Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002827.1 Hibiscus syriacus cultivar Beakdansim tig00005812_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: 80602
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2594 original size:89 final size:88
Alignment explanation
Indices: 2486--2655 Score: 241
Period size: 89 Copynumber: 1.9 Consensus size: 88
2476 ATTCCACTAT
* * * *
2486 TCTTCAGGGAAGATTGAATCTAGGAAGACTTGTTCCACTGCTGCTCAGGGAAGATCAAATCTGGA
1 TCTTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGCTCCTCAAGGAAGACCAAATCTGG-
*
2551 AAAAGGGGGATATGCTCCACTGCA
65 AAAAGGGAGATATGCTCCACTGCA
* * * *
2575 TCTTTAGGGAAGATTGAATCGAGGCATACTTGTTCCACTGCTCCTCAAGGAAGACCAAATTTGGA
1 TCTTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGCTCCTCAAGGAAGACCAAATCTGGA
*
2640 CAAGGGAGATATGCTC
66 AAAGGGAGATATGCTC
2656 TTTACTTCTT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 15 0.21
89 56 0.79
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (88 bp):
TCTTCAGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGCTCCTCAAGGAAGACCAAATCTGGA
AAAGGGAGATATGCTCCACTGCA
Found at i:4170 original size:7 final size:7
Alignment explanation
Indices: 4160--4250 Score: 75
Period size: 7 Copynumber: 12.7 Consensus size: 7
4150 CCCTTTTATT
4160 TTTTTTC
1 TTTTTTC
4167 -TTTTTC
1 TTTTTTC
4173 -TTTTTC
1 TTTTTTC
4179 TTTTTCTC
1 TTTTT-TC
4187 TTTTGTTTC
1 -TTT-TTTC
4196 TTTCTTT-
1 TTT-TTTC
4203 TTTCTTTC
1 TTT-TTTC
4211 TTTTTTC
1 TTTTTTC
4218 TTTTTT-
1 TTTTTTC
4224 TTCTTTT-
1 TT-TTTTC
4231 TTTTTTC
1 TTTTTTC
*
4238 ATTTTTTA
1 -TTTTTTC
4246 TTTTT
1 TTTTT
4251 CATTTTTTTC
Statistics
Matches: 74, Mismatches: 2, Indels: 16
0.80 0.02 0.17
Matches are distributed among these distances:
6 18 0.24
7 32 0.43
8 17 0.23
9 5 0.07
10 2 0.03
ACGTcount: A:0.02, C:0.13, G:0.01, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:4182 original size:20 final size:19
Alignment explanation
Indices: 4159--4250 Score: 105
Period size: 20 Copynumber: 4.7 Consensus size: 19
4149 CCCCTTTTAT
4159 TTTTTTTCTTTTTCTTTTTC
1 TTTTTTTCTTTTT-TTTTTC
*
4179 TTTTTCTCTTTTGTTTCTTTC
1 TTTTTTTCTTTT-TTT-TTTC
*
4200 -TTTTTTCTTTCTTTTTTC
1 TTTTTTTCTTTTTTTTTTC
4218 TTTTTTTTCTTTTTTTTTTC
1 -TTTTTTTCTTTTTTTTTTC
* *
4238 ATTTTTTATTTTT
1 TTTTTTTCTTTTT
4251 CATTTTTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.06
19 14 0.23
20 39 0.63
21 5 0.08
ACGTcount: A:0.02, C:0.13, G:0.01, T:0.84
Consensus pattern (19 bp):
TTTTTTTCTTTTTTTTTTC
Found at i:4199 original size:27 final size:27
Alignment explanation
Indices: 4169--4237 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
4159 TTTTTTTCTT
4169 TTTCTTTTTCTTTTTCTCTTTT-GTTTC
1 TTTCTTTTT-TTTTTCTCTTTTCGTTTC
* * * *
4196 TTTCTTTTTTCTTTCTTTTTTCTTTTT
1 TTTCTTTTTTTTTTCTCTTTTCGTTTC
4223 TTTCTTTTTTTTTTC
1 TTTCTTTTTTTTTTC
4238 ATTTTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
26 10 0.28
27 26 0.72
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.83
Consensus pattern (27 bp):
TTTCTTTTTTTTTTCTCTTTTCGTTTC
Found at i:4242 original size:27 final size:28
Alignment explanation
Indices: 4153--4264 Score: 97
Period size: 26 Copynumber: 4.0 Consensus size: 28
4143 CTTGAACCCC
* *
4153 TTTTATTTTTTTTCTTTTTCTTTTTC-T
1 TTTTCTTTTTTTTCTTTTTTTTTTTCAT
*
4180 TTTTCTCTTTTGTTTCTTTCTTTTTTCTTTCTT
1 TTTTCT-TTTT-TTTC-TT-TTTTTT-TTTCAT
4213 TTTTCTTTTTTTTC-TTTTTTTTTTCA-
1 TTTTCTTTTTTTTCTTTTTTTTTTTCAT
* * *
4239 TTTT-TTATTTTTCATTTTTTTCTTCA
1 TTTTCTTTTTTTTCTTTTTTTTTTTCA
4265 GGTGAAGTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
25 8 0.11
26 15 0.21
27 9 0.12
28 10 0.14
29 5 0.07
30 2 0.03
31 9 0.12
32 8 0.11
33 7 0.10
ACGTcount: A:0.04, C:0.13, G:0.01, T:0.81
Consensus pattern (28 bp):
TTTTCTTTTTTTTCTTTTTTTTTTTCAT
Found at i:4243 original size:11 final size:10
Alignment explanation
Indices: 4152--4262 Score: 84
Period size: 11 Copynumber: 10.3 Consensus size: 10
4142 TCTTGAACCC
4152 CTTTTATTTTT
1 CTTTT-TTTTT
*
4163 -TTTCTTTTT
1 CTTTTTTTTT
4172 CTTTTTCTTTTT
1 C-TTTT-TTTTT
*
4184 CTCTTTTGTTT
1 CT-TTTTTTTT
4195 CTTTCTTTTTT
1 CTTT-TTTTTT
4206 CTTTCTTTTTT
1 CTTT-TTTTTT
4217 C-TTTTTTTT
1 CTTTTTTTTT
4226 CTTTTTTTTTT
1 C-TTTTTTTTT
4237 CATTTTTTATTT
1 C-TTTTTT-TTT
4249 -TTCATTTTTTT
1 CTT--TTTTTTT
4260 CTT
1 CTT
4263 CAGGTGAAGT
Statistics
Matches: 84, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
9 12 0.14
10 9 0.11
11 45 0.54
12 18 0.21
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.82
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:4259 original size:1 final size:1
Alignment explanation
Indices: 4153--4250 Score: 52
Period size: 1 Copynumber: 98.0 Consensus size: 1
4143 CTTGAACCCC
* * * * * * * * * * * *
4153 TTTTATTTTTTTTCTTTTTCTTTTTCTTTTTCTCTTTTGTTTCTTTCTTTTTTCTTTCTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** *
4218 TTTTTTTTCTTTTTTTTTTCATTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4251 CATTTTTTTC
Statistics
Matches: 66, Mismatches: 31, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.03, C:0.12, G:0.01, T:0.84
Consensus pattern (1 bp):
T
Found at i:39160 original size:12 final size:13
Alignment explanation
Indices: 39137--39192 Score: 59
Period size: 12 Copynumber: 4.7 Consensus size: 13
39127 AAGAACTAGA
39137 TTGAAGCTCGATT
1 TTGAAGCTCGATT
39150 TTGAA-CTCGA--
1 TTGAAGCTCGATT
* *
39160 TTCAAGCTTGATT
1 TTGAAGCTCGATT
39173 TTGAA-CTCGATT
1 TTGAAGCTCGATT
39185 TTG-AGCTC
1 TTGAAGCTC
39193 AATTCGAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
10 4 0.11
11 5 0.14
12 17 0.49
13 9 0.26
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (13 bp):
TTGAAGCTCGATT
Found at i:39161 original size:23 final size:23
Alignment explanation
Indices: 39129--39184 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
39119 AAAAATTCAA
* *
39129 GAACTAGATTGAAGCTCGATTTT
1 GAACTCGATTCAAGCTCGATTTT
*
39152 GAACTCGATTCAAGCTTGATTTT
1 GAACTCGATTCAAGCTCGATTTT
39175 GAACTCGATT
1 GAACTCGATT
39185 TTGAGCTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (23 bp):
GAACTCGATTCAAGCTCGATTTT
Found at i:39213 original size:24 final size:23
Alignment explanation
Indices: 39178--39227 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
39168 TGATTTTGAA
* *
39178 CTCGATTTTGAGCTCAATTCGAG
1 CTCGATTATGAGCTCAATTCAAG
*
39201 CTCGAATTATGAGCTCGATTCAAG
1 CTCG-ATTATGAGCTCAATTCAAG
39225 CTC
1 CTC
39228 ATTGGGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (23 bp):
CTCGATTATGAGCTCAATTCAAG
Found at i:39216 original size:13 final size:12
Alignment explanation
Indices: 39141--39218 Score: 52
Period size: 12 Copynumber: 6.6 Consensus size: 12
39131 ACTAGATTGA
*
39141 AGCTCGATTTTG
1 AGCTCGAATTTG
* **
39153 AACTCG-ATTCA
1 AGCTCGAATTTG
* *
39164 AGCTTGATTTTG
1 AGCTCGAATTTG
* *
39176 AACTCGATTTTG
1 AGCTCGAATTTG
*
39188 AGCTC-AATTCG
1 AGCTCGAATTTG
39199 AGCTCGAATTATG
1 AGCTCGAATT-TG
39212 AGCTCGA
1 AGCTCGA
39219 TTCAAGCTCA
Statistics
Matches: 48, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
11 15 0.31
12 25 0.52
13 8 0.17
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (12 bp):
AGCTCGAATTTG
Found at i:40435 original size:7 final size:7
Alignment explanation
Indices: 40402--40435 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
40392 ACTCGAATAA
40402 AGGGTTT
1 AGGGTTT
*
40409 AGGATTT
1 AGGGTTT
40416 AGGGTTT
1 AGGGTTT
*
40423 AAGGTTT
1 AGGGTTT
40430 AGGGTT
1 AGGGTT
40436 CATTACAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (7 bp):
AGGGTTT
Found at i:40620 original size:19 final size:19
Alignment explanation
Indices: 40582--40629 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
40572 AAAAATTAGT
*
40582 TATTAAAAATATTATCATTA
1 TATTAAATA-ATTATCATTA
*
40602 TATTAAATAATTCTCATTA
1 TATTAAATAATTATCATTA
*
40621 GA-TAAATAA
1 TATTAAATAA
40630 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.28
19 10 0.40
20 8 0.32
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (19 bp):
TATTAAATAATTATCATTA
Found at i:43085 original size:15 final size:15
Alignment explanation
Indices: 43065--43096 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
43055 TAGTGCTTAA
43065 ATTATACATTATTTT
1 ATTATACATTATTTT
43080 ATTATACATTATTTT
1 ATTATACATTATTTT
43095 AT
1 AT
43097 GATCAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATACATTATTTT
Found at i:43588 original size:15 final size:15
Alignment explanation
Indices: 43568--43599 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
43558 TAGTGTTTAA
43568 ATTATACATTATTTT
1 ATTATACATTATTTT
43583 ATTATACATTATTTT
1 ATTATACATTATTTT
43598 AT
1 AT
43600 GACCAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATACATTATTTT
Found at i:48762 original size:2 final size:2
Alignment explanation
Indices: 48755--48784 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
48745 AACTACATGA
*
48755 AT AT AT AT GT 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
48785 TAAATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57872 original size:21 final size:21
Alignment explanation
Indices: 57846--57885 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
57836 TCAATTGTGT
57846 ATCGATGCACTGCTACAGTGC
1 ATCGATGCACTGCTACAGTGC
*
57867 ATCGATGTACTGCTACAGT
1 ATCGATGCACTGCTACAGT
57886 AACTTTCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (21 bp):
ATCGATGCACTGCTACAGTGC
Found at i:60985 original size:42 final size:42
Alignment explanation
Indices: 60899--61215 Score: 216
Period size: 43 Copynumber: 7.3 Consensus size: 42
60889 TAAGGGCTTA
* * *
60899 AATTATAAAAATAAAAAGT-ATTATTGAAAAAATTACGGACCTC
1 AATTAT-AAAGTAAAAAGTGA-GATTGAAAAAATTAGGGACCTC
* * *
60942 AATTATAAAGATAAAAAGTGATATTTAAAAAA-TAGGGGCCTC
1 AATTATAAAG-TAAAAAGTGAGATTGAAAAAATTAGGGACCTC
* * * *
60984 AATTTTAAAGTAAAAAATGAGATTGAAAAAACTAAGGG-CCTA
1 AATTATAAAGTAAAAAGTGAGATTGAAAAAA-TTAGGGACCTC
* * *
61026 AATTATGTAAGTAAAAAGTGGGATTGAAAAAATTAGGGACCTT
1 AATTAT-AAAGTAAAAAGTGAGATTGAAAAAATTAGGGACCTC
* * * * *
61069 AATTATGAAGGTAGAAAGTGAGACTGGAAAAAATTA-GAAGCTC
1 AATTAT-AAAGTAAAAAGTGAGA-TTGAAAAAATTAGGGACCTC
* * * *
61112 AATTATAAAGGTACAAAGTGAGAATGAAAAACTTAGTATGA--TC
1 AATTATAAA-GTAAAAAGTGAGATTGAAAAAATTAG--GGACCTC
* **
61155 AATCATAAATGTAAAAAGT-ATGATTGAAAAAAAAATTAAAGACCTC
1 AATTATAAA-GTAAAAAGTGA-GATTG---AAAAAATTAGGGACCTC
61201 AATTATAAAGATAAA
1 AATTATAAAG-TAAA
61216 TTAAATTGAA
Statistics
Matches: 217, Mismatches: 39, Indels: 33
0.75 0.13 0.11
Matches are distributed among these distances:
41 18 0.08
42 45 0.21
43 116 0.53
44 14 0.06
45 2 0.01
46 22 0.10
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (42 bp):
AATTATAAAGTAAAAAGTGAGATTGAAAAAATTAGGGACCTC
Found at i:66076 original size:603 final size:603
Alignment explanation
Indices: 64932--66129 Score: 2281
Period size: 603 Copynumber: 2.0 Consensus size: 603
64922 AAAACACTAA
64932 GCATTTTTGGATTAATGAGATTATTTCGGGATCTTCGGCTCAGAATTTGGTAAAACGAACAACAA
1 GCATTTTTGGATTAATGAGATTATTTCGGGATCTTCGGCTCAGAATTTGGTAAAACGAACAACAA
64997 AATTGAACTCATGACGTCGAAAATGTTAAGAGGGAGATTTTTAAAAAAATGTTAACATCAGTCAA
66 AATTGAACTCATGACGTCGAAAATGTTAAGAGGGAGATTTTTAAAAAAATGTTAACATCAGTCAA
65062 TGGTCAAAGTCAATGTCGATGAACAGTCAATGGTTAATAGATCAATATTTCAATTCGTTCAATGG
131 TGGTCAAAGTCAATGTCGATGAACAGTCAATGGTTAATAGATCAATATTTCAATTCGTTCAATGG
* *
65127 CTCGGTTCGGTTTGGTCAATGGTTCGATTTAGTTGGTCCCATTCGGGTAGGTCAATCTGACTGGG
196 CTCGGTTCGGTTTGGTCAATGGTTCAATTTAGTTGGTCCCATACGGGTAGGTCAATCTGACTGGG
65192 ATGATTTTGGGTTTGGGTTTGGGCCGAGTGGGTCAAGCGGGACACACTGGTCGGATTGGCCAAAT
261 ATGATTTTGGGTTTGGGTTTGGGCCGAGTGGGTCAAGCGGGACACACTGGTCGGATTGGCCAAAT
*
65257 GGTTTAATGGATCAACCCACTTTTAGAAGCCCACCAAGCGATGAACCTTCCCCATGAGCAACAGC
326 GGGTTAATGGATCAACCCACTTTTAGAAGCCCACCAAGCGATGAACCTTCCCCATGAGCAACAGC
** *
65322 GATGTGTAGAGGCACGTGTGATGATTTTTTGGCTCAGAAAAATTTCTAAAAAATTAATATAAAGG
391 GATGTGTAGAGGCACGTGTGATGACGTTTTGGCTCAGAAAAAGTTCTAAAAAATTAATATAAAGG
65387 GTTTTGAATCACTTACAAGGTTTTATTAACCAAGATGAACGGTATAGAGCTTGATTACACTTCAA
456 GTTTTGAATCACTTACAAGGTTTTATTAACCAAGATGAACGGTATAGAGCTTGATTACACTTCAA
* *
65452 TGAAAACTTGATATTGCTCACCCCTCCACATACAAACGACAGAAACAACGAAACAACCACCATTG
521 TGAAAACTTGATATTGCTCACCCCTCCACACACAAACGACAGAAACAACGAAACAACCACCAATG
65517 GACTCTAAACTTGATATC
586 GACTCTAAACTTGATATC
65535 GCATTTTTGGATTAATGAGATTATTTCGGGATCTTCGGCTCAGAATTTGGTAAAACGAACAACAA
1 GCATTTTTGGATTAATGAGATTATTTCGGGATCTTCGGCTCAGAATTTGGTAAAACGAACAACAA
65600 AATTGAACTCATGACGTCGAAAATGTTAAGAGGGAGATTTTTAAAAAAATGTTAACATCAGTCAA
66 AATTGAACTCATGACGTCGAAAATGTTAAGAGGGAGATTTTTAAAAAAATGTTAACATCAGTCAA
65665 TGGTCAAAGTCAATGTCGATGAACAGTCAATGGTTAATAGATCAATATTTCAATTCGTTCAATGG
131 TGGTCAAAGTCAATGTCGATGAACAGTCAATGGTTAATAGATCAATATTTCAATTCGTTCAATGG
65730 CTCGGTTCGGTTTGGTCAATGGTTCAATTTAGTTGGTCCCATACGGGTAGGTCAATCTGACTGGG
196 CTCGGTTCGGTTTGGTCAATGGTTCAATTTAGTTGGTCCCATACGGGTAGGTCAATCTGACTGGG
65795 ATGATTTTGGGTTTGGGTTTGGGCCGAGTGGGTCAAGCGGGACACACTGGTCGGATTGGCCAAAT
261 ATGATTTTGGGTTTGGGTTTGGGCCGAGTGGGTCAAGCGGGACACACTGGTCGGATTGGCCAAAT
*
65860 GGGTTAATGGATCAACCCGCTTTTAGAAGCCCACCAAGCGATGGAA-CTTCCCCATGAGCAACAG
326 GGGTTAATGGATCAACCCACTTTTAGAAGCCCACCAAGCGAT-GAACCTTCCCCATGAGCAACAG
65924 CGATGTGTAGAGGCACGTGTGATGACGTTTTGGCTCAGAAAAAGTTCTAAAAAATTAATATAAAG
390 CGATGTGTAGAGGCACGTGTGATGACGTTTTGGCTCAGAAAAAGTTCTAAAAAATTAATATAAAG
*
65989 GGTTTTGAATCACTTACAAGGTTTTATTCACCAAGATGAACGGTATAGAGCTTGATTACACTTCA
455 GGTTTTGAATCACTTACAAGGTTTTATTAACCAAGATGAACGGTATAGAGCTTGATTACACTTCA
*
66054 ATGAAAACTTGATATTGCTCACCCCTCCACACACAAACGACAGAAACAATGAAACAACCACCAAT
520 ATGAAAACTTGATATTGCTCACCCCTCCACACACAAACGACAGAAACAACGAAACAACCACCAAT
66119 GGACTCTAAAC
585 GGACTCTAAAC
66130 AACACGATGA
Statistics
Matches: 583, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
603 580 0.99
604 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (603 bp):
GCATTTTTGGATTAATGAGATTATTTCGGGATCTTCGGCTCAGAATTTGGTAAAACGAACAACAA
AATTGAACTCATGACGTCGAAAATGTTAAGAGGGAGATTTTTAAAAAAATGTTAACATCAGTCAA
TGGTCAAAGTCAATGTCGATGAACAGTCAATGGTTAATAGATCAATATTTCAATTCGTTCAATGG
CTCGGTTCGGTTTGGTCAATGGTTCAATTTAGTTGGTCCCATACGGGTAGGTCAATCTGACTGGG
ATGATTTTGGGTTTGGGTTTGGGCCGAGTGGGTCAAGCGGGACACACTGGTCGGATTGGCCAAAT
GGGTTAATGGATCAACCCACTTTTAGAAGCCCACCAAGCGATGAACCTTCCCCATGAGCAACAGC
GATGTGTAGAGGCACGTGTGATGACGTTTTGGCTCAGAAAAAGTTCTAAAAAATTAATATAAAGG
GTTTTGAATCACTTACAAGGTTTTATTAACCAAGATGAACGGTATAGAGCTTGATTACACTTCAA
TGAAAACTTGATATTGCTCACCCCTCCACACACAAACGACAGAAACAACGAAACAACCACCAATG
GACTCTAAACTTGATATC
Found at i:73521 original size:12 final size:12
Alignment explanation
Indices: 73499--73540 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
73489 AATAAACCAC
73499 ACCC-AAACCCA
1 ACCCAAAACCCA
* *
73510 ACCTATAACCCA
1 ACCCAAAACCCA
73522 ACCCAAAACCCA
1 ACCCAAAACCCA
73534 A-CCAAAA
1 ACCCAAAA
73541 TCCGACCGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.50, C:0.45, G:0.00, T:0.05
Consensus pattern (12 bp):
ACCCAAAACCCA
Found at i:73530 original size:24 final size:24
Alignment explanation
Indices: 73490--73536 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
73480 AAAACCAAAA
73490 ATAAACCACACCCAAACCCAACCT
1 ATAAACCACACCCAAACCCAACCT
*
73514 ATAACCCA-ACCCAAAACCCAACC
1 ATAAACCACACCC-AAACCCAACC
73537 AAAATCCGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.47, C:0.47, G:0.00, T:0.06
Consensus pattern (24 bp):
ATAAACCACACCCAAACCCAACCT
Found at i:78267 original size:12 final size:13
Alignment explanation
Indices: 78250--78282 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
78240 ACGTTCGATA
78250 TATGTTCGTT-TT
1 TATGTTCGTTATT
78262 TATGTTCGTTCATT
1 TATGTTCGTT-ATT
78276 TATGTTC
1 TATGTTC
78283 AAACAGAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
14 9 0.47
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.61
Consensus pattern (13 bp):
TATGTTCGTTATT
Found at i:79576 original size:241 final size:239
Alignment explanation
Indices: 79106--79581 Score: 572
Period size: 241 Copynumber: 2.0 Consensus size: 239
79096 ATATATATGT
* * * *
79106 ACTTCTAAATTTTAGGAGAGCTAACTTATAAAATTATAGAGGGACGAAACATACTATTAATACAA
1 ACTTCTAAATTTTAGGAGAACTAACTTATAAAATTATAGAGGGAAGAAACATACTATTAAAAAAA
* *
79171 AATACATAAAAGAATATCTAAATATATGTTTTTAAAATTTTTAAAAATAAAAACTACCCCGATTG
66 AATACATAAAAGAATATCTAAATATATGTATTTAAAACTTTTAAAAATAAAAACTACCCCGATTG
* **
79236 TCGCCTGGGTCCATCCTACCTACACAATCATCTTCCGATGAGATTATTAGTGAAACACCACACCA
131 TCCCCTAAGTCCATCCTACCTACACAATCATCTTCCGATGAGATTATTAGTGAAACACCACACCA
*
79301 TTTTCAAACCAAAGTGAAATGGGAAAGGAATAATGCTAGAGGAGA
196 TTTGCAAACCAAAGTGAAATGGGAAA-GAATAATGCTAGAGGAGA
* * * *
79346 ACTTCTGAAATTTTAGGAGATACTAACTTATTAAATT-T-TATGGAAGAAAACATATTA-TAAAA
1 ACTTCT-AAATTTTAGGAGA-ACTAACTTATAAAATTATAGAGGGAAG-AAACATACTATTAAAA
* * * * *
79408 AAAAATACATAAAA-AA-ATCTAAAATATTTGATAATTTAAAACTTTTAAAGATGACAACTACCT
63 AAAAATACATAAAAGAATATCT-AAATATATG-T-ATTTAAAACTTTTAAAAATAAAAACTACCC
* * *
79471 CGGTTGTCCCCTAAGTCCATCCCTACCTACACTATCATC-TCCGGTGAGATTATATTAGTGAAAC
125 CGATTGTCCCCTAAGTCCAT-CCTACCTACACAATCATCTTCCGATGAGA-T-TATTAGTGAAAC
* * *
79535 ACACTCACCATTTGCAAACCAAATTGCAAT-GGAAA-AATAATGCTAGA
187 AC-CACACCATTTGCAAACCAAAGTGAAATGGGAAAGAATAATGCTAGA
79582 TTAGCACCCC
Statistics
Matches: 201, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
238 4 0.02
239 10 0.05
240 29 0.14
241 84 0.42
242 32 0.16
243 19 0.09
244 23 0.11
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.29
Consensus pattern (239 bp):
ACTTCTAAATTTTAGGAGAACTAACTTATAAAATTATAGAGGGAAGAAACATACTATTAAAAAAA
AATACATAAAAGAATATCTAAATATATGTATTTAAAACTTTTAAAAATAAAAACTACCCCGATTG
TCCCCTAAGTCCATCCTACCTACACAATCATCTTCCGATGAGATTATTAGTGAAACACCACACCA
TTTGCAAACCAAAGTGAAATGGGAAAGAATAATGCTAGAGGAGA
Done.