Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003778.1 Hibiscus syriacus cultivar Beakdansim tig00008087_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: 71797
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:3900 original size:21 final size:21
Alignment explanation
Indices: 3876--3920 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3866 TGATTTTAAA
3876 AAAACTAAAAATTTAAATACT
1 AAAACTAAAAATTTAAATACT
* * * *
3897 AAAACTGATAGTTTAAGTACT
1 AAAACTAAAAATTTAAATACT
3918 AAA
1 AAA
3921 CTTATACTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAACTAAAAATTTAAATACT
Found at i:4729 original size:21 final size:21
Alignment explanation
Indices: 4705--4744 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4695 GCAATTCATA
*
4705 GTACTGACATGACGATCCACG
1 GTACTGACATGACAATCCACG
*
4726 GTACTGACGTGACAATCCA
1 GTACTGACATGACAATCCA
4745 TCTTCATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (21 bp):
GTACTGACATGACAATCCACG
Found at i:14060 original size:109 final size:109
Alignment explanation
Indices: 13860--14074 Score: 276
Period size: 109 Copynumber: 2.0 Consensus size: 109
13850 ACATTTAGTA
* * * * *
13860 CCTAAACTATCAGTATTAGTCTGTTTTAGTACTTAATTTTTGTTAAAATCATACATAATATTTAA
1 CCTAAACTATCAGTATGAGTCCGTTTTAATACCTAATTTTTGTTAAAACCATACATAATATTTAA
**
13925 TTTTTGTTTCATTTTAGTACCATTGTTAAAA-TCTTAACACAGTT
66 TTTTTCATTCATTTTAGTACCATTGTTAAAAGT-TTAACACAGTT
* *
13969 CCTAAACTATCAGTATCGA-TCCGTTTTAATACCTAATTTTT-TT-AAACCATACCTAATGTTTA
1 CCTAAACTATCAGTAT-GAGTCCGTTTTAATACCTAATTTTTGTTAAAACCATACATAATATTTA
*
14031 GTTTTTCATTCATTTTAGTACCACGTTGTTAAAAGTTTAACACA
65 ATTTTTCATTCATTTTAGTACCA--TTGTTAAAAGTTTAACACA
14075 ATACATAAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
107 36 0.39
108 2 0.02
109 52 0.57
110 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (109 bp):
CCTAAACTATCAGTATGAGTCCGTTTTAATACCTAATTTTTGTTAAAACCATACATAATATTTAA
TTTTTCATTCATTTTAGTACCATTGTTAAAAGTTTAACACAGTT
Found at i:24145 original size:15 final size:16
Alignment explanation
Indices: 24122--24193 Score: 64
Period size: 15 Copynumber: 4.6 Consensus size: 16
24112 TTCCCTTCTT
24122 CCTTC-TTCTCTCC-C
1 CCTTCTTTCTCTCCTC
24136 CCTTCTTTCTTCTCCTC
1 CCTTCTTTC-TCTCCTC
*
24153 CTCTTTCTTT-TCTCCTT
1 C-C-TTCTTTCTCTCCTC
24170 CCTTCTTT-TCTCC-C
1 CCTTCTTTCTCTCCTC
*
24184 TCTTCTTTCT
1 CCTTCTTTCT
24194 TCGCTTCTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
14 12 0.24
15 15 0.31
16 6 0.12
17 9 0.18
18 1 0.02
19 6 0.12
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (16 bp):
CCTTCTTTCTCTCCTC
Found at i:24161 original size:33 final size:33
Alignment explanation
Indices: 24124--24209 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 33
24114 CCCTTCTTCC
24124 TTCTTCTCTCC-CCCTTC-TTTCTTCTCCTCCTCT
1 TTCTTCTCTCCTCCCTTCTTTTC-TC-CCTCCTCT
* * *
24157 TTCTTTTCTCCTTCCTTCTTTTCTCCCTCTTCT
1 TTCTTCTCTCCTCCCTTCTTTTCTCCCTCCTCT
* * *
24190 TTCTTCGCTTCTTCCTTCTT
1 TTCTTCTCTCCTCCCTTCTT
24210 CGGCTCCTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 34 0.76
34 7 0.16
35 4 0.09
ACGTcount: A:0.00, C:0.42, G:0.01, T:0.57
Consensus pattern (33 bp):
TTCTTCTCTCCTCCCTTCTTTTCTCCCTCCTCT
Found at i:24176 original size:30 final size:30
Alignment explanation
Indices: 24136--24225 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 30
24126 CTTCTCTCCC
* **
24136 CCTTCTTTCTTCTCCTCCTCTTTCTTTTCT
1 CCTTCCTTCTTCTCCTCCTCTTTCTTCGCT
*
24166 CCTTCCTTCTTTTCTCCCTCTTCTTTCTTCGCT
1 CCTTCCTTC--TTCT-CCTCCTCTTTCTTCGCT
* **
24199 TCTTCCTTCTTCGGCTCCTCTTTCTTC
1 CCTTCCTTCTTCTCCTCCTCTTTCTTC
24226 TCCGGTTCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
30 20 0.41
31 3 0.06
32 4 0.08
33 22 0.45
ACGTcount: A:0.00, C:0.41, G:0.03, T:0.56
Consensus pattern (30 bp):
CCTTCCTTCTTCTCCTCCTCTTTCTTCGCT
Found at i:24188 original size:18 final size:18
Alignment explanation
Indices: 24113--24194 Score: 59
Period size: 15 Copynumber: 4.8 Consensus size: 18
24103 TCCTCCTCCT
*
24113 TCCCTTCTTCCTTCTTCTC
1 TCCC-TCTTCCTTCTTTTC
* *
24132 TCCCCCTT-CTT-TCTTC
1 TCCCTCTTCCTTCTTTTC
* *
24148 T-CCTCCTCTTTCTTTTC
1 TCCCTCTTCCTTCTTTTC
24165 T--C-CTTCCTTCTTTTC
1 TCCCTCTTCCTTCTTTTC
*
24180 TCCCTCTTCTTTCTT
1 TCCCTCTTCCTTCTT
24195 CGCTTCTTCC
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
15 16 0.33
16 7 0.15
17 9 0.19
18 12 0.25
19 4 0.08
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (18 bp):
TCCCTCTTCCTTCTTTTC
Found at i:25929 original size:24 final size:24
Alignment explanation
Indices: 25902--25947 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25892 TTCGTGAACA
*
25902 TTCGATTATATTCGTTTATGTTCG
1 TTCGATTATATTCATTTATGTTCG
* *
25926 TTCGGTTATGTTCATTTATGTT
1 TTCGATTATATTCATTTATGTT
25948 TAATCAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.11, G:0.17, T:0.57
Consensus pattern (24 bp):
TTCGATTATATTCATTTATGTTCG
Found at i:26431 original size:16 final size:16
Alignment explanation
Indices: 26410--26452 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
26400 TTTATGTTCG
26410 TTTATGTTCGTGATCA
1 TTTATGTTCGTGATCA
* *
26426 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGATCA
26442 TTTATGTTCGT
1 TTTATGTTCGT
26453 TTATTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.56
Consensus pattern (16 bp):
TTTATGTTCGTGATCA
Found at i:26546 original size:16 final size:15
Alignment explanation
Indices: 26525--26562 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
26515 TAAAATTTGT
26525 TTATTTATATTCGTG
1 TTATTTATATTCGTG
*
26540 TTCATTTATGTTCGT-
1 TT-ATTTATATTCGTG
26555 TTATTTAT
1 TTATTTAT
26563 TAAATGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 4 0.19
16 11 0.52
ACGTcount: A:0.18, C:0.08, G:0.11, T:0.63
Consensus pattern (15 bp):
TTATTTATATTCGTG
Found at i:26953 original size:3 final size:3
Alignment explanation
Indices: 26945--26992 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
26935 ATGTATACCA
26945 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26993 GTGTCACGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28988 original size:42 final size:42
Alignment explanation
Indices: 28932--29019 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
28922 AAATCTCGTA
* * * *
28932 TTTGTTTCATGTAATTCATTTTTCGGAAAATATTTTCCCGTG
1 TTTGTTTCACGTAATTCATTTTCCGAAAAATATTTTCCAGTG
* * *
28974 TTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTTCAGTG
1 TTTGTTTCACGTAATTCATTTTCCGAAAAATATTTTCCAGTG
29016 TTTG
1 TTTG
29020 GTTGGAGGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (42 bp):
TTTGTTTCACGTAATTCATTTTCCGAAAAATATTTTCCAGTG
Found at i:29259 original size:21 final size:23
Alignment explanation
Indices: 29233--29282 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
29223 TAATTATTAA
29233 AATATTTAAAAT-ATATT-TATT
1 AATATTTAAAATAATATTATATT
*
29254 AATATTTATAATAATATTATATT
1 AATATTTAAAATAATATTATATT
29277 -ATATTT
1 AATATTT
29283 TTAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTAAAATAATATTATATT
Found at i:29260 original size:10 final size:10
Alignment explanation
Indices: 29245--29290 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
29235 TATTTAAAAT
29245 ATATTTATTA
1 ATATTTATTA
29255 ATATTTATAATA
1 ATATTTAT--TA
29267 ATATTATATT-
1 ATATT-TATTA
29277 ATATTT-TTA
1 ATATTTATTA
29286 ATATT
1 ATATT
29291 ATAATAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 13 0.41
11 1 0.03
12 7 0.22
13 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTATTA
Found at i:29278 original size:26 final size:25
Alignment explanation
Indices: 29216--29278 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
29206 CATTTTCATC
29216 AAAATATTA-ATTATTAAAATATTT
1 AAAATATTATATTATTAAAATATTT
*
29240 AAAATA-TAT-TTATTAATAT-TTAT
1 AAAATATTATATTATTAAAATATT-T
29263 AATAATATTATATTAT
1 AA-AATATTATATTAT
29279 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 14 0.42
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATATTATATTATTAAAATATTT
Found at i:29280 original size:22 final size:22
Alignment explanation
Indices: 29233--29288 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
29223 TAATTATTAA
*
29233 AATATTTAAAAT-ATATTTATT
1 AATATTTATAATAATATTTATT
29254 AATATTTATAATAATATTATATT
1 AATATTTATAATAATATT-TATT
*
29277 -ATATTTTTAATA
1 AATATTTATAATA
29289 TTATAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 11 0.35
22 16 0.52
23 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATTTATAATAATATTTATT
Found at i:29310 original size:32 final size:32
Alignment explanation
Indices: 29244--29323 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
29234 ATATTTAAAA
* *
29244 TATATTTATTAATATTTATAATAATATTATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
29276 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
29308 TATATTGTAATAATAT
1 TATATT-TATTAATAT
29324 AAGATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:29347 original size:26 final size:26
Alignment explanation
Indices: 29318--29367 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
29308 TATATTGTAA
*
29318 TAATATAAGATAT-TATATTTTTATTT
1 TAATA-AAGATATAAATATTTTTATTT
*
29344 TAATAAATATATAAATATTTTTAT
1 TAATAAAGATATAAATATTTTTAT
29368 ATATTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TAATAAAGATATAAATATTTTTATTT
Found at i:29410 original size:24 final size:23
Alignment explanation
Indices: 29352--29412 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 23
29342 TTTAATAAAT
*
29352 ATATAAATATTTTTATATATTTA
1 ATATTAATATTTTTATATATTTA
29375 ATAATGAATAATATTATTTATATATTTA
1 AT-AT---TAATATT-TTTATATATTTA
29403 ATATTAATAT
1 ATATTAATAT
29413 AATAATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
23 2 0.06
24 8 0.25
27 8 0.25
28 14 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATTAATATTTTTATATATTTA
Found at i:29457 original size:23 final size:23
Alignment explanation
Indices: 29431--29475 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29421 AATAATATTT
29431 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
29454 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
29476 AAATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:29788 original size:15 final size:15
Alignment explanation
Indices: 29752--29818 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
29742 TTCCGTAAAT
**
29752 GTAATTCATTTTTCA
1 GTAATTCAAATTTCA
29767 G-AATTCAAATTTCA
1 GTAATTCAAATTTCA
* **
29781 ATAATTCATTTTTCA
1 GTAATTCAAATTTCA
*
29796 GTAATTCAAATTCCA
1 GTAATTCAAATTTCA
29811 GTAATTCA
1 GTAATTCA
29819 TATAGAATCA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 11 0.26
15 31 0.74
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (15 bp):
GTAATTCAAATTTCA
Found at i:29795 original size:29 final size:30
Alignment explanation
Indices: 29753--29819 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
29743 TCCGTAAATG
*
29753 TAATTCATTTTTCAG-AATTCAAATTTCAA
1 TAATTCATTTTTCAGTAATTCAAATTCCAA
*
29782 TAATTCATTTTTCAGTAATTCAAATTCCAG
1 TAATTCATTTTTCAGTAATTCAAATTCCAA
29812 TAATTCAT
1 TAATTCAT
29820 ATAGAATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 15 0.43
30 20 0.57
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (30 bp):
TAATTCATTTTTCAGTAATTCAAATTCCAA
Found at i:31158 original size:15 final size:15
Alignment explanation
Indices: 31138--31168 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31128 TTTAAAATTA
31138 TTATATATTTTTTAT
1 TTATATATTTTTTAT
31153 TTATATATTTTTTAT
1 TTATATATTTTTTAT
31168 T
1 T
31169 AAAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATATATTTTTTAT
Found at i:31958 original size:31 final size:31
Alignment explanation
Indices: 31890--31965 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
31880 TTTTAATAGT
* *
31890 TATTATATTTTATATTAATATATTTATGTATA
1 TATTAT-TTTTATATTAAAATATATATGTATA
* *
31922 TATTATTTTTTTATTAAAATA-ATATTTATA
1 TATTATTTTTATATTAAAATATATATGTATA
31952 TAATTATTATTTAT
1 T-ATTATT-TTTAT
31966 TTAGAATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 8 0.22
31 19 0.51
32 10 0.27
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (31 bp):
TATTATTTTTATATTAAAATATATATGTATA
Found at i:46643 original size:177 final size:177
Alignment explanation
Indices: 46347--46690 Score: 643
Period size: 177 Copynumber: 1.9 Consensus size: 177
46337 TAAAAATAAA
46347 TGATCTCTAACGTTATCGATCGTTCGACTTAAATTCCATTAAATTCTTCGAAATCATCATAGTTC
1 TGATCTCTAACGTTATCGATCGTTCGACTTAAATTCCATTAAATTCTTCGAAATCATCATAGTTC
*
46412 CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTTGATGTTATATATATTCAC
66 CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTCGATGTTATATATATTCAC
* *
46477 AACGCTGTTTAGAAATGCATTTTCGTCTGATAATGATCTGCGTTTGG
131 AAAGCTATTTAGAAATGCATTTTCGTCTGATAATGATCTGCGTTTGG
*
46524 TGATCTCTAACGTTATCGATCGTTCGATTTAAATTCCATTAAATTCTTCGAAATCATCATAGTTC
1 TGATCTCTAACGTTATCGATCGTTCGACTTAAATTCCATTAAATTCTTCGAAATCATCATAGTTC
46589 CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTCGATGTTATATATATTCAC
66 CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTCGATGTTATATATATTCAC
*
46654 AAAGCTATTTAGAAATGCATTTTCGTTTGATAATGAT
131 AAAGCTATTTAGAAATGCATTTTCGTCTGATAATGAT
46691 GGAATCCATG
Statistics
Matches: 162, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
177 162 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (177 bp):
TGATCTCTAACGTTATCGATCGTTCGACTTAAATTCCATTAAATTCTTCGAAATCATCATAGTTC
CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTCGATGTTATATATATTCAC
AAAGCTATTTAGAAATGCATTTTCGTCTGATAATGATCTGCGTTTGG
Found at i:47070 original size:41 final size:42
Alignment explanation
Indices: 47005--47100 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 42
46995 TTTCTTGTAA
* * * *
47005 AAACGCCGCAATATATTTGAAATTTTGCGGCGTTTTAG-CC-T
1 AAACGCCGCAATAGAGTTGAAATTTAGCGGC-ATTTAGACCAT
*
47046 AAACGCCGCAATAGAGTTGTAATTTAGCGGCATTTAGACCAT
1 AAACGCCGCAATAGAGTTGAAATTTAGCGGCATTTAGACCAT
47088 AAACGCCGCAATA
1 AAACGCCGCAATA
47101 AGTATTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 5 0.10
41 29 0.60
42 14 0.29
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
AAACGCCGCAATAGAGTTGAAATTTAGCGGCATTTAGACCAT
Found at i:47573 original size:21 final size:21
Alignment explanation
Indices: 47547--47597 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
47537 AGTGTTTTAC
47547 TGGTTTACTGCTTGGGAGCAA
1 TGGTTTACTGCTTGGGAGCAA
47568 TGGTTTACTGCTTGGGAGCAA
1 TGGTTTACTGCTTGGGAGCAA
*
47589 TGTTTTACT
1 TGGTTTACT
47598 ACTTTCGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.39
Consensus pattern (21 bp):
TGGTTTACTGCTTGGGAGCAA
Found at i:49342 original size:20 final size:20
Alignment explanation
Indices: 49297--49354 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
49287 GCATGGGTAG
49297 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
49321 TGTATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
49341 TGCATCGATGCACT
1 TGCATCGATGCACT
49355 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:50396 original size:29 final size:30
Alignment explanation
Indices: 50270--50393 Score: 151
Period size: 30 Copynumber: 4.1 Consensus size: 30
50260 TCGAGACATA
* * * * *
50270 TGGACAGTTTACCTAGGTTCTTCAGGACCTA
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
50301 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
50331 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
50361 TGGATAGTTACCG-GGGTCTATGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
50390 TGGA
1 TGGA
50394 TAGGTCCTTC
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
29 17 0.20
30 60 0.71
31 7 0.08
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:50727 original size:2 final size:2
Alignment explanation
Indices: 50666--50719 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
50656 GTATGCGTGG
50666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50708 AT AT AT AT AT AT
1 AT AT AT AT AT AT
50720 GAATATATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56843 original size:21 final size:21
Alignment explanation
Indices: 56799--56844 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
56789 CGGAAGTAAT
*
56799 GAGAGAAGCAGCGATAGCATA
1 GAGAGAAGCAGCCATAGCATA
*
56820 GAGAGAAGCA-CCATATCATCA
1 GAGAGAAGCAGCCATAGCAT-A
56841 GAGA
1 GAGA
56845 TATGAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.43, C:0.17, G:0.28, T:0.11
Consensus pattern (21 bp):
GAGAGAAGCAGCCATAGCATA
Found at i:57295 original size:44 final size:44
Alignment explanation
Indices: 57179--57306 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 44
57169 AAATGTTGCA
* * *** * *
57179 ATATACCATACATTTAGCGATGTTTGTAGGATACAAACGTCACT
1 ATATACCAGACCTTTAGCGATGTTTGTATCCTAAAAACGCCACT
* **
57223 ATATATCAGACCTTTAGCGGCGTTTGTATCCTAAAAACGCCACT
1 ATATACCAGACCTTTAGCGATGTTTGTATCCTAAAAACGCCACT
* *
57267 ATATACCAGACCTTTAGCGATATTTGTATTCTAAAAACGC
1 ATATACCAGACCTTTAGCGATGTTTGTATCCTAAAAACGC
57307 TGTTTAGCGA
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (44 bp):
ATATACCAGACCTTTAGCGATGTTTGTATCCTAAAAACGCCACT
Found at i:57315 original size:30 final size:30
Alignment explanation
Indices: 57279--57338 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
57269 ATACCAGACC
* *
57279 TTTAGCGATATTTGTATTC-TAAAAACGCTG
1 TTTAGCGACATTTGTA-TCAAAAAAACGCTG
*
57309 TTTAGCGACGTTTGTATCAAAAAAACGCTG
1 TTTAGCGACATTTGTATCAAAAAAACGCTG
57339 CCAAATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTAGCGACATTTGTATCAAAAAAACGCTG
Found at i:57417 original size:43 final size:42
Alignment explanation
Indices: 57341--57580 Score: 250
Period size: 43 Copynumber: 5.6 Consensus size: 42
57331 AAACGCTGCC
* **
57341 AAATTTCAACACCTATTGCGGCGTTTGCAAGAAAAATCCTGCT
1 AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAATCC-GCT
* * * * *
57384 ACATCTCAAAACTTATTGCGGCGTTTTTGAGAAAAGTGCCGCT
1 AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAAT-CCGCT
* * * * * *
57427 AAATCTCTACACTTATTGTGGCGTTTTTGAGAAAAACGCCGCG
1 AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAA-TCCGCT
** *
57470 AAATAGCAACACCTATTGCGGCGTTTGTGATAAAAATGCCGCT
1 AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAAT-CCGCT
*
57513 AAATCTCAACACCTATTGCGGCGTTTGT-AGAAAAAAACCGCT
1 AAATCTCAACACCTATTGCGGCGTTTGTGAG-AAAAATCCGCT
57555 AAA-CATCAACACCTATTGCGGCGTTT
1 AAATC-TCAACACCTATTGCGGCGTTT
57581 TTCGTTAACA
Statistics
Matches: 164, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 30 0.18
43 131 0.80
44 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (42 bp):
AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAATCCGCT
Found at i:68412 original size:21 final size:21
Alignment explanation
Indices: 68386--68426 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
68376 AGTTTCAGAT
68386 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
68407 TCGCAACGCGAACTTCGACT
1 TCGCAACGCGAACATCGACT
68427 CGCAATGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:68492 original size:42 final size:42
Alignment explanation
Indices: 68440--68621 Score: 207
Period size: 42 Copynumber: 4.5 Consensus size: 42
68430 AATGCGATAG
* *
68440 TCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
* * *
68482 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGAGA--TAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
* *
68522 TCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
* * *
68566 TCTAA----ATT-CAATAGTCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
68603 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
68622 AGAATAAGGG
Statistics
Matches: 114, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
37 31 0.27
38 2 0.02
40 8 0.07
41 2 0.02
42 65 0.57
44 6 0.05
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
Found at i:68514 original size:21 final size:21
Alignment explanation
Indices: 68432--68561 Score: 151
Period size: 21 Copynumber: 6.3 Consensus size: 21
68422 CGACTCGCAA
68432 TGCGATAGTCCAAGTT--CGT
1 TGCGATAGTCCAAGTTCGCGT
* *
68451 TGTGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
* *
68472 TGCGATTTATTCCAAATT--CGT
1 TGCGA--TAGTCCAAGTTCGCGT
68493 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
* *
68514 TGAGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
*
68535 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
68556 TGCGAT
1 TGCGAT
68562 TTATTCTAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
19 23 0.24
21 63 0.67
23 8 0.09
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCGCGT
Found at i:68557 original size:63 final size:60
Alignment explanation
Indices: 68432--68621 Score: 176
Period size: 63 Copynumber: 3.1 Consensus size: 60
68422 CGACTCGCAA
* *
68432 TGCGATAGTCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGT
1 TGCGATAGTCCAAGTTCGTTGAGATAGTCGAAGTTCGCGTTGCGA-TTAGTCCAAATTCGT
* *
68493 TGCGATAGTCCAAGTTCGCGTTGAGATAGTCGAAGTTCGCGTTGCGA-TAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTT--CGTTGAGATAGTCGAAGTTCGCGTTGCGATTAGTCCAAATT--CGT
* * * * * *
68556 TGCGATTTATTCTAAATTC----A-ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGT
1 TGCGA--TAGTCCAAGTTCGTTGAGATAGTCGAAGTTCGCGTTGCGA-TTAGTCCAAATTCGT
68614 TGCGATAG
1 TGCGATAG
68622 AGAATAAGGG
Statistics
Matches: 110, Mismatches: 11, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
56 2 0.02
58 29 0.26
59 1 0.01
60 9 0.08
61 24 0.22
63 37 0.34
65 8 0.07
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (60 bp):
TGCGATAGTCCAAGTTCGTTGAGATAGTCGAAGTTCGCGTTGCGATTAGTCCAAATTCGT
Found at i:68863 original size:20 final size:20
Alignment explanation
Indices: 68834--68871 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
68824 ATCGCAATGA
*
68834 ATGTATATCGCAATGCGAAT
1 ATGTAAATCGCAATGCGAAT
68854 ATGTAAATCGCAATGCGA
1 ATGTAAATCGCAATGCGA
68872 TAGTCGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (20 bp):
ATGTAAATCGCAATGCGAAT
Found at i:70901 original size:16 final size:17
Alignment explanation
Indices: 70877--70922 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
70867 TAGTGTAAGA
70877 ATTTATTTTATATTAG-T
1 ATTT-TTTTATATTAGTT
*
70894 ATTTTTTTA-AATAGTT
1 ATTTTTTTATATTAGTT
70910 ATATTTTTTATAT
1 AT-TTTTTTATAT
70923 AATATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 4 0.17
16 8 0.33
17 11 0.46
18 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
ATTTTTTTATATTAGTT
Found at i:70916 original size:17 final size:16
Alignment explanation
Indices: 70886--70964 Score: 61
Period size: 17 Copynumber: 4.7 Consensus size: 16
70876 AATTTATTTT
70886 ATATTAGTATTTTTTTAA
1 ATATTA-TA-TTTTTTAA
*
70904 ATAGTTATATTTTTTAT
1 ATA-TTATATTTTTTAA
* *
70921 ATAATATATTTATGTAA
1 ATATTATATTT-TTTAA
*
70938 ATATTATTTTTTATTAA
1 ATATTATATTTT-TTAA
*
70955 A-ATAATATTT
1 ATATTATATTT
70965 ATATAATTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
16 15 0.31
17 26 0.53
18 5 0.10
19 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
ATATTATATTTTTTAA
Found at i:70976 original size:33 final size:31
Alignment explanation
Indices: 70911--70979 Score: 93
Period size: 33 Copynumber: 2.2 Consensus size: 31
70901 TAAATAGTTA
* *
70911 TATTTTTTATATAATATATTTATGTAAATAT
1 TATTTTTTATAAAATATATTTATATAAATAT
*
70942 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTTTA-TAAAAT-ATATTTATATAAATAT
70975 TATTT
1 TATTT
70980 ATTAGAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 9 0.27
32 5 0.15
33 19 0.58
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
TATTTTTTATAAAATATATTTATATAAATAT
Found at i:70990 original size:16 final size:15
Alignment explanation
Indices: 70940--70992 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
70930 TTATGTAAAT
*
70940 ATTATTTTTTATTAA
1 ATTATTATTTATTAA
* *
70955 AATAATATTTA-TATA
1 ATTATTATTTATTA-A
70970 ATTATTATTTATTAGA
1 ATTATTATTTATTA-A
70986 ATTATTA
1 ATTATTA
70993 ATTTTTTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 2 0.07
15 18 0.60
16 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
ATTATTATTTATTAA
Found at i:71137 original size:26 final size:27
Alignment explanation
Indices: 71093--71157 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
71083 GATATGGTAA
* *
71093 TTTTTTATAATTAATGTTAATATTAATT
1 TTTTTTAT-TTTAATGTTAATATGAATT
*
71121 TTTTTTATTTTAA-GTTATTATGAATT
1 TTTTTTATTTTAATGTTAATATGAATT
* *
71147 TATATTATTTT
1 TTTTTTATTTT
71158 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 20 0.62
27 4 0.12
28 8 0.25
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (27 bp):
TTTTTTATTTTAATGTTAATATGAATT
Done.