Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002762.1 Hibiscus syriacus cultivar Beakdansim tig00005693_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: 53341
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:13072 original size:37 final size:37
Alignment explanation
Indices: 13021--13091 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
13011 ACTAAGTGTA
*
13021 CAACCCACATAATTCATAATAAGTTTATGAACGAGTG
1 CAACCCACATAATTCATAATAAGTTTATAAACGAGTG
13058 CAACCCACGA-AATTCATAATAAGTTTATAAACGA
1 CAACCCAC-ATAATTCATAATAAGTTTATAAACGA
13092 TCGTATCGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
37 31 0.97
38 1 0.03
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (37 bp):
CAACCCACATAATTCATAATAAGTTTATAAACGAGTG
Found at i:14267 original size:47 final size:47
Alignment explanation
Indices: 14210--14305 Score: 167
Period size: 47 Copynumber: 2.0 Consensus size: 47
14200 AATTAAACTT
*
14210 TAATCGTATTTATTAAATTTAAT-ATTCTATCTCATTAAATCAATTAA
1 TAATCATATTTATTAAATTTAATAATT-TATCTCATTAAATCAATTAA
14257 TAATCATATTTATTAAATTTAATAATTTATCTCATTAAATCAATTAA
1 TAATCATATTTATTAAATTTAATAATTTATCTCATTAAATCAATTAA
14304 TA
1 TA
14306 TTAAAAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 44 0.94
48 3 0.06
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.47
Consensus pattern (47 bp):
TAATCATATTTATTAAATTTAATAATTTATCTCATTAAATCAATTAA
Found at i:14271 original size:25 final size:22
Alignment explanation
Indices: 14221--14296 Score: 82
Period size: 22 Copynumber: 3.3 Consensus size: 22
14211 AATCGTATTT
*
14221 ATTAAATTTAATATTCTATCTC
1 ATTAAATTTAATAATCTATCTC
*
14243 ATTAAATCAATTAATAATCATAT-TT
1 ATTAAAT---TTAATAATC-TATCTC
*
14268 ATTAAATTTAATAATTTATCTC
1 ATTAAATTTAATAATCTATCTC
14290 ATTAAAT
1 ATTAAAT
14297 CAATTAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
21 3 0.07
22 23 0.51
25 16 0.36
26 3 0.07
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTAAATTTAATAATCTATCTC
Found at i:14303 original size:25 final size:25
Alignment explanation
Indices: 14228--14305 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 25
14218 TTTATTAAAT
14228 TTAAT-ATTCTATCTCATTAAATCAA
1 TTAATAATT-TATCTCATTAAATCAA
* *
14253 TTAATAATCATAT-TTATTAAAT---
1 TTAATAAT-TTATCTCATTAAATCAA
14275 TTAATAATTTATCTCATTAAATCAA
1 TTAATAATTTATCTCATTAAATCAA
14300 TTAATA
1 TTAATA
14306 TTAAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
21 3 0.07
22 16 0.37
25 19 0.44
26 5 0.12
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATAATTTATCTCATTAAATCAA
Found at i:14568 original size:16 final size:17
Alignment explanation
Indices: 14534--14572 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
14524 AGAAATTTGG
14534 AAGAAATAAAAATTGAA
1 AAGAAATAAAAATTGAA
14551 AAGAAA-AAAAA-TGAA
1 AAGAAATAAAAATTGAA
14566 AA-AAATA
1 AAGAAATA
14573 TTTTCTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.14
15 7 0.33
16 5 0.24
17 6 0.29
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (17 bp):
AAGAAATAAAAATTGAA
Found at i:15802 original size:22 final size:19
Alignment explanation
Indices: 15769--15821 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
15759 TAGGAGCTAA
15769 ATTATTAAAATAATACTTT
1 ATTATTAAAATAATACTTT
15788 ATTATTAAAATAATACTTT
1 ATTATTAAAATAATACTTT
*
15807 ATTATTAAAACAATA
1 ATTATTAAAATAATA
15822 TCCAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTATTAAAATAATACTTT
Found at i:16914 original size:81 final size:81
Alignment explanation
Indices: 16766--17210 Score: 545
Period size: 81 Copynumber: 5.4 Consensus size: 81
16756 TGGGAAATTC
* * *
16766 GCTCCACTCTTCTTTCATGG-GATATCGGACTTGATCTGTTCCTCTTTTTTCGGGTAGTCAGATC
1 GCTCCACTCTTCTTTCAAGGAGATA--AGACTTGATTTGTTCCTC-TTTTTCGGGTAGTCAGATC
*
16830 AATTTTGGAAAATGAGTAT
63 AATTTTGGAAAACGAGTAT
* * * * * *
16849 GCTCCACTATTCTTTCAGGGAGATACA-ATTTGATTTGTTCATCTTTTTCAGGTAGTTAGATCAA
1 GCTCCACTCTTCTTTCAAGGAGATA-AGACTTGATTTGTTCCTCTTTTTCGGGTAGTCAGATCAA
*
16913 TTTTGGAAAACGAGTCT
65 TTTTGGAAAACGAGTAT
* * *
16930 GCTCTACTCTTCTTTCAGGGAGATAAGACTTGATTCGTTCCTCTTTTTCGGGTAGTCAGATCAAT
1 GCTCCACTCTTCTTTCAAGGAGATAAGACTTGATTTGTTCCTCTTTTTCGGGTAGTCAGATCAAT
* *
16995 ATTGGAAAATGAGTAT
66 TTTGGAAAACGAGTAT
* *
17011 GCTCCACTCTTCTTTCAAGGAGATAAGACTTGATTTGTTCCTCTTTTTTTTTTTTTTGAGTAGTC
1 GCTCCACTCTTCTTTCAAGGAGATAAGACTTGATTTGTTCCTC--------TTTTTCGGGTAGTC
17076 AGATCAATTTTGGAAAACGAGTAT
58 AGATCAATTTTGGAAAACGAGTAT
* * * *
17100 GCTCCAATATTCTTTCAAGGAGATAAAACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAAT
1 GCTCCACTCTTCTTTCAAGGAGATAAGACTTGATTTGTTCCTCTTTTTCGGGTAGTCAGATCAAT
*
17165 ATTGGAAAACGAGTCA-
66 TTTGGAAAACGAGT-AT
17181 GCTCCACTCTTCTTTCAAGGAGATAAGACT
1 GCTCCACTCTTCTTTCAAGGAGATAAGACT
17211 CGAGAAATCT
Statistics
Matches: 314, Mismatches: 37, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
80 1 0.00
81 203 0.65
82 14 0.04
83 19 0.06
84 4 0.01
89 73 0.23
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (81 bp):
GCTCCACTCTTCTTTCAAGGAGATAAGACTTGATTTGTTCCTCTTTTTCGGGTAGTCAGATCAAT
TTTGGAAAACGAGTAT
Found at i:17156 original size:170 final size:161
Alignment explanation
Indices: 16794--17210 Score: 559
Period size: 170 Copynumber: 2.5 Consensus size: 161
16784 GGGATATCGG
* *
16794 ACTTGATCTGTTCCTCTTTTTTCGGGTAGTCAGATCAATTTTGGAAAATGAGTATGCTCCACTAT
1 ACTTGAT-TGTTCCTC-TTTTTCGGGTAGTCAGATCAATATTGGAAAATGAGTATGCTCCACTCT
* * *
16859 TCTTTCAGGGAGATACA-ATTTGATTTGTTCATCTTTTTCAGGTAGTTAGATCAATTTTGGAAAA
64 TCTTTCAAGGAGATA-AGACTTGATTTGTTCATCTTTTTCAGGTAGTCAGATCAATTTTGGAAAA
* * * * * *
16923 CGAGTCTGCTCTACTCTTCTTTCAGGGAGATAAG
128 CGAGTATGCTCCAATATTCTTTCAAGGAGATAAA
16957 ACTTGATTCGTTCCTCTTTTTCGGGTAGTCAGATCAATATTGGAAAATGAGTATGCTCCACTCTT
1 ACTTGATT-GTTCCTCTTTTTCGGGTAGTCAGATCAATATTGGAAAATGAGTATGCTCCACTCTT
* **
17022 CTTTCAAGGAGATAAGACTTGATTTGTTCCTCTTTTTTTTTTTTTTGAGTAGTCAGATCAATTTT
65 CTTTCAAGGAGATAAGACTTGATTTGTTCATC-------TTTTTCAG-GTAGTCAGATCAATTTT
17087 GGAAAACGAGTATGCTCCAATATTCTTTCAAGGAGATAAA
122 GGAAAACGAGTATGCTCCAATATTCTTTCAAGGAGATAAA
*
17127 ACTTGATATGTTCCTCTTTTTCGGGTAGTCAGATCAATATTGGAAAACGAGTCA-GCTCCACTCT
1 ACTTGAT-TGTTCCTCTTTTTCGGGTAGTCAGATCAATATTGGAAAATGAGT-ATGCTCCACTCT
17191 TCTTTCAAGGAGATAAGACT
64 TCTTTCAAGGAGATAAGACT
17211 CGAGAAATCT
Statistics
Matches: 227, Mismatches: 15, Indels: 17
0.88 0.06 0.07
Matches are distributed among these distances:
161 1 0.00
162 75 0.33
163 14 0.06
169 6 0.03
170 129 0.57
171 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (161 bp):
ACTTGATTGTTCCTCTTTTTCGGGTAGTCAGATCAATATTGGAAAATGAGTATGCTCCACTCTTC
TTTCAAGGAGATAAGACTTGATTTGTTCATCTTTTTCAGGTAGTCAGATCAATTTTGGAAAACGA
GTATGCTCCAATATTCTTTCAAGGAGATAAA
Found at i:17295 original size:136 final size:137
Alignment explanation
Indices: 17084--17398 Score: 418
Period size: 136 Copynumber: 2.3 Consensus size: 137
17074 TCAGATCAAT
* * * * * *
17084 TTTGGAAAACGAGTATGCTCCAATATTCTTTCAA-GGAGATAAAACTTGATATGTTCCTCTTTTT
1 TTTGGAAGACGGGTATGCTCCACTCTTATTTCAAGGGAGATCAAACTTGATATGTTCCTCTTTTT
* * *
17148 CGGGTAGTCAGATCAATATTGGAAAACGAGTCAGCTCCACTCTTCTTTCAAGGAGATAAGACTCG
66 AGGGTAGTCAGATCAATATTGGAAAACGAGTCAGCTCCACTATTCTTTCAAGGAGATAAGACTCA
17213 AGAAATC
131 AGAAATC
* * * *
17220 TTTGGAAGACGGGTCTGCTCTACTCTTATTTCAAGGGAGATCAGACTTGATATGTTTCTC-TTTT
1 TTTGGAAGACGGGTATGCTCCACTCTTATTTCAAGGGAGATCAAACTTGATATGTTCCTCTTTTT
* * * * * *
17284 AGGGTAGTCAGATCAATGTTTGAAGATGAGTCTGCTCCACTATTCTTTCATGGAGATAAGACTCA
66 AGGGTAGTCAGATCAATATTGGAAAACGAGTCAGCTCCACTATTCTTTCAAGGAGATAAGACTCA
*
17349 AGAAGTC
131 AGAAATC
* *
17356 TTTGGAAGACGGGTATGCTCCACTCTTCTTTCAGGGGAGATCA
1 TTTGGAAGACGGGTATGCTCCACTCTTATTTCAAGGGAGATCA
17399 TACATTTTCA
Statistics
Matches: 154, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
136 132 0.86
137 22 0.14
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (137 bp):
TTTGGAAGACGGGTATGCTCCACTCTTATTTCAAGGGAGATCAAACTTGATATGTTCCTCTTTTT
AGGGTAGTCAGATCAATATTGGAAAACGAGTCAGCTCCACTATTCTTTCAAGGAGATAAGACTCA
AGAAATC
Found at i:18197 original size:90 final size:90
Alignment explanation
Indices: 18058--18339 Score: 297
Period size: 90 Copynumber: 3.1 Consensus size: 90
18048 GATACTACTA
* * * * *
18058 AAAAG-TTGACTCATCTCCGCGAGAAAGTCAA-GAATGACAACATTAAAAGATCGACTTCTCTTT
1 AAAAGATTGACTCATCTTCGCAAGAAAGTCAAGGAATGACAACACTAAAAGATTGACTTCTCTTC
* *
18121 GTGAGAAAGTCAAGAAAGATAACACT
66 GCGAGAAAGTCAAGAAA-ACAACACT
* * * * *
18147 AAAAGATTGATTCCTCTTCGCAAGAAAGTCAAGGAA-GGCAACACGAAAAGATTGAC-CCATCTT
1 AAAAGATTGACTCATCTTCGCAAGAAAGTCAAGGAATGACAACACTAAAAGATTGACTTC-TCTT
*
18210 CGCGATAAAGTCAAGGAAAACAACACT
65 CGCGAGAAAGTCAA-GAAAACAACACT
* * * * *
18237 AAAAGATTAACTAATCTTCACAAGAAAGT--AGAGAATGACAATACTAAAAGATTGATTTCTCTT
1 AAAAGATTGACTCATCTTCGCAAGAAAGTCAAG-GAATGACAACACTAAAAGATTGACTTCTCTT
* *
18300 CACGAGGAAGTCAAGAATAACAACACT
65 CGCGAGAAAGTCAAGAA-AACAACACT
18327 AAAAGATTGACTC
1 AAAAGATTGACTC
18340 CTATTCATGA
Statistics
Matches: 157, Mismatches: 28, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
88 2 0.01
89 12 0.08
90 135 0.86
91 8 0.05
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (90 bp):
AAAAGATTGACTCATCTTCGCAAGAAAGTCAAGGAATGACAACACTAAAAGATTGACTTCTCTTC
GCGAGAAAGTCAAGAAAACAACACT
Found at i:18362 original size:45 final size:45
Alignment explanation
Indices: 18058--18364 Score: 248
Period size: 45 Copynumber: 6.8 Consensus size: 45
18048 GATACTACTA
* * * * *
18058 AAAAG-TTGACTCATCTCCGCGAGAAAGTCAAGAATGACAACATT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACAACACT
* * *** *
18102 AAAAGATCGACTTCTCTTTGTGAGAAAGTCAAGAA-AGATAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATA-ACAACACT
* * * ** *
18147 AAAAGATTGATTCCTCTTCGCAAGAAAGTCAAGGAA-GGCAACACG
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAATAACAACACT
* *
18192 AAAAGATTGAC-CCATCTTCGCGATAAAGTCAAGGAA-AACAACACT
1 AAAAGATTGACTCC-TCTTCACGAGAAAGTCAA-GAATAACAACACT
* ** * * *
18237 AAAAGATTAACTAATCTTCACAAGAAAGT-AGAGAATGACAATACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCA-AGAATAACAACACT
* * *
18282 AAAAGATTGATTTCTCTTCACGAGGAAGTCAAGAATAACAACACT
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACAACACT
* * *
18327 AAAAGATTGACTCCTATTCATGAGGAAGTCAAGAATAA
1 AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAA
18365 TATCGAAATA
Statistics
Matches: 210, Mismatches: 45, Indels: 15
0.78 0.17 0.06
Matches are distributed among these distances:
44 11 0.05
45 195 0.93
46 4 0.02
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (45 bp):
AAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACAACACT
Found at i:20135 original size:1 final size:1
Alignment explanation
Indices: 20131--20183 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
20121 TTTTTCTCGC
* * * * *
20131 TTTTTTCTTTTTTCTTTTTTTTTTTTTTTTCTTTTTTTTTTCTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20184 CTATATTTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:20148 original size:6 final size:6
Alignment explanation
Indices: 20132--20185 Score: 76
Period size: 6 Copynumber: 9.2 Consensus size: 6
20122 TTTTCTCGCT
*
20132 TTTTTC TTTTTTC TTTTT- TTTTTT TTTTTC TTTTT- TTTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
20179 TTTTTC T
1 TTTTTC T
20186 ATATTTTCCC
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
5 10 0.23
6 28 0.64
7 6 0.14
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (6 bp):
TTTTTC
Found at i:20151 original size:17 final size:16
Alignment explanation
Indices: 20131--20183 Score: 79
Period size: 17 Copynumber: 3.2 Consensus size: 16
20121 TTTTTCTCGC
*
20131 TTTTTTCTTTTTTCTTT
1 TTTTTTTTTTTTTC-TT
20148 TTTTTTTTTTTTTCTT
1 TTTTTTTTTTTTTCTT
20164 TTTTTTTTCTTTTTCTT
1 TTTTTTTT-TTTTTCTT
20181 TTT
1 TTT
20184 CTATATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
16 10 0.29
17 24 0.71
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
TTTTTTTTTTTTTCTT
Found at i:20176 original size:24 final size:24
Alignment explanation
Indices: 20131--20236 Score: 81
Period size: 24 Copynumber: 4.0 Consensus size: 24
20121 TTTTTCTCGC
*
20131 TTTTTTCTTTTTTCTTTTTTTTTT
1 TTTTTTCTTTTTTCTTTTTTTTTC
20155 TTTTTTCTTTTTT-TTTTCTTTTTC
1 TTTTTTCTTTTTTCTTTT-TTTTTC
*
20179 -TTTTTCTATATTTTCCCTTTCCTTTTTC
1 TTTTTTCT-T-TTTT--CTTT-TTTTTTC
20207 TATCTTTTCTATTTTTCATTTTTTTCTTC
1 T-T-TTTTCT-TTTTTC-TTTTTTT-TTC
20236 T
1 T
20237 ATATCCTCTT
Statistics
Matches: 67, Mismatches: 3, Indels: 19
0.75 0.03 0.21
Matches are distributed among these distances:
23 11 0.16
24 19 0.28
25 4 0.06
28 13 0.19
29 7 0.10
30 5 0.07
31 8 0.12
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTTCTTTTTTCTTTTTTTTTC
Found at i:21942 original size:23 final size:23
Alignment explanation
Indices: 21912--21989 Score: 138
Period size: 23 Copynumber: 3.4 Consensus size: 23
21902 GCACAGGTAC
21912 TGCATCGATGCACACGTTAGGGA
1 TGCATCGATGCACACGTTAGGGA
*
21935 TGCATCGATGCACACTTTAGGGA
1 TGCATCGATGCACACGTTAGGGA
*
21958 TGCATTGATGCACACGTTAGGGA
1 TGCATCGATGCACACGTTAGGGA
21981 TGCATCGAT
1 TGCATCGAT
21990 ACATACCTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACACGTTAGGGA
Found at i:27896 original size:3 final size:3
Alignment explanation
Indices: 27888--27921 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
27878 TGGGTTTGGG
27888 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
27922 AAAAAAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:28209 original size:29 final size:27
Alignment explanation
Indices: 28171--28285 Score: 78
Period size: 27 Copynumber: 4.3 Consensus size: 27
28161 AAATTTACAA
* *
28171 AATATGTTATAATTATTTTTTTATATATT
1 AATATATTATAATTA-TTTATTATAT-TT
* *
28200 TATATATTATATTTATTTATTATATTT
1 AATATATTATAATTATTTATTATATTT
* *
28227 AATA-ATTAATAATTA---ATAATAATT
1 AATATATT-ATAATTATTTATTATATTT
* *
28251 ATTATTATTATATTTATTTATT-TATTT
1 AATA-TATTATAATTATTTATTATATTT
*
28278 ATTATATT
1 AATATATT
28286 CATTTAATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
24 10 0.15
25 6 0.09
26 10 0.15
27 19 0.28
28 11 0.16
29 12 0.18
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (27 bp):
AATATATTATAATTATTTATTATATTT
Found at i:28212 original size:13 final size:13
Alignment explanation
Indices: 28194--28285 Score: 68
Period size: 13 Copynumber: 7.1 Consensus size: 13
28184 TATTTTTTTA
28194 TATATTTATATAT
1 TATATTTATATAT
*
28207 TATATTTATTTAT
1 TATATTTATATAT
28220 TATATTTA-ATAAT
1 TATATTTATAT-AT
*
28233 TAATAATTA-ATA-
1 T-ATATTTATATAT
*
28245 -ATAATTATTATTAT
1 TATATTTA-TA-TAT
*
28259 TATATTTATTTAT
1 TATATTTATATAT
28272 T-TATTTATTATAT
1 TATATTTA-TATAT
28285 T
1 T
28286 CATTTAATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
10 7 0.11
12 8 0.12
13 35 0.54
14 9 0.14
15 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATATTTATATAT
Found at i:28218 original size:4 final size:4
Alignment explanation
Indices: 28183--28291 Score: 53
Period size: 4 Copynumber: 26.8 Consensus size: 4
28173 TATGTTATAA
* * * * *
28183 TTAT TTTT TTAT ATAT TTAT ATAT TATAT TTAT TTAT TATAT TTA- ATAA
1 TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT T-TAT TTAT TTAT
* * * * *
28232 TTAA TAAT TAAT AATAA TTA- TTA- TTAT TATAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT -TTAT TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTAT
*
28280 TATAT TCAT TTA
1 T-TAT TTAT TTA
28292 ATTTCTATGT
Statistics
Matches: 82, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
3 8 0.10
4 57 0.70
5 17 0.21
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (4 bp):
TTAT
Found at i:30664 original size:65 final size:64
Alignment explanation
Indices: 30549--30694 Score: 204
Period size: 65 Copynumber: 2.3 Consensus size: 64
30539 TTGAATGCAT
* * * *
30549 TTTGTGTATCGATGCACAACCATGCATCGATGCACTCTTGAATTTATTGAAACATCGAATGTAG
1 TTTGTGTACCGATGCACAACCATGCATCGATGCACTCCTGAATTTATTGAAACATCGAATATAA
**
30613 TTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTT-TTGAAACATCGAATATA
1 TTTGTGTACCGATGCACA-ACCATGCATCGATGCACTCCTGAAT-TTATTGAAACATCGAATATA
30677 A
64 A
*
30678 TTAGTGTACCGATGCAC
1 TTTGTGTACCGATGCAC
30695 CCCTAGTGTA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 17 0.23
65 54 0.74
66 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (64 bp):
TTTGTGTACCGATGCACAACCATGCATCGATGCACTCCTGAATTTATTGAAACATCGAATATAA
Found at i:37174 original size:29 final size:29
Alignment explanation
Indices: 37136--37291 Score: 172
Period size: 29 Copynumber: 5.4 Consensus size: 29
37126 CATTTTACAT
* * *
37136 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* **
37165 AAATATCACCCTTTTCAAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
*
37194 AAATAGCA-CATTTTTGAATTAAATTCCCA
1 AAATAGCACCCTTTTTGAATT-AATTCCCA
**
37223 AAATAGCA-TATTTTTGAATTAAATTCCCA
1 AAATAGCACCCTTTTTGAATT-AATTCCCA
* *
37252 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
*
37281 AAATATCACCC
1 AAATAGCACCC
37292 GATCAACTGG
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
28 9 0.08
29 94 0.85
30 8 0.07
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATAGCACCCTTTTTGAATTAATTCCCA
Found at i:37321 original size:18 final size:18
Alignment explanation
Indices: 37294--37328 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37284 TATCACCCGA
*
37294 TCAACTGGTCAGGTCGGG
1 TCAACGGGTCAGGTCGGG
*
37312 TCAACGGGTCGGGTCGG
1 TCAACGGGTCAGGTCGG
37329 AACTGGTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.23, G:0.43, T:0.20
Consensus pattern (18 bp):
TCAACGGGTCAGGTCGGG
Found at i:48137 original size:19 final size:19
Alignment explanation
Indices: 48113--48151 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
48103 TCAAATGCAT
48113 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
48132 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
48151 T
1 T
48152 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:48175 original size:65 final size:63
Alignment explanation
Indices: 48050--48258 Score: 174
Period size: 65 Copynumber: 3.2 Consensus size: 63
48040 TATTCAAAGG
* * *
48050 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATTGAACATCAAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAACATCGAATGCA
*
48112 TTC
61 TTT
48115 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCCAAGCATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTT-CAA-CATCGAATGCATTT
** * * *** * **
48180 GGTGCATCAATGCACAAACCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTC-AACATCGAATGCATTT
*
48244 CATGCATCGATGCAC
1 CATGCACCGATGCAC
48259 ACTTGGTGCA
Statistics
Matches: 120, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
63 7 0.06
64 50 0.42
65 61 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAACATCGAATGCATTT
Found at i:48276 original size:64 final size:65
Alignment explanation
Indices: 48099--48261 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 65
48089 GAATTAATTG
* * * * *
48099 AACATCAAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCCA
* ** * ** ** *
48164 AGCATCGAATGCATTTGGTGCATCAATGCACAAACCATGCATCGATGCAC-CAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCCA
48228 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
48262 TGGTGCACCG
Statistics
Matches: 78, Mismatches: 20, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
64 38 0.49
65 40 0.51
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCCA
Found at i:50379 original size:20 final size:21
Alignment explanation
Indices: 50346--50385 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
50336 TTTTAACGTA
50346 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
50366 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
50386 ATTTGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATTCATTTTCAAACC
Done.