Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008767.1 Hibiscus syriacus cultivar Beakdansim tig00111866_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: 108381
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2507 original size:21 final size:21
Alignment explanation
Indices: 2482--2532 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
2472 TAGTCTAATT
2482 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGTTCA
*
2503 CGTTGCGATAGTCGAAGTTCA
1 CGTTGCGATAGTCCAAGTTCA
2524 CGTTGCGAT
1 CGTTGCGAT
2533 TTTCCACGAC
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:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCA
Found at i:10170 original size:22 final size:22
Alignment explanation
Indices: 10117--10163 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
10107 GGTCAGGTGG
10117 TCAACTCTTTATCTTTGTTCTC
1 TCAACTCTTTATCTTTGTTCTC
10139 TCAACTCTTTATCTTTGTTCTC
1 TCAACTCTTTATCTTTGTTCTC
10161 TCA
1 TCA
10164 TATCTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.15, C:0.28, G:0.04, T:0.53
Consensus pattern (22 bp):
TCAACTCTTTATCTTTGTTCTC
Found at i:11385 original size:2 final size:2
Alignment explanation
Indices: 11378--11432 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
11368 AGATGGTGGG
11378 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11420 TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA
11433 ATTGTATTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14265 original size:29 final size:29
Alignment explanation
Indices: 14230--14311 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
14220 AAACTAAATT
*
14230 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
14259 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
14288 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
14312 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:19032 original size:29 final size:29
Alignment explanation
Indices: 18997--19078 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
18987 AAACTAAATT
*
18997 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
19026 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
19055 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
19079 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:21712 original size:37 final size:37
Alignment explanation
Indices: 21671--21744 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
21661 TAATTTGTAA
*
21671 GACACATCTATCTCATTACAACCTTTTTAAACATAGG
1 GACACATCTATCTCATTACAACATTTTTAAACATAGG
21708 GACACATCTATCTCATTACAACATTTTTAAACATAGG
1 GACACATCTATCTCATTACAACATTTTTAAACATAGG
21745 AGATGTACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.32
Consensus pattern (37 bp):
GACACATCTATCTCATTACAACATTTTTAAACATAGG
Found at i:24896 original size:37 final size:36
Alignment explanation
Indices: 24847--24955 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
24837 ATATTTCAAC
* *
24847 AAACATCTACCAAACTTTGAAAAGTCATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAA-CCATTTTTCAAAG
*
24884 AAATATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
24919 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
24956 TTGGTTGCCA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
35 34 0.52
36 2 0.03
37 30 0.45
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.31
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:24912 original size:21 final size:21
Alignment explanation
Indices: 24888--24947 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
24878 TCAAAGAAAT
24888 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
*
24909 ATTT-TCAAA----G-AAA-C
1 ATTTACCAAACTTTGAAAACC
24923 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
24944 ATTT
1 ATTT
24948 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
ATTTACCAAACTTTGAAAACC
Found at i:28269 original size:16 final size:16
Alignment explanation
Indices: 28248--28280 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28238 TAATAAATAG
28248 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
28264 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
28280 A
1 A
28281 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:28365 original size:10 final size:10
Alignment explanation
Indices: 28347--28421 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
28337 CATTTAATAA
*
28347 ATAAGCGAAC
1 ATAAACGAAC
28357 ATAAACGAAC
1 ATAAACGAAC
28367 ----ACGAAC
1 ATAAACGAAC
28373 ATAAACGAAC
1 ATAAACGAAC
** *
28383 ACGAAC-ATAA
1 ATAAACGA-AC
28393 ATGAACACGAAC
1 AT-AA-ACGAAC
28405 ATAAACGAAC
1 ATAAACGAAC
28415 ATAAACG
1 ATAAACG
28422 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.56, C:0.21, G:0.13, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:28373 original size:16 final size:16
Alignment explanation
Indices: 28352--28415 Score: 119
Period size: 16 Copynumber: 4.0 Consensus size: 16
28342 AATAAATAAG
28352 CGAACATAAACGAACA
1 CGAACATAAACGAACA
28368 CGAACATAAACGAACA
1 CGAACATAAACGAACA
*
28384 CGAACATAAATGAACA
1 CGAACATAAACGAACA
28400 CGAACATAAACGAACA
1 CGAACATAAACGAACA
28416 TAAACGTTGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.56, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:29186 original size:14 final size:14
Alignment explanation
Indices: 29169--29224 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
29159 ATGAACATAA
29169 AACGAACATAATCG
1 AACGAACATAATCG
29183 AACGAACAT-A---
1 AACGAACATAATCG
* *
29193 AACAAACATAACCG
1 AACGAACATAATCG
*
29207 AACAAACATAATCG
1 AACGAACATAATCG
29221 AACG
1 AACG
29225 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:29200 original size:24 final size:24
Alignment explanation
Indices: 29147--29217 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
29137 AGATTGAGTT
*
29147 AAACATAAAT-GAATGAACATAAAAC
1 AAACAT-AATCGAACGAACAT-AAAC
*
29172 GAACATAATCGAACGAACATAAAC
1 AAACATAATCGAACGAACATAAAC
* *
29196 AAACATAACCGAACAAACATAA
1 AAACATAATCGAACGAACATAA
29218 TCGAACGTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 26 0.65
25 14 0.35
ACGTcount: A:0.61, C:0.18, G:0.08, T:0.13
Consensus pattern (24 bp):
AAACATAATCGAACGAACATAAAC
Found at i:30640 original size:37 final size:36
Alignment explanation
Indices: 30598--30706 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
30588 ATATTTCAAC
*
30598 AAACATCTACCAAACTTTGAAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCATTTTTCAAAG
* *
30635 AAACATTTATCAAACTTTGAAAACCA-TTTTCAAAA
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
30670 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
30707 TTGGTTGGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 33 0.51
36 7 0.11
37 25 0.38
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:37814 original size:24 final size:24
Alignment explanation
Indices: 37782--37861 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 24
37772 TCAGGCTTCT
37782 AAAGAAGAAGAGAAGGAC-GATGGA
1 AAAGAAGAAGAGAAGGACAG-TGGA
37806 AAAGAAGAAGAGAAGGACAGTGGA
1 AAAGAAGAAGAGAAGGACAGTGGA
*
37830 AAAGCAG-A-AG-AGGACAGTGGA
1 AAAGAAGAAGAGAAGGACAGTGGA
*
37851 AAAGCAGAAGA
1 AAAGAAGAAGA
37862 AGAGGAAAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
21 18 0.35
22 3 0.06
23 2 0.04
24 28 0.54
25 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.36, T:0.04
Consensus pattern (24 bp):
AAAGAAGAAGAGAAGGACAGTGGA
Found at i:37862 original size:24 final size:24
Alignment explanation
Indices: 37802--37867 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 24
37792 AGAAGGACGA
*
37802 TGGAAAAGAAGAAG-AGAAGGACAG
1 TGGAAAAGCAGAAGAAG-AGGACAG
37826 TGGAAAAGC---AGAAGAGGACAG
1 TGGAAAAGCAGAAGAAGAGGACAG
37847 TGGAAAAGCAGAAGAAGAGGA
1 TGGAAAAGCAGAAGAAGAGGA
37868 AAAGAAAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
21 18 0.49
22 2 0.05
24 17 0.46
ACGTcount: A:0.52, C:0.06, G:0.38, T:0.05
Consensus pattern (24 bp):
TGGAAAAGCAGAAGAAGAGGACAG
Found at i:37879 original size:18 final size:18
Alignment explanation
Indices: 37856--38181 Score: 102
Period size: 18 Copynumber: 17.4 Consensus size: 18
37846 GTGGAAAAGC
37856 AGAAGAAGAGGAAAAGAA
1 AGAAGAAGAGGAAAAGAA
*
37874 AGAAGAAGAAGAAGAAGAA
1 AGAAGAAGAGGAA-AAGAA
* * * *
37893 A-AAGCAGAAGAAGAGGA
1 AGAAGAAGAGGAAAAGAA
37910 A-AAGAA-AGTAGAAAA-AA
1 AGAAGAAGAG--GAAAAGAA
37927 AGAAGAAGAGG-AAAGAA
1 AGAAGAAGAGGAAAAGAA
* *
37944 AGAAGAAAAAGCATTAGAAGAGGA
1 AGAAG-AAGAGGA--A-AAGA--A
* *
37968 A-AAGAAAGAAGTAAAAG-C
1 AGAAG-AAG-AGGAAAAGAA
*
37986 AGAAGAAGAGGTAAAGAA
1 AGAAGAAGAGGAAAAGAA
* ** *
38004 AGAAGTAAAATCAGAAG-A
1 AGAAG-AAGAGGAAAAGAA
* *
38022 AGAGGAAGA--AAAAG-C
1 AGAAGAAGAGGAAAAGAA
38037 AGAAGAAGAGGAAAAGAA
1 AGAAGAAGAGGAAAAGAA
*
38055 AGAAGAAAAAGCAGAAGAAGAGGA
1 AGAAG-AAGAG--GAA-AAGA--A
**
38079 A-AAGAA-AGTAGAAAAGGC
1 AGAAGAAGAG--GAAAAGAA
38097 AGAAGAAGAGGAAAAGAA
1 AGAAGAAGAGGAAAAGAA
* * *
38115 AGAAGAAAATGCAGAAGAA
1 AGAAGAAGA-GGAAAAGAA
* **
38134 GAGGTAAAGAAAGAAGAAAAGGC
1 -A-G--AAG-AAGAGGAAAAGAA
38157 AGAAGAAGAGGAAAAGAA
1 AGAAGAAGAGGAAAAGAA
38175 AGAAGAA
1 AGAAGAA
38182 AATGCAGAAG
Statistics
Matches: 229, Mismatches: 45, Indels: 68
0.67 0.13 0.20
Matches are distributed among these distances:
15 12 0.05
16 4 0.02
17 32 0.14
18 86 0.38
19 36 0.16
20 6 0.03
21 15 0.07
22 12 0.05
23 16 0.07
24 10 0.04
ACGTcount: A:0.64, C:0.03, G:0.30, T:0.03
Consensus pattern (18 bp):
AGAAGAAGAGGAAAAGAA
Found at i:37925 original size:30 final size:30
Alignment explanation
Indices: 37885--38245 Score: 501
Period size: 30 Copynumber: 12.4 Consensus size: 30
37875 GAAGAAGAAG
37885 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
* *
37915 AAGTAGAAAAA-AAGAAGAAGAGG-AAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
**
37943 AAGAAGAAAAAGCATTAGAAGAGGAAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
* *
37973 AAGAAGTAAAAGCAGAAGAAGAGGTAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
* *
38003 AAGAAGTAAAATCAGAAG-A-A-G---AG-
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
38026 --GAAGAAAAAGCAGAAGAAGAGGAAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
38054 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
* *
38084 AAGTAGAAAAGGCAGAAGAAGAGGAAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
* *
38114 AAGAAGAAAATGCAGAAGAAGAGGTAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
*
38144 AAGAAGAAAAGGCAGAAGAAGAGGAAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
*
38174 AAGAAGAAAATGCAGAAGAAGAGGAAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
* *
38204 AAGAAGAAAAAGCAGTAGAAGAGGTAAAGA
1 AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
38234 AAGAAGAAAAAG
1 AAGAAGAAAAAG
38246 AAGTCCATGA
Statistics
Matches: 296, Mismatches: 24, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
21 14 0.05
22 1 0.00
23 1 0.00
24 3 0.01
27 3 0.01
28 16 0.05
29 21 0.07
30 237 0.80
ACGTcount: A:0.63, C:0.03, G:0.30, T:0.04
Consensus pattern (30 bp):
AAGAAGAAAAAGCAGAAGAAGAGGAAAAGA
Found at i:37928 original size:11 final size:12
Alignment explanation
Indices: 37861--38213 Score: 99
Period size: 12 Copynumber: 25.8 Consensus size: 12
37851 AAAGCAGAAG
*
37861 AAGAGGAAAAGA
1 AAGAAGAAAAGA
37873 AAGAAGAAGAAG-
1 AAGAAGAA-AAGA
37885 AAGAAGAAAAAGCA
1 AAGAAG-AAAAG-A
37899 GAAGAAGAGGAAAAGA
1 -AAG-A-A-GAAAAGA
*
37915 AAGTAGAAAA-A
1 AAGAAGAAAAGA
*
37926 AAGAAGAAGAGGA
1 AAGAAGAA-AAGA
*
37939 AAGAA-AGAAGA
1 AAGAAGAAAAGA
**
37950 AA-AAGCATTAG-
1 AAGAAG-AAAAGA
*
37961 AAGAGGAAAAGA
1 AAGAAGAAAAGA
37973 AAGAAGTAAAAGCA
1 AAGAAG-AAAAG-A
37987 GAAGAAGAGGTAAAGA
1 -AAGAAGA---AAAGA
*
38003 AAGAAGTAAAATCA
1 AAGAAG-AAAA-GA
*
38017 GAAGAAGAGGAAGA
1 -AAGAAGA-AAAGA
*
38031 AA-AAGCAGAAG-
1 AAGAAG-AAAAGA
*
38042 AAGAGGAAAAGA
1 AAGAAGAAAAGA
38054 AAGAAGAAAAAGCA
1 AAGAAG-AAAAG-A
38068 GAAGAAGAGGAAAAGA
1 -AAG-A-A-GAAAAGA
*
38084 AAGTAGAAAAGGCA
1 AAGAAGAAAA-G-A
38098 GAAGAAGAGGAAAAGA
1 -AAG-A-A-GAAAAGA
38114 AAGAAGAAAATGCA
1 AAGAAGAAAA-G-A
38128 GAAGAAGAGGTAAAGA
1 -AAGAAGA---AAAGA
38144 AAGAAGAAAAGGCA
1 AAGAAGAAAA-G-A
38158 GAAGAAGAGGAAAAGA
1 -AAG-A-A-GAAAAGA
38174 AAGAAGAAAATGCA
1 AAGAAGAAAA-G-A
38188 GAAGAAGAGGAAAAGA
1 -AAG-A-A-GAAAAGA
38204 AAGAAGAAAA
1 AAGAAGAAAA
38214 AGCAGTAGAA
Statistics
Matches: 264, Mismatches: 20, Indels: 114
0.66 0.05 0.29
Matches are distributed among these distances:
10 2 0.01
11 24 0.09
12 70 0.27
13 36 0.14
14 13 0.05
15 64 0.24
16 12 0.05
17 23 0.09
18 20 0.08
ACGTcount: A:0.64, C:0.03, G:0.30, T:0.03
Consensus pattern (12 bp):
AAGAAGAAAAGA
Found at i:38195 original size:18 final size:17
Alignment explanation
Indices: 37880--38225 Score: 144
Period size: 15 Copynumber: 22.5 Consensus size: 17
37870 AGAAAGAAGA
37880 AGAAGAAGAAGAAAAAGC
1 AGAAGAAGAAG-AAAAGC
*
37898 AGAAGAAGAGGAAAAG-
1 AGAAGAAGAAGAAAAGC
*
37914 A-AAGTAGAA-AAAA--
1 AGAAGAAGAAGAAAAGC
*
37927 AGAAGAAG-AGGAAAG-
1 AGAAGAAGAAGAAAAGC
37942 A-AAGAAG-A-AAAAGC
1 AGAAGAAGAAGAAAAGC
** *
37956 ATTAGAAGAGGAAAAG-
1 AGAAGAAGAAGAAAAGC
*
37972 A-AAGAAG--TAAAAGC
1 AGAAGAAGAAGAAAAGC
* *
37986 AGAAGAAGAGGTAAAG-
1 AGAAGAAGAAGAAAAGC
* *
38002 A-AAGAAGTAA-AATCAGA
1 AGAAGAAG-AAGAA-AAGC
*
38019 AGAAGAGGAAGAAAAAGC
1 AGAAGAAGAAG-AAAAGC
*
38037 AGAAGAAGAGGAAAAG-
1 AGAAGAAGAAGAAAAGC
38053 A-AAGAAG-A-AAAAGC
1 AGAAGAAGAAGAAAAGC
*
38067 AGAAGAAGAGGAAAAG-
1 AGAAGAAGAAGAAAAGC
* *
38083 A-AAGTAG-A-AAAGGC
1 AGAAGAAGAAGAAAAGC
*
38097 AGAAGAAGAGGAAAAG-
1 AGAAGAAGAAGAAAAGC
*
38113 A-AAGAAG-A-AAATGC
1 AGAAGAAGAAGAAAAGC
* *
38127 AGAAGAAGAGGTAAAG-
1 AGAAGAAGAAGAAAAGC
*
38143 A-AAGAAG-A-AAAGGC
1 AGAAGAAGAAGAAAAGC
*
38157 AGAAGAAGAGGAAAAG-
1 AGAAGAAGAAGAAAAGC
*
38173 A-AAGAAG-A-AAATGC
1 AGAAGAAGAAGAAAAGC
*
38187 AGAAGAAGAGGAAAAG-
1 AGAAGAAGAAGAAAAGC
38203 A-AAGAAG-A-AAAAGC
1 AGAAGAAGAAGAAAAGC
*
38217 AGTAGAAGA
1 AGAAGAAGA
38226 GGTAAAGAAA
Statistics
Matches: 244, Mismatches: 44, Indels: 82
0.66 0.12 0.22
Matches are distributed among these distances:
13 36 0.15
14 27 0.11
15 99 0.41
16 12 0.05
17 42 0.17
18 26 0.11
19 2 0.01
ACGTcount: A:0.63, C:0.03, G:0.30, T:0.03
Consensus pattern (17 bp):
AGAAGAAGAAGAAAAGC
Found at i:42866 original size:44 final size:44
Alignment explanation
Indices: 42801--42936 Score: 177
Period size: 44 Copynumber: 3.1 Consensus size: 44
42791 GCTCAGTTAG
* *
42801 CTTCGAATGCTATCAACTTCACCTGACATGGACCATCAATGGCA
1 CTTCGAATGCTATCAAATTCACCTAACATGGACCATCAATGGCA
* *
42845 CTTCGAATGCTATGAAATTCACCTAACATGGACCATCAATGGTA
1 CTTCGAATGCTATCAAATTCACCTAACATGGACCATCAATGGCA
* * *
42889 CTT-GTAATTCTATCAAGTTCGCCTAACATGGA-CAGTCAATGGCA
1 CTTCG-AATGCTATCAAATTCACCTAACATGGACCA-TCAATGGCA
42933 CTTC
1 CTTC
42937 AACTCATGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
43 3 0.04
44 77 0.96
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (44 bp):
CTTCGAATGCTATCAAATTCACCTAACATGGACCATCAATGGCA
Found at i:44195 original size:17 final size:17
Alignment explanation
Indices: 44173--44209 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
44163 CGATTTTGAG
*
44173 CTCGATTCAAGCTCGAA
1 CTCGATTAAAGCTCGAA
44190 CTCGATTAAAGCTCGAA
1 CTCGATTAAAGCTCGAA
44207 CTC
1 CTC
44210 AAACTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (17 bp):
CTCGATTAAAGCTCGAA
Found at i:44617 original size:26 final size:26
Alignment explanation
Indices: 44581--44667 Score: 129
Period size: 26 Copynumber: 3.3 Consensus size: 26
44571 CCTGCAGACA
44581 CACAAAACAAGGGACAGAGCACCAAG
1 CACAAAACAAGGGACAGAGCACCAAG
*
44607 CACAAAACAAGGGACATAGCACCAAG
1 CACAAAACAAGGGACAGAGCACCAAG
* * *
44633 CAAAAAACAAGGGACAGAGAACCAAA
1 CACAAAACAAGGGACAGAGCACCAAG
44659 CACCAAAAC
1 CA-CAAAAC
44668 CAATACTAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
26 49 0.91
27 5 0.09
ACGTcount: A:0.54, C:0.26, G:0.18, T:0.01
Consensus pattern (26 bp):
CACAAAACAAGGGACAGAGCACCAAG
Found at i:46697 original size:14 final size:14
Alignment explanation
Indices: 46680--46720 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
46670 TTTATTCATC
46680 AATAATGTATTTTT
1 AATAATGTATTTTT
46694 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
46705 AATAATGTAATTTT
1 AATAATGTATTTTT
46719 AA
1 AA
46721 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:48173 original size:37 final size:38
Alignment explanation
Indices: 48118--48201 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
48108 TGGTAACCAA
48118 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
48155 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
48192 -GTTGAAAAAT
1 CTTTGAAAAAT
48202 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:48629 original size:16 final size:16
Alignment explanation
Indices: 48608--48641 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
48598 TTACTATTCA
*
48608 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
48624 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
48640 CG
1 CG
48642 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:50462 original size:16 final size:13
Alignment explanation
Indices: 50429--50463 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
50419 CCCATAACAC
50429 CGCAGCAGAATGG
1 CGCAGCAGAATGG
50442 CGCAGCAGAATGG
1 CGCAGCAGAATGG
*
50455 CGTAGCAGA
1 CGCAGCAGA
50464 GCGCATGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.37, T:0.09
Consensus pattern (13 bp):
CGCAGCAGAATGG
Found at i:52743 original size:21 final size:21
Alignment explanation
Indices: 52719--52779 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
52709 AACTTTGAAA
52719 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
52740 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
52754 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
52775 AAATG
1 AAATG
52780 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:52818 original size:37 final size:36
Alignment explanation
Indices: 52711--52829 Score: 152
Period size: 35 Copynumber: 3.3 Consensus size: 36
52701 TGGTAACCAA
*
52711 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
52748 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
* * *
52783 CTTTGAAAAATAATTTTTTAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-AGTTTTCAAAGTTTGGTAAATGTTT
*
52820 -GTTGAAAAAT
1 CTTTGAAAAAT
52830 GATAATGGGA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 35 0.47
36 14 0.19
37 26 0.35
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:60762 original size:24 final size:24
Alignment explanation
Indices: 60727--60782 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
60717 TTCATCCTTC
*
60727 GTATCAGCACGATGCTGAGCTGAT
1 GTATCAGTACGATGCTGAGCTGAT
60751 GTATCAGTACGATGCTGAGCTGAT
1 GTATCAGTACGATGCTGAGCTGAT
60775 GTATCAGT
1 GTATCAGT
60783 TGACTGTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (24 bp):
GTATCAGTACGATGCTGAGCTGAT
Found at i:65241 original size:27 final size:27
Alignment explanation
Indices: 65203--65268 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
65193 GATAATGGCT
*
65203 CTGAATCATTCAGAATGTACTTCTAAG
1 CTGAATCATTCAGAATGCACTTCTAAG
*
65230 CTGAATCATTCAGAATGCACTTCTATG
1 CTGAATCATTCAGAATGCACTTCTAAG
65257 CTGAATCATTCA
1 CTGAATCATTCA
65269 TCACTGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (27 bp):
CTGAATCATTCAGAATGCACTTCTAAG
Found at i:82516 original size:23 final size:24
Alignment explanation
Indices: 82490--82537 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
82480 ATAAGTTTAC
82490 AATTAAATAATAAAATAAT-ATAA
1 AATTAAATAATAAAATAATAATAA
**
82513 AATTATTTAATAAAATAATAATAA
1 AATTAAATAATAAAATAATAATAA
82537 A
1 A
82538 TTTATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTAAATAATAAAATAATAATAA
Found at i:82538 original size:23 final size:24
Alignment explanation
Indices: 82497--82557 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
82487 TACAATTAAA
82497 TAATAAAATAAT-ATAAAA-TTATT
1 TAATAAAATAATAATAAAATTTA-T
82520 TAATAAAATAATAAT-AAATTTAT
1 TAATAAAATAATAATAAAATTTAT
*
82543 TAATATAAAAAATAA
1 TAATA-AAATAATAA
82558 CAACATACCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TAATAAAATAATAATAAAATTTAT
Found at i:82550 original size:20 final size:18
Alignment explanation
Indices: 82503--82552 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
82493 TAAATAATAA
*
82503 AATAATATAAAATTATTT
1 AATAATATAAAATAATTT
*
82521 AATAAAATAATAATAAATTT
1 AATAATATAA-AAT-AATTT
*
82541 ATTAATATAAAA
1 AATAATATAAAA
82553 AATAACAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 9 0.35
19 5 0.19
20 12 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAATATAAAATAATTT
Found at i:83985 original size:116 final size:116
Alignment explanation
Indices: 83779--84011 Score: 333
Period size: 116 Copynumber: 2.0 Consensus size: 116
83769 AAACAACCCT
** * * **
83779 ACCTTAAAAAAATAACTGATCCTATTTTCATATGTAATAGGATGAGGGGAGGTAAGGTTGTAGGC
1 ACCTTAAAAAAATAACTGATCCTATTCCCATATATAATAGGATGAGGGGAGATAAGGTAATAGGC
* * *
83844 TGCCTCCAACATCAGGTTGAAAGCAGTTTCCGTGGAAGACTTCCGGCAGTC
66 TGCCCCCAACATCAGGTTGAAAGCAGCTTCCGTGGAAGACCTCCGGCAGTC
* *
83895 ACCTTAAAAAAATAGCTG-TCCCTATTCCCATATATAATGGGATGAGGGGAGATAAGGTAATAGG
1 ACCTTAAAAAAATAACTGAT-CCTATTCCCATATATAATAGGATGAGGGGAGATAAGGTAATAGG
* *
83959 TTGCCCCCAACATCAGGTTGAGAGCAGCTTCCGTGGAAGACCTCCGGCAGTC
65 CTGCCCCCAACATCAGGTTGAAAGCAGCTTCCGTGGAAGACCTCCGGCAGTC
84011 A
1 A
84012 GAATTACGAA
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
115 1 0.01
116 102 0.99
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (116 bp):
ACCTTAAAAAAATAACTGATCCTATTCCCATATATAATAGGATGAGGGGAGATAAGGTAATAGGC
TGCCCCCAACATCAGGTTGAAAGCAGCTTCCGTGGAAGACCTCCGGCAGTC
Found at i:91322 original size:30 final size:30
Alignment explanation
Indices: 91264--91323 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
91254 TTAGACCTTA
* **
91264 CCCGCCCCGCATCTGCCCACCCGGCATTCG
1 CCCGCCCCGCATCCGCCCACCCCACATTCG
* *
91294 CCCGCCCCGTATCCGCTCACCCCACATTCG
1 CCCGCCCCGCATCCGCCCACCCCACATTCG
91324 ACCACCCACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.57, G:0.17, T:0.15
Consensus pattern (30 bp):
CCCGCCCCGCATCCGCCCACCCCACATTCG
Found at i:95496 original size:27 final size:26
Alignment explanation
Indices: 95457--95515 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
95447 GAAACTAAAT
* *
95457 TAAATAAATAAAGGCTAAAAT-AAAAA
1 TAAAAAAATAAAGG-AAAAATCAAAAA
*
95483 TAAAAAAATAAAAGGAAAAATCAATAA
1 TAAAAAAAT-AAAGGAAAAATCAAAAA
95510 TAAAAA
1 TAAAAA
95516 TACTGAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (26 bp):
TAAAAAAATAAAGGAAAAATCAAAAA
Found at i:97387 original size:15 final size:15
Alignment explanation
Indices: 97367--97406 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
97357 GTAGCTTTAG
97367 GCATGAATTTTTCAA
1 GCATGAATTTTTCAA
97382 GCATGAATTTTTCAA
1 GCATGAATTTTTCAA
97397 GCATGAATTT
1 GCATGAATTT
97407 AATTTCTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (15 bp):
GCATGAATTTTTCAA
Done.