Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004864.1 Hibiscus syriacus cultivar Beakdansim tig00010970_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: 79539
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:15358 original size:14 final size:14
Alignment explanation
Indices: 15339--15365 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15329 GATCAGAACT
15339 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
15353 TCAAGATTCCAGA
1 TCAAGATTCCAGA
15366 CATGCAACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:15853 original size:43 final size:43
Alignment explanation
Indices: 15733--15854 Score: 181
Period size: 43 Copynumber: 2.8 Consensus size: 43
15723 ATGAAGGGGC
* * * * *
15733 CATCCGCGATTTCAACCCCATGACGGAGGATATCATACCCATA
1 CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCCATA
*
15776 CATCCACGATTTCAACTCCACGATAGAGGATATCGTACCCATA
1 CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCCATA
*
15819 CATCCACGATTTCAACTCCACGATGGAAGATATCGT
1 CATCCACGATTTCAACTCCACGATGGAGGATATCGT
15855 GCTATTTGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCCATA
Found at i:16093 original size:110 final size:110
Alignment explanation
Indices: 15896--16099 Score: 300
Period size: 110 Copynumber: 1.9 Consensus size: 110
15886 GCTTCCCAGT
* * *
15896 TTCAGAGCCAATTTTAATTTCACAACGAATGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAATGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* *
15961 TAACAAATGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
66 CAACAAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
* * * *
16006 TTCAGAGTCAATTTCAACTTCACAGCGAATGATATTAGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAATGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* * *
16071 CAGCGAAGGGGCGACTGGTTGTCAACAAA
66 CAACAAAGGGGCGACTGATTGTCAACAAA
16100 TAATTTCCCA
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
110 82 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAATGATATTAGACTCAAGACAACACAAGCTCAACTTCA
CAACAAAGGGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCA
Found at i:16903 original size:13 final size:13
Alignment explanation
Indices: 16885--16914 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16875 TTTGTTATTA
16885 ATATTGTATAATT
1 ATATTGTATAATT
16898 ATATTGTATAATT
1 ATATTGTATAATT
16911 ATAT
1 ATAT
16915 ATATAATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
ATATTGTATAATT
Found at i:18470 original size:25 final size:25
Alignment explanation
Indices: 18432--18481 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
18422 TTCCCTACTT
** *
18432 CTGTACTTGGTTGCCTGTCTCTAAG
1 CTGTACTTCCTTGCCTGTATCTAAG
18457 CTGTACTTCCTTGCCTGTATCTAAG
1 CTGTACTTCCTTGCCTGTATCTAAG
18482 TAGGTACGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (25 bp):
CTGTACTTCCTTGCCTGTATCTAAG
Found at i:19878 original size:2 final size:2
Alignment explanation
Indices: 19835--19866 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19825 CTGTACACAC
*
19835 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19867 TTTATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19878 original size:17 final size:16
Alignment explanation
Indices: 19855--19902 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
19845 ATATATATAT
19855 ATATATAAATATTTTA
1 ATATATAAATATTTTA
* **
19871 TTTATATACCTATTATTA
1 -ATATATAAATATT-TTA
19889 ATATATAAATATTT
1 ATATATAAATATTT
19903 AATTATTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
16 1 0.04
17 20 0.83
18 3 0.12
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATATAAATATTTTA
Found at i:19959 original size:2 final size:2
Alignment explanation
Indices: 19952--19980 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19942 ATCTTATAAT
19952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19981 TTCCATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20074 original size:23 final size:23
Alignment explanation
Indices: 20042--20086 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
20032 TTTTTACCTT
20042 TATATATATAC-ATTGTTTTTTTA
1 TATATATATACTATT-TTTTTTTA
*
20065 TATATCTATACTATTTTTTTTT
1 TATATATATACTATTTTTTTTT
20087 CTTTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (23 bp):
TATATATATACTATTTTTTTTTA
Found at i:20203 original size:13 final size:13
Alignment explanation
Indices: 20172--20213 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
20162 TCTATTTATT
* *
20172 TTTATTTTATCTA
1 TTTATTTTGTTTA
*
20185 TCTATTTTGTTTA
1 TTTATTTTGTTTA
20198 TTTATTTTGTTTA
1 TTTATTTTGTTTA
20211 TTT
1 TTT
20214 TTCTATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTATTTTGTTTA
Found at i:20242 original size:26 final size:25
Alignment explanation
Indices: 20194--20247 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
20184 ATCTATTTTG
* *
20194 TTTATTTATTTTGTTTATTTTTCTAT
1 TTTATTCATTTTCTTTATTTTTC-AT
20220 TTTATTCATGTTTCTTTA-TTTTCAT
1 TTTATTCAT-TTTCTTTATTTTTCAT
20245 TTT
1 TTT
20248 GCTTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 13 0.52
27 7 0.28
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTATTCATTTTCTTTATTTTTCAT
Found at i:21514 original size:21 final size:20
Alignment explanation
Indices: 21463--21514 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
21453 TTTTCCCAAT
*
21463 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
21483 TCGAAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
21504 TCGCAATGCGA
1 TCGCAATGCGA
21515 TACTGACTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:21578 original size:20 final size:20
Alignment explanation
Indices: 21555--21596 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21545 TCACAACGAA
*
21555 ATACTTACTTTAGCAACACG
1 ATACTGACTTTAGCAACACG
* *
21575 ATACTGACTTTCGCAACGCG
1 ATACTGACTTTAGCAACACG
21595 AT
1 AT
21597 TTACTTAGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (20 bp):
ATACTGACTTTAGCAACACG
Found at i:22174 original size:19 final size:19
Alignment explanation
Indices: 22150--22194 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
22140 GCAACGAGAT
*
22150 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
22169 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
22188 AATCGCA
1 AATCGCA
22195 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:22212 original size:19 final size:19
Alignment explanation
Indices: 22190--22360 Score: 174
Period size: 19 Copynumber: 9.1 Consensus size: 19
22180 GAAACCAAAA
*
22190 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22209 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22228 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22247 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
22267 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
22283 TAGTCG-T--GATAGTCATT
1 TCG-CGTTGCGATTTTCATT
**
22300 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
22319 TCCGCATTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
22339 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
22359 TC
1 TC
22361 AACCAAAAGA
Statistics
Matches: 131, Mismatches: 11, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
14 6 0.05
16 5 0.04
17 5 0.04
19 65 0.50
20 49 0.37
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:22267 original size:39 final size:38
Alignment explanation
Indices: 22190--22360 Score: 174
Period size: 39 Copynumber: 4.6 Consensus size: 38
22180 GAAACCAAAA
*
22190 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
22228 TCGCGTTGCGATTTTCATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
22267 TCGCGTTGCGATTGTC---TAGTCG-T--GATAGTCATT
1 TCGCGTTGCGATTTTCATTTCG-CGTTGCGATTTTCATT
** * *
22300 TCGCGTTGCGATAGTCATTTCCGCATTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTT-CGCGTTGCGATTTTCATT
*
22339 ATCTCGTTGCGATTTTCATTTC
1 -TCGCGTTGCGATTTTCATTTC
22361 AACCAAAAGA
Statistics
Matches: 110, Mismatches: 13, Indels: 19
0.77 0.09 0.13
Matches are distributed among these distances:
33 23 0.21
35 1 0.01
36 5 0.05
37 3 0.03
38 22 0.20
39 39 0.35
40 17 0.15
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:22337 original size:20 final size:19
Alignment explanation
Indices: 22295--22360 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
22285 GTCGTGATAG
**
22295 TCATTT-CGCGTTGCGATAG
1 TCATTTCCGC-TTGCGATTC
22314 TCATTTCCGCATTGCGATTC
1 TCATTTCCGC-TTGCGATTC
*
22334 TCATTATCTCG-TTGCGATTT
1 TCATT-TC-CGCTTGCGATTC
22354 TCATTTC
1 TCATTTC
22361 AACCAAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 8 0.20
20 28 0.70
21 2 0.05
22 2 0.05
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (19 bp):
TCATTTCCGCTTGCGATTC
Found at i:24421 original size:42 final size:42
Alignment explanation
Indices: 24361--24483 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
24351 GCCCGACTCG
* * *
24361 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
24403 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
24445 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
24484 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:24441 original size:21 final size:21
Alignment explanation
Indices: 24417--24483 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
24407 TCATTCCTCG
24417 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
24438 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
24459 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
24480 AGAG
1 AGAG
24484 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:25861 original size:14 final size:14
Alignment explanation
Indices: 25842--25877 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
25832 ATTGTTTAAT
25842 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
25856 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
25870 TGATTTGT
1 TGATTTGT
25878 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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:26078 original size:19 final size:19
Alignment explanation
Indices: 26056--26173 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
26046 CGAAATTAAA
26056 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
26075 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
26090 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
26108 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
26123 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
26141 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
26160 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
26174 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:26102 original size:33 final size:33
Alignment explanation
Indices: 26060--26153 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
26050 ATTAAATTCG
26060 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
26093 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
26126 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
26154 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:28465 original size:12 final size:12
Alignment explanation
Indices: 28448--28472 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28438 TCTTCGGGGA
28448 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28460 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28472 C
1 C
28473 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:29784 original size:20 final size:20
Alignment explanation
Indices: 29759--29809 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
29749 ATTCATTTGA
*
29759 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
29779 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
29799 TTATCGCAACG
1 CTATCGCAACG
29810 AGAATATCGC
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:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:29859 original size:14 final size:15
Alignment explanation
Indices: 29839--29911 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
29829 TGAAAATCGC
29839 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
29854 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
29871 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
29889 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
29905 -TTGCGAT
1 ATTGCGAT
29912 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:29876 original size:19 final size:19
Alignment explanation
Indices: 29835--29901 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
29825 GAAATGAAAA
29835 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
29851 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29868 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
29886 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
29902 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:30037 original size:14 final size:14
Alignment explanation
Indices: 30018--30054 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
30008 CATCAATTAA
30018 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
30032 ACAAATCATCTTTT
1 ACAAATCAACATTT
30046 ACAAATCAA
1 ACAAATCAA
30055 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:31517 original size:42 final size:42
Alignment explanation
Indices: 31466--31547 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
31456 TTCAACGATG
* * *
31466 ATAGTGGCCTCTTGAACGGTGGGGGGGGAATCTTGAGGGAGA
1 ATAGGGGCCTCTTGAACGATGGGAGGGGAATCTTGAGGGAGA
* *
31508 ATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGGGA
1 ATAGGGGCCTCTTGAACGATGGGAGGGGAATCTTGAGGGA
31548 TGACCGGTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.13, G:0.43, T:0.22
Consensus pattern (42 bp):
ATAGGGGCCTCTTGAACGATGGGAGGGGAATCTTGAGGGAGA
Found at i:31951 original size:20 final size:19
Alignment explanation
Indices: 31916--31982 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
31906 GAAACTTAAA
31916 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
31935 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
31955 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
31974 ATCGCAACG
1 ATCGCAACG
31983 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:31990 original size:14 final size:14
Alignment explanation
Indices: 31971--32028 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
31961 ATGCGAAATG
31971 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
31985 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
32001 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
32017 AAAATCGCAACG
1 AAAATCGCAACG
32029 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:32013 original size:32 final size:33
Alignment explanation
Indices: 31955--32033 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
31945 GGAAATGGCT
*
31955 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
31988 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
32020 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
32034 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:32062 original size:19 final size:18
Alignment explanation
Indices: 32040--32103 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
32030 GAAACACAAA
32040 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* *
32059 TCGCGTTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
32075 TCG--TTGCGATTTTTATT
1 TCGCATTGCGA-TTTTATT
32092 TCGCATTGCGAT
1 TCGCATTGCGAT
32104 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
14 6 0.16
16 7 0.19
17 4 0.11
18 4 0.11
19 16 0.43
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:32111 original size:19 final size:20
Alignment explanation
Indices: 32089--32131 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
32079 TGCGATTTTT
32089 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
32108 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
32128 ATTT
1 ATTT
32132 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:32122 original size:20 final size:20
Alignment explanation
Indices: 32097--32142 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
32087 TTATTTCGCA
32097 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
32117 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
32137 TTGCGA
1 TTGCGA
32143 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:32640 original size:18 final size:18
Alignment explanation
Indices: 32614--32658 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
32604 GTCGATCAGA
32614 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGTGAGG
* *
32632 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTAGGTGAGG
32650 TGATGGCTC
1 TGATGGCTC
32659 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.42, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTAGGTGAGG
Found at i:34003 original size:20 final size:20
Alignment explanation
Indices: 33978--34015 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33968 AATAGTTTCT
33978 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
33998 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
34016 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:34295 original size:22 final size:22
Alignment explanation
Indices: 34270--34313 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34260 GATTTAGATA
34270 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
34292 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
34314 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:34526 original size:20 final size:20
Alignment explanation
Indices: 34501--34594 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
34491 GATTATGTAT
34501 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
34521 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
34541 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
34562 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
34582 TATCGCATTGCGA
1 TATCGCGTTGCGA
34595 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:34595 original size:20 final size:20
Alignment explanation
Indices: 34481--34595 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
34471 CGCTTTGAAA
*
34481 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
34502 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
34522 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
34542 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
34563 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
34583 ATCGCATTGCGAT
1 ATCGCATTGCGAT
34596 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:34614 original size:41 final size:41
Alignment explanation
Indices: 34523--34657 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
34513 AAAGTCAGTA
* * * ** *
34523 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
34563 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
34605 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
34646 TCGCGTTGCGAT
1 TCGCGTTGCGAT
34658 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:34628 original size:20 final size:20
Alignment explanation
Indices: 34584--34676 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
34574 ATAGTCAGTA
* **
34584 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
34605 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
34625 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
34646 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
34666 TCGCATTGCGA
1 TCGCATTGCGA
34677 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:34658 original size:41 final size:41
Alignment explanation
Indices: 34584--34679 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
34574 ATAGTCAGTA
*
34584 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
34625 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
34666 TCGCATTGCGAATT
1 TCGCATTGCGAATT
34680 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:42911 original size:22 final size:22
Alignment explanation
Indices: 42885--42927 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
42875 GACGACACTA
42885 ACTTGATGTCTGATGATCTCCG
1 ACTTGATGTCTGATGATCTCCG
42907 ACTTGATGTCTGATGATCTCC
1 ACTTGATGTCTGATGATCTCC
42928 TTACTCAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (22 bp):
ACTTGATGTCTGATGATCTCCG
Found at i:43636 original size:59 final size:59
Alignment explanation
Indices: 43217--43609 Score: 652
Period size: 59 Copynumber: 6.7 Consensus size: 59
43207 TACCATACAA
* * * *
43217 AAATTCATACACTTAGTATGAATTTCATATCATTTTAGCATAC-AAGGTGCCCAATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAA-GTGCCCTATACGG
*
43276 AAATTCATACACTTAGTATGAATTTCTTAACATTTT----CACGAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
*
43331 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGA
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
43390 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* **
43449 AAATTCATACACTTAGTATGAATTTCTTCACATTTTAGCACACGAAGTGCCCTATACAT
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
43508 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
*
43567 AAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACAC
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
43610 TTAGTGCCAT
Statistics
Matches: 314, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
55 49 0.16
56 2 0.01
59 263 0.84
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
Found at i:43983 original size:22 final size:21
Alignment explanation
Indices: 43953--44010 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
43943 ATCAATACTT
43953 CTACCATGGTATCGATACTACC
1 CTACCATGGTATCGATACT-CC
* *
43975 CTACTATGGTATTGATACTCC
1 CTACCATGGTATCGATACTCC
*
43996 CTTCCA--GTATCGATA
1 CTACCATGGTATCGATA
44011 TCAAAATTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 8 0.26
21 6 0.19
22 17 0.55
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (21 bp):
CTACCATGGTATCGATACTCC
Found at i:44057 original size:20 final size:21
Alignment explanation
Indices: 44032--44089 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
44022 TTCAATGTGG
*
44032 CATGGTATCAATACCCT-TAC
1 CATGGTATCGATACCCTATAC
*
44052 CATGGTATCGATACTACTATAC
1 CATGGTATCGATAC-CCTATAC
*
44074 TATGGTATCGATACCC
1 CATGGTATCGATACCC
44090 CCTTCTGGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 13 0.41
21 3 0.09
22 16 0.50
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (21 bp):
CATGGTATCGATACCCTATAC
Found at i:44081 original size:95 final size:95
Alignment explanation
Indices: 43941--44164 Score: 306
Period size: 95 Copynumber: 2.4 Consensus size: 95
43931 TGGTTCTTCA
* * * *
43941 GTATCAATA-CTTCTACCATGGTATCGATACTACCCTACTATGGTATTGATACTCCCTTCCAGTA
1 GTATCAATACCCT-TACCATGGTATCGATACTACCATACTATGGTATCGATACCCCCTTCCAGTA
* *
44005 TCGATATCAAAATTAGATTCAATGTGGCATG
65 TCGATACCAAAATTAGATTCAATGTGACATG
* **
44036 GTATCAATACCCTTACCATGGTATCGATACTACTATACTATGGTATCGATACCCCCTTCTGGTAT
1 GTATCAATACCCTTACCATGGTATCGATACTACCATACTATGGTATCGATACCCCCTTCCAGTAT
* * * *
44101 CGATACCAAAATTAGGTTCGATGTTACCTG
66 CGATACCAAAATTAGATTCAATGTGACATG
*
44131 GTATCAATACCCTTACCATGGTACCGATACTACC
1 GTATCAATACCCTTACCATGGTATCGATACTACC
44165 TCGTTCGTAC
Statistics
Matches: 113, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
95 111 0.98
96 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (95 bp):
GTATCAATACCCTTACCATGGTATCGATACTACCATACTATGGTATCGATACCCCCTTCCAGTAT
CGATACCAAAATTAGATTCAATGTGACATG
Found at i:45015 original size:23 final size:24
Alignment explanation
Indices: 44973--45021 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
44963 CCTAAATCGA
44973 TATTTAGGGAATTACATATTTATT
1 TATTTAGGGAATTACATATTTATT
**
44997 TATTTA-GGAATTAGTTATTTATT
1 TATTTAGGGAATTACATATTTATT
45020 TA
1 TA
45022 GAACTCTCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (24 bp):
TATTTAGGGAATTACATATTTATT
Found at i:48231 original size:56 final size:56
Alignment explanation
Indices: 48145--48255 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
48135 TAGAATATTT
48145 GAAGTGCACAATTTTGAGCGAAGGATATGTATTGTCAATTATTATTTCAAACAAGA
1 GAAGTGCACAATTTTGAGCGAAGGATATGTATTGTCAATTATTATTTCAAACAAGA
48201 GAAGTGCACAATTTTGAGCGAAGGATATGTATTGTCAATTATTATTTCAAACAAG
1 GAAGTGCACAATTTTGAGCGAAGGATATGTATTGTCAATTATTATTTCAAACAAG
48256 TTAGAAAAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (56 bp):
GAAGTGCACAATTTTGAGCGAAGGATATGTATTGTCAATTATTATTTCAAACAAGA
Found at i:48738 original size:21 final size:20
Alignment explanation
Indices: 48714--48758 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
48704 CCTTTATTTC
*
48714 GAATAAGCTTGATTTTCTGTT
1 GAATAAGCTTGAATTTC-GTT
*
48735 GAAT-ATCTTGAATTTCGTT
1 GAATAAGCTTGAATTTCGTT
48754 GAATA
1 GAATA
48759 TCTTAGAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (20 bp):
GAATAAGCTTGAATTTCGTT
Found at i:48756 original size:19 final size:20
Alignment explanation
Indices: 48721--48767 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
48711 TTCGAATAAG
*
48721 CTTGATTTTCTGTTGAATAT
1 CTTGAATTTCTGTTGAATAT
48741 CTTGAATTTC-GTTGAATAT
1 CTTGAATTTCTGTTGAATAT
48760 CTTAGAAT
1 CTT-GAAT
48768 GCCATGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTGAATTTCTGTTGAATAT
Found at i:49330 original size:18 final size:19
Alignment explanation
Indices: 49307--49354 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
49297 AATGTGTTCG
49307 AAAAGAAAAAAAATGAA-A
1 AAAAGAAAAAAAATGAAGA
**
49325 AAAAG-AAAAATGTGAAGA
1 AAAAGAAAAAAAATGAAGA
49343 AAAAGAAAAAAA
1 AAAAGAAAAAAA
49355 TGGTTGAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 11 0.44
19 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (19 bp):
AAAAGAAAAAAAATGAAGA
Found at i:50293 original size:25 final size:25
Alignment explanation
Indices: 50253--50302 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
50243 ATTTTAGTTG
*
50253 ATTAGATTATTATATTTTATTTAGAA
1 ATTAGATTATTATA-TTTACTTAGAA
*
50279 ATTAG-TTATTTTATTTACTTAGAA
1 ATTAGATTATTATATTTACTTAGAA
50303 CTCTCGAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 7 0.32
26 5 0.23
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (25 bp):
ATTAGATTATTATATTTACTTAGAA
Found at i:51438 original size:43 final size:45
Alignment explanation
Indices: 51377--51490 Score: 196
Period size: 45 Copynumber: 2.6 Consensus size: 45
51367 TTTATCTTGT
51377 CATGGTAGTGAGTAAGGTGAGTAAAGCCTTA-TT-TACACATTGC
1 CATGGTAGTGAGTAAGGTGAGTAAAGCCTTATTTATACACATTGC
51420 CATGGTAGTGAGTAAGGTGAGTAAAGCCTTATTTATACACATTGC
1 CATGGTAGTGAGTAAGGTGAGTAAAGCCTTATTTATACACATTGC
* *
51465 CATGGTAATGAGTAAGGTGATTAAAG
1 CATGGTAGTGAGTAAGGTGAGTAAAG
51491 TCGACTATAA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
43 31 0.46
44 2 0.03
45 34 0.51
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (45 bp):
CATGGTAGTGAGTAAGGTGAGTAAAGCCTTATTTATACACATTGC
Found at i:51763 original size:17 final size:18
Alignment explanation
Indices: 51736--51774 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
51726 TCCACCTTTG
51736 TCTTATCTTTTTTCTTCA
1 TCTTATCTTTTTTCTTCA
*
51754 TCTT-TCTTTTTTCTTCT
1 TCTTATCTTTTTTCTTCA
51771 TCTT
1 TCTT
51775 CATTCTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (18 bp):
TCTTATCTTTTTTCTTCA
Found at i:52279 original size:20 final size:20
Alignment explanation
Indices: 52251--52289 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52241 TTATGGGTTT
*
52251 TAGTGTCAACATTGTTCATG
1 TAGTATCAACATTGTTCATG
*
52271 TAGTATCAATATTGTTCAT
1 TAGTATCAACATTGTTCAT
52290 ATTCTGGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TAGTATCAACATTGTTCATG
Found at i:52390 original size:20 final size:20
Alignment explanation
Indices: 52364--52412 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
52354 GAGGGTAAAA
* *
52364 GTATCAATACTAGA-GGTTG
1 GTATCAATACCAGATGCTTG
*
52383 GATATCAACACCAGATGCTTG
1 G-TATCAATACCAGATGCTTG
52404 GTATCAATA
1 GTATCAATA
52413 TTTGAAGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.75
21 5 0.21
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (20 bp):
GTATCAATACCAGATGCTTG
Found at i:60324 original size:2 final size:2
Alignment explanation
Indices: 60270--60310 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
60260 CATAATATTT
60270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60311 GTACGCATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61993 original size:21 final size:21
Alignment explanation
Indices: 61967--62022 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
61957 TGTTATATGT
61967 GGTCCTTCGGGACATCTACAG
1 GGTCCTTCGGGACATCTACAG
61988 GGTCCTTCGGGACATCTACAG
1 GGTCCTTCGGGACATCTACAG
*
62009 GGTCCTTCGAGACA
1 GGTCCTTCGGGACA
62023 GTTTTACATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.23
Consensus pattern (21 bp):
GGTCCTTCGGGACATCTACAG
Found at i:64598 original size:22 final size:22
Alignment explanation
Indices: 64572--64616 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
64562 AAAAAATTTG
64572 AAAAT-GAAAATTATTTTCTAAA
1 AAAATAGAAAA-TATTTTCTAAA
64594 AAAATAGAAAATATTTTCTAAA
1 AAAATAGAAAATATTTTCTAAA
64616 A
1 A
64617 CCAAACATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAATAGAAAATATTTTCTAAA
Found at i:67697 original size:7 final size:7
Alignment explanation
Indices: 67685--67709 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
67675 ACTAATTCAC
67685 AAATCCA
1 AAATCCA
67692 AAATCCA
1 AAATCCA
67699 AAATCCA
1 AAATCCA
67706 AAAT
1 AAAT
67710 TTAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATCCA
Found at i:68029 original size:28 final size:27
Alignment explanation
Indices: 67975--68028 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
67965 CTATTAGATT
*
67975 TATGGGATTTGAGGTATTTGTTAAAAA
1 TATGAGATTTGAGGTATTTGTTAAAAA
68002 TATGAGATTTGAGGT-TATTGTTAAAAA
1 TATGAGATTTGAGGTAT-TTGTTAAAAA
68029 AAATCTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (27 bp):
TATGAGATTTGAGGTATTTGTTAAAAA
Found at i:69629 original size:2 final size:2
Alignment explanation
Indices: 69622--69647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69612 ATAGGTTTGC
69622 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
69648 CTACAGTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69675 original size:19 final size:19
Alignment explanation
Indices: 69651--69691 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
69641 TATATATCTA
**
69651 CAGTCCCATCGGATGCACT
1 CAGTCCCATAAGATGCACT
69670 CAGTCCCATAAGATGCACT
1 CAGTCCCATAAGATGCACT
69689 CAG
1 CAG
69692 CAAGTGCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.20
Consensus pattern (19 bp):
CAGTCCCATAAGATGCACT
Found at i:69818 original size:2 final size:2
Alignment explanation
Indices: 69811--69844 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
69801 ATTCTTAAAT
69811 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
69845 GTCGTAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.