Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006865.1 Hibiscus syriacus cultivar Beakdansim tig00017464_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: 189683
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:146424 original size:29 final size:29
Alignment explanation
Indices: 146362--146426 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
146352 TAAAATTTTG
146362 TTTTATTT-ATTTTAGTCCTTAAGATTCTA
1 TTTT-TTTCATTTTAGTCCTTAAGATTCTA
* *
146391 TTTTTTTCATTTTAGTCCTTGAGGTTTCTA
1 TTTTTTTCATTTTAGTCCTT-AAGATTCTA
146421 TTTTTT
1 TTTTTT
146427 ACTTTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 3 0.09
29 16 0.50
30 13 0.41
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (29 bp):
TTTTTTTCATTTTAGTCCTTAAGATTCTA
Found at i:146459 original size:30 final size:30
Alignment explanation
Indices: 146425--146482 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
146415 TTTCTATTTT
146425 TTACT-TTTTGATCC-TCTTAACTTTATGTAA
1 TTACTGTTTT-ATCCAT-TTAACTTTATGTAA
*
146455 TTACTGTTTTATCCATTTAAGTTTATGT
1 TTACTGTTTTATCCATTTAACTTTATGT
146483 TTTGGCCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.22, C:0.14, G:0.09, T:0.55
Consensus pattern (30 bp):
TTACTGTTTTATCCATTTAACTTTATGTAA
Found at i:146580 original size:31 final size:30
Alignment explanation
Indices: 146516--146585 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
146506 TTCCTATTTG
* * *
146516 TACTATTTTTGTCCTTTGAGTTTATGTGTT
1 TACTATTTTGGTCCTTTAAGTTTATATGTT
146546 TACTATTTTGGTCCTTGTAAGTTTATAT-TCT
1 TACTATTTTGGTCCTT-TAAGTTTATATGT-T
146577 TACT-TTTTG
1 TACTATTTTG
146586 CTCATTTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (30 bp):
TACTATTTTGGTCCTTTAAGTTTATATGTT
Found at i:146585 original size:30 final size:29
Alignment explanation
Indices: 146521--146585 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
146511 ATTTGTACTA
* *
146521 TTTTT-GTCCTTTGAGTTTATGTGTTTAC
1 TTTTTGGTCCTTTAAGTTTATATGTTTAC
146549 TATTTTGGTCCTTGTAAGTTTATAT-TCTTAC
1 T-TTTTGGTCCTT-TAAGTTTATATGT-TTAC
146580 TTTTTG
1 TTTTTG
146586 CTCATTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 1 0.03
29 4 0.13
30 12 0.39
31 14 0.45
ACGTcount: A:0.14, C:0.11, G:0.15, T:0.60
Consensus pattern (29 bp):
TTTTTGGTCCTTTAAGTTTATATGTTTAC
Found at i:150227 original size:21 final size:19
Alignment explanation
Indices: 150203--150269 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 19
150193 AAGATCAAAT
150203 CAAAGTGAAGAGACAAAAAAA
1 CAAAGTGAA-AGA-AAAAAAA
*
150224 CAAAGAGAAAAGAAACAAAGAA
1 CAAAGTG-AAAGAAA-AAA-AA
* *
150246 AAAAGTCAAAGAAAAAAAA
1 CAAAGTGAAAGAAAAAAAA
150265 CAAAG
1 CAAAG
150270 AAAGGAAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 6 0.16
20 5 0.13
21 19 0.50
22 8 0.21
ACGTcount: A:0.72, C:0.09, G:0.16, T:0.03
Consensus pattern (19 bp):
CAAAGTGAAAGAAAAAAAA
Found at i:150231 original size:16 final size:15
Alignment explanation
Indices: 150210--150270 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 15
150200 AATCAAAGTG
150210 AAGAGACAAAAAAACA
1 AAGAGA-AAAAAAACA
*
150226 AAGAGAAAAGAAAC-
1 AAGAGAAAAAAAACA
**
150240 AA-AGAAAAAAGTC-
1 AAGAGAAAAAAAACA
150253 AA-AGAAAAAAAACA
1 AAGAGAAAAAAAACA
150267 AAGA
1 AAGA
150271 AAGGAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
13 19 0.51
14 4 0.11
15 8 0.22
16 6 0.16
ACGTcount: A:0.75, C:0.08, G:0.15, T:0.02
Consensus pattern (15 bp):
AAGAGAAAAAAAACA
Found at i:150241 original size:23 final size:21
Alignment explanation
Indices: 150210--150280 Score: 61
Period size: 23 Copynumber: 3.2 Consensus size: 21
150200 AATCAAAGTG
*
150210 AAGAGACAAAAAAACAAAGAGAA
1 AAGAAACAAAAAAA-AAAG-GAA
* **
150233 AAGAAACAAAGAAAAAAGTCA
1 AAGAAACAAAAAAAAAAGGAA
*
150254 AAGAAAAAAAACAAAGAAAGGAA
1 AAGAAACAAAA-AAA-AAAGGAA
150277 AAGA
1 AAGA
150281 GGACAAAGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 10 0.26
22 7 0.18
23 21 0.55
ACGTcount: A:0.75, C:0.07, G:0.17, T:0.01
Consensus pattern (21 bp):
AAGAAACAAAAAAAAAAGGAA
Found at i:150278 original size:15 final size:13
Alignment explanation
Indices: 150217--150272 Score: 76
Period size: 13 Copynumber: 4.2 Consensus size: 13
150207 GTGAAGAGAC
150217 AAAAAAACAAAGA
1 AAAAAAACAAAGA
150230 GAAAAGAAACAAAGA
1 -AAAA-AAACAAAGA
**
150245 AAAAAGTCAAAGA
1 AAAAAAACAAAGA
150258 AAAAAAACAAAGA
1 AAAAAAACAAAGA
150271 AA
1 AA
150273 GGAAAAGAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 20 0.54
14 8 0.22
15 9 0.24
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (13 bp):
AAAAAAACAAAGA
Found at i:151559 original size:36 final size:36
Alignment explanation
Indices: 151491--151596 Score: 126
Period size: 36 Copynumber: 3.0 Consensus size: 36
151481 TTGAGATCGT
*
151491 TTTCTC-AAAAGCAAACTTTGTCTTGCTGGAGACAA
1 TTTCTCTAAAAGCAAATTTTGTCTTGCTGGAGACAA
* *
151526 TTTCTCTAAAAACAAATTTTGT-TTCGCTTGAGACAA
1 TTTCTCTAAAAGCAAATTTTGTCTT-GCTGGAGACAA
* * * *
151562 TTTCTCTCAAAGCAAATTTCGTCTTGTTTGAGACA
1 TTTCTCTAAAAGCAAATTTTGTCTTGCTGGAGACA
151597 TTTTTTTCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
35 8 0.13
36 51 0.84
37 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (36 bp):
TTTCTCTAAAAGCAAATTTTGTCTTGCTGGAGACAA
Found at i:152034 original size:26 final size:28
Alignment explanation
Indices: 151986--152038 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
151976 CTTGAGATAA
151986 TTTCTTTTGAAATAAAAATCTTTGAGTT
1 TTTCTTTTGAAATAAAAATCTTTGAGTT
152014 TTTCTTTT-AAA-AAAAATCTTTGAGT
1 TTTCTTTTGAAATAAAAATCTTTGAGT
152039 ATACTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 14 0.56
27 3 0.12
28 8 0.32
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (28 bp):
TTTCTTTTGAAATAAAAATCTTTGAGTT
Found at i:152046 original size:28 final size:26
Alignment explanation
Indices: 151987--152063 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 26
151977 TTGAGATAAT
*
151987 TTCTTTTGAAATAAAAATCTTTGAGTTT
1 TTCTTTT-AAA-AAAAATCTTTGAGTTC
152015 TTCTTTTAAAAAAAATCTTTGAGTATAC
1 TTCTTTTAAAAAAAATCTTTGAGT-T-C
*
152043 TTCTTTTTAAACAAAAT-TTTG
1 TTC-TTTTAAAAAAAATCTTTG
152064 TCTCTCTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
26 14 0.32
27 4 0.09
28 14 0.32
29 12 0.27
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (26 bp):
TTCTTTTAAAAAAAATCTTTGAGTTC
Found at i:152111 original size:93 final size:96
Alignment explanation
Indices: 151958--152132 Score: 216
Period size: 93 Copynumber: 1.9 Consensus size: 96
151948 GTTTTTTTGG
* * * * * *
151958 AAACAAAATTTTGTCTCCCTTGAGATAATTTCTTTTGAAATAAAAATCTTTGAGTTTTTCT-TTT
1 AAACAAAATTTTGTCTCCCTTAAGACAATTTCTTTCGAAATAAAAATCTTTAAGTGTTTCTGTTG
152022 AAA-A-AAAATCTTTGAGTATACTTCTTTTT
66 AAATACAAAATCTTTGAGTATACTTCTTTTT
* * *
152051 AAACAAAATTTTGTCTCTCTTAAGACAGTTT-TTTCGCGAA-AAAAATCTTTAAGTAGTTTCTGT
1 AAACAAAATTTTGTCTCCCTTAAGACAATTTCTTTCG-AAATAAAAATCTTTAAGT-GTTTCTGT
152114 TGAAATACAAAATCTTTGA
64 TGAAATACAAAATCTTTGA
152133 TAACAAAGCT
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
92 17 0.25
93 34 0.50
94 5 0.07
95 1 0.01
96 11 0.16
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (96 bp):
AAACAAAATTTTGTCTCCCTTAAGACAATTTCTTTCGAAATAAAAATCTTTAAGTGTTTCTGTTG
AAATACAAAATCTTTGAGTATACTTCTTTTT
Found at i:152326 original size:31 final size:30
Alignment explanation
Indices: 152278--152337 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
152268 ACAAACCATC
*
152278 ATCTTTTAGTCGTTTCTTTTGAAACAAAAG
1 ATCTTTGAGTCGTTTCTTTTGAAACAAAAG
152308 ATCTTTGAGTCTGTTTCTTTTGAAACAAAA
1 ATCTTTGAGTC-GTTTCTTTTGAAACAAAA
152338 TTTTATTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (30 bp):
ATCTTTGAGTCGTTTCTTTTGAAACAAAAG
Found at i:152527 original size:276 final size:277
Alignment explanation
Indices: 152014--152764 Score: 1129
Period size: 277 Copynumber: 2.7 Consensus size: 277
152004 TCTTTGAGTT
* ** * * *
152014 TTTCTTTT-AAA-AAAA-ATCTTTGAGTATACTTCTTTTTAAACAAAATTTTGTCTCTCTTAAGA
1 TTTCTTTTGAAACAAAAGATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTCTTGAGA
152076 CAGTTTTTTCGCGAAAAAAATCTTTAAGTAGTTTCTGTTGAAATACAAAATCTTTGATAACAAAG
66 CAGTTTTTT-GC-AAAAAAATCTTTAAGTAGTTTCTGTTGAAATACAAAATCTTTGATAACAAAG
* *
152141 CTTTGTCTCTTTTGAGGCAGTTTCTTTTGGGGAAAAAATATTTGAGTCTGTTTCCTTTGAAACAA
129 CTTTGTCTCTTTTGAGGCAGTTTCTTTT-GGAAAAAAATCTTTGAGTCTGTTTCCTTTGAAACAA
* *
152206 AGCGTTGTCTCACTTGAGACAATTTTCCTCAAAATACCAAATTATGAATTTG-TTCACTGAAAAC
193 AGTGTTATCTCACTTGAGACAATTTTCCTCAAAATACCAAATTATGAATTTGTTTCACTGAAAAC
152270 AAACCATCATCTTTTAGTCG
258 AAACCATCATCTTTTAGTCG
*
152290 TTTCTTTTGAAACAAAAGATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATTTCTCTTGAGA
1 TTTCTTTTGAAACAAAAGATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTCTTGAGA
* * *
152355 CAGTTTTTTGCAAAAAAATCTTTAAGTAGTTTTTGTTGAAATACAAAATCTTTGATAATAAGGCT
66 CAGTTTTTTGCAAAAAAATCTTTAAGTAGTTTCTGTTGAAATACAAAATCTTTGATAACAAAGCT
*
152420 TTGTCTCTTTTGAGGCAGTTTCTTTTGGAAAAAAATCTTTAAGTCTGTTTCCTTTGAAACAAAGT
131 TTGTCTCTTTTGAGGCAGTTTCTTTTGGAAAAAAATCTTTGAGTCTGTTTCCTTTGAAACAAAGT
152485 GTTATCTCACTTGAGACAATTTTCCTCAAAATACCAAATTATGAATTTGTTTCACTGAAAACAAA
196 GTTATCTCACTTGAGACAATTTTCCTCAAAATACCAAATTATGAATTTGTTTCACTGAAAACAAA
152550 CCATCATCTTTTAGTCG
261 CCATCATCTTTTAGTCG
*
152567 TTTCTTTTGAAACAAAAGATCTTTGAGTCCGTTTCTTTTGAAACAAAATTTTATCTCT-TTGGAG
1 TTTCTTTTGAAACAAAAGATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTCTT-GAG
* * * * * * *
152631 ATAGTTTTTCCGCGAAAAAATCTTTGAGTAGTTTCTGTTGAAACACAAAATCTTTGAGAACAAAA
65 ACAGTTTTT-TGCAAAAAAATCTTTAAGTAGTTTCTGTTGAAATACAAAATCTTTGATAACAAAG
* * ** * *
152696 CTTTGTCTCTCTCGAGAAAATTTCTTTT-GAGAAAAAATCTTTGAGTCTATTT-CTTTCGAAACA
129 CTTTGTCTCTTTTGAGGCAGTTTCTTTTGGA-AAAAAATCTTTGAGTCTGTTTCCTTT-GAAACA
152759 AAGTGT
192 AAGTGT
152765 CGTTAGCGAG
Statistics
Matches: 433, Mismatches: 34, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
276 93 0.21
277 185 0.43
278 106 0.24
279 49 0.11
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (277 bp):
TTTCTTTTGAAACAAAAGATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTCTTGAGA
CAGTTTTTTGCAAAAAAATCTTTAAGTAGTTTCTGTTGAAATACAAAATCTTTGATAACAAAGCT
TTGTCTCTTTTGAGGCAGTTTCTTTTGGAAAAAAATCTTTGAGTCTGTTTCCTTTGAAACAAAGT
GTTATCTCACTTGAGACAATTTTCCTCAAAATACCAAATTATGAATTTGTTTCACTGAAAACAAA
CCATCATCTTTTAGTCG
Found at i:152603 original size:31 final size:30
Alignment explanation
Indices: 152555--152614 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
152545 ACAAACCATC
*
152555 ATCTTTTAGTCGTTTCTTTTGAAACAAAAG
1 ATCTTTGAGTCGTTTCTTTTGAAACAAAAG
152585 ATCTTTGAGTCCGTTTCTTTTGAAACAAAA
1 ATCTTTGAGT-CGTTTCTTTTGAAACAAAA
152615 TTTTATCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (30 bp):
ATCTTTGAGTCGTTTCTTTTGAAACAAAAG
Found at i:152911 original size:29 final size:30
Alignment explanation
Indices: 152866--152927 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
152856 AAAATTTACA
152866 ATCTTTGAGTCTGTTTCGTTTGAAA-CATT
1 ATCTTTGAGTCTGTTTCGTTTGAAACCATT
*
152895 ATCTTTGAGTC-GATTTCTTTTGAAACCATT
1 ATCTTTGAGTCTG-TTTCGTTTGAAACCATT
152925 ATC
1 ATC
152928 CCTAAAGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 1 0.03
29 22 0.73
30 7 0.23
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.47
Consensus pattern (30 bp):
ATCTTTGAGTCTGTTTCGTTTGAAACCATT
Found at i:153099 original size:49 final size:49
Alignment explanation
Indices: 153009--153203 Score: 277
Period size: 49 Copynumber: 4.0 Consensus size: 49
152999 GGAGCCGTGT
** *
153009 CAACCATAGATAACCAATCGT-CTCATCACGTAGGAATCGAGTTATCAC
1 CAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCAC
153057 CAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCAC
1 CAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCAC
* *
153106 CAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCGAGTTATCAT
1 CAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCAC
* * ** *
153155 C-ACTCTTAGATAACCAGCCGTCCTTATCGTGTAGGAACCGAGTTGTCAC
1 CAAC-CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCAC
153204 AATTCCTAAA
Statistics
Matches: 133, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
48 21 0.16
49 112 0.84
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (49 bp):
CAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCAC
Found at i:153144 original size:24 final size:24
Alignment explanation
Indices: 153068--153144 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
153058 AACCATAGAT
*
153068 AACCAGCCGTCCTCATCACGTAGG
1 AACCAGCCATCCTCATCACGTAGG
** * * *
153092 AACCGAGTTATCAC-CAAC-CATAGAT
1 AACC-AGCCATC-CTCATCACGTAG-G
153117 AACCAGCCATCCTCATCACGTAGG
1 AACCAGCCATCCTCATCACGTAGG
153141 AACC
1 AACC
153145 GAGTTATCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
23 1 0.03
24 20 0.54
25 15 0.41
26 1 0.03
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.17
Consensus pattern (24 bp):
AACCAGCCATCCTCATCACGTAGG
Found at i:153522 original size:3 final size:3
Alignment explanation
Indices: 153516--153559 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
153506 TATTATTTAA
* *
153516 ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT AAT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
153560 TACAATTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:154980 original size:30 final size:30
Alignment explanation
Indices: 154917--154997 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
154907 TTGTAATTAC
* *
154917 TTTTAAGTCCTTTAAGTTTCTATTTTTGTTA
1 TTTT-AGTCCTTTAAGTTTCTATTTATGATA
*
154948 TTTTAGTCTTTTAAGTTTCTATTTCAT-ATA
1 TTTTAGTCCTTTAAGTTTCTATTT-ATGATA
* *
154978 TTTTAGACCTTAAAGTTTCT
1 TTTTAGTCCTTTAAGTTTCT
154998 GTGAATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
30 38 0.88
31 5 0.12
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (30 bp):
TTTTAGTCCTTTAAGTTTCTATTTATGATA
Found at i:155079 original size:29 final size:28
Alignment explanation
Indices: 155009--155106 Score: 81
Period size: 30 Copynumber: 3.4 Consensus size: 28
154999 TGAATTATTG
* * * *
155009 TTTACTCCTTTAATTTTTGTTTCTTCTAA
1 TTTAGTCCTTAAATTTTTGTTT-TTTTAT
*
155038 TTTAGCCCTTTAAATTTTTGTTTTATTTAT
1 TTTAGTCC-TTAAATTTTTGTTTT-TTTAT
* *
155068 TTTAGTCCTTAAGATTCTAT-TTTTTTCAT
1 TTTAGTCCTTAA-ATT-TTTGTTTTTTTAT
155097 TTTAGTCCTT
1 TTTAGTCCTT
155107 GAGGTTTCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 25 0.44
30 30 0.53
31 2 0.04
ACGTcount: A:0.18, C:0.14, G:0.06, T:0.61
Consensus pattern (28 bp):
TTTAGTCCTTAAATTTTTGTTTTTTTAT
Found at i:155122 original size:30 final size:29
Alignment explanation
Indices: 155057--155122 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
155047 TTAAATTTTT
*
155057 GTTTTATTTATTTTAGTCCTTAAGATTCTA
1 GTTTT-TTCATTTTAGTCCTTAAGATTCTA
* * *
155087 TTTTTTTCATTTTAGTCCTTGAGGTTTCTA
1 GTTTTTTCATTTTAGTCCTT-AAGATTCTA
155117 GTTTTT
1 GTTTTT
155123 ACTTTTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.17, C:0.11, G:0.12, T:0.61
Consensus pattern (29 bp):
GTTTTTTCATTTTAGTCCTTAAGATTCTA
Found at i:155128 original size:29 final size:28
Alignment explanation
Indices: 155063--155128 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
155053 TTTTGTTTTA
*
155063 TTTA-TTTTAGTCCTTAAGATTCTATTT
1 TTTACTTTTAGTCCTTAAGATTCTAGTT
* * *
155090 TTTTCATTTTAGTCCTTGAGGTTTCTAGTT
1 TTTAC-TTTTAGTCCTT-AAGATTCTAGTT
155120 TTTACTTTT
1 TTTACTTTT
155129 TTATCCCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 3 0.10
29 15 0.48
30 13 0.42
ACGTcount: A:0.17, C:0.12, G:0.11, T:0.61
Consensus pattern (28 bp):
TTTACTTTTAGTCCTTAAGATTCTAGTT
Found at i:156662 original size:24 final size:24
Alignment explanation
Indices: 156634--156710 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
156624 TATTCAAATG
*
156634 ATAAACGAACACAAATGAACAAAC
1 ATAAACGAACACAAACGAACAAAC
* * * *
156658 GTAAATGAATACAAACGAACGAAC
1 ATAAACGAACACAAACGAACAAAC
* **
156682 ATAAACAAACGTAAACGAACAAAC
1 ATAAACGAACACAAACGAACAAAC
156706 ATAAA
1 ATAAA
156711 ATTATTTGGG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.61, C:0.18, G:0.10, T:0.10
Consensus pattern (24 bp):
ATAAACGAACACAAACGAACAAAC
Found at i:158166 original size:30 final size:30
Alignment explanation
Indices: 158139--158233 Score: 76
Period size: 30 Copynumber: 3.4 Consensus size: 30
158129 AGGTCCTTCT
158139 AGTTTTTGTTTATACTATTTTAATCCTTTA
1 AGTTTTTGTTTATACTATTTTAATCCTTTA
* * * ** *
158169 ATTTTTTGTTTGTGCTATTTTGGTACTTTA
1 AGTTTTTGTTTATACTATTTTAATCCTTTA
*
158199 A--TTTT-TTT-T-CTA-TTTAATCCCTTA
1 AGTTTTTGTTTATACTATTTTAATCCTTTA
*
158223 AGTTTATGTTT
1 AGTTTTTGTTT
158234 TTCTCTTGTA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
24 9 0.18
25 3 0.06
26 4 0.08
27 6 0.12
28 4 0.08
30 25 0.49
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.62
Consensus pattern (30 bp):
AGTTTTTGTTTATACTATTTTAATCCTTTA
Found at i:164234 original size:27 final size:25
Alignment explanation
Indices: 164204--164253 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
164194 AAATGATTGT
*
164204 AATACACTGGATCTGTAAAATGACCAA
1 AATACACTGGA-ATG-AAAATGACCAA
*
164231 AATACCCTGGAATGAAAATGACC
1 AATACACTGGAATGAAAATGACC
164254 GATGAATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 2 0.10
27 10 0.48
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (25 bp):
AATACACTGGAATGAAAATGACCAA
Found at i:172210 original size:32 final size:32
Alignment explanation
Indices: 172170--172291 Score: 147
Period size: 32 Copynumber: 3.8 Consensus size: 32
172160 AGGAATAATG
*
172170 GGGGCATCTTTAAAGGTTCAACATCAAATGTT
1 GGGGCATCTTTGAAGGTTCAACATCAAATGTT
*
172202 GGGGCATCTTTGAAGGTTCAACATTAAATGTT
1 GGGGCATCTTTGAAGGTTCAACATCAAATGTT
* * * * *
172234 GAGGCATTTTTGAAGATTCAACATCGAATATT
1 GGGGCATCTTTGAAGGTTCAACATCAAATGTT
* *
172266 GGGTCATCTTTG-GGGATTCAACATCA
1 GGGGCATCTTTGAAGG-TTCAACATCA
172292 TGATGTGAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
31 1 0.01
32 74 0.99
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (32 bp):
GGGGCATCTTTGAAGGTTCAACATCAAATGTT
Found at i:172750 original size:64 final size:65
Alignment explanation
Indices: 172582--172760 Score: 324
Period size: 65 Copynumber: 2.8 Consensus size: 65
172572 TCAATAAATA
172582 AAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAACAACTTTCC
1 AAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAACAACTTTCC
* * *
172647 AAGTTTCATTCAGAATCAATTTCAACTTCACAACAAAGGATATTGGACTCAACAAACAACTTTCC
1 AAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAACAACTTTCC
172712 -AGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTC
1 AAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTC
172761 GAAGTGACAT
Statistics
Matches: 108, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 46 0.43
65 62 0.57
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (65 bp):
AAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAACAAACAACTTTCC
Found at i:173137 original size:227 final size:226
Alignment explanation
Indices: 172844--173513 Score: 954
Period size: 227 Copynumber: 2.9 Consensus size: 226
172834 GAAATAGTAC
* *
172844 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAATGG-GCCA
1 TTGGATTTCAACTTCACGAC-AAAGATATCCAATTCAAAGCTCAACTTCACAACGAA-GGAGCCA
172908 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCATTCATATTTAGATTGGATTTCAACTTC
64 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCATTCATATTTAGATTGGATTTCAACTTC
*
172973 ACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAA-GAAGGAGCCATCCACGATTTCAACTT
129 ACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGTCATCCACGATTTCAACTT
173037 CACGACGAAGGATATCATGT-CATTCATCTTTAG
194 CACGACGAAGGATATCAT-TCCATTCATCTTTAG
* * *
173070 ATTGGATTTTAACTTCACGACAAAGGATATCCAATTTAAAGCTCAACTTCACAACTAAGGAGCCA
1 -TTGGATTTCAACTTCACGACAAA-GATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCA
* *
173135 TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGATTGGATTTCAACTTC
64 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCATTCATATTTAGATTGGATTTCAACTTC
* *
173200 ACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCATCCACGATTTCAACTT
129 ACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGTCATCCACGATTTCAACTT
* *
173265 CACAACGAAGGATATCGTTCCATTCATCTTTAG
194 CACGACGAAGGATATCATTCCATTCATCTTTAG
*
173298 TTGGGATTTCAACTTCACGACAAAAGATATCCAATTCAAAGCTCAAC-TCACAACGAATGAGCCA
1 TT-GGATTTCAACTTCACGAC-AAAGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCA
* ** * **
173362 TCCATGATTTCAACTTCACGACGAAGGATATCGTGCACACAAGCAGCAATGCA-ACCCTTGGATT
64 TCCACGATTTCAACTTCACGACGAAGGATATCGTG--C-CATTCA--TATTTAGA---TTGGATT
* ***
173426 TCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGTCATCTGTGAT
121 TCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGTCATCCACGAT
*
173491 TTCAAATTCACGACGAAGGATAT
186 TTCAACTTCACGACGAAGGATAT
173514 TGTCCCCAAC
Statistics
Matches: 397, Mismatches: 32, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
226 5 0.01
227 204 0.51
228 91 0.23
229 3 0.01
230 4 0.01
231 1 0.00
232 2 0.01
234 87 0.22
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (226 bp):
TTGGATTTCAACTTCACGACAAAGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATC
CACGATTTCAACTTCACGACGAAGGATATCGTGCCATTCATATTTAGATTGGATTTCAACTTCAC
GACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGTCATCCACGATTTCAACTTCA
CGACGAAGGATATCATTCCATTCATCTTTAG
Found at i:173182 original size:114 final size:114
Alignment explanation
Indices: 172844--173513 Score: 913
Period size: 114 Copynumber: 5.8 Consensus size: 114
172834 GAAATAGTAC
* *
172844 TTGGATTTCAACTTCACAACGAAA-GATATCCAATTCAAGGCTCAACTTCACAACGAATGG-GCC
1 TTGGATTTCAACTTCACGAC-AAAGGATATCCAATTCAAAGCTCAACTTCACAACGAA-GGAGCC
* *
172907 ATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCATTCATATTTAGA
64 ATCCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
*
172958 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAA-GAAGGAGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
*
173022 CCACGATTTCAACTTCACGACGAAGGATATCATGTCATTCATCTTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
* * *
173071 TTGGATTTTAACTTCACGACAAAGGATATCCAATTTAAAGCTCAACTTCACAACTAAGGAGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
173136 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
* * * *
173185 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGTCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
*
173250 CCACGATTTCAACTTCACAACGAAGGATATCGT-TCCATTCATCTTTAG-
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGT-CATTCATCTTTAGA
* *
173298 TTGGGATTTCAACTTCACGACAAAAGATATCCAATTCAAAGCTCAAC-TCACAACGAATGAGCCA
1 TT-GGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCA
* ** * ***
173362 TCCATGATTTCAACTTCACGACGAAGGATATCGTG-CACACAAGCAGCAATGCAA
65 TCCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTC-ATC-TTTA-G--A
* * *
173416 CCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGT
1 ---TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGC
*** *
173481 CATCTGTGATTTCAAATTCACGACGAAGGATAT
63 CATCCACGATTTCAACTTCACGACGAAGGATAT
173514 TGTCCCCAAC
Statistics
Matches: 501, Mismatches: 39, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
112 5 0.01
113 157 0.31
114 250 0.50
115 1 0.00
120 42 0.08
121 46 0.09
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (114 bp):
TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGTCATTCATCTTTAGA
Found at i:174017 original size:84 final size:84
Alignment explanation
Indices: 173735--174017 Score: 304
Period size: 84 Copynumber: 3.4 Consensus size: 84
173725 GATTACATTC
* * * ** * *
173735 AGCTCAAGGCAAGAATGGTTATCTTTC-ATTAAAGACCTTCGAGTTTGATTACATTCAGCACAAA
1 AGCTCAAGGCAAGAAGGGATATCTGTCAACAAAAGACCTTCAAGTTTGATTACATTCAGCTCAAA
* * *
173799 GGCATATCAAATTTATA-TCAT
66 GGCACAT--TATTTGTAGT-AT
* * *
173820 AACTCAAGGCTAGAAGGGATATCTGTCAAC-AAAGACCTTCAAGTTCGATTACATTCAGCTCAAA
1 AGCTCAAGGCAAGAAGGGATATCTGTCAACAAAAGACCTTCAAGTTTGATTACATTCAGCTCAAA
*
173884 GGCACATTATTTGCAGCT-T
66 GGCACATTATTTGTAG-TAT
* * * *
173903 AGCTCAAGGCAAGAAGAGCTATCTGCCAACAAAAGACCTTCAAGTTTGATTACACTCAGCTCAAA
1 AGCTCAAGGCAAGAAGGGATATCTGTCAACAAAAGACCTTCAAGTTTGATTACATTCAGCTCAAA
*
173968 GACACATTATTTGTAGTAT
66 GGCACATTATTTGTAGTAT
* * *
173987 AGCTCAAGGCGAGAAGGGTTATATGTCAACA
1 AGCTCAAGGCAAGAAGGGATATCTGTCAACA
174018 GGAAACTGCT
Statistics
Matches: 166, Mismatches: 27, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
83 32 0.19
84 73 0.44
85 60 0.36
86 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (84 bp):
AGCTCAAGGCAAGAAGGGATATCTGTCAACAAAAGACCTTCAAGTTTGATTACATTCAGCTCAAA
GGCACATTATTTGTAGTAT
Found at i:174046 original size:84 final size:84
Alignment explanation
Indices: 173822--174048 Score: 228
Period size: 84 Copynumber: 2.7 Consensus size: 84
173812 TATATCATAA
* * * * * * *
173822 CTCAAGGCTAGAAGGGATATCTGTCAAC-AAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGG
1 CTCAAGGCAAGAAGAGCTATATGCCAACAAAAGACCTGCAAGTTCGATTACATTCAGCTCAAAGA
173886 CACATTATTTGCAGCTTAG
66 CACATTATTTGCAGCTTAG
* * * *
173905 CTCAAGGCAAGAAGAGCTATCTGCCAACAAAAGACCTTCAAGTTTGATTACACTCAGCTCAAAGA
1 CTCAAGGCAAGAAGAGCTATATGCCAACAAAAGACCTGCAAGTTCGATTACATTCAGCTCAAAGA
*
173970 CACATTATTTGTAG-TATAG
66 CACATTATTTGCAGCT-TAG
* * * * * * *
173989 CTCAAGGCGAGAAGGGTTATATGTCAACAGGAA-A-CTGCTGAGTTCGATTCCATTCAGCTC
1 CTCAAGGCAAGAAGAGCTATATGCCAACA-AAAGACCTGC-AAGTTCGATTACATTCAGCTC
174049 GATGACATAT
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
83 28 0.23
84 91 0.75
85 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (84 bp):
CTCAAGGCAAGAAGAGCTATATGCCAACAAAAGACCTGCAAGTTCGATTACATTCAGCTCAAAGA
CACATTATTTGCAGCTTAG
Found at i:175651 original size:14 final size:14
Alignment explanation
Indices: 175619--175653 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
175609 CGTTTTTATT
175619 TTATTTTATTTTAG
1 TTATTTTATTTTAG
* *
175633 GTATTTTATTTTTG
1 TTATTTTATTTTAG
175647 TTATTTT
1 TTATTTT
175654 CAATTTGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (14 bp):
TTATTTTATTTTAG
Found at i:179653 original size:14 final size:15
Alignment explanation
Indices: 179634--179678 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
179624 GGGTTTGGAG
179634 AACATAAACGAACA-
1 AACATAAACGAACAT
*
179648 AACATAAATGAACAT
1 AACATAAACGAACAT
*
179663 AA-ACAAACGAACAT
1 AACATAAACGAACAT
179677 AA
1 AA
179679 ATGATCGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 25 0.93
15 2 0.07
ACGTcount: A:0.64, C:0.18, G:0.07, T:0.11
Consensus pattern (15 bp):
AACATAAACGAACAT
Found at i:179661 original size:24 final size:24
Alignment explanation
Indices: 179633--179682 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
179623 CGGGTTTGGA
*
179633 GAACATAAACGAACAAACATAAAT
1 GAACATAAACAAACAAACATAAAT
*
179657 GAACATAAACAAACGAACATAAAT
1 GAACATAAACAAACAAACATAAAT
179681 GA
1 GA
179683 TCGATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.16, G:0.10, T:0.12
Consensus pattern (24 bp):
GAACATAAACAAACAAACATAAAT
Found at i:181484 original size:18 final size:20
Alignment explanation
Indices: 181461--181497 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
181451 TCAGTAATCC
181461 TATTCCC-C-GGTAATCTTT
1 TATTCCCACTGGTAATCTTT
181479 TATTCCCACTGGTAATCTT
1 TATTCCCACTGGTAATCTT
181498 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.43
Consensus pattern (20 bp):
TATTCCCACTGGTAATCTTT
Found at i:181773 original size:2 final size:2
Alignment explanation
Indices: 181768--182257 Score: 241
Period size: 2 Copynumber: 239.0 Consensus size: 2
181758 TATGTGTGTG
181768 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
* * *
181810 TA TA TA TA CA TA TA CT- TA TA TA CTT TA CA CT- 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
* *
181851 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CT- TA TC 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
* * * *
181893 CT- TA T- TT TCA TA CA TCA TA CA TA TA TA CT- TA TG TA TA TA GT-
1 -TA TA TA TA T-A TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA -TA
*
181934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
181977 GTT TA TA TA GTT TA TA TA TA CTA TA TA GTT TA TA TA T- TCA TA GTT
1 -TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA T-A TA -TA
*
182022 TA TA GT- TA TA TA T- TA TA CTA TA TA GTT TA TA TA CT- TA TA CTA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA -TA
* * * *
182064 TA TA TA TG TA CT- TT TA TA TA TA TA TA TA TA TA TA CA TCA TA CA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* * * * *
182107 TA TG TA CA TA CA TA TA TA TG TA CA TA TA TCA TGA TCA T- TGA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A T-A T-A TA T-A T-A
* *
182151 -A TGA TA -A TA TA TA TA TA TA TA TA T- TCA TA CT- TA TG TA CA
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA
* * * *
182190 TA CA TCA TA CA CA TA TA CT- TA TA TA TA T- TA TA TA TT TA TA -A
1 TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
182231 TT TA TA TA TA TA TA CT- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
182258 CACACATCAT
Statistics
Matches: 374, Mismatches: 61, Indels: 106
0.69 0.11 0.20
Matches are distributed among these distances:
1 22 0.06
2 310 0.83
3 42 0.11
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:181985 original size:9 final size:9
Alignment explanation
Indices: 181973--182012 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
181963 ATATATACTT
181973 TATAGTTTA
1 TATAGTTTA
181982 TATAGTTTA
1 TATAGTTTA
*
181991 TATA-TACTA
1 TATAGT-TTA
182000 TATAGTTTA
1 TATAGTTTA
182009 TATA
1 TATA
182013 TTCATAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 25 0.93
10 1 0.04
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (9 bp):
TATAGTTTA
Found at i:182228 original size:17 final size:17
Alignment explanation
Indices: 182202--182257 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 17
182192 CATCATACAC
*
182202 ATATACTTATATATATT
1 ATATATTTATATATATT
182219 ATATATTTATA-AT-TT
1 ATATATTTATATATATT
*
182234 ATATATATATACTTATATT
1 ATATATTTATA--TATATT
182253 ATATA
1 ATATA
182258 CACACATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 12 0.36
16 2 0.06
17 10 0.30
18 2 0.06
19 7 0.21
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATATTTATATATATT
Done.