAATGATT-TAATAATGATTTAAATATTTAATGA-T
1 -TAATAATTATTATAATAATGATTT-AATA-ATAATGATT
* * * * *
206040 T--TGATGATT-TAGTAATGATTTGATAATAATCATT
1 TAATAATTATTATAATAATGATTTAATAATAATGATT
* * *
206074 ATAGTAATGATTTGATAATAATCA-TT-ATAATAATGATTT
1 -TAATAATTA-TT-ATAATAATGATTTAATAATAATGA-TT
* * *
206113 AGTAATAATCATTATAAAAATGA-TT--TAATAATGTTT
1 --TAATAATTATTATAATAATGATTTAATAATAATGATT
* * * * * *
206149 TAAATATTTAATGAT-TTGATGATTTAGTAATGAT--TT
1 T-AATAATT-ATTATAATAATGATTTAATAATAATGATT
* * *
206185 GATAATAATCATTATAATAATGATTTTATAATAATTATT
1 --TAATAATTATTATAATAATGATTTAATAATAATGATT
* *
206224 TAGTAATTATTTATAATAATGATTTAATACTAATGATT
1 TAATAATTA-TTATAATAATGATTTAATAATAATGATT
206262 TAATAATTATTACTAATAAT
1 TAATAATTATTA-TAATAAT
206282 TATAAAATAC
Statistics
Matches: 214, Mismatches: 42, Indels: 46
0.71 0.14 0.15
Matches are distributed among these distances:
33 5 0.02
34 5 0.02
35 27 0.13
36 14 0.07
37 55 0.26
38 81 0.38
39 13 0.06
40 14 0.07
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (37 bp):
TAATAATTATTATAATAATGATTTAATAATAATGATT
Found at i:206291 original size:38 final size:38
Alignment explanation
Indices: 206176--206294 Score: 105
Period size: 38 Copynumber: 3.1 Consensus size: 38
206166 GATGATTTAG
* * *** *
206176 TAATGATTTGATAATAATCATTATAATAATGATTTTATAA
1 TAATGATTTAATAATTAT--TTATAATAATGATAAAATAC
* * **
206216 TAATTATTTAGTAATTATTTATAATAATGATTTAATAC
1 TAATGATTTAATAATTATTTATAATAATGATAAAATAC
*
206254 TAATGATTTAATAATTA-TTACTAATAATTATAAAATAC
1 TAATGATTTAATAATTATTTA-TAATAATGATAAAATAC
206292 TAA
1 TAA
206295 CAAATGAGTG
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
37 3 0.04
38 50 0.75
40 14 0.21
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (38 bp):
TAATGATTTAATAATTATTTATAATAATGATAAAATAC
Found at i:207013 original size:29 final size:29
Alignment explanation
Indices: 206971--207103 Score: 205
Period size: 29 Copynumber: 4.6 Consensus size: 29
206961 TCGTGAGCTA
**
206971 GGACTACATGGCGACCTACTTGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
207000 GGACTACATGGCGACCTACAAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
207029 GGACTACATGGCGACCTACAAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
* *
207058 GGACTACATGACGACCTACAAGGTCGCCCA
1 GGACTACATGGCGACCTACAAGGTCG-CCG
*
207088 GG-CTGCATGGCGACCT
1 GGACTACATGGCGACCT
207104 CTCCATTGGC
Statistics
Matches: 97, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 93 0.96
30 4 0.04
ACGTcount: A:0.23, C:0.32, G:0.30, T:0.16
Consensus pattern (29 bp):
GGACTACATGGCGACCTACAAGGTCGCCG
Found at i:207182 original size:20 final size:20
Alignment explanation
Indices: 207153--207191 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
207143 ACCTCTCCAT
207153 TGGCTCGTATGGCTCGTATA
1 TGGCTCGTATGGCTCGTATA
*
207173 TGGCTTGTATGGCTCGTAT
1 TGGCTCGTATGGCTCGTAT
207192 GTCACCCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (20 bp):
TGGCTCGTATGGCTCGTATA
Found at i:207205 original size:21 final size:21
Alignment explanation
Indices: 207179--207225 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
207169 TATATGGCTT
207179 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
207200 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
207221 GTATG
1 GTATG
207226 TCGCCTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (21 bp):
GTATGGCTCGTATGTCACCCC
Found at i:207211 original size:9 final size:9
Alignment explanation
Indices: 207153--207192 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
207143 ACCTCTCCAT
207153 TGGCTCGTA
1 TGGCTCGTA
207162 TGGCTCGTATA
1 TGGCTCG--TA
*
207173 TGGCTTGTA
1 TGGCTCGTA
207182 TGGCTCGTA
1 TGGCTCGTA
207191 TG
1 TG
207193 TCACCCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:210015 original size:41 final size:41
Alignment explanation
Indices: 209927--210084 Score: 120
Period size: 42 Copynumber: 3.8 Consensus size: 41
209917 AATTGATACT
** * * *
209927 TTAGCGGCGTTTTTAGTAAAAACGCTGCAATAGAGTTGACA
1 TTAGCGGCGTTTTTACCAAAAACGCCGCAATAGAGTGGAAA
* *
209968 TATAGCGGCGTTTTTA-CAAAAATGCCGCAATAGGGTGGCAAA
1 T-TAGCGGCGTTTTTACCAAAAACGCCGCAATAGAGTGG-AAA
* * * * ***
210010 TTAGCGGCGTTTATACCAAAAAACGCCACAATAAAATAGTTCA
1 TTAGCGGCGTTTTTACC-AAAAACGCCGCAATAGAGT-GGAAA
* **
210053 TTTGCGGCGTTTTTATTAAAAACGCCGCAATA
1 TTAGCGGCGTTTTTACCAAAAACGCCGCAATA
210085 TTCTGATATA
Statistics
Matches: 92, Mismatches: 20, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
41 31 0.34
42 32 0.35
43 28 0.30
44 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGTTTTTACCAAAAACGCCGCAATAGAGTGGAAA
Found at i:211515 original size:11 final size:11
Alignment explanation
Indices: 211499--211527 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
211489 TTTTACTCGT
211499 ACCAAATTCTA
1 ACCAAATTCTA
211510 ACCAAATTCTA
1 ACCAAATTCTA
211521 ACCAAAT
1 ACCAAAT
211528 ATCTGAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (11 bp):
ACCAAATTCTA
Found at i:213045 original size:28 final size:28
Alignment explanation
Indices: 213014--213067 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
213004 TTATGAGTGC
213014 ATATAATAT-TTGTCATGGAAGTTTATCA
1 ATAT-ATATCTTGTCATGGAAGTTTATCA
* *
213042 ATATTTCTCTTGTCATGGAAGTTTAT
1 ATATATATCTTGTCATGGAAGTTTAT
213068 ATTTTCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (28 bp):
ATATATATCTTGTCATGGAAGTTTATCA
Found at i:219245 original size:22 final size:20
Alignment explanation
Indices: 219207--219254 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
219197 TGGGTAGATG
*
219207 TTTTAAATTTACCTGAC-TT
1 TTTTATATTTACCTGACATT
219226 TATTTATATTGTACCATGACATT
1 T-TTTATATT-TACC-TGACATT
219249 TTTTAT
1 TTTTAT
219255 TTAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 7 0.29
21 4 0.17
22 9 0.38
23 3 0.12
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTATATTTACCTGACATT
Found at i:219592 original size:21 final size:21
Alignment explanation
Indices: 219574--219658 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
219564 ATGAAGCAAG
*
219574 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
219595 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
219616 GGAAGCAGAGAGA-AAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
219636 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
219657 GG
1 GG
219659 CAGAACAGAG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 18 0.33
21 36 0.67
ACGTcount: A:0.38, C:0.20, G:0.41, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:219659 original size:21 final size:20
Alignment explanation
Indices: 219610--219670 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
219600 CAGCTAGAGC
* *
219610 AGCAGCGGAAGCAGAGAGAA
1 AGCAGCGGCAGCACAGAGAA
219630 AGCAGCGGCAGCACAGAGAGA
1 AGCAGCGGCAGCACAGAGA-A
* *
219651 GGCAGCGGCAGAACAGAGAA
1 AGCAGCGGCAGCACAGAGAA
219671 GTAATGTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.41, C:0.20, G:0.39, T:0.00
Consensus pattern (20 bp):
AGCAGCGGCAGCACAGAGAA
Found at i:220209 original size:43 final size:42
Alignment explanation
Indices: 220007--220231 Score: 143
Period size: 43 Copynumber: 5.2 Consensus size: 42
219997 CATACATTTA
* * * * *
220007 GCGGCGTTTTTGATAAAAACGCCGCAAAATCTCAATA-CATATTCT
1 GCGGCG-TTTTAATGAAAACGCCGCTAAATATCAAAATC-TA-T-T
* * * * * * *
220052 GCGGCGTTTTTAGGAAAACGCCGGTAAAAATAAAAATTTACT
1 GCGGCGTTTTAATGAAAACGCCGCTAAATATCAAAATCTATT
* *
220094 GCGGCGTTTTGGAA-GAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTT--AATGAAAACGCCGCTAAATATCAA-AATCTATT
* * * *
220137 GCGGCG-TTTATCTGCCAAATGCCGTTAAATATCAAAATCTATT
1 GCGGCGTTTTA-ATG-AAAACGCCGCTAAATATCAAAATCTATT
* * *
220180 GCGGCGTTTTAATGATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTTAATGA-AAACGCCGCTAAATATCAAAATCTATT
220223 GCGGCGTTT
1 GCGGCGTTT
220232 GTTGAACAAT
Statistics
Matches: 139, Mismatches: 31, Indels: 22
0.72 0.16 0.11
Matches are distributed among these distances:
40 1 0.01
42 16 0.12
43 87 0.63
44 29 0.21
45 6 0.04
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTTAATGAAAACGCCGCTAAATATCAAAATCTATT
Found at i:220246 original size:43 final size:42
Alignment explanation
Indices: 220007--220275 Score: 136
Period size: 43 Copynumber: 6.2 Consensus size: 42
219997 CATACATTTA
* * * *
220007 GCGGCGTTTT-TGATAAAAACGCCGCAAAATCTCAATACATATTCT
1 GCGGCGTTTTATGAT--AAACGCCGCTAAATATCAAAACCTA-T-T
* * * * ** *
220052 GCGGCGTTTTTAGGA-AAACGCCGGTAAAAATAAAAATTTACT
1 GCGGCG-TTTTATGATAAACGCCGCTAAATATCAAAACCTATT
* * *
220094 GCGGCGTTTTGGAAGA-AAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTT--ATGATAAACGCCGCTAAATATCAA-AACCTATT
* ** * * *
220137 GCGGCGTTTATCTGCCAAATGCCGTTAAATATCAAAATCTATT
1 GCGGCGTTT-TATGATAAACGCCGCTAAATATCAAAACCTATT
* *
220180 GCGGCGTTTTAATGATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTT-ATGATAAACGCCGCTAAATATCAAAACCTATT
* * ***
220223 GCGGCGTTTGT-TGA-ACAATCGCCGCTATATGTTGTAACCTATT
1 GCGGCGTTT-TATGATA-AA-CGCCGCTAAATATCAAAACCTATT
220266 GCGGCGTTTT
1 GCGGCGTTTT
220276 TTGTTGAAAA
Statistics
Matches: 173, Mismatches: 39, Indels: 27
0.72 0.16 0.11
Matches are distributed among these distances:
41 5 0.03
42 16 0.09
43 120 0.69
44 20 0.12
45 6 0.03
46 4 0.02
47 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (42 bp):
GCGGCGTTTTATGATAAACGCCGCTAAATATCAAAACCTATT
Found at i:220317 original size:15 final size:14
Alignment explanation
Indices: 220297--220340 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 14
220287 CGCCGCAAAC
220297 TTTAGCGGCGTTATT
1 TTTAGCGGCGTT-TT
*
220312 TTTAGCGGCG--CT
1 TTTAGCGGCGTTTT
220324 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
220338 TTT
1 TTT
220341 TACGCCGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 11 0.44
14 4 0.16
15 10 0.40
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (14 bp):
TTTAGCGGCGTTTT
Found at i:222170 original size:26 final size:26
Alignment explanation
Indices: 222140--222479 Score: 224
Period size: 26 Copynumber: 13.7 Consensus size: 26
222130 TTTGATGATT
222140 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
222166 CAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
222192 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
222218 TAAAAATGA-TT--TAATAA-GATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
222239 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
222263 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
222289 TAGTAATGA-TTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
222314 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
* * *
222340 TA-AAATGA-TT--TAATAAT-GTTT
1 TAGTAATGATTTGATAATAATCATTA
* * * *
222361 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
222385 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
222411 TAATAATGATTTTATAAT-ATTATT-
1 TAGTAATGATTTGATAATAATCATTA
* *
222435 TAGTAATTATTT-ATAATAATGATTTAA
1 TAGTAATGATTTGATAATAATCA-TT-A
* *
222462 TACTAATGATTTAATAAT
1 TAGTAATGATTTGATAAT
222480 TATTCTAATA
Statistics
Matches: 256, Mismatches: 30, Indels: 54
0.75 0.09 0.16
Matches are distributed among these distances:
18 1 0.00
19 6 0.02
20 5 0.02
21 7 0.03
22 12 0.05
23 14 0.05
24 26 0.10
25 54 0.21
26 104 0.41
27 22 0.09
28 5 0.02
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:222375 original size:122 final size:124
Alignment explanation
Indices: 222085--222479 Score: 642
Period size: 122 Copynumber: 3.2 Consensus size: 124
222075 ATGTATTTAT
222085 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
222150 TTGATAATAATCATTACAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
222209 TAATCATTATAAAAATGATTTAATAA-GATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
222273 TTGATAATAATCATTATAGTAATGA-TTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
222331 TAATCATTAT-AAAATGATTTAATAATGTTTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * *
222395 TTGATAATAATCATTATAATAATGATTTTATAAT-ATTATT-TAGTAATTATTTA-TAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
*
222451 TAATGATT-TAATACTAATGATTTAATAAT
1 TAATCATTATAA-A--AATGATTTAATAAT
222480 TATTCTAATA
Statistics
Matches: 257, Mismatches: 8, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
119 1 0.00
120 11 0.04
121 27 0.11
122 109 0.42
123 83 0.32
124 26 0.10
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:222418 original size:148 final size:145
Alignment explanation
Indices: 222137--222479 Score: 333
Period size: 148 Copynumber: 2.3 Consensus size: 145
222127 TGATTTGATG
* *
222137 ATTTAGTAATGATTTGATAATAATCATTACAGTAATGATTT-GATAATAATCATTATAATAATGA
1 ATTTAGTAATGA-TTGATAATAATCATTATAATAATGATTTAG-TAATAATCATTATAATAATGA
* * * * *
222201 TTTAGTAATAATCATTATAAAAATGATTTAATAAGATTTAAATATTTAATGATTTGATGATTTAG
64 TTTAATAATAATCATTATAAAAATGATTTAAT-AGATTTAAATATTTAATGATATAATCATTTAA
222266 TAATGATTTGATAATAATC
128 TAATGATTTGATAAT-ATC
222285 ATTATAGTAATGATTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAA-AATGAT
1 ATT-TAGTAATGATTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGAT
* * * *
222349 TTAATAAT-GT-TTTA-AATATTTAATGATTTGAT-GATTTAGTAATGATTTGAT-A-ATAATCA
65 TTAATAATAATCATTATAA-A---AATGATTTAATAGATTTA--AAT-ATTTAATGATATAATCA
* *
222408 TTATAATAATGATTTTATAATATT
123 TT-TAATAATGATTTGATAATATC
* * * * *
222432 ATTTAGTAATTATTTATAATAATGATTTAATACTAATGATTTAATAAT
1 ATTTAGTAATGATTGATAATAATCA-TT-ATAATAATGATTTAGTAAT
222480 TATTCTAATA
Statistics
Matches: 165, Mismatches: 18, Indels: 24
0.80 0.09 0.12
Matches are distributed among these distances:
144 2 0.01
145 4 0.02
146 26 0.16
147 26 0.16
148 91 0.55
149 16 0.10
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (145 bp):
ATTTAGTAATGATTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATT
TAATAATAATCATTATAAAAATGATTTAATAGATTTAAATATTTAATGATATAATCATTTAATAA
TGATTTGATAATATC
Found at i:222489 original size:37 final size:36
Alignment explanation
Indices: 222399--222491 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 36
222389 AATGATTTGA
* * *
222399 TAATAATCATTATAATAATGATTTTATAATATTATT
1 TAATAATTATTATAATAATGATTTAATAATATGATT
* *
222435 TAGTAATTATTTATAATAATGATTTAATACTAATGATT
1 TAATAATTA-TTATAATAATGATTTAATAAT-ATGATT
*
222473 TAATAATTATTCTAATAAT
1 TAATAATTATTATAATAAT
222492 TATAAATACT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 7 0.15
37 28 0.58
38 13 0.27
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.48
Consensus pattern (36 bp):
TAATAATTATTATAATAATGATTTAATAATATGATT
Found at i:222783 original size:16 final size:17
Alignment explanation
Indices: 222748--222785 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
222738 CAAATTAAAC
**
222748 ATTTATAATATAAACTA
1 ATTTATAATATAAAAAA
222765 ATTTA-AATATAAAAAA
1 ATTTATAATATAAAAAA
222781 ATTTA
1 ATTTA
222786 CCTTATCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTATAATATAAAAAA
Found at i:223225 original size:29 final size:29
Alignment explanation
Indices: 223183--223316 Score: 216
Period size: 29 Copynumber: 4.6 Consensus size: 29
223173 AGGACTACAT
**
223183 GGGACTACATGGCGACCTACTTGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
223212 GGGACTACATGGCGACCTACAAGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
223241 GGGACTACATGGCGACCTACAAGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
223270 GGGACTACATGGCGACCTACAAGGTCGCCC
1 GGGACTACATGGCGACCTACAAGGTCG-CC
* *
223300 AGG-CTGCATGGCGACCT
1 GGGACTACATGGCGACCT
223317 CTCCATTGGC
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 96 0.96
30 4 0.04
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.16
Consensus pattern (29 bp):
GGGACTACATGGCGACCTACAAGGTCGCC
Found at i:223395 original size:20 final size:20
Alignment explanation
Indices: 223366--223404 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
223356 ACCTCTCCAT
223366 TGGCTCGTATGGCTCGTATA
1 TGGCTCGTATGGCTCGTATA
*
223386 TGGCTTGTATGGCTCGTAT
1 TGGCTCGTATGGCTCGTAT
223405 GTCACCCCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.31, T:0.38
Consensus pattern (20 bp):
TGGCTCGTATGGCTCGTATA
Found at i:223418 original size:21 final size:21
Alignment explanation
Indices: 223392--223438 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
223382 TATATGGCTT
223392 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
223413 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
*
223434 TTATG
1 GTATG
223439 TCGCCTGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.30, G:0.23, T:0.32
Consensus pattern (21 bp):
GTATGGCTCGTATGTCACCCC
Found at i:223424 original size:9 final size:9
Alignment explanation
Indices: 223366--223405 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
223356 ACCTCTCCAT
223366 TGGCTCGTA
1 TGGCTCGTA
223375 TGGCTCGTATA
1 TGGCTCG--TA
*
223386 TGGCTTGTA
1 TGGCTCGTA
223395 TGGCTCGTA
1 TGGCTCGTA
223404 TG
1 TG
223406 TCACCCCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.12, C:0.17, G:0.33, T:0.38
Consensus pattern (9 bp):
TGGCTCGTA
Found at i:228347 original size:21 final size:21
Alignment explanation
Indices: 228323--228370 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
228313 TTTTAAGCTC
228323 GAGTCTTGAGATTGCATAAAT
1 GAGTCTTGAGATTGCATAAAT
228344 GAGTCTTGAGATTGCATAAAT
1 GAGTCTTGAGATTGCATAAAT
228365 GAGTCT
1 GAGTCT
228371 CAAGACTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.33
Consensus pattern (21 bp):
GAGTCTTGAGATTGCATAAAT
Done.