Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009313.1 Hibiscus syriacus cultivar Beakdansim tig00113059_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: 105643
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7326 original size:17 final size:18
Alignment explanation
Indices: 7300--7337 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
7290 ATGTTGTTCA
7300 TTAAAGCATGCATTGCAT
1 TTAAAGCATGCATTGCAT
* *
7318 TTAAA-CATGTATTTCAT
1 TTAAAGCATGCATTGCAT
7335 TTA
1 TTA
7338 GGGAAGTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (18 bp):
TTAAAGCATGCATTGCAT
Found at i:7364 original size:17 final size:17
Alignment explanation
Indices: 7344--7402 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
7334 TTTAGGGAAG
7344 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
7361 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
7377 TAATTCATTCATGCATT
1 TAGTTCATTTATGCATC
7394 TAGTTCATT
1 TAGTTCATT
7403 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:10200 original size:17 final size:17
Alignment explanation
Indices: 10175--10214 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
10165 GTATGTTGTT
*
10175 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
10192 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
10209 CATTTA
1 CATTTA
10215 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:10293 original size:18 final size:18
Alignment explanation
Indices: 10270--10315 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
10260 ATTCATGCAT
10270 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
10288 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
10306 TTAATTCATT
1 TTAGTTCATT
10316 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:13101 original size:17 final size:17
Alignment explanation
Indices: 13076--13115 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
13066 GTATGTTGTT
*
13076 CATTGAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
13093 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
13110 CATTTA
1 CATTTA
13116 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:13194 original size:18 final size:18
Alignment explanation
Indices: 13171--13216 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
13161 AATCATGCAT
13171 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
13189 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
13207 TTAATTCATT
1 TTAGTTCATT
13217 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:16000 original size:17 final size:17
Alignment explanation
Indices: 15975--16014 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
15965 GTATGTTGTT
*
15975 CATTGAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
15992 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
16009 CATTTA
1 CATTTA
16015 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:16093 original size:18 final size:18
Alignment explanation
Indices: 16070--16115 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
16060 AATCATGCAT
16070 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
16088 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
16106 TTATTTCATT
1 TTAGTTCATT
16116 AATCATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:18851 original size:17 final size:17
Alignment explanation
Indices: 18826--18865 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
18816 GTATGTTGTT
*
18826 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
18843 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
18860 CATTTA
1 CATTTA
18866 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:18892 original size:17 final size:17
Alignment explanation
Indices: 18872--18930 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
18862 TTTAGGGAAG
18872 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
18889 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
18905 TAATTCATTCATGCATT
1 TAGTTCATTTATGCATC
18922 TAGTTCATT
1 TAGTTCATT
18931 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:18944 original size:18 final size:18
Alignment explanation
Indices: 18921--18966 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
18911 ATTCATGCAT
18921 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
18939 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
18957 TTATTTCATT
1 TTAGTTCATT
18967 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:21770 original size:18 final size:19
Alignment explanation
Indices: 21747--21782 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21737 TTTCAACAAA
21747 GAAAGAGA-AATAAGAGTT
1 GAAAGAGACAATAAGAGTT
*
21765 GAAAGAGACATTAAGAGT
1 GAAAGAGACAATAAGAGT
21783 GGAGAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.03, G:0.28, T:0.17
Consensus pattern (19 bp):
GAAAGAGACAATAAGAGTT
Found at i:22525 original size:17 final size:17
Alignment explanation
Indices: 22500--22539 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
22490 GTATGTTGTT
*
22500 CATTGAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
22517 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
22534 CATTTA
1 CATTTA
22540 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:25350 original size:17 final size:17
Alignment explanation
Indices: 25325--25364 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
25315 GTATGTTGTT
*
25325 CATTGAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
25342 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
25359 CATTTA
1 CATTTA
25365 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:25439 original size:17 final size:18
Alignment explanation
Indices: 25419--25463 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
25409 AATCATGCAT
25419 TTAGTTCATTGAATAA-G
1 TTAGTTCATTGAATAATG
25436 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAATG
*
25454 TTATTTCATT
1 TTAGTTCATT
25464 AATCAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (18 bp):
TTAGTTCATTGAATAATG
Found at i:28182 original size:17 final size:17
Alignment explanation
Indices: 28157--28196 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
28147 GTATGTTGTT
*
28157 CATTGAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
28174 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
28191 CATTTA
1 CATTTA
28197 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:29533 original size:252 final size:248
Alignment explanation
Indices: 29031--29539 Score: 934
Period size: 252 Copynumber: 2.0 Consensus size: 248
29021 AAAATAAAAA
29031 AAAGG-AAAAAAAAAGAAAATTAAAGAGGGGGCATTCTTTTCATCTTTGAAAAAAATAATCAAGA
1 AAAGGAAAAAAAAAAGAAAATTAAAGAGGGGGCATTCTTTTCATCTTTGAAAAAAATAATCAAGA
29095 AGGTTTCGTATTCGTTCATCGTTTCTTTCATTATCTTTACGATTTCATTGCCTTTTCTCATATTC
66 AGGTTTCGTATTCGTTCATCGTTTCTTTCATTATCTTTACGATTTCATTGCCTTTTCTCATATTC
29160 GTCTTTATTGTAGCCAATTCTTTCTTTACTCACATCATTCTTCCAACCAAGCCCCAAATTATTTC
131 GTCTTTATTGTAGCCAATTCTTTCTTTACT-ACATCATTCTTCCAACCAAGCCCCAAATTATTTC
29225 AGTCGAAGTCTACAAGACACCTTGTAAACCTCGAGGGAGTTCTACAAGAACTTT
195 AGTCGAAGTCTACAAGACACCTTGTAAACCTCGAGGGAGTTCTACAAGAACTTT
29279 AAAGGAAAAAAAAAAGAAAATTTAAAGAGGGGGAGCAATTCTTTTCATCTTTGAAAAAAATAATC
1 AAAGGAAAAAAAAAAGAAAA-TTAAAGA-GGGG-GC-ATTCTTTTCATCTTTGAAAAAAATAATC
29344 AAGAAGGTTTCGTATTCGTTTCATCGTTTCTTTCATTATCTTTACGATTTCATTGCCTTTTCTCA
62 AAGAAGGTTTCGTATTCG-TTCATCGTTTCTTTCATTATCTTTACGATTTCATTGCCTTTTCTCA
29409 TATTCGTTCTTTATTGTAGCCAATTCTTTCTTTACT-CATCATTCTTCCAACCAAG-CCCAAATT
126 TATTCG-TCTTTATTGTAGCCAATTCTTTCTTTACTACATCATTCTTCCAACCAAGCCCCAAATT
29472 ATTTCAGTCGAAGTCTACAAGACACCTTGTAAACCTCGAGGGAGTTCTACAAGAACTTT
190 ATTTCAGTCGAAGTCTACAAGACACCTTGTAAACCTCGAGGGAGTTCTACAAGAACTTT
29531 AAAGGAAAA
1 AAAGGAAAA
29540 CAAGAGCGGT
Statistics
Matches: 254, Mismatches: 0, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
248 5 0.02
249 14 0.06
250 7 0.03
251 4 0.02
252 78 0.31
253 65 0.26
254 52 0.20
255 29 0.11
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (248 bp):
AAAGGAAAAAAAAAAGAAAATTAAAGAGGGGGCATTCTTTTCATCTTTGAAAAAAATAATCAAGA
AGGTTTCGTATTCGTTCATCGTTTCTTTCATTATCTTTACGATTTCATTGCCTTTTCTCATATTC
GTCTTTATTGTAGCCAATTCTTTCTTTACTACATCATTCTTCCAACCAAGCCCCAAATTATTTCA
GTCGAAGTCTACAAGACACCTTGTAAACCTCGAGGGAGTTCTACAAGAACTTT
Found at i:31242 original size:17 final size:17
Alignment explanation
Indices: 31217--31256 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
31207 GTATGTTGTT
*
31217 CATTGAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
31234 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
31251 CATTTA
1 CATTTA
31257 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:31335 original size:18 final size:18
Alignment explanation
Indices: 31312--31357 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
31302 AATCATGCAT
31312 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
31330 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
31348 TTATTTCATT
1 TTAGTTCATT
31358 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:34121 original size:17 final size:17
Alignment explanation
Indices: 34101--34159 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
34091 TTTAGGGAAG
34101 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
34118 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
34134 TAATTCATTCATGCATT
1 TAGTTCATTTATGCATC
34151 TAGTTCATT
1 TAGTTCATT
34160 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:34173 original size:18 final size:18
Alignment explanation
Indices: 34150--34195 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
34140 ATTCATGCAT
34150 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
34168 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
34186 TTATTTCATT
1 TTAGTTCATT
34196 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:37695 original size:17 final size:17
Alignment explanation
Indices: 37670--37709 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
37660 GTATATTGTT
*
37670 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
37687 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
37704 CATTTA
1 CATTTA
37710 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:39240 original size:22 final size:22
Alignment explanation
Indices: 39215--39256 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
39205 CAATTCATTT
39215 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
39237 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
39257 CCAGCACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:42416 original size:12 final size:12
Alignment explanation
Indices: 42399--42423 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42389 AACAAGACAC
42399 TTACGGCTATCT
1 TTACGGCTATCT
42411 TTACGGCTATCT
1 TTACGGCTATCT
42423 T
1 T
42424 AGCCACACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TTACGGCTATCT
Found at i:45220 original size:22 final size:21
Alignment explanation
Indices: 45187--45227 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
45177 TTTTTCAAAA
*
45187 CAAAAAACAAAAAAAAAGAGG
1 CAAAAAAAAAAAAAAAAGAGG
45208 CAAAAAAGAAAAAAAAAAGA
1 CAAAAAA-AAAAAAAAAAGA
45228 AAAAAAAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAAAAAAAAGAGG
Found at i:45223 original size:11 final size:11
Alignment explanation
Indices: 45195--45234 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
45185 AACAAAAAAC
45195 AAAAAAAAAGA
1 AAAAAAAAAGA
***
45206 GGCAAAAAAGA
1 AAAAAAAAAGA
45217 AAAAAAAAAGA
1 AAAAAAAAAGA
45228 AAAAAAA
1 AAAAAAA
45235 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:45230 original size:29 final size:28
Alignment explanation
Indices: 45183--45241 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
45173 TATTTTTTTC
* * *
45183 AAAACAAAAAACAAAAAAAAAGAGGCAA
1 AAAACAAAAAAAAAAAAAAAAAAGCCAA
*
45211 AAAAGAAAAAAAAAAGAAAAAAAAGCCAA
1 AAAACAAAAAAAAAA-AAAAAAAAGCCAA
45240 AA
1 AA
45242 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.81, C:0.08, G:0.10, T:0.00
Consensus pattern (28 bp):
AAAACAAAAAAAAAAAAAAAAAAGCCAA
Found at i:52064 original size:9 final size:9
Alignment explanation
Indices: 52050--52074 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52040 TCGGGTTAGT
52050 AAAAAAATA
1 AAAAAAATA
52059 AAAAAAATA
1 AAAAAAATA
52068 AAAAAAA
1 AAAAAAA
52075 AGAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:56592 original size:20 final size:20
Alignment explanation
Indices: 56567--56617 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
56557 TGATTATGGT
56567 GATGTGAGCTATGTTTGAAG
1 GATGTGAGCTATGTTTGAAG
56587 GATGTGAGCTATGTTTGAAG
1 GATGTGAGCTATGTTTGAAG
* *
56607 GTTATGAGCTA
1 GATGTGAGCTA
56618 ATTATATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.06, G:0.33, T:0.35
Consensus pattern (20 bp):
GATGTGAGCTATGTTTGAAG
Found at i:61437 original size:17 final size:17
Alignment explanation
Indices: 61412--61451 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
61402 GTATGTTGTT
*
61412 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
61429 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
61446 CATTTA
1 CATTTA
61452 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:61530 original size:18 final size:18
Alignment explanation
Indices: 61507--61545 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
61497 ATTCATGCAT
61507 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
61525 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
61543 TTA
1 TTA
61546 TTTTATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:68562 original size:17 final size:17
Alignment explanation
Indices: 68531--68583 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
68521 TCTTTTTGAA
*
68531 TTCTTTTTCTT-TTCTT
1 TTCTTCTTCTTCTTCTT
68547 TTCTTCTTCTTCTTCTT
1 TTCTTCTTCTTCTTCTT
*
68564 TT-TGTCTTTTTCTTTCTT
1 TTCT-TCTTCTTC-TTCTT
68582 TT
1 TT
68584 TGCACTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 11 0.34
17 14 0.44
18 7 0.22
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (17 bp):
TTCTTCTTCTTCTTCTT
Found at i:73182 original size:18 final size:17
Alignment explanation
Indices: 73141--73182 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
73131 GCAAAGGAAA
73141 AAGAAACACTCAAAAAG
1 AAGAAACACTCAAAAAG
*
73158 ATTGAAAGCACTCAAAAAG
1 A-AGAAA-CACTCAAAAAG
73177 AAGAAA
1 AAGAAA
73183 AAGAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 8 0.38
19 12 0.57
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (17 bp):
AAGAAACACTCAAAAAG
Found at i:75963 original size:11 final size:13
Alignment explanation
Indices: 75931--75960 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
75921 TGGCCAAAGA
75931 TGAAAAGGTATGT
1 TGAAAAGGTATGT
75944 TGAAAAGGTATG-
1 TGAAAAGGTATGT
75956 TGAAA
1 TGAAA
75961 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:102988 original size:7 final size:8
Alignment explanation
Indices: 102969--103005 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
102959 GTTTGCAATT
*
102969 TTTTTGAA
1 TTTTTGGA
102977 TTTTTGGA
1 TTTTTGGA
102985 TTTTTGGA
1 TTTTTGGA
*
102993 TTTTTGGC
1 TTTTTGGA
103001 TTTTT
1 TTTTT
103006 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.11, C:0.03, G:0.19, T:0.68
Consensus pattern (8 bp):
TTTTTGGA
Found at i:103005 original size:1 final size:1
Alignment explanation
Indices: 103001--103038 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
102991 GATTTTTGGC
* *
103001 TTTTTTTTTTTTTTTTTTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
103039 GAAAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (1 bp):
T
Found at i:103015 original size:11 final size:11
Alignment explanation
Indices: 103001--103038 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
102991 GATTTTTGGC
103001 TTTTTTTTT-T
1 TTTTTTTTTGT
103011 TTTTTTTTTGT
1 TTTTTTTTTGT
103022 TTTTTTTTTGT
1 TTTTTTTTTGT
103033 TTTTTT
1 TTTTTT
103039 GAAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:103018 original size:22 final size:20
Alignment explanation
Indices: 103001--103038 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
102991 GATTTTTGGC
*
103001 TTTTTTTTTTTTTTTTTTTG
1 TTTTTTTTTTGTTTTTTTTG
103021 TTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTGTTTTTTT
103039 GAAAAAAAAT
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:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (20 bp):
TTTTTTTTTTGTTTTTTTTG
Done.