Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001794.1 Hibiscus syriacus cultivar Beakdansim tig00003626_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: 36389
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1499 original size:83 final size:83
Alignment explanation
Indices: 1337--1503 Score: 309
Period size: 83 Copynumber: 2.0 Consensus size: 83
1327 ATGGAAAATT
*
1337 AAACCAAATTTATTTAAACAATGAGTTTTTGCTAATGATGGACTAAGGGAGTTAAGGAACACCTG
1 AAACCAAATTTATTTAAACAATGAGTTTTTGCTAATGATGGACTAAGGGAGTTAAAGAACACCTG
1402 TTATAGTTAATTCACATG
66 TTATAGTTAATTCACATG
1420 AAACCAAATTTATTTAAACAATGAGTTTTTGCTAATGATGG-CTAAGGGAGTTAAAGAACACCTG
1 AAACCAAATTTATTTAAACAATGAGTTTTTGCTAATGATGGACTAAGGGAGTTAAAGAACACCTG
1484 TTATAGTTAATTTCACATG
66 TTATAGTTAA-TTCACATG
1503 A
1 A
1504 GCACTCAAGA
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
82 32 0.39
83 50 0.61
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (83 bp):
AAACCAAATTTATTTAAACAATGAGTTTTTGCTAATGATGGACTAAGGGAGTTAAAGAACACCTG
TTATAGTTAATTCACATG
Found at i:3000 original size:85 final size:84
Alignment explanation
Indices: 2734--3513 Score: 1000
Period size: 85 Copynumber: 9.4 Consensus size: 84
2724 GAAATTGTTC
**
2734 ACAGCATAGCTCAA-G-GAGAAAAGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATT---
1 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAG
2794 -T-AA--CTATATCAAATTT
66 CTCAAGGC-ATATCAAATTT
* * * *
2810 ACAGCATACCTCAAGGTGAGAAGGG-TCATCTGTCAACGAAAACCTTCAAGTTCGATTCTATTCA
1 ACAGCATAGCTCAAGGTGAGAAGGGCT-ATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCA
*
2874 GCTC-GGGCATATCAAATTT
65 GCTCAAGGCATATCAAATTT
* *
2893 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACGAAAACCTTCGAGTTTCGATTCCATTAA
1 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAG-TTCGATTCCATTCA
2958 GCTCAAGGCATATCAAATTT
65 GCTCAAGGCATATCAAATTT
** *
2978 ACAGCATAGCTCAAGACGAGAA-GGCTATCTGTCAACAAAAACCTTCAAGTTCGATTCCATTCAG
1 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAG
*
3042 CTCAAGGGCATTTC-AATTT
66 CTCAA-GGCATATCAAATTT
* **
3061 ACAGCATAGCTCAAGGTGAGAAGGG-T-TATGTCAACAAAAACCTTCGAGTTTAATTCCATTCAG
1 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAG
*
3124 CTCATA-GTATATCAAATTT
66 CTCA-AGGCATATCAAATTT
* * ** * *
3143 ACAGCATAACTCAAGGCGAGAAGGTATATCTGTCAATAAAAACCTTCGAGTTCGATTCTATTCAG
1 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAG
3208 CTCAAGGGCATATCAAATTT
66 CTCAA-GGCATATCAAATTT
* * * * * * * *
3228 ACAACATAACTCAAGGCGAAAATGGTTATTTGTCAACAAAAGCCTTCGAGTTCGATTCCATTCAG
1 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAG
3293 CTCAAGGGCATATCAAATTT
66 CTCAA-GGCATATCAAATTT
* *
3313 ACAGCATAACTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAA
1 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAG
3378 CTCAAGGGCATATCAAATTT
66 CTCAA-GGCATATCAAATTT
* * * *
3398 ACAGCATAGTTTAAGGTGAGAAGGGCTATCTGTCAA-AAAAACCTTCAAGTTTGATTCCATTCAG
1 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAG
* *
3462 CTCAAGGCCTGTCAAATTT
66 CTCAAGGCATATCAAATTT
* *
3481 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGT
1 ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGT
3514 TATTGAAGAC
Statistics
Matches: 619, Mismatches: 64, Indels: 35
0.86 0.09 0.05
Matches are distributed among these distances:
76 13 0.02
77 2 0.00
78 38 0.06
81 5 0.01
82 65 0.11
83 146 0.24
84 118 0.19
85 232 0.37
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (84 bp):
ACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCAG
CTCAAGGCATATCAAATTT
Found at i:4009 original size:34 final size:34
Alignment explanation
Indices: 3954--4090 Score: 199
Period size: 34 Copynumber: 4.0 Consensus size: 34
3944 TGTGTAATAC
* *
3954 ATATATTATATAATAGTTTTTGAAAACA-TTTCAAA
1 ATATATAATAT-ATAG-TTTTGAAAACATTTTGAAA
3989 ATATATAATATATAGTTTTTGAAAACATTTTGAAA
1 ATATATAATATATAG-TTTTGAAAACATTTTGAAA
4024 ATATATAATATATAGTTTTGAAAACATTTTGAAA
1 ATATATAATATATAGTTTTGAAAACATTTTGAAA
*
4058 ATTTATAATATATA-TTTTGAAAACA-TTTGAAA
1 ATATATAATATATAGTTTTGAAAACATTTTGAAA
4090 A
1 A
4091 AAAAAATATA
Statistics
Matches: 98, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
32 8 0.08
33 11 0.11
34 48 0.49
35 31 0.32
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (34 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAA
Found at i:4184 original size:25 final size:25
Alignment explanation
Indices: 4151--4199 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
4141 ATTGCACATA
4151 TATTATATTATAGTATTATATTATT
1 TATTATATTATAGTATTATATTATT
* * *
4176 TATTATATTTTATTATTTTATTAT
1 TATTATATTATAGTATTATATTAT
4200 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TATTATATTATAGTATTATATTATT
Found at i:4190 original size:30 final size:29
Alignment explanation
Indices: 4149--4208 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
4139 TTATTGCACA
4149 TATATTATATTATAGTATTATATTATTTAT
1 TATATTATATTATAGTATTATATT-TTTAT
* **
4179 TATATTTTATTATTTTATTATATTTTTAT
1 TATATTATATTATAGTATTATATTTTTAT
4208 T
1 T
4209 TTTATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (29 bp):
TATATTATATTATAGTATTATATTTTTAT
Found at i:4202 original size:13 final size:13
Alignment explanation
Indices: 4151--4253 Score: 55
Period size: 13 Copynumber: 8.6 Consensus size: 13
4141 ATTGCACATA
* *
4151 TATTATATTATAG
1 TATTTTATTATAT
*
4164 TATTATATTAT-T
1 TATTTTATTATAT
* *
4176 TATTATATTTTAT
1 TATTTTATTATAT
4189 TATTTTATTATA-
1 TATTTTATTATAT
*
4201 T-TTTTATTTTTAT
1 TATTTTA-TTATAT
*
4214 T-TTTTATT-TTT
1 TATTTTATTATAT
4225 TATTTT-TTAT-T
1 TATTTTATTATAT
*
4236 T-TTTT-TTTTAT
1 TATTTTATTATAT
4247 T-TTTTAT
1 TATTTTAT
4254 AGGTCCAAAG
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
10 7 0.09
11 18 0.24
12 23 0.30
13 28 0.37
ACGTcount: A:0.23, C:0.00, G:0.01, T:0.76
Consensus pattern (13 bp):
TATTTTATTATAT
Found at i:4214 original size:39 final size:34
Alignment explanation
Indices: 4171--4250 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 34
4161 TAGTATTATA
4171 TTATTTATTATATTTTATTATTTTATTATATTTTTATTT
1 TTATTT-TTATATTTT-TTATTTT-TTAT-TTTTT-TTT
4210 TTATTTTT-TATTTTTTATTTTTTATTTTTTTTT
1 TTATTTTTATATTTTTTATTTTTTATTTTTTTTT
4243 TTATTTTT
1 TTATTTTT
4251 TATAGGTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
33 11 0.27
34 5 0.12
35 4 0.10
36 7 0.17
37 6 0.15
38 2 0.05
39 6 0.15
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (34 bp):
TTATTTTTATATTTTTTATTTTTTATTTTTTTTT
Found at i:4217 original size:7 final size:7
Alignment explanation
Indices: 4171--4253 Score: 100
Period size: 7 Copynumber: 11.6 Consensus size: 7
4161 TAGTATTATA
4171 TTATTTAT
1 TTATTT-T
4179 TATATTTT
1 T-TATTTT
4187 ATTATTTT
1 -TTATTTT
4195 ATTATATTT
1 -TTAT-TTT
4204 TTA-TTT
1 TTATTTT
4210 TTATTTT
1 TTATTTT
4217 TTATTTT
1 TTATTTT
4224 TTATTTT
1 TTATTTT
4231 TTA-TTT
1 TTATTTT
4237 TT-TTTT
1 TTATTTT
4243 TTATTTT
1 TTATTTT
4250 TTAT
1 TTAT
4254 AGGTCCAAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 13
0.84 0.00 0.16
Matches are distributed among these distances:
6 16 0.23
7 28 0.41
8 16 0.23
9 9 0.13
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (7 bp):
TTATTTT
Found at i:7280 original size:20 final size:20
Alignment explanation
Indices: 7244--7281 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7234 ATCCTATTCC
**
7244 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
7264 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
7282 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:7917 original size:67 final size:66
Alignment explanation
Indices: 7812--7939 Score: 152
Period size: 67 Copynumber: 1.9 Consensus size: 66
7802 ACTTAAAAAA
* * *
7812 ACCCGACCCAACTCGACCCGAATATCAAACTTAAAAATCCGACTCGACCCGAACAAAATAAAGCT
1 ACCCGACCCAACCCGACCCGAATATCAAACTTAAAAATCCAACCCGACCCGAA-AAAATAAAGCT
7877 TC
65 TC
* * * *
7879 ACCCGACCCGACCCGACCCGAATAT-ATGTA-TTAGAAATCCAACCCGACCCGAAATAATAAA
1 ACCCGACCCAACCCGACCCGAATATCA--AACTTAAAAATCCAACCCGACCCGAAAAAATAAA
7940 AAATATTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
66 8 0.15
67 43 0.83
68 1 0.02
ACGTcount: A:0.40, C:0.34, G:0.12, T:0.15
Consensus pattern (66 bp):
ACCCGACCCAACCCGACCCGAATATCAAACTTAAAAATCCAACCCGACCCGAAAAAATAAAGCTT
C
Found at i:8518 original size:29 final size:28
Alignment explanation
Indices: 8480--8548 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 28
8470 CTGGAGGTTA
8480 TTTTAGTCATTTCAAAACTTGAGTGTATTT
1 TTTTA-TCATTTCAAAACTTGAGTGTA-TT
8510 TTTTATCATTTCAAAACTTGAGTGTATT
1 TTTTATCATTTCAAAACTTGAGTGTATT
8538 TTTTATCATTT
1 TTTTATCATTT
8549 AATTTAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 13 0.33
29 21 0.54
30 5 0.13
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (28 bp):
TTTTATCATTTCAAAACTTGAGTGTATT
Found at i:9369 original size:11 final size:10
Alignment explanation
Indices: 9347--9385 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
9337 ACAACAGCCA
9347 ATCAACGACG
1 ATCAACGACG
9357 ATCAACGATCG
1 ATCAACGA-CG
*
9368 ATCAATGACG
1 ATCAACGACG
*
9378 GTCAACGA
1 ATCAACGA
9386 TCAATCAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (10 bp):
ATCAACGACG
Found at i:9371 original size:21 final size:21
Alignment explanation
Indices: 9345--9403 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
9335 ACACAACAGC
*
9345 CAATCAACGACGATCAACGAT
1 CAATCAACGACGGTCAACGAT
* *
9366 CGATCAATGACGGTCAACGAT
1 CAATCAACGACGGTCAACGAT
*
9387 CAATCAACAACGGTCAA
1 CAATCAACGACGGTCAA
9404 TGGCCAGTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (21 bp):
CAATCAACGACGGTCAACGAT
Found at i:11397 original size:18 final size:19
Alignment explanation
Indices: 11374--11419 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
11364 AATAAGTCAA
*
11374 TGCAATTGTTCG-TTTCTC
1 TGCAATTGTTCGTTTTCGC
11392 TGCAATTGTTCGTTTTCGC
1 TGCAATTGTTCGTTTTCGC
11411 TGCAATTGT
1 TGCAATTGT
11420 CGCTTAAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
TGCAATTGTTCGTTTTCGC
Found at i:12126 original size:21 final size:21
Alignment explanation
Indices: 12011--12126 Score: 58
Period size: 21 Copynumber: 5.6 Consensus size: 21
12001 GCGAAATAAA
*
12011 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
* ** * *
12031 AATCGTAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* * **
12051 AATCGCAACGTGATTATGAAG
1 AATCGCAACGCGATTTTCCAG
* ** *
12072 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
12092 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
12114 AATCGCAACGCGA
1 AATCGCAACGCGA
12127 ATATGAAAAT
Statistics
Matches: 66, Mismatches: 26, Indels: 7
0.67 0.26 0.07
Matches are distributed among these distances:
19 1 0.02
20 22 0.33
21 41 0.62
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:12139 original size:20 final size:20
Alignment explanation
Indices: 12114--12368 Score: 149
Period size: 20 Copynumber: 12.7 Consensus size: 20
12104 GATTTTCCAG
**
12114 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
** *
12134 AATCGCAACGCGAA-CATAT
1 AATCGCAACGCGAATCCGAA
* * *
12153 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATCCGAA
* * *
12173 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* * *
12194 AATCGCAACGCGTATTCGTA
1 AATCGCAACGCGAATCCGAA
**
12214 AATCGCAACGAC-AATATGTAA
1 AATCGCAACG-CGAATCCG-AA
* * *
12235 AATCGCAAAGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* *
12255 AATCGCAACGC-ATATCTGTA
1 AATCGCAACGCGA-ATCCGAA
* * *
12275 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGAA
* * *
12295 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
*
12315 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCG-AA
* * *
12336 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
12356 AATCGCAACGCGA
1 AATCGCAACGCGA
12369 TTTTTAAAGC
Statistics
Matches: 178, Mismatches: 47, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
19 14 0.08
20 118 0.66
21 46 0.26
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:12219 original size:41 final size:40
Alignment explanation
Indices: 12114--12368 Score: 198
Period size: 41 Copynumber: 6.3 Consensus size: 40
12104 GATTTTCCAG
* * * * *
12114 AATCGCAACGCGAATATGAAAATCGCAACGCG-A-ACATA
1 AATCGCAACGCGAATACGTAAATCGCAACGAGTATCCGTA
* *
12152 TAATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A-AATCGCAACGAGTATCCGT-A
* * ** **
12194 AATCGCAACGCGTATTCGTAAATCGCAACGACAATATGTAA
1 AATCGCAACGCGAATACGTAAATCGCAACGAGTATCCGT-A
* * * *
12235 AATCGCAAAGCGTATCCGTAAATCGCAACGCA-TATCTGTA
1 AATCGCAACGCGAATACGTAAATCGCAACG-AGTATCCGTA
* * *
12275 AATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTAAATCGCAACGAGTATCCGTA
* *
12315 AATCGCAACGAC-AATACGTAAAATCGCAATGCGTATCCGTA
1 AATCGCAACG-CGAATACGT-AAATCGCAACGAGTATCCGTA
12356 AATCGCAACGCGA
1 AATCGCAACGCGA
12369 TTTTTAAAGC
Statistics
Matches: 180, Mismatches: 24, Indels: 22
0.80 0.11 0.10
Matches are distributed among these distances:
38 3 0.02
39 22 0.12
40 52 0.29
41 95 0.53
42 7 0.04
43 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGAATACGTAAATCGCAACGAGTATCCGTA
Found at i:12237 original size:101 final size:101
Alignment explanation
Indices: 12114--12370 Score: 337
Period size: 101 Copynumber: 2.6 Consensus size: 101
12104 GATTTTCCAG
* * * *
12114 AATCGCAACG-CGAATATG-AAAATCGCAACGCG-A-ACATATAATCGCAACGCGATTCTG-ACT
1 AATCGCAACGAC-AATATGTAAAATCGCAAAGCGTATCCGTA-AATCGCAACGCGATTCTGTA-A
* * *
12174 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATTCGTA
63 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTA
12214 AATCGCAACGACAATATGTAAAATCGCAAAGCGTATCCGTAAATCGCAACGC-ATATCTGTAAAT
1 AATCGCAACGACAATATGTAAAATCGCAAAGCGTATCCGTAAATCGCAACGCGAT-TCTGTAAAT
*
12278 CGCAACGAGAATACGTAAATCGCAATGCGTATCCGTA
65 CGCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
* *
12315 AATCGCAACGACAATACGTAAAATCGCAATGCGTATCCGTAAATCGCAACGCGATT
1 AATCGCAACGACAATATGTAAAATCGCAAAGCGTATCCGTAAATCGCAACGCGATT
12371 TTTAAAGCGC
Statistics
Matches: 140, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
100 16 0.11
101 86 0.61
102 34 0.24
103 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (101 bp):
AATCGCAACGACAATATGTAAAATCGCAAAGCGTATCCGTAAATCGCAACGCGATTCTGTAAATC
GCAACGAGAATACGTAAATCGCAACGCGTATCCGTA
Found at i:12985 original size:21 final size:20
Alignment explanation
Indices: 12924--12999 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
12914 TTCTAAACTT
12924 AAAATCGCAAC-ATGAAAATG
1 AAAATCGCAACGA-GAAAATG
12944 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGA-GAAAATG
**
12964 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGA-AAATG
12985 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
13000 TAATCGCAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 30 0.61
21 19 0.39
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGAGAAAATG
Found at i:13085 original size:20 final size:20
Alignment explanation
Indices: 13060--13106 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
13050 GATTCTCTCA
13060 TTGCGATAGTCATT-TCCGCG
1 TTGCGATAGTCATTAT-CGCG
*
13080 TTGCGATAGTCATTATCTCG
1 TTGCGATAGTCATTATCGCG
13100 TTGCGAT
1 TTGCGAT
13107 TTCATTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTATCGCG
Found at i:14970 original size:94 final size:94
Alignment explanation
Indices: 14809--15170 Score: 591
Period size: 94 Copynumber: 3.9 Consensus size: 94
14799 TAGATTGCTT
* * * *
14809 AGTAAATTTATTCGGTTGCTACCAATACTGCTAAATTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
14874 ATTTGTCTTTTGTTTTTTCTTTTGCTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
14903 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAATGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
14968 ATTTGTCTTTTTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
14997 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
15062 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
15091 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTTTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
15156 ATTTGTCTTTGTTTT
66 ATTTGTCTTTGTTTT
15171 CACTGTTTAA
Statistics
Matches: 253, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
93 17 0.07
94 236 0.93
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:15440 original size:42 final size:42
Alignment explanation
Indices: 15364--15452 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
15354 GACTCGCCTG
* * *
15364 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
15406 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
15448 TCATC
1 TCATC
15453 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:16643 original size:14 final size:14
Alignment explanation
Indices: 16624--16659 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
16614 ATTGTTTAAT
16624 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
16638 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
16652 TGATTTGT
1 TGATTTGT
16660 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:16787 original size:19 final size:19
Alignment explanation
Indices: 16765--16823 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
16755 CAAAATGTCT
16765 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
16784 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
16798 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
16817 ATCGCAA
1 ATCGCAA
16824 CGATAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.52
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:16811 original size:33 final size:33
Alignment explanation
Indices: 16769--16844 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
16759 ATGTCTATCG
*
16769 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCA
* *
16802 CAATGCGAAATGAAAATCGCAACGATAAAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCA
*
16835 CAACGCGAAA
1 CAATGCGAAA
16845 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAAAATCA
Found at i:16872 original size:19 final size:19
Alignment explanation
Indices: 16850--17007 Score: 120
Period size: 19 Copynumber: 8.7 Consensus size: 19
16840 CGAAACTAAA
16850 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
16869 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
16884 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
16902 TTCGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
16917 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * **
16935 TTCGCATTGTGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
16954 TTCCGCGTTGCGATATTCAT
1 TT-CGCGTTGCGATTTTCAT
16974 ATTCGCGTTGCGATTTTCAT
1 -TTCGCGTTGCGATTTTCAT
*
16994 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
17008 CTCTCGTTGC
Statistics
Matches: 106, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
14 16 0.15
16 6 0.06
17 6 0.06
19 46 0.43
20 30 0.28
21 2 0.02
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:16944 original size:33 final size:33
Alignment explanation
Indices: 16854--16947 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
16844 ACTAAATTCG
* *
16854 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
*
16887 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
16920 CGTTGCGATTTTCATTTCGCATTGTGAT
1 CGTTGCGATTTTCATTTCGCATTGTGAT
16948 AGTCATTTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
Found at i:16973 original size:20 final size:19
Alignment explanation
Indices: 16920--17006 Score: 102
Period size: 20 Copynumber: 4.5 Consensus size: 19
16910 GTGATTCTCT
*
16920 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* * *
16939 CATTGTGATAGTCATTTCCG
1 CGTTGCGATATTCATTT-CG
16959 CGTTGCGATATTCATATTCG
1 CGTTGCGATATTCAT-TTCG
*
16979 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
*
16998 CATTGCGAT
1 CGTTGCGAT
17007 TCTCTCGTTG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 25 0.44
20 30 0.53
21 2 0.04
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:17039 original size:53 final size:56
Alignment explanation
Indices: 16920--17040 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 56
16910 GTGATTCTCT
* * *
16920 CGTTGCGATTTTCATTTCGCATTGTGATAGTCATTTCCGCGTTGCGATATTCATATTCG
1 CGTTGCGATTTTCATTTCGCATTGCGATA-TC--TTCCGCGTTGCGATAGTAATATTCG
*
16979 CGTTGCGATTTTCATTTCGCATTGCGAT-TC-T-CTCGTTGCGATAGTAAT-TTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGATATCTTCCGCGTTGCGATAGTAATATT-CG
17032 CGTTGCGAT
1 CGTTGCGAT
17041 AAACATTAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
52 2 0.04
53 25 0.44
54 1 0.02
57 2 0.04
59 27 0.47
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (56 bp):
CGTTGCGATTTTCATTTCGCATTGCGATATCTTCCGCGTTGCGATAGTAATATTCG
Found at i:17086 original size:20 final size:20
Alignment explanation
Indices: 17013--17086 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
17003 CGATTCTCTC
* *
17013 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
** **
17033 GTTGCGATAAACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
17053 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
17074 GTTGCGATAGTCA
1 GTTGCGATAGTCA
17087 AATGAATGCC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.56
21 11 0.28
22 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:19364 original size:15 final size:14
Alignment explanation
Indices: 19329--19359 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
19319 TCCCGTGGCA
19329 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
19343 TTTTCTTTGGGGA-
1 TTTTCTTTGGGGAC
19356 TTTT
1 TTTT
19360 TTCTTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.06, C:0.10, G:0.26, T:0.58
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:20495 original size:20 final size:20
Alignment explanation
Indices: 20468--20718 Score: 196
Period size: 20 Copynumber: 12.5 Consensus size: 20
20458 GTTAGAATCT
20468 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACAGATTCG
* * *
20488 CATTGCGA-TTACTA-AATCA
1 CGTTGCGATTTAC-AGATTCG
* *
20507 CATTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATTCG
*
20527 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACAGATTCG
*
20547 CGTTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATTCG
20567 CGTTGCGATTTACAG-TTACG
1 CGTTGCGATTTACAGATT-CG
20587 CGTTGCGATTTTAC-GTATT-G
1 CGTTGCGA-TTTACAG-ATTCG
* *
20607 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACAGATTCG
* * *
20628 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACAGATTCG
* *
20649 CGTTGCGATAGT-CAGAATCG
1 CGTTGCGAT-TTACAGATTCG
*
20669 CGTTGCGATTTATATG-TTCG
1 CGTTGCGATTTACA-GATTCG
* *
20689 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACAGATTCG
20709 CGTTGCGATT
1 CGTTGCGATT
20719 ATGAAAAATT
Statistics
Matches: 188, Mismatches: 24, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
19 19 0.10
20 129 0.69
21 38 0.20
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACAGATTCG
Found at i:20612 original size:41 final size:40
Alignment explanation
Indices: 20509--20718 Score: 253
Period size: 40 Copynumber: 5.2 Consensus size: 40
20499 CTAAATCACA
20509 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
*
20549 TTGCGATTTACGTATTCTCGTTGCGATTTACAGTTACGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
* *
20589 TTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCG
1 TTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACGCG
* * *
20630 TTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATCGCG
1 TTGCGA-TTTACGTATTCTCGTTGCGAT-TTACAGATA-CGCG
** * * * * *
20671 TTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCG
1 TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
20711 TTGCGATT
1 TTGCGATT
20719 ATGAAAAATT
Statistics
Matches: 147, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 76 0.52
41 69 0.47
42 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACGTATTCTCGTTGCGATTTACAGATACGCG
Found at i:20617 original size:81 final size:81
Alignment explanation
Indices: 20509--20718 Score: 250
Period size: 81 Copynumber: 2.6 Consensus size: 81
20499 CTAAATCACA
* * *
20509 TTGCGA-TTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGC
1 TTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACTCGTTGC
* *
20573 GAT-TTACAG-TTACGCG
66 GATAGT-CAGAAT-CGCG
*
20589 TTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTG
1 TTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGGATACTCGTTG
20654 CGATAGTCAGAATCGCG
65 CGATAGTCAGAATCGCG
* * * * *
20671 TTGCGATTTATATGT-TCG-CGTTGCGATTTTCATATTCGCGTTGCGATT
1 TTGCGATTT-TACGTATTGTCGTTGCGATTTACAGATACGCGTTGCGATT
20719 ATGAAAAATT
Statistics
Matches: 113, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
80 8 0.07
81 62 0.55
82 37 0.33
83 6 0.05
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (81 bp):
TTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACTCGTTGC
GATAGTCAGAATCGCG
Found at i:24693 original size:62 final size:63
Alignment explanation
Indices: 24617--24741 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 63
24607 ACACACTTAT
** *
24617 ATACAAAGCAAAAATAACTTTGGTGTATATTTGATAAATACATATAAATGAATTAAATTCATC
1 ATACAAAGCAAAAATAACAATGCTGTATATTTGATAAATACATATAAATGAATTAAATTCATC
* *
24680 ATAC-AAGTAAAAATAACAATGCTGTATATTTGATAAATACATATAAATGTATTAAATTCATC
1 ATACAAAGCAAAAATAACAATGCTGTATATTTGATAAATACATATAAATGAATTAAATTCATC
24742 CTATATTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 53 0.93
63 4 0.07
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.34
Consensus pattern (63 bp):
ATACAAAGCAAAAATAACAATGCTGTATATTTGATAAATACATATAAATGAATTAAATTCATC
Found at i:24826 original size:59 final size:59
Alignment explanation
Indices: 24642--24826 Score: 162
Period size: 62 Copynumber: 3.1 Consensus size: 59
24632 AACTTTGGTG
* * ** * *
24642 TATATTTGATAAATACATATAAATGAATTAAATTCATCATACAAGTA-AAAATAACAATGCTG
1 TATATTTGATAAATACATATAAATGTATTAAATTCATCATATATTTATGAAA-AA-AAT-C-A
* *
24704 TATATTTGATAAATACATATAAATGTATTAAATTCATCCTATATTTATGAATAAAATCA
1 TATATTTGATAAATACATATAAATGTATTAAATTCATCATATATTTATGAAAAAAATCA
* ** * *
24763 TATATTTGA-AACATTCATATACTTGTATTAAATT-ATTATATATTTGT-AAGAAAAATCA
1 TATATTTGATAA-ATACATATAAATGTATTAAATTCATCATATATTTATGAA-AAAAATCA
24821 TTATAT
1 -TATAT
24827 ATTTTTCAAG
Statistics
Matches: 104, Mismatches: 15, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.02
58 19 0.18
59 33 0.32
60 1 0.01
61 3 0.03
62 44 0.42
63 2 0.02
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.39
Consensus pattern (59 bp):
TATATTTGATAAATACATATAAATGTATTAAATTCATCATATATTTATGAAAAAAATCA
Found at i:28389 original size:23 final size:23
Alignment explanation
Indices: 28363--28415 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
28353 AAACTGCCAA
*
28363 AAAGACAGAGATAAACGTGTCAC
1 AAAGACAGAGATAAACATGTCAC
*
28386 AAAGACAGAGATAAACATGTCAT
1 AAAGACAGAGATAAACATGTCAC
28409 AAAGACA
1 AAAGACA
28416 TAAATATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.15, G:0.19, T:0.13
Consensus pattern (23 bp):
AAAGACAGAGATAAACATGTCAC
Done.