Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007793.1 Hibiscus syriacus cultivar Beakdansim tig00110082_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: 216588
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:134187 original size:23 final size:23
Alignment explanation
Indices: 134161--134230 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
134151 AACGAACGAA
* * *
134161 AAAAATGAACGTGTCACAAAGAT
1 AAAAATAAACATGTCTCAAAGAT
134184 AAAAATAAACATGTCTCAAAGAT
1 AAAAATAAACATGTCTCAAAGAT
134207 AAAAATAAACATGTCTCAAAGAT
1 AAAAATAAACATGTCTCAAAGAT
134230 A
1 A
134231 GAGATATACG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.56, C:0.13, G:0.11, T:0.20
Consensus pattern (23 bp):
AAAAATAAACATGTCTCAAAGAT
Found at i:138022 original size:31 final size:31
Alignment explanation
Indices: 137987--138045 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
137977 TAAAAATTTA
*
137987 GGTACTAAAATGAAACAAAAAGTTAACAATG
1 GGTACTAAAATGAAACAAAAAGTAAACAATG
138018 GGTACTAAAATGAAACAAAAAGTAAACA
1 GGTACTAAAATGAAACAAAAAGTAAACA
138046 TTAGATATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (31 bp):
GGTACTAAAATGAAACAAAAAGTAAACAATG
Found at i:138295 original size:25 final size:25
Alignment explanation
Indices: 138267--138316 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
138257 TCTTACAAAG
* *
138267 AATATAATGACTAAACTCAAAATAA
1 AATAAAATAACTAAACTCAAAATAA
138292 AATAAAATAACTAAACTCAAAATAA
1 AATAAAATAACTAAACTCAAAATAA
138317 TGAAGATCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.22
Consensus pattern (25 bp):
AATAAAATAACTAAACTCAAAATAA
Found at i:143749 original size:12 final size:12
Alignment explanation
Indices: 143731--143766 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
143721 TATATGTGTT
143731 CATGTGATATGA
1 CATGTGATATGA
*
143743 TATGTGATATGA
1 CATGTGATATGA
143755 CATGTGATATGA
1 CATGTGATATGA
143767 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:143788 original size:23 final size:26
Alignment explanation
Indices: 143731--143799 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
143721 TATATGTGTT
**
143731 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
143755 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
143780 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
143800 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:143929 original size:15 final size:15
Alignment explanation
Indices: 143911--143944 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
143901 GAGGGTATAA
143911 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
* *
143926 TAGTTCTTCTGGATG
1 TAGTCCTTCGGGATG
143941 TAGT
1 TAGT
143945 GGTCCTACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.41
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:151179 original size:9 final size:9
Alignment explanation
Indices: 151165--151200 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
151155 ATCTGCAAAA
151165 AAATTAAAT
1 AAATTAAAT
151174 AAATTAAAT
1 AAATTAAAT
*
151183 -ACTTAAAT
1 AAATTAAAT
151191 AAATTAAAT
1 AAATTAAAT
151200 A
1 A
151201 CAAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:151190 original size:17 final size:17
Alignment explanation
Indices: 151168--151201 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
151158 TGCAAAAAAA
151168 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
151185 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
151202 AAAATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:159167 original size:17 final size:15
Alignment explanation
Indices: 159127--159169 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
159117 GAATTCAAAA
*
159127 TTTTAAATTAGGATT
1 TTTTTAATTAGGATT
159142 TTCTTTAATTATGGAATT
1 TT-TTTAATTA-GG-ATT
159160 TTTTTAATTA
1 TTTTTAATTA
159170 CTAATGTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 7 0.29
17 10 0.42
18 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (15 bp):
TTTTTAATTAGGATT
Found at i:164253 original size:11 final size:12
Alignment explanation
Indices: 164234--164281 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
164224 ATTTAAAAAT
164234 TTATT-AATATA
1 TTATTAAATATA
*
164245 TT-TTAAATATCT
1 TTATTAAATAT-A
164257 TTATTAAA-ATA
1 TTATTAAATATA
164268 TTATTAAAT-TA
1 TTATTAAATATA
164279 TTA
1 TTA
164282 AATTAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 2 0.06
11 20 0.65
12 4 0.13
13 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (12 bp):
TTATTAAATATA
Found at i:164281 original size:19 final size:19
Alignment explanation
Indices: 164257--164295 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
164247 TTAAATATCT
*
164257 TTATTAAAATATTATTAAA
1 TTATTAAAATAATATTAAA
*
164276 TTATTAAATTAATATTAAA
1 TTATTAAAATAATATTAAA
164295 T
1 T
164296 ACATAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTAAAATAATATTAAA
Found at i:164406 original size:29 final size:29
Alignment explanation
Indices: 164385--164482 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 29
164375 TATTTTATTG
164385 TATATTATTAAAATAAAAATATAATATCT
1 TATATTATTAAAATAAAAATATAATATCT
* * *
164414 TATATTATTATAAT-ATAAT-TGAGTAT-T
1 TATATTATTAAAATAAAAATAT-AATATCT
*
164441 T-TATTA-TAATATTAAAAATATAATA-C-
1 TATATTATTAA-AATAAAAATATAATATCT
164467 TATATTATTAGAAATA
1 TATATTATTA-AAATA
164483 TTAATAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
25 2 0.04
26 8 0.15
27 15 0.28
28 14 0.26
29 14 0.26
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
TATATTATTAAAATAAAAATATAATATCT
Found at i:164475 original size:22 final size:23
Alignment explanation
Indices: 164445--164488 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
164435 AGTATTTTAT
164445 TATAATATTAAAAATA-TAATAC
1 TATAATATTAAAAATATTAATAC
* *
164467 TATATTATTAGAAATATTAATA
1 TATAATATTAAAAATATTAATA
164489 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAC
Found at i:164493 original size:22 final size:22
Alignment explanation
Indices: 164450--164493 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
164440 TTTATTATAA
*
164450 TATTAAAAATATAATACTATAT
1 TATTAAAAATATAATACAATAT
*
164472 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATACAATAT
164494 ATTTTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TATTAAAAATATAATACAATAT
Found at i:180363 original size:112 final size:112
Alignment explanation
Indices: 180166--180600 Score: 696
Period size: 112 Copynumber: 3.9 Consensus size: 112
180156 ATCTCAATTT
*
180166 AATGGATCAACTCCTCCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGATCTCTCTTTCCAA
1 AATGGATCAACTCCTCCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCCAA
* * *
180231 GATTTGATATTTCTTTCAGAGTAAGTGGAACAAGTCTTCCTCGATTC
66 GATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTTCCTCGATTC
* *
180278 AATGGATCAACTCCTCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTTTCTTTCCAA
1 AATGGATCAACTCCTCCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCCAA
*
180343 GATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTTCCTCAATAT-
66 GATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTTCCTCGAT-TC
* *
180390 AATGGATCAACTCCTCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCTAA
1 AATGGATCAACTCCTCCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCCAA
* * *
180455 GATTTGATATTCCCTTTAGAGTAAGTGGAATAAGTCTTCCTCGATTC
66 GATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTTCCTCGATTC
*
180502 AATGGATCAACGTCC-CCAGATATGATATTCCCTTCAGAGTAAGC-GACACATGTCTCTCTTTCC
1 AATGGATCAAC-TCCTCCAGATATGATATTCCCTTCAGAGTAAGCGGA-ACAGGTCTCTCTTT-C
180565 CAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAA
63 CAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAA
180601 ATTTATCTTT
Statistics
Matches: 299, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
111 3 0.01
112 259 0.87
113 37 0.12
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (112 bp):
AATGGATCAACTCCTCCAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCCAA
GATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTTCCTCGATTC
Found at i:180610 original size:48 final size:50
Alignment explanation
Indices: 180514--180646 Score: 170
Period size: 48 Copynumber: 2.8 Consensus size: 50
180504 TGGATCAACG
* * * *
180514 TCCCCAGATATGATATTCCCTTCAGAGTAAGC-G-ACACATGTCTCTCTT
1 TCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATGTCTATCTT
180562 TCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAAT-T-TATCTT
1 TCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATGTCTATCTT
* *
180610 T--TAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
1 TCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAA
180647 GTCTTCCTCG
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
46 34 0.44
48 36 0.47
49 2 0.03
50 5 0.06
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (50 bp):
TCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATGTCTATCTT
Found at i:180626 original size:159 final size:158
Alignment explanation
Indices: 180407--180757 Score: 519
Period size: 159 Copynumber: 2.2 Consensus size: 158
180397 CAACTCCTCC
* ** * *
180407 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTCTAAGATTTGATATTCCCTTT
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATCTATCTTTCTAAGATTTGATATTCCCTTC
* *
180472 AGAGTAAGTGGAATAAGTCTTCCTCGATTCAATGGATCAACGTCCCCAGATATGATATTCCCTTC
66 AGAGTAAGTGGAACAAGTCTTCCTCGATTCAATGGATCAACGTCCCAAGATATGATATTCCCTTC
*
180537 AGAGTAAGC-G-ACACATGTCTCTCTTTCCCA
131 AGAGTAAGCGGAACAAAT-T-TCT-TTT-CCA
*
180567 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATTTATCTTT-TAAGATTTGATATTCCCTTC
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATCTATCTTTCTAAGATTTGATATTCCCTTC
* *
180631 AGAGTAAGTGGAACAAGTCTTCCTCGATTCAATGGATCAACTTCCCAAGATTTGATATTCCCTTC
66 AGAGTAAGTGGAACAAGTCTTCCTCGATTCAATGGATCAACGTCCCAAGATATGATATTCCCTTC
**
180696 AGAGTAAGCGGAACAAATTTCTTTTTTA
131 AGAGTAAGCGGAACAAATTTCTTTTCCA
*
180724 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAA
180758 GTCTTCCTCG
Statistics
Matches: 175, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
157 34 0.19
158 3 0.02
159 92 0.53
160 41 0.23
161 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (158 bp):
AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATCTATCTTTCTAAGATTTGATATTCCCTTC
AGAGTAAGTGGAACAAGTCTTCCTCGATTCAATGGATCAACGTCCCAAGATATGATATTCCCTTC
AGAGTAAGCGGAACAAATTTCTTTTCCA
Found at i:180633 original size:46 final size:49
Alignment explanation
Indices: 180519--180646 Score: 167
Period size: 46 Copynumber: 2.7 Consensus size: 49
180509 CAACGTCCCC
* * *
180519 AGATATGATATTCCCTTCAGAGTAAGC-G-ACACATGTCTCTCTTTCCCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATGTCTATCTTT-CCA
*
180567 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAAT-T-TATCTTT-TA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATGTCTATCTTTCCA
*
180613 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAA
180647 GTCTTCCTCG
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
46 34 0.47
48 32 0.44
49 2 0.03
50 5 0.07
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (49 bp):
AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATGTCTATCTTTCCA
Found at i:180755 original size:111 final size:112
Alignment explanation
Indices: 180561--180867 Score: 474
Period size: 111 Copynumber: 2.7 Consensus size: 112
180551 ATGTCTCTCT
* *
180561 TTCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATTTATCTTTTAAGATTTGATATTC
1 TTCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATTTCTTTTTTAAGATTTGATATTC
180626 CCTTCAGAGTAAGTGGAACAAGTCTTCCTCGATTCAATGGATC-AAC
66 CCTTCAGAGTAAGTGGAACAAGTCTTCCTCGATTCAATGGATCAAAC
180672 TTCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATTTCTTTTTTAAGATTTGATATTC
1 TTCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATTTCTTTTTTAAGATTTGATATTC
*
180737 CCTTCAGAGTAAGTGGAACAAGTCTTCCTCGATTCAATGGATCAAAT
66 CCTTCAGAGTAAGTGGAACAAGTCTTCCTCGATTCAATGGATCAAAC
* ** *** * *
180784 TTCCC-AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTCCCAAGATCTGATTT
1 TTCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAAT-T-TCTTTTTTAAGATTTGATAT
*
180848 TCCCTTCAGAGTAAGCGGAA
64 TCCCTTCAGAGTAAGTGGAA
180868 TAGGTCTCTC
Statistics
Matches: 181, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
111 139 0.77
112 8 0.04
113 34 0.19
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (112 bp):
TTCCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATTTCTTTTTTAAGATTTGATATTC
CCTTCAGAGTAAGTGGAACAAGTCTTCCTCGATTCAATGGATCAAAC
Found at i:180853 original size:48 final size:48
Alignment explanation
Indices: 180783--180917 Score: 193
Period size: 48 Copynumber: 2.8 Consensus size: 48
180773 ATGGATCAAA
*
180783 TTTCCC-AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTC
1 TTTCCCAAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTC
* * *
180830 TTTCCCAAGATCTGATTTTCCCTTCAGAGTAAGCGGAATAGGTCTCTC
1 TTTCCCAAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTC
* *
180878 -TTCTCAAAGATTTGATATTCCCTTCAGAGTAAGCGGAACA
1 TTTC-CCAAGATATGATATTCCCTTCAGAGTAAGCGGAACA
180918 AATTTCTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
47 9 0.12
48 69 0.88
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (48 bp):
TTTCCCAAGATATGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTC
Found at i:183439 original size:429 final size:429
Alignment explanation
Indices: 182640--183497 Score: 1662
Period size: 429 Copynumber: 2.0 Consensus size: 429
182630 AGGGTTAGAG
*
182640 GGTTTATAATATGTACGGGGCATGAAAGGAGATTTTCGTCTGATTGTGCCAGTTCTAAAAAACCT
1 GGTTTATAATATGTACGGGGCACGAAAGGAGATTTTCGTCTGATTGTGCCAGTTCTAAAAAACCT
*
182705 CAAAGAAACCTGAGCAAAGATTTCATGCCGCTGGAACAACGTCTCTGTCAGTCTAAACATCTCCC
66 CAAAGAAACCTGAGCAAAGATTTCATGCCGCTGGAACAACATCTCTGTCAGTCTAAACATCTCCC
182770 TCATGGAGAAACTTGTTGCGCCTATTCCAAATGTTCCACAACAACAAGGTTATCCTAGCAAGCCC
131 TCATGGAGAAACTTGTTGCGCCTATTCCAAATGTTCCACAACAACAAGGTTATCCTAGCAAGCCC
182835 TTTTTGGTCCATCTGAGTGGCAATCCAATCTAGTCATTCCTTGCAAGAGTTTCCTTTACAGTCAA
196 TTTTTGGTCCATCTGAGTGGCAATCCAATCTAGTCATTCCTTGCAAGAGTTTCCTTTACAGTCAA
182900 TAATAGAGATATTAAGTCCTGAGAAATGTAAAATAGATTTGGATTTAGGGCATTCTTTTAGGTTA
261 TAATAGAGATATTAAGTCCTGAGAAATGTAAAATAGATTTGGATTTAGGGCATTCTTTTAGGTTA
182965 TGGAGCGTGTTTTCTATGGCGTCCCCATACATAGGGCATTTACCCTCCGAAAGGCGAGCATTGAG
326 TGGAGCGTGTTTTCTATGGCGTCCCCATACATAGGGCATTTACCCTCCGAAAGGCGAGCATTGAG
183030 GAGTTTTTTCGCTTGTTAAGATTGCATTGTGACAGATTC
391 GAGTTTTTTCGCTTGTTAAGATTGCATTGTGACAGATTC
* *
183069 GGTTTATACTATGTACGGGGCACGAAAGGAGATTTTCGTCTGATTGTGCCAGTTCTAAGAAACCT
1 GGTTTATAATATGTACGGGGCACGAAAGGAGATTTTCGTCTGATTGTGCCAGTTCTAAAAAACCT
183134 CAAAGAAACCTGAGCAAAGATTTCATGCCGCTGGAACAACATCTCTGTCAGTCTAAACATCTCCC
66 CAAAGAAACCTGAGCAAAGATTTCATGCCGCTGGAACAACATCTCTGTCAGTCTAAACATCTCCC
*
183199 TCATGGAGAAACTTGTTGCGCCTATTCTAAATGTTCCACAACAACAAGGTTATCCTAGCAAGCCC
131 TCATGGAGAAACTTGTTGCGCCTATTCCAAATGTTCCACAACAACAAGGTTATCCTAGCAAGCCC
183264 TTTTTGGTCCATCTGAGTGGCAATCCAATCTAGTCATTCCTTGCAAGAGTTTCCTTTACAGTCAA
196 TTTTTGGTCCATCTGAGTGGCAATCCAATCTAGTCATTCCTTGCAAGAGTTTCCTTTACAGTCAA
183329 TAATAGAGATATTAAGTCCTGAGAAATGTAAAATAGATTTGGATTTAGGGCATTCTTTTAGGTTA
261 TAATAGAGATATTAAGTCCTGAGAAATGTAAAATAGATTTGGATTTAGGGCATTCTTTTAGGTTA
*
183394 TGGAGCGTGTTTTCTATGGCGTCCCCATATATAGGGCATTTACCCTCCGAAAGGCGAGCATTGAG
326 TGGAGCGTGTTTTCTATGGCGTCCCCATACATAGGGCATTTACCCTCCGAAAGGCGAGCATTGAG
183459 GAGTTTTTTCGCTTGTTAAGATTGCATTGTGACAGATTC
391 GAGTTTTTTCGCTTGTTAAGATTGCATTGTGACAGATTC
183498 TCCAACCAAA
Statistics
Matches: 423, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
429 423 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (429 bp):
GGTTTATAATATGTACGGGGCACGAAAGGAGATTTTCGTCTGATTGTGCCAGTTCTAAAAAACCT
CAAAGAAACCTGAGCAAAGATTTCATGCCGCTGGAACAACATCTCTGTCAGTCTAAACATCTCCC
TCATGGAGAAACTTGTTGCGCCTATTCCAAATGTTCCACAACAACAAGGTTATCCTAGCAAGCCC
TTTTTGGTCCATCTGAGTGGCAATCCAATCTAGTCATTCCTTGCAAGAGTTTCCTTTACAGTCAA
TAATAGAGATATTAAGTCCTGAGAAATGTAAAATAGATTTGGATTTAGGGCATTCTTTTAGGTTA
TGGAGCGTGTTTTCTATGGCGTCCCCATACATAGGGCATTTACCCTCCGAAAGGCGAGCATTGAG
GAGTTTTTTCGCTTGTTAAGATTGCATTGTGACAGATTC
Found at i:184633 original size:30 final size:30
Alignment explanation
Indices: 184597--184657 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
184587 GCTCCCATAA
*
184597 TGGGCCTCTACAAAACCTTATCTGAATTAG
1 TGGGCCTCTACAAAACCTGATCTGAATTAG
184627 TGGGCCTCTACAAAACCTGATCTGAATTAG
1 TGGGCCTCTACAAAACCTGATCTGAATTAG
184657 T
1 T
184658 CAGTCAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (30 bp):
TGGGCCTCTACAAAACCTGATCTGAATTAG
Found at i:194232 original size:2 final size:2
Alignment explanation
Indices: 194225--194311 Score: 53
Period size: 2 Copynumber: 47.0 Consensus size: 2
194215 TCAGGCCGGG
* * * *
194225 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
* * * *
194265 TA TA TA TA T- TA -A TT TA -A TT TA AA TT TA T- TA -A 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
194302 TA TA TA TA TA
1 TA TA TA TA TA
194312 ATAATTATTT
Statistics
Matches: 62, Mismatches: 16, Indels: 14
0.67 0.17 0.15
Matches are distributed among these distances:
1 7 0.11
2 55 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:194258 original size:15 final size:16
Alignment explanation
Indices: 194240--194314 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 16
194230 ATATATTTAA
194240 ATTAA-ATATATAAAT
1 ATTAATATATATAAAT
*
194255 ATTATATATATATATAT
1 ATTA-ATATATATAAAT
* *
194272 ATTAATTTAATTTAAATTT
1 ATTAATAT-ATATAAA--T
*
194291 ATTAATATATATATAT
1 ATTAATATATATAAAT
194307 ATATAATA
1 AT-TAATA
194315 ATTATTTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
15 4 0.09
16 7 0.15
17 23 0.49
18 5 0.11
19 8 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAATATATATAAAT
Found at i:194325 original size:39 final size:40
Alignment explanation
Indices: 194257--194332 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
194247 ATATAAATAT
*
194257 TATATATATATATATATTAATTTAATTTAA-ATTTATTAA
1 TATATATATATATATAATAATTTAATTTAATATTTATTAA
*
194296 TATATATATATATATAATAA-TTATTTTTAATATTTAT
1 TATATATATATATATAATAATTTA-ATTTAATATTTAT
194333 CGGTCGGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 3 0.09
39 24 0.73
40 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (40 bp):
TATATATATATATATAATAATTTAATTTAATATTTATTAA
Found at i:198138 original size:23 final size:21
Alignment explanation
Indices: 198090--198162 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 21
198080 AGAATAATTA
*
198090 TGTCTTTGTGACATGTTT-TC
1 TGTCTTTGTGACACGTTTCTC
198110 TGTCTTTGTGACACGTTTAACTC
1 TGTCTTTGTGACACGTTT--CTC
**
198133 TGTCTTTGTGGCACATTTTTCTC
1 TGTCTTTGT-G-ACACGTTTCTC
198156 TGTCTTT
1 TGTCTTT
198163 TGGTAGCTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
20 17 0.38
23 21 0.47
24 1 0.02
25 6 0.13
ACGTcount: A:0.11, C:0.19, G:0.18, T:0.52
Consensus pattern (21 bp):
TGTCTTTGTGACACGTTTCTC
Found at i:202679 original size:44 final size:44
Alignment explanation
Indices: 202596--202969 Score: 224
Period size: 44 Copynumber: 8.7 Consensus size: 44
202586 TTAGGGACCT
* * *
202596 TTGAGAAAA-TTAGG-GCCTCAATTATAAAGATACGTAGAAATTGAAA
1 TTGAAAAAACTTAGGAGCCTCAATTATAAAG----GTAGAAAGTGAGA
*
202642 TTGAAAAAACTTAGGAGCCTCAATTGTAAAGGTAGAAAGTGAGA
1 TTGAAAAAACTTAGGAGCCTCAATTATAAAGGTAGAAAGTGAGA
* *
202686 TTGAAAAAACTTAAGGA-CCTCAATTATAAAGTTAAAAAGTGAGA
1 TTGAAAAAACTT-AGGAGCCTCAATTATAAAGGTAGAAAGTGAGA
* * *
202730 TT-AAAAAA-TTGGGGGTCTCAATTATAAAGGTAGAAAGTGAGA
1 TTGAAAAAACTTAGGAGCCTCAATTATAAAGGTAGAAAGTGAGA
* * ** * * * *
202772 TTGAAAAAACATAAGAGAATCAATTATATAGTTAAAAAATG-GA
1 TTGAAAAAACTTAGGAGCCTCAATTATAAAGGTAGAAAGTGAGA
* * ** * **
202815 TT-AAAAAAATTAGGGGTATCAATTATAAAGGTAAAAAAAG-GA
1 TTGAAAAAACTTAGGAGCCTCAATTATAAAGGTAGAAAGTGAGA
* * * * *
202857 TTG-AAAAA-TTA-GAGACTTCAATTATAAAGATTAAAAATTAAGA
1 TTGAAAAAACTTAGGAG-CCTCAATTATAAAG-GTAGAAAGTGAGA
*** * *
202900 TTGAATAAAA-TTA-GAATATCAATTATAAAGATA-AAAGGTAAGA
1 TTGAA-AAAACTTAGGAGCCTCAATTATAAAGGTAGAAA-GTGAGA
* *
202943 TT-TAAAAA-TTAGAAGCCT-AATTATAAA
1 TTGAAAAAACTTAGGAGCCTCAATTATAAA
202970 TATGTAAAAA
Statistics
Matches: 267, Mismatches: 47, Indels: 33
0.77 0.14 0.10
Matches are distributed among these distances:
40 2 0.01
41 33 0.12
42 79 0.30
43 30 0.11
44 83 0.31
45 13 0.05
46 8 0.03
47 5 0.02
48 14 0.05
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.26
Consensus pattern (44 bp):
TTGAAAAAACTTAGGAGCCTCAATTATAAAGGTAGAAAGTGAGA
Found at i:202758 original size:86 final size:88
Alignment explanation
Indices: 202645--202913 Score: 311
Period size: 86 Copynumber: 3.1 Consensus size: 88
202635 ATTGAAATTG
* * * * *
202645 AAAAAACTTAGGAGCCTCAATTGTAAAGGTAGAAAGTGAGATTGAAAAAACTTAAG-GACCTCAA
1 AAAAAAATTAGGGGTCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGAGACATCAA
*
202709 TTATAAAGTTAAAAAGTGAGATT
66 TTATAAAGTTAAAAAATGAGATT
* *
202732 -AAAAAATTGGGGGTCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACATAAGAGA-ATCAA
1 AAAAAAATTAGGGGTCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGAGACATCAA
*
202795 TTATATAGTTAAAAAATG-GATT
66 TTATAAAGTTAAAAAATGAGATT
* * ** *
202817 AAAAAAATTAGGGGTATCAATTATAAAGGTAAAAAAAG-GATTG-AAAAA-TT-AGAGACTTCAA
1 AAAAAAATTAGGGGTCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGAGACATCAA
* *
202878 TTATAAAGATTAAAAATTAAGATT
66 TTATAAAG-TTAAAAAATGAGATT
*
202902 GAATAAAATTAG
1 -AAAAAAATTAG
202914 AATATCAATT
Statistics
Matches: 156, Mismatches: 20, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
82 5 0.03
83 12 0.08
84 13 0.08
85 13 0.08
86 111 0.71
87 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.26
Consensus pattern (88 bp):
AAAAAAATTAGGGGTCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGAGACATCAA
TTATAAAGTTAAAAAATGAGATT
Found at i:202903 original size:43 final size:42
Alignment explanation
Indices: 202833--202980 Score: 137
Period size: 41 Copynumber: 3.5 Consensus size: 42
202823 ATTAGGGGTA
*
202833 TCAATTATAAAG-GTAAAAA--AAGGATTGAAAAATTAGAGACT
1 TCAATTATAAAGATTAAAAATTAA-GATTGAAAAATTAGA-ACT
202874 TCAATTATAAAGATTAAAAATTAAGATTGAATAAAATTAGAA-T
1 TCAATTATAAAGATTAAAAATTAAGATTG-A-AAAATTAGAACT
** * *
202917 ATCAATTATAAAGA-TAAAAGGTAAGATTTAAAAATTAGAAGCC
1 -TCAATTATAAAGATTAAAAATTAAGATTGAAAAATTAGAA-CT
*
202960 T-AATTATAAATATGTAAAAAT
1 TCAATTATAAAGAT-TAAAAAT
202981 GGGAGCCCTA
Statistics
Matches: 89, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
41 32 0.36
42 8 0.09
43 23 0.26
44 17 0.19
45 9 0.10
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (42 bp):
TCAATTATAAAGATTAAAAATTAAGATTGAAAAATTAGAACT
Found at i:202965 original size:41 final size:44
Alignment explanation
Indices: 202677--202979 Score: 131
Period size: 42 Copynumber: 7.1 Consensus size: 44
202667 GTAAAGGTAG
* * *
202677 AAAGTGAGATTGAA-AAAACTTAAGGACCTCAATTATAAAG-TTAA
1 AAAGTAAGATTGAATAAAA-TT-AGAACATCAATTATAAAGATTAA
* * ** * *
202721 AAAGTGAGATT-AA-AAAATTGGGGGTC-TCAATTATAAAG-GTAG
1 AAAGTAAGATTGAATAAAATT--AGAACATCAATTATAAAGATTAA
* * * *
202763 AAAGTGAGATTGAAAAAACATAAGAGA-ATCAATTATATAG-TTAA
1 AAAGTAAGATTGAATAAA-ATTAGA-ACATCAATTATAAAGATTAA
* * * *** *
202807 AAAAT-GGATT-AAAAAAATTAGGGGTATCAATTATAAAG-GTAA
1 AAAGTAAGATTGAATAAAATTA-GAACATCAATTATAAAGATTAA
*
202849 AAA--AAGGATTG-A-AAAATTAGAGACTTCAATTATAAAGATTAA
1 AAAGTAA-GATTGAATAAAATTAGA-ACATCAATTATAAAGATTAA
* *
202891 AAATTAAGATTGAATAAAATTAGAATATCAATTATAAAGA-TAA
1 AAAGTAAGATTGAATAAAATTAGAACATCAATTATAAAGATTAA
* * * *
202934 AAGGTAAGATT-TA-AAAATTAGAAGCCT-AATTATAAATATGTAA
1 AAAGTAAGATTGAATAAAATTAGAA-CATCAATTATAAAGAT-TAA
202977 AAA
1 AAA
202980 TGGGAGCCCT
Statistics
Matches: 205, Mismatches: 34, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
40 1 0.00
41 42 0.20
42 65 0.32
43 38 0.19
44 48 0.23
45 11 0.05
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (44 bp):
AAAGTAAGATTGAATAAAATTAGAACATCAATTATAAAGATTAA
Found at i:209298 original size:27 final size:29
Alignment explanation
Indices: 209245--209313 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 29
209235 GTTTAACTTT
*
209245 ATTTATTTAATTTTTTTAATTTCAT-A-A
1 ATTTATTTATTTTTTTTAATTTCATAATA
**
209272 ATTTATTTATTTTTTATTTGTTT-ATAATA
1 ATTTATTTATTTTTT-TTAATTTCATAATA
209301 ATTT-TTTATTTTT
1 ATTTATTTATTTTT
209314 AAATATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 16 0.44
28 15 0.42
29 5 0.14
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (29 bp):
ATTTATTTATTTTTTTTAATTTCATAATA
Done.