Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002063.1 Hibiscus syriacus cultivar Beakdansim tig00004207_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: 31281
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:191 original size:14 final size:14
Alignment explanation
Indices: 172--207 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
162 GATTGTTAAT
172 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
186 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
200 TGATTTGT
1 TGATTTGT
208 GTAATTGATG
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:329 original size:19 final size:19
Alignment explanation
Indices: 313--414 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
303 AAAAATGACT
313 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
332 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
351 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
365 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
384 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
404 ATCGCAATGCG
1 ATCGCAATGCG
415 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:447 original size:13 final size:14
Alignment explanation
Indices: 429--482 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
419 TAATTTCGCA
429 TTGCGATTC-TTCG
1 TTGCGATTCTTTCG
442 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
459 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
475 TTGCGATT
1 TTGCGATT
483 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 6 0.17
14 8 0.23
15 3 0.09
16 5 0.14
17 7 0.20
19 6 0.17
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:466 original size:19 final size:19
Alignment explanation
Indices: 442--673 Score: 276
Period size: 19 Copynumber: 13.4 Consensus size: 19
432 CGATTCTTCG
442 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
461 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
475 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
494 -TGCGA-TTTC--TTCGCA
1 TTGCGATTTTCATTTCGCA
509 TTGCGATTTTC-TTTCGCA
1 TTGCGATTTTCATTTCGCA
527 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
545 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
564 TTGCGA--TT--TGTCG--
1 TTGCGATTTTCATTTCGCA
577 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
596 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
615 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
629 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
648 TTGCGATTTTTCATTTCGCA
1 TTGCGA-TTTTCATTTCGCA
668 -TGCGAT
1 TTGCGAT
674 CTCTCGTTGA
Statistics
Matches: 187, Mismatches: 4, Indels: 45
0.79 0.02 0.19
Matches are distributed among these distances:
13 6 0.03
14 12 0.06
15 12 0.06
16 20 0.11
17 33 0.18
18 31 0.17
19 60 0.32
20 13 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:480 original size:33 final size:33
Alignment explanation
Indices: 421--737 Score: 288
Period size: 32 Copynumber: 9.5 Consensus size: 33
411 TGCGTTTATA
421 ATTTCGCATTGCGATTC-TTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
453 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
486 ATTTCGCA-TGCGATT-TCTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCT-TTCG--TTGCGATTTTC
520 -TTTCGCATTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTC-TTTCG--TTGCGATTTTC
*
556 ATTTCGCATTGCGATT-TGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
588 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTC
*
624 -TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTTC
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGA-TTTTC
*
660 ATTTCGCA-TGCGA-TCTCTCGTT--GATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
* *
689 ATTTCCGCATTGCGATT-TCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCT-TTCGTTGCGATTTTC
*
722 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
738 GTAATTTCCG
Statistics
Matches: 251, Mismatches: 7, Indels: 54
0.80 0.02 0.17
Matches are distributed among these distances:
29 9 0.04
30 6 0.02
31 10 0.04
32 68 0.27
33 66 0.26
34 26 0.10
35 8 0.03
36 29 0.12
37 18 0.07
38 11 0.04
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
Found at i:498 original size:51 final size:52
Alignment explanation
Indices: 442--706 Score: 379
Period size: 51 Copynumber: 5.2 Consensus size: 52
432 CGATTCTTCG
*
442 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
494 -TGCGA-TTTC--TTCGCATTGCGATTTTCTTTCGCATTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTCTCTCG--TTGCGATTTTCATTTCGCA
*
545 TTGCGATTTTCATTTCGCATTGCGATT-TGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
596 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
648 TTGCGATTTTTCATTTCGCA-TGCGA-TCTCTCGTT--GATTTTCATTTCCGCA
1 TTGCGA-TTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
698 TTGCGATTT
1 TTGCGATTT
707 CATGTTGGGA
Statistics
Matches: 199, Mismatches: 2, Indels: 27
0.87 0.01 0.12
Matches are distributed among these distances:
48 12 0.06
49 14 0.07
50 28 0.14
51 65 0.33
52 49 0.25
53 19 0.10
55 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:3229 original size:24 final size:24
Alignment explanation
Indices: 3195--3241 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3185 CTGAAACATC
3195 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3219 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3242 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3948 original size:20 final size:20
Alignment explanation
Indices: 3920--4129 Score: 215
Period size: 20 Copynumber: 10.5 Consensus size: 20
3910 AAATTTCAGT
* * *
3920 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3940 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
3960 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3980 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
4000 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
4020 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
4040 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
4060 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
4080 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
4100 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
4120 GTTGCGATTT
1 GTTGCGATTT
4130 TGGAAAATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
20 163 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:4146 original size:21 final size:20
Alignment explanation
Indices: 4096--4193 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
4086 ATTTATGTGT
* * * *
4096 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
4116 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
4137 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
4157 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
4178 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
4194 GACACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:4188 original size:41 final size:41
Alignment explanation
Indices: 4096--4252 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
4086 ATTTATGTGT
* * *
4096 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
4137 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
4178 TCGCGTTGCGATTTTGGACACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
4218 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
4253 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:14750 original size:20 final size:19
Alignment explanation
Indices: 14722--14762 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
14712 ATCCATAAAA
*
14722 TATATTTTTATGAATTTTTT
1 TATAGTTTTA-GAATTTTTT
*
14742 TATAGTTTTAGGATTTTTT
1 TATAGTTTTAGAATTTTTT
14761 TA
1 TA
14763 CAACTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (19 bp):
TATAGTTTTAGAATTTTTT
Found at i:14961 original size:29 final size:29
Alignment explanation
Indices: 14924--14979 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
14914 AATATCAAAA
*
14924 TTAATAATATAGTACAGTTACTAAAACTT
1 TTAATAATATAGTACAGGTACTAAAACTT
14953 TTAATAATATAGTACAGGTACTAAAAC
1 TTAATAATATAGTACAGGTACTAAAAC
14980 ATGTATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (29 bp):
TTAATAATATAGTACAGGTACTAAAACTT
Found at i:18097 original size:19 final size:20
Alignment explanation
Indices: 18073--18119 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
18063 GAGTATTATT
18073 TAAAATGTTATTTT-TTACC
1 TAAAATGTTATTTTCTTACC
* *
18092 TAAAATATTATTTTCGTTACT
1 TAAAATGTTATTTTC-TTACC
18113 TAAAATG
1 TAAAATG
18120 AATATTTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 13 0.57
21 10 0.43
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (20 bp):
TAAAATGTTATTTTCTTACC
Found at i:18140 original size:15 final size:15
Alignment explanation
Indices: 18120--18148 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18110 ACTTAAAATG
18120 AATATTTCTGATATT
1 AATATTTCTGATATT
18135 AATATTTCTGATAT
1 AATATTTCTGATAT
18149 AAAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (15 bp):
AATATTTCTGATATT
Found at i:18325 original size:24 final size:25
Alignment explanation
Indices: 18298--18347 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
18288 TTTGATTTTT
*
18298 TAATATTAGTTTT-ACTATT-TAAAA
1 TAATAATA-TTTTAACTATTGTAAAA
18322 TAATAATATTTTAACTATTGTAAAA
1 TAATAATATTTTAACTATTGTAAAA
18347 T
1 T
18348 GTGAAAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 13 0.57
25 6 0.26
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
TAATAATATTTTAACTATTGTAAAA
Found at i:18917 original size:105 final size:105
Alignment explanation
Indices: 18735--18946 Score: 424
Period size: 105 Copynumber: 2.0 Consensus size: 105
18725 TGCCTTTTGG
18735 TTAGGTCAGGTGTAGGGAACTAGGGATTTGTTATGTTCCTGGCCCGTACAAGAGTTGGGCGAATG
1 TTAGGTCAGGTGTAGGGAACTAGGGATTTGTTATGTTCCTGGCCCGTACAAGAGTTGGGCGAATG
18800 GCATGCATGCACTAATCACCCATAACCAGGAGCCATAAGC
66 GCATGCATGCACTAATCACCCATAACCAGGAGCCATAAGC
18840 TTAGGTCAGGTGTAGGGAACTAGGGATTTGTTATGTTCCTGGCCCGTACAAGAGTTGGGCGAATG
1 TTAGGTCAGGTGTAGGGAACTAGGGATTTGTTATGTTCCTGGCCCGTACAAGAGTTGGGCGAATG
18905 GCATGCATGCACTAATCACCCATAACCAGGAGCCATAAGC
66 GCATGCATGCACTAATCACCCATAACCAGGAGCCATAAGC
18945 TT
1 TT
18947 CGTTGAACAG
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 107 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (105 bp):
TTAGGTCAGGTGTAGGGAACTAGGGATTTGTTATGTTCCTGGCCCGTACAAGAGTTGGGCGAATG
GCATGCATGCACTAATCACCCATAACCAGGAGCCATAAGC
Found at i:20559 original size:21 final size:19
Alignment explanation
Indices: 20512--20551 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20502 TTTAAACAAA
20512 TAAAATTAATATATATTTT
1 TAAAATTAATATATATTTT
* *
20531 TAAAATTACTTTATATTTT
1 TAAAATTAATATATATTTT
20550 TA
1 TA
20552 GAAAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TAAAATTAATATATATTTT
Found at i:21333 original size:18 final size:19
Alignment explanation
Indices: 21300--21340 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
21290 TTTAAGGGTC
21300 AATTAATAATTTATCATGA
1 AATTAATAATTTATCATGA
*
21319 AATTAGTAA-TTATCATGA
1 AATTAATAATTTATCATGA
21337 AATT
1 AATT
21341 TTTATGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (19 bp):
AATTAATAATTTATCATGA
Found at i:22839 original size:48 final size:48
Alignment explanation
Indices: 22782--22943 Score: 207
Period size: 48 Copynumber: 3.4 Consensus size: 48
22772 ACGTCACTTT
* * *
22782 TGTGACGATGGTGCTACCATTAAAGATAATTAGCACGTCTGACGTCTG
1 TGTGACGATGGTGCTACTATTAATGATAATTAGCACGTTTGACGTCTG
* *
22830 TGTGACGATGATGCTACTATTAATGATAATTAGCACGTTTGACGTCCG
1 TGTGACGATGGTGCTACTATTAATGATAATTAGCACGTTTGACGTCTG
* * * * **
22878 TGTGACGGTGGTGTTAATATTAATGGTACCTAGCACGTTTGACGTCTG
1 TGTGACGATGGTGCTACTATTAATGATAATTAGCACGTTTGACGTCTG
* *
22926 TGTGACGGTAGTGCTACT
1 TGTGACGATGGTGCTACT
22944 TTCAATCGTA
Statistics
Matches: 98, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 98 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.33
Consensus pattern (48 bp):
TGTGACGATGGTGCTACTATTAATGATAATTAGCACGTTTGACGTCTG
Found at i:22955 original size:48 final size:46
Alignment explanation
Indices: 22812--22960 Score: 165
Period size: 48 Copynumber: 3.1 Consensus size: 46
22802 TAAAGATAAT
* * **
22812 TAGCACGTCTGACGTCTGTGTGACGATGATGCTACTATTAATGATAAT
1 TAGCACGTTTGACGTCTGTGTGACGGTG-TGCTACTATTAATG-TACC
* * *
22860 TAGCACGTTTGACGTCCGTGTGACGGTGGTGTTAATATTAATGGTACC
1 TAGCACGTTTGACGTCTGTGTGACGGT-GTGCTACTATTAAT-GTACC
22908 TAGCACGTTTGACGTCTGTGTGACGGTAGTGCTACT-TTCAATCGTACC
1 TAGCACGTTTGACGTCTGTGTGACGGT-GTGCTACTATT-AAT-GTACC
22956 TAGCA
1 TAGCA
22961 TGTCCGACGT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
47 2 0.02
48 82 0.95
49 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (46 bp):
TAGCACGTTTGACGTCTGTGTGACGGTGTGCTACTATTAATGTACC
Found at i:23097 original size:34 final size:34
Alignment explanation
Indices: 23051--23129 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
23041 TACATTGTGC
* *
23051 TATGAAAAGAATAAAATGAAAGGCACATGTTTGA
1 TATGAAATGAATAAAATGAAAGGCACAAGTTTGA
* * *
23085 TGTGAAATGAATAAAGTGAAAGGTACAAGTTTGA
1 TATGAAATGAATAAAATGAAAGGCACAAGTTTGA
23119 TATGAAATGAA
1 TATGAAATGAA
23130 AATATACTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (34 bp):
TATGAAATGAATAAAATGAAAGGCACAAGTTTGA
Found at i:23408 original size:2 final size:2
Alignment explanation
Indices: 23399--23436 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
23389 TAATGTTTTC
23399 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23437 CTATTTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25525 original size:25 final size:24
Alignment explanation
Indices: 25497--25557 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 24
25487 CATTTTAGTC
25497 AAAATATTAATTATTAAATATTTAT
1 AAAATA-TAATTATTAAATATTTAT
25522 AAAATAT--TTATT-AATATTTAT
1 AAAATATAATTATTAAATATTTAT
25543 AATAATATAA-TATTA
1 AA-AATATAATTATTA
25558 TATAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
21 11 0.34
22 10 0.31
23 4 0.12
24 1 0.03
25 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATAATTATTAAATATTTAT
Found at i:25526 original size:11 final size:11
Alignment explanation
Indices: 25507--25550 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
25497 AAAATATTAA
*
25507 TTATTAAATAT
1 TTATAAAATAT
25518 TTATAAAATAT
1 TTATAAAATAT
*
25529 TTAT-TAATAT
1 TTATAAAATAT
25539 TTATAATAATAT
1 TTATAA-AATAT
25551 AATATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.32
11 14 0.50
12 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTATAAAATAT
Found at i:25535 original size:22 final size:22
Alignment explanation
Indices: 25507--25650 Score: 75
Period size: 21 Copynumber: 6.4 Consensus size: 22
25497 AAAATATTAA
25507 TTATTAAATATTTATAA-AATAT
1 TTATT-AATATTTATAATAATAT
25529 TTATTAATATTTATAATAATAT
1 TTATTAATATTTATAATAATAT
* * * *
25551 AATATTATATAATAATAATAATCAA
1 -TTATTA-ATATTTATAATAAT-AT
**
25576 TTA-TAATA-AAATAATCAAT-T
1 TTATTAATATTTATAAT-AATAT
* *
25596 ATATATAATATAATATAATAATAT
1 TTAT-TAATAT-TTATAATAATAT
* *
25620 AATATTAATA--TATAATAATAAA
1 -TTATTAATATTTATAATAAT-AT
25642 TTATTAATA
1 TTATTAATA
25651 AAATTTATAT
Statistics
Matches: 99, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
20 2 0.02
21 34 0.34
22 22 0.22
23 10 0.10
24 26 0.26
25 5 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATTAATATTTATAATAATAT
Found at i:25549 original size:3 final size:3
Alignment explanation
Indices: 25541--25640 Score: 84
Period size: 3 Copynumber: 33.3 Consensus size: 3
25531 ATTAATATTT
* *
25541 ATA ATA AT- ATA ATA TTA TATA ATA ATA ATA ATCA ATT ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A ATA ATA ATA ATA
* *
25586 ATA ATCA ATT ATA TATA AT- ATA AT- ATA ATA AT- ATA ATA TTA ATA
1 ATA AT-A ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25630 TATA ATA ATA A
1 -ATA ATA ATA A
25641 ATTATTAATA
Statistics
Matches: 79, Mismatches: 8, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
2 10 0.13
3 55 0.70
4 14 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:25554 original size:5 final size:5
Alignment explanation
Indices: 25544--25631 Score: 65
Period size: 5 Copynumber: 16.6 Consensus size: 5
25534 AATATTTATA
* *
25544 ATAAT ATAAT ATTAT ATAAT AATAAT AATCAATT ATAAT AAAAT AATCAAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT -AT-AA-T ATAAT ATAAT -AT-AAT
25595 -TATAT ATAAT ATAAT AT-A- ATAAT ATAAT ATTAAT ATA
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATA
25632 TAATAATAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
3 2 0.03
4 3 0.04
5 38 0.55
6 18 0.26
7 7 0.10
8 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:25560 original size:10 final size:10
Alignment explanation
Indices: 25513--25650 Score: 61
Period size: 10 Copynumber: 14.4 Consensus size: 10
25503 TTAATTATTA
*
25513 AATATTTATAA
1 AATA-TTATAT
25524 AATATT-TATT
1 AATATTATA-T
25534 AATATT-TAT
1 AATATTATAT
25543 AATA--ATAT
1 AATATTATAT
25551 AATATTATAT
1 AATATTATAT
*
25561 AATAATA-AT
1 AATATTATAT
25570 AATCAATTATAAT
1 AAT--ATTAT-AT
*
25583 AA-AATA-AT
1 AATATTATAT
25591 CAAT-TATATAT
1 -AATAT-TATAT
*
25602 AATATAATAT
1 AATATTATAT
25612 AATA--ATAT
1 AATATTATAT
25620 AATATTA-AT
1 AATATTATAT
*
25629 -ATATAATAAT
1 AATATTAT-AT
25639 AA-ATTAT-T
1 AATATTATAT
25647 AATA
1 AATA
25651 AAATTTATAT
Statistics
Matches: 100, Mismatches: 8, Indels: 40
0.68 0.05 0.27
Matches are distributed among these distances:
8 25 0.25
9 17 0.17
10 43 0.43
11 11 0.11
13 4 0.04
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (10 bp):
AATATTATAT
Found at i:25568 original size:24 final size:24
Alignment explanation
Indices: 25541--25640 Score: 97
Period size: 24 Copynumber: 4.3 Consensus size: 24
25531 ATTAATATTT
25541 ATAATAATATAATATTATATAATA
1 ATAATAATATAATATTATATAATA
*
25565 ATAAT-A-ATCA-ATTATAATAA-A
1 ATAATAATATAATATTAT-ATAATA
*
25586 ATAATCAAT-TATATATAATATAAT-
1 ATAAT-AATATA-ATATTATATAATA
25610 ATAATAATATAATATTA-ATATATA
1 ATAATAATATAATATTATATA-ATA
25634 ATAATAA
1 ATAATAA
25641 ATTATTAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
21 11 0.18
22 10 0.16
23 13 0.21
24 24 0.39
25 4 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
ATAATAATATAATATTATATAATA
Found at i:25938 original size:20 final size:19
Alignment explanation
Indices: 25891--25942 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
25881 AATAAAATTA
25891 TAAAAATAATATTTAATAAT
1 TAAAAATAAT-TTTAATAAT
* *
25911 AAATAAATAATTTTAATATTT
1 TAA-AAATAATTTTAATA-AT
25932 TAAAAATAATT
1 TAAAAATAATT
25943 ATATTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAAATAATTTTAATAAT
Found at i:27761 original size:38 final size:39
Alignment explanation
Indices: 27710--27788 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 39
27700 GAATCAGTGT
*
27710 TGCTCAAAACGGGAGATATCTTAAATGAAATCGTATGCA
1 TGCTCAAAACGGGAGATATCTTAAATGAAAGCGTATGCA
27749 TGCTC-AAACGGGAGATATCTTAAATGAAAGCGTATGCA
1 TGCTCAAAACGGGAGATATCTTAAATGAAAGCGTATGCA
27787 TG
1 TG
27789 TGAAACGTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 34 0.87
39 5 0.13
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (39 bp):
TGCTCAAAACGGGAGATATCTTAAATGAAAGCGTATGCA
Done.