Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004613.1 Hibiscus syriacus cultivar Beakdansim tig00010318_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: 50078
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:6534 original size:17 final size:18
Alignment explanation
Indices: 6512--6545 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6502 TTGAAAGGTC
*
6512 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
6529 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
6546 ATAGAATGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:9854 original size:3 final size:3
Alignment explanation
Indices: 9846--9875 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
9836 ATGTAATTTG
9846 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
9876 TTTAATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:10367 original size:44 final size:44
Alignment explanation
Indices: 10304--10396 Score: 168
Period size: 44 Copynumber: 2.1 Consensus size: 44
10294 CTTATACCCG
* *
10304 ACCCCATTCTGCCTTGATAATTTTTAGTTTTTCTCCCATCTCCA
1 ACCCCATTCTACCTTGATAATATTTAGTTTTTCTCCCATCTCCA
10348 ACCCCATTCTACCTTGATAATATTTAGTTTTTCTCCCATCTCCA
1 ACCCCATTCTACCTTGATAATATTTAGTTTTTCTCCCATCTCCA
10392 ACCCC
1 ACCCC
10397 TCTTGACCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.20, C:0.34, G:0.05, T:0.40
Consensus pattern (44 bp):
ACCCCATTCTACCTTGATAATATTTAGTTTTTCTCCCATCTCCA
Found at i:13159 original size:18 final size:18
Alignment explanation
Indices: 13138--13180 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
13128 TTATTATTGA
13138 TATTATTATTTCTT-TTTT
1 TATTATTATTT-TTCTTTT
13156 TATT-TATATTTTTCTTTT
1 TATTAT-TATTTTTCTTTT
13174 TATTATT
1 TATTATT
13181 TTTGCAGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.14
18 18 0.82
19 1 0.05
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTATTATTTTTCTTTT
Found at i:13174 original size:21 final size:21
Alignment explanation
Indices: 13141--13181 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13131 TTATTGATAT
*
13141 TATTATTTCTTTTTTTATTTA
1 TATTATTTCTTTTATTATTTA
13162 TATT-TTTCTTTTTATTATTT
1 TATTATTTC-TTTTATTATTT
13182 TTGCAGGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (21 bp):
TATTATTTCTTTTATTATTTA
Found at i:25144 original size:19 final size:20
Alignment explanation
Indices: 25120--25170 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
25110 AATGACCAAT
25120 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
25139 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
25159 AAAATCGCAACG
1 AAAATCGCAACG
25171 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:25164 original size:20 final size:20
Alignment explanation
Indices: 25120--25437 Score: 165
Period size: 20 Copynumber: 15.6 Consensus size: 20
25110 AATGACCAAT
* *
25120 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
25139 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
25159 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
25179 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
25199 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
25220 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
25243 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
25263 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
25283 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
25303 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
25326 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
25346 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
25366 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
25386 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
25406 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
25426 AAAATCGCAACG
1 AAAATCGCAACG
25438 TTGAAAATAA
Statistics
Matches: 246, Mismatches: 41, Indels: 23
0.79 0.13 0.07
Matches are distributed among these distances:
19 17 0.07
20 186 0.76
21 14 0.06
23 29 0.12
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:25298 original size:40 final size:40
Alignment explanation
Indices: 25245--25435 Score: 238
Period size: 40 Copynumber: 4.7 Consensus size: 40
25235 TTTAGAAGAA
* * * *
25245 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
* * * *
25285 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGA-CT-G-AGAG
*
25328 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
*
25368 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
* * *
25408 AATCGCAACGCGATTTAGAAAATCGCAA
1 AATCGCAATGCGATTGAGAGAATCGCAA
25436 CGTTGAAAAT
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 97 0.73
41 3 0.02
42 1 0.01
43 32 0.24
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
Found at i:25334 original size:83 final size:83
Alignment explanation
Indices: 25224--25400 Score: 282
Period size: 83 Copynumber: 2.1 Consensus size: 83
25214 GCTTCCAAGT
* * * * *
25224 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* *
25289 GCAATGCGATTGAGAGAG
66 GCAATGCGACTGAGAGAA
25307 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
25372 GCAATGCGACTGAGAGAA
66 GCAATGCGACTGAGAGAA
*
25390 TCGCAATGCGA
1 TCGCAACGCGA
25401 CTGAGAGAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGACTGAGAGAA
Found at i:25536 original size:6 final size:6
Alignment explanation
Indices: 25525--25605 Score: 162
Period size: 6 Copynumber: 13.5 Consensus size: 6
25515 GACACGTATT
25525 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
25573 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
25606 CGAGACGAGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:26311 original size:6 final size:6
Alignment explanation
Indices: 26295--26362 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
26285 TCTCGTCTCG
26295 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
26342 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
26363 AATACGTGTC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.08
6 57 0.92
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:26495 original size:20 final size:20
Alignment explanation
Indices: 26472--26642 Score: 189
Period size: 20 Copynumber: 8.4 Consensus size: 20
26462 ATTTTCAACG
* *
26472 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
26492 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
* *
26512 TTGCGATTCTCTCAGTCGCG
1 TTGCGATTCTCTCAATCGCA
* *
26532 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
* *
26555 TTGCGACTCTCTCAATCGCG
1 TTGCGATTCTCTCAATCGCA
*
26575 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
26595 TTGCGATTATATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
26615 TTGTGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
26635 TTGCGATT
1 TTGCGATT
26643 TTCTTCTAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
20 113 0.85
21 2 0.02
22 3 0.02
23 15 0.11
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:26566 original size:63 final size:63
Alignment explanation
Indices: 26483--26640 Score: 187
Period size: 63 Copynumber: 2.6 Consensus size: 63
26473 TGCGATTCTA
* * * * *
26483 TAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCGTTGCGATTTTCTTC
1 TAAATCGCATTGCGACTCTCTCAATCGCATTGCGACTCTCTCAATCGCATTGCGATTTTCTTC
* * * *
26546 TAAATCGCGTTGCGACTCTCTCAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTAT-ATC
1 TAAATCGCATTGCGACTCTCTCAATCGCATTGCGACTCTCTCAATCGCATTGCGATTTTCTTC
* * *
26608 --AATCGCATTGTGATTCTATCAATCGCATTGCGA
1 TAAATCGCATTGCGACTCTCTCAATCGCATTGCGA
26641 TTTTCTTCTA
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
60 28 0.35
62 2 0.02
63 51 0.63
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (63 bp):
TAAATCGCATTGCGACTCTCTCAATCGCATTGCGACTCTCTCAATCGCATTGCGATTTTCTTC
Found at i:26639 original size:103 final size:103
Alignment explanation
Indices: 26470--26663 Score: 298
Period size: 103 Copynumber: 1.9 Consensus size: 103
26460 TTATTTTCAA
* * * * * * *
26470 CGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCGTTG
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
26535 CGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
66 CGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
* * *
26573 CGTTGCGACTCTCTCAATCGCATTGCGATTATATCAATCGCATTGTGATTCTATCAATCGCATTG
1 CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
26638 CGATTTTCTTCTAAATCGCGTTGCGA
66 CGATTTTCTTCTAAATCGCGTTGCGA
26664 ACTTGGAAGC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 81 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.36
Consensus pattern (103 bp):
CGTTGCGACTCTATAAATCGCATTGCGATTATATCAATCGCATTGCGATTCTATCAATCGCATTG
CGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCG
Found at i:26704 original size:20 final size:20
Alignment explanation
Indices: 26679--26730 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
26669 GAAGCTCGCA
*
26679 TTGCGATTTTCTTTTGACCG
1 TTGCGATTTTCTTTTGAACG
*
26699 TTGCGATTTTCTTTTTAACG
1 TTGCGATTTTCTTTTGAACG
26719 TTGCGATTTTCT
1 TTGCGATTTTCT
26731 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTCTTTTGAACG
Found at i:26757 original size:19 final size:20
Alignment explanation
Indices: 26717--26767 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
26707 TTCTTTTTAA
*
26717 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
26737 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
26756 CGTTGCGATTTT
1 CGTTGCGATTTT
26768 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:28694 original size:21 final size:21
Alignment explanation
Indices: 28668--28716 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
28658 TGAAAAGTGT
*
28668 CTGATTACAAAAGAATATGTA
1 CTGATTACAAAAGAATATGGA
*
28689 CTGATTACAGAAGAATATGGA
1 CTGATTACAAAAGAATATGGA
28710 CTGATTA
1 CTGATTA
28717 TTCTGTCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (21 bp):
CTGATTACAAAAGAATATGGA
Found at i:29718 original size:8 final size:8
Alignment explanation
Indices: 29705--29775 Score: 63
Period size: 8 Copynumber: 8.5 Consensus size: 8
29695 ATTTCGCCTG
29705 AAAAAAGA
1 AAAAAAGA
29713 AAAAAAGA
1 AAAAAAGA
29721 AAAATGAAGA
1 AAAA--AAGA
**
29731 AAACTAG-
1 AAAAAAGA
*
29738 AAAAATGA
1 AAAAAAGA
29746 AAAAAAGA
1 AAAAAAGA
29754 AAGAGAAAGA
1 AA-A-AAAGA
*
29764 AAAGAAGA
1 AAAAAAGA
29772 AAAA
1 AAAA
29776 GAAAATAGGG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
7 4 0.08
8 30 0.60
9 2 0.04
10 14 0.28
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:29732 original size:18 final size:18
Alignment explanation
Indices: 29709--29780 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
29699 CGCCTGAAAA
29709 AAGAAAAAAAGAAAAATG
1 AAGAAAAAAAGAAAAATG
**
29727 AAGAAAACTAGAAAAATG
1 AAGAAAAAAAGAAAAATG
* *
29745 AAAAAAAGAAAGAGAAAGA-A
1 AAGAAAA-AAAGA-AAA-ATG
29765 AAGAAGAAAAAGAAAA
1 AAGAA-AAAAAGAAAA
29781 TAGGGTTCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 22 0.51
19 6 0.14
20 12 0.28
21 3 0.07
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (18 bp):
AAGAAAAAAAGAAAAATG
Found at i:29742 original size:33 final size:33
Alignment explanation
Indices: 29704--29780 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
29694 TATTTCGCCT
*
29704 GAAAAAAGAAAAAAAGAAAAATG-AAGAAAACTA
1 GAAAAAAGAAAAAAAGAAAAA-GAAAGAAAACAA
* * *
29737 GAAAAATGAAAAAAAGAAAGAGAAAGAAAAGAA
1 GAAAAAAGAAAAAAAGAAAAAGAAAGAAAACAA
29770 G-AAAAAGAAAA
1 GAAAAAAGAAAA
29781 TAGGGTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 10 0.26
33 28 0.74
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (33 bp):
GAAAAAAGAAAAAAAGAAAAAGAAAGAAAACAA
Found at i:29771 original size:14 final size:15
Alignment explanation
Indices: 29744--29780 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
29734 CTAGAAAAAT
29744 GAAA-AAAAGAAAGA
1 GAAAGAAAAGAAAGA
29758 GAAAGAAAAG-AAGA
1 GAAAGAAAAGAAAGA
*
29772 AAAAGAAAA
1 GAAAGAAAA
29781 TAGGGTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAGAAAGA
Found at i:42842 original size:23 final size:22
Alignment explanation
Indices: 42789--42842 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
42779 GGAATCGATA
*
42789 CCCCTTGAAGGGGAACCGATTC
1 CCCCTTGAAGGGGAACCAATTC
*
42811 CCCCTTTGAATGGGAACCAATTC
1 CCCC-TTGAAGGGGAACCAATTC
42834 CCTCCTTGA
1 CC-CCTTGA
42843 GGGAATCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 22 0.79
24 2 0.07
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.24
Consensus pattern (22 bp):
CCCCTTGAAGGGGAACCAATTC
Found at i:49733 original size:41 final size:41
Alignment explanation
Indices: 49640--49736 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 41
49630 TCCAAAATTT
* * *
49640 ATAAGTCCTTCAGGCATCAGTATGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCAGGCATCAGTAAGCCTTTCGAGCAAGATGC
* * * **
49681 TTAAATTCTTCAGGTCATCTTTAAGCCTTTCGAGCAAGATG-
1 ATAAGTCCTTCAGG-CATCAGTAAGCCTTTCGAGCAAGATGC
49722 ATAAGTCCTTCAGGC
1 ATAAGTCCTTCAGGC
49737 CATCCATAAG
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
40 1 0.02
41 22 0.50
42 21 0.48
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (41 bp):
ATAAGTCCTTCAGGCATCAGTAAGCCTTTCGAGCAAGATGC
Found at i:49993 original size:228 final size:231
Alignment explanation
Indices: 49489--50058 Score: 794
Period size: 228 Copynumber: 2.5 Consensus size: 231
49479 TCCAAAATTT
* * * * * * * **
49489 ATAAGTCCTTTGGGTCATTCATAAGACCTTT-AGACATGATGTTTTTACTTGTCTATCAAAATAT
1 ATAAGTCCTTCGGGCCATCCATAAGA-CTTTCAGGCATGATGTTTTCACATGTCTTTTGAAATAT
* *
49553 GAGAAAGGTTTCTCATTCAAATTTGAAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACT
65 GAGAAAGGTTTCTCATTTAAATCTGAAAA-TTGAAA-TTTTGAAAAGTAAGAAAGGTTTCTTACT
*
49618 TAGTAAACTATTTCCAAAATTTATAAGTCCTTCAGGCATCAGTATGTCTTTCGAGCATGATGCTT
128 TAGTAAACTATTTCCAAAATTTATAAGTCCTTCAGGCATCAGTAAGTCTTTCGAGCATGATGCTT
* * *
49683 AAATTCTTCAGGTCATCTTTAAGCCTTTCGAGCAAGATG
193 AAATCCTTCAGGTAATCTATAAGCCTTTCGAGCAAGATG
* * * *
49722 ATAAGTCCTTCAGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTTTTGAAATATG
1 ATAAGTCCTTCGGGCCATCCATAAGACTTTCAGGCATGATGTTTTCACATGTCTTTTGAAATATG
49787 -GAAAGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGG-TTCTTACTTA
66 AGAAAGGTTTCTCAT-TTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACTTA
* *
49850 GTAAACTATTTCCAAAA-TTATAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGCTT-
130 GTAAACTATTTCCAAAATTTATAAGTCCTTCAGG-CATCAGTAAGTCTTTCGAGCATGATGCTTA
49913 AATCCTTC-GGTAATCTATAAGCCTTTCGAGCAAGATG
194 AATCCTTCAGGTAATCTATAAGCCTTTCGAGCAAGATG
*
49950 ATAAGTCCTTCGGGCCATCCATAAGACTTTCAGGCATGATGTTTTCACATG-CCTTTGAAATATG
1 ATAAGTCCTTCGGGCCATCCATAAGACTTTCAGGCATGATGTTTTCACATGTCTTTTGAAATATG
* * * *
50014 AGAAATGTTTCTCATGTTAAACCTAAAAATTGAAAATTTTAAAAA
66 AGAAAGGTTTCTCAT-TTAAATCTGAAAATTG-AAATTTTGAAAA
50059 ATCTGATATT
Statistics
Matches: 301, Mismatches: 31, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
227 12 0.04
228 101 0.34
229 33 0.11
230 54 0.18
231 19 0.06
232 23 0.08
233 59 0.20
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (231 bp):
ATAAGTCCTTCGGGCCATCCATAAGACTTTCAGGCATGATGTTTTCACATGTCTTTTGAAATATG
AGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACTTAG
TAAACTATTTCCAAAATTTATAAGTCCTTCAGGCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
TCCTTCAGGTAATCTATAAGCCTTTCGAGCAAGATG
Done.