Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002176.1 Hibiscus syriacus cultivar Beakdansim tig00004435_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: 65208
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:560 original size:2 final size:2
Alignment explanation
Indices: 553--581 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
543 AATCTCAATG
553 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 A
582 CAATTGTTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2552 original size:12 final size:12
Alignment explanation
Indices: 2534--2569 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2524 TATATATGTT
2534 CATGTGATATGA
1 CATGTGATATGA
*
2546 TATGTGATATGA
1 CATGTGATATGA
*
2558 CCTGTGATATGA
1 CATGTGATATGA
2570 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:9574 original size:15 final size:15
Alignment explanation
Indices: 9556--9588 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
9546 GAGGGTATAA
9556 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
9571 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
9586 TAG
1 TAG
9589 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:11162 original size:22 final size:22
Alignment explanation
Indices: 11132--11176 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
11122 AGTTATGAAT
*
11132 TTGGCAAATTCATGTTTCGAAA
1 TTGGAAAATTCATGTTTCGAAA
*
11154 TTGGAAAATTCGTGTTTCGAAA
1 TTGGAAAATTCATGTTTCGAAA
11176 T
1 T
11177 GTAAAATCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (22 bp):
TTGGAAAATTCATGTTTCGAAA
Found at i:11255 original size:4 final size:4
Alignment explanation
Indices: 11238--11268 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
11228 GTTAAAGTTA
*
11238 AACG AACA AACG AACG AACG AACG AACG AAC
1 AACG AACG AACG AACG AACG AACG AACG AAC
11269 ATGAACATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.55, C:0.26, G:0.19, T:0.00
Consensus pattern (4 bp):
AACG
Found at i:12225 original size:21 final size:21
Alignment explanation
Indices: 12209--12389 Score: 222
Period size: 21 Copynumber: 8.7 Consensus size: 21
12199 GCGTTGCATT
12209 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
12230 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
12250 TTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
12271 TTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
12292 TCGCGTTGCGCT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
12312 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
12333 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
12354 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
12375 TCGTGTTGCGATAGT
1 TCGCGTTGCGATAGT
12390 CTACAGTTGT
Statistics
Matches: 133, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
20 28 0.21
21 105 0.79
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:12281 original size:62 final size:62
Alignment explanation
Indices: 12209--12365 Score: 287
Period size: 62 Copynumber: 2.5 Consensus size: 62
12199 GCGTTGCATT
*
12209 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* *
12271 TTGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
12333 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
12366 AGTTGAAAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 90 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (62 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:12318 original size:41 final size:42
Alignment explanation
Indices: 12209--12389 Score: 204
Period size: 41 Copynumber: 4.4 Consensus size: 42
12199 GCGTTGCATT
* * ** **
12209 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAA
* * *
12250 TTGCGTTGCGATAGTTGAAAATTGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAA
* * * **
12292 TCGCGTTGCGCT-TTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAA
*
12333 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAA
*
12375 TCGTGTTGCGATAGT
1 TCGCGTTGCGATAGT
12390 CTACAGTTGT
Statistics
Matches: 116, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
41 65 0.56
42 51 0.44
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (42 bp):
TCGCGTTGCGATAGTTCAAAATCGCGTTGCGATAGTTGAAAA
Found at i:12444 original size:22 final size:22
Alignment explanation
Indices: 12379--12469 Score: 93
Period size: 22 Copynumber: 4.4 Consensus size: 22
12369 TGAAAATCGT
12379 GTTGCGATAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTTGTC
* * **
12401 G-T-CGAT--TTTCCAAAT-TC
1 GTTGCGATAGTCTACAGTTGTC
*
12418 ATTGCGATAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTTGTC
*
12440 GTTGCCATAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTTGTC
12462 GTTGCGAT
1 GTTGCGAT
12470 TTTCCAAATT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
17 2 0.04
18 6 0.12
19 4 0.08
20 4 0.08
21 6 0.12
22 30 0.58
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (22 bp):
GTTGCGATAGTCTACAGTTGTC
Found at i:12585 original size:6 final size:6
Alignment explanation
Indices: 12574--12624 Score: 75
Period size: 6 Copynumber: 8.0 Consensus size: 6
12564 GACACGTATT
12574 ACCACG ACCACG ACCACG ACCACG ACCACGGCG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCA---CG ACCACG ACCACG ACCACG
12625 GCGACCACGG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
6 36 0.86
9 6 0.14
ACGTcount: A:0.31, C:0.49, G:0.20, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:12610 original size:15 final size:15
Alignment explanation
Indices: 12578--12649 Score: 78
Period size: 15 Copynumber: 5.0 Consensus size: 15
12568 CGTATTACCA
12578 CGACCACGACCA---
1 CGACCACGACCACGG
12590 CGACCACGACCACGG
1 CGACCACGACCACGG
*
12605 CGACCACGACCACGA
1 CGACCACGACCACGG
* **
12620 CCACGGCGACCACGG
1 CGACCACGACCACGG
*
12635 TGACCACGACCACGG
1 CGACCACGACCACGG
12650 GACGAGACGA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
12 12 0.25
15 36 0.75
ACGTcount: A:0.28, C:0.46, G:0.25, T:0.01
Consensus pattern (15 bp):
CGACCACGACCACGG
Found at i:12610 original size:21 final size:21
Alignment explanation
Indices: 12584--12649 Score: 105
Period size: 21 Copynumber: 3.0 Consensus size: 21
12574 ACCACGACCA
12584 CGACCACGACCACGACCACGG
1 CGACCACGACCACGACCACGG
12605 CGACCACGACCACGACCACGG
1 CGACCACGACCACGACCACGG
12626 CGACCACGGTGACCACGACCACGG
1 CGACCAC---GACCACGACCACGG
12650 GACGAGACGA
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
21 28 0.67
24 14 0.33
ACGTcount: A:0.27, C:0.45, G:0.26, T:0.02
Consensus pattern (21 bp):
CGACCACGACCACGACCACGG
Found at i:13272 original size:19 final size:19
Alignment explanation
Indices: 13248--13333 Score: 100
Period size: 19 Copynumber: 4.4 Consensus size: 19
13238 TTAACTATCA
13248 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
13267 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
*
13289 CAACGAATTTGAAAAATCG
1 CAACGAATTTGGAAAATCG
13308 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
13327 CAACGAA
1 CAACGAA
13334 AACTGTAGAC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 37 0.69
20 2 0.04
21 2 0.04
22 13 0.24
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.19
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:13364 original size:41 final size:41
Alignment explanation
Indices: 13342--13483 Score: 239
Period size: 41 Copynumber: 3.5 Consensus size: 41
13332 AAAACTGTAG
*
13342 ACTATCGCAACGCGAAATGAAAAATTGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
* *
13383 ACTATCGCAACGTGAAATGAAAAATTGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
* *
13424 ACTATCGCAACGCGAAATGGAAAATCGCAACTCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
13465 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
13484 CAACGCGAAT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:13393 original size:82 final size:80
Alignment explanation
Indices: 13304--13476 Score: 204
Period size: 82 Copynumber: 2.1 Consensus size: 80
13294 AATTTGAAAA
* * *
13304 ATCGCAACGAATTTGGAAAATCGCAACGAAAACTGT-AGACTATCGCAACGCGAAATGAAAAATT
1 ATCGCAACGAA-ATGAAAAATCGCAACG-AAACTGTCA-ACTATCGCAACGCGAAATGAAAAATC
13368 GCAACGCGATTTTCAACT
63 GCAACGCGATTTTCAACT
* ** * * *
13386 ATCGCAACGTGAAATGAAAAATTGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAAC--GAAATGAAAAATCGCAACGAAACTGTCAACTATCGCAACGCGAAATGAAAAATCG
*
13451 CAACTCGATTTTCAACT
64 CAACGCGATTTTCAACT
13468 ATCGCAACG
1 ATCGCAACG
13477 CGAAATGCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
80 1 0.01
82 60 0.77
83 14 0.18
84 3 0.04
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (80 bp):
ATCGCAACGAAATGAAAAATCGCAACGAAACTGTCAACTATCGCAACGCGAAATGAAAAATCGCA
ACGCGATTTTCAACT
Found at i:13452 original size:20 final size:20
Alignment explanation
Indices: 13345--13454 Score: 76
Period size: 20 Copynumber: 5.4 Consensus size: 20
13335 ACTGTAGACT
13345 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
* ** * **
13365 ATTGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
13386 ATCGCAACGTGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
* ** * **
13406 ATTGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
13427 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
13447 ATCGCAAC
1 ATCGCAAC
13455 TCGATTTTCA
Statistics
Matches: 61, Mismatches: 27, Indels: 4
0.66 0.29 0.04
Matches are distributed among these distances:
20 34 0.56
21 27 0.44
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:13487 original size:21 final size:21
Alignment explanation
Indices: 13342--13487 Score: 100
Period size: 21 Copynumber: 7.1 Consensus size: 21
13332 AAAACTGTAG
13342 ACTATCGCAACGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** * ** *
13362 AAAATTGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
13383 ACTATCGCAACGTGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** * ** *
13403 AAAATTGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
13424 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
13445 A-AATCGCAACTCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
13465 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
13486 AC
1 AC
13488 GCGAATTTGC
Statistics
Matches: 85, Mismatches: 38, Indels: 5
0.66 0.30 0.04
Matches are distributed among these distances:
20 40 0.47
21 45 0.53
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:19693 original size:22 final size:23
Alignment explanation
Indices: 19649--19694 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
19639 TAGGTGCTGG
19649 AAACAAGATAAGAAATAAGATTA
1 AAACAAGATAAGAAATAAGATTA
19672 AAACAAGATAA-AGAA-AAGATTA
1 AAACAAGATAAGA-AATAAGATTA
19694 A
1 A
19695 GGAATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.67, C:0.04, G:0.13, T:0.15
Consensus pattern (23 bp):
AAACAAGATAAGAAATAAGATTA
Found at i:39825 original size:41 final size:41
Alignment explanation
Indices: 39755--39991 Score: 157
Period size: 41 Copynumber: 5.8 Consensus size: 41
39745 TTTTCCCAAT
39755 TCGCAATGCGAA-TAAGTAAATCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATTAAGTAAATCGCAATGCGAATAAGTAAA
** * * *
39795 TCGCAATGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTA
1 TCGCAATGCGAATTAAGTAAATCGCAATGCGAATAAGT-A-AA
*** * * * * *
39836 TCGCAATGC-AATTTTCCTAATTCGCATTGCGATTTACGT-AT
1 TCGCAATGCGAA-TTAAGTAAATCGCAATGCGA-ATAAGTAAA
** * * * *
39877 TCGCGTTGCGATTTTCA-TAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGA-ATTAAGTAAATCGCAATGCGAATAAGTAAA
* * *
39918 TCGCAACGCG-ATTAAGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAAGTAAATCGCAATGCGAA-TAAGTAAA
*
39959 TCGCAATGCGAA-TACGTAAATCGCAATGCGAAT
1 TCGCAATGCGAATTAAGTAAATCGCAATGCGAAT
39992 CTTACTATCG
Statistics
Matches: 151, Mismatches: 33, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
39 5 0.03
40 38 0.25
41 102 0.68
42 4 0.03
43 1 0.01
44 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (41 bp):
TCGCAATGCGAATTAAGTAAATCGCAATGCGAATAAGTAAA
Found at i:39870 original size:21 final size:21
Alignment explanation
Indices: 39836--39908 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
39826 ATACTGACTA
* *
39836 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
39857 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
39877 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
39898 TCGCAATGCGA
1 TCGCAATGCGA
39909 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:40001 original size:20 final size:20
Alignment explanation
Indices: 39755--40009 Score: 169
Period size: 20 Copynumber: 12.6 Consensus size: 20
39745 TTTTCCCAAT
*
39755 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
*
39775 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATACGTAAA
** *
39795 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
39816 TCGCAATGCG-ATAC-TGACTA
1 TCGCAATGCGAATACGT-A-AA
* * *
39836 TCGCAATGC-AATTTTCCTAAT
1 TCGCAATGCGAA--TACGTAAA
* * *
39857 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGA-ATACGTAAA
** * * * *
39877 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGA-ATACGTAAA
39898 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
39918 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
39938 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
39959 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
39979 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
39999 TCGCAATGCGA
1 TCGCAATGCGA
40010 TTTACATAGC
Statistics
Matches: 189, Mismatches: 34, Indels: 24
0.77 0.14 0.10
Matches are distributed among these distances:
19 5 0.03
20 124 0.66
21 55 0.29
22 4 0.02
23 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:40588 original size:19 final size:19
Alignment explanation
Indices: 40564--40608 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
40554 GCAACGAGAG
* *
40564 AATCGCAACGCGGAATAAA
1 AATCGCAACGCGAAACAAA
*
40583 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
40602 AATCGCA
1 AATCGCA
40609 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:40693 original size:52 final size:53
Alignment explanation
Indices: 40609--40710 Score: 152
Period size: 52 Copynumber: 1.9 Consensus size: 53
40599 CAAAATCGCA
** ** *
40609 TTGCGATTTTCATTTCGCGTTGCGATTTTCA-TTTCGCGTTGCTATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
40661 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTCTC
40711 ATTATCTCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 27 0.61
53 17 0.39
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.44
Consensus pattern (53 bp):
TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:40698 original size:20 final size:20
Alignment explanation
Indices: 40659--40726 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
40649 GCTATTCTCT
40659 CGTTGCGATAGTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
40678 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
** * *
40698 CGTTGCGATTCTCATTATCT
1 CGTTGCGATAGTCATTTTCG
40718 CGTTGCGAT
1 CGTTGCGAT
40727 TTTCATTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:40732 original size:20 final size:19
Alignment explanation
Indices: 40604--40735 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
40594 GAAACCAAAA
*
40604 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
40623 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
40642 TCGCGTTGC--TATTC---
1 TCGCGTTGCGATTTTCATT
* **
40656 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
40675 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
40695 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
40714 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
40734 TC
1 TC
40736 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
14 8 0.08
16 4 0.04
17 4 0.04
19 47 0.48
20 34 0.35
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:44282 original size:14 final size:14
Alignment explanation
Indices: 44263--44298 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
44253 ATTGTTTAAT
44263 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
44277 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
44291 TGATTTGT
1 TGATTTGT
44299 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:44429 original size:19 final size:19
Alignment explanation
Indices: 44405--44541 Score: 134
Period size: 19 Copynumber: 7.7 Consensus size: 19
44395 AAAAAGTACT
*
44405 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
44424 ATCGCAACGCGAATTGAAA
1 ATCGCAACGCGAAATGAAA
*
44443 ATCGCAACGCGAATTGAAA
1 ATCGCAACGCGAAATGAAA
*
44462 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
44476 ATCGCAACGTGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
44495 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
44509 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
44528 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
44542 CTAAATTCGC
Statistics
Matches: 99, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.20
15 1 0.01
16 3 0.03
17 3 0.03
18 2 0.02
19 70 0.71
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:44484 original size:33 final size:33
Alignment explanation
Indices: 44405--44541 Score: 159
Period size: 33 Copynumber: 4.0 Consensus size: 33
44395 AAAAAGTACT
*
44405 ATCGCAATGCGAAATGAAAATCGCAACGCGAATTGAAA
1 ATCGCAACGCGAAATGAAAATCGCAA--CG-A--GAAA
* *
44443 ATCGCAACGCGAATTGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
* *
44476 ATCGCAACGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
*
44509 ATCGCAACGCGAAACT-AAAATCGCAACGCGAAA
1 ATCGCAACGCGAAA-TGAAAATCGCAACGAGAAA
44542 CTAAATTCGC
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
33 60 0.68
34 1 0.01
35 1 0.01
36 2 0.02
38 24 0.27
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
Found at i:44531 original size:52 final size:50
Alignment explanation
Indices: 44405--44541 Score: 132
Period size: 52 Copynumber: 2.7 Consensus size: 50
44395 AAAAAGTACT
* * *
44405 ATCGCAATGCGAAA-TGAAAATCGCAACGCGAATTGAAAATCGCAACGCGA
1 ATCGCAAAGCGAAACT-AAAATCGCAACGCGAAATGAAAATCGCAACGCAA
* * * * * *
44455 ATTGAAAATCGCAACGAGAGAATCGCAACGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAAAGCGAAACTA-A-AATCGCAACGCGAAATGAAAATCGCAACG-C-AA
*
44509 ATCGCAACGCGAAACTAAAATCGCAACGCGAAA
1 ATCGCAAAGCGAAACTAAAATCGCAACGCGAAA
44542 CTAAATTCGC
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
50 10 0.15
51 1 0.02
52 41 0.62
53 2 0.03
54 12 0.18
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (50 bp):
ATCGCAAAGCGAAACTAAAATCGCAACGCGAAATGAAAATCGCAACGCAA
Found at i:44595 original size:33 final size:32
Alignment explanation
Indices: 44551--44677 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
44541 ACTAAATTCG
44551 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
44584 CGTTGCAATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
44617 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
44650 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
44678 AGTAATTTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:44627 original size:66 final size:66
Alignment explanation
Indices: 44544--44676 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
44534 ACGCGAAACT
44544 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
44609 G
66 G
* * *
44610 AAATTCGCGTTGTGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
44675 G
66 G
44676 A
1 A
44677 TAGTAATTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
G
Found at i:46984 original size:12 final size:12
Alignment explanation
Indices: 46967--46991 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46957 TCTTCGGGGA
46967 CTTTTTCTTCTT
1 CTTTTTCTTCTT
46979 CTTTTTCTTCTT
1 CTTTTTCTTCTT
46991 C
1 C
46992 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:48029 original size:20 final size:20
Alignment explanation
Indices: 48004--48075 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
47994 TTTTCCTAAT
*
48004 TCGCAATGTGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
48024 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
** *
48044 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
48065 TCGCAATGCGA
1 TCGCAATGCGA
48076 TACTGACTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 31 0.66
21 16 0.34
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:48089 original size:20 final size:20
Alignment explanation
Indices: 48064--48121 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
48054 AATTTGGAAA
* *
48064 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
*
48084 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
48104 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
48122 AAATCGCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:48128 original size:20 final size:20
Alignment explanation
Indices: 48060--48130 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
48050 TGCGAATTTG
* * *
48060 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATTCT
**
48080 GACTATCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
***
48100 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
48120 GAAAATCGCAA
1 GAAAATCGCAA
48131 TCATCTTCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
GAAAATCGCAACGAGATTCT
Found at i:48417 original size:20 final size:20
Alignment explanation
Indices: 48344--48419 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
48334 CAACGGGGAA
*
48344 ATCGCAACGCGAAAATGGCT
1 ATCGCAACTCGAAAATGGCT
* ***
48364 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACTCGAAAATG-GCT
48384 ATCGCAACGT-GAAAATGGCT
1 ATCGCAAC-TCGAAAATGGCT
*
48404 ATCGCAACTAGAAAAT
1 ATCGCAACTCGAAAAT
48420 CGCAATGCGA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
19 6 0.14
20 31 0.72
21 6 0.14
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACTCGAAAATGGCT
Found at i:48481 original size:19 final size:19
Alignment explanation
Indices: 48438--48562 Score: 197
Period size: 19 Copynumber: 6.8 Consensus size: 19
48428 GAAATGAAAA
48438 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
48454 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
48471 CCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
48490 TCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
48509 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
48528 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
48547 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
48563 TCGTTGCGAT
Statistics
Matches: 100, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
14 11 0.11
16 3 0.03
17 2 0.02
19 84 0.84
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:50193 original size:43 final size:42
Alignment explanation
Indices: 50146--50239 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
50136 CCTCTTCAAC
* * *
50146 GATGACAGTGGCCTCTTGAACGGTGGGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGGGGACTCTTGAGG
* *
50189 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
*
50231 AATGACAGG
1 GATGACAGG
50240 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 23 0.52
43 21 0.48
ACGTcount: A:0.21, C:0.15, G:0.43, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
Found at i:50601 original size:20 final size:20
Alignment explanation
Indices: 50576--50614 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50566 GAAGAATAGT
50576 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
* *
50596 TTACTTTTGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
50615 ATGACAATCG
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:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:50627 original size:20 final size:19
Alignment explanation
Indices: 50604--50668 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
50594 ACTTACTTTT
50604 GCAACGCGAAAATGACAATC
1 GCAACGCG-AAATGACAATC
* *
50624 GCAACGCGGAAATGGCTATC
1 GCAACGC-GAAATGACAATC
* *
50644 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGACAATC
50663 GCAACG
1 GCAACG
50669 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 14 0.38
20 22 0.59
21 1 0.03
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (19 bp):
GCAACGCGAAATGACAATC
Found at i:50721 original size:19 final size:19
Alignment explanation
Indices: 50699--50829 Score: 84
Period size: 19 Copynumber: 7.3 Consensus size: 19
50689 ACAAACCGCA
50699 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
50718 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
50732 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
50751 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
50765 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
50784 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
** *
50804 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
50824 TTGCGA
1 TTGCGA
50830 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 13, Indels: 23
0.71 0.11 0.19
Matches are distributed among these distances:
14 15 0.17
15 6 0.07
16 4 0.05
17 4 0.05
18 6 0.07
19 26 0.30
20 23 0.26
21 3 0.03
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:50735 original size:14 final size:14
Alignment explanation
Indices: 50716--50774 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
50706 TTTCATTTCG
50716 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
50730 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
50747 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
50763 CGTTGCGATTTT
1 CGTTGCGATTTT
50775 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:50741 original size:33 final size:33
Alignment explanation
Indices: 50699--50790 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
50689 ACAAACCGCA
*
50699 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
50732 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
50765 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
50791 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:50809 original size:20 final size:19
Alignment explanation
Indices: 50775--50829 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
50765 TTGCGATTTT
*
50775 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
50794 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
50814 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
50830 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:51392 original size:18 final size:18
Alignment explanation
Indices: 51369--51416 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
51359 CGGGTCGATC
51369 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
51387 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
51405 AGGTGATGGCTC
1 AGGTGATGGCTC
51417 CCAAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:52761 original size:20 final size:20
Alignment explanation
Indices: 52736--52778 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
52726 AATAGTTTCT
*
52736 GAAAATGAAAATTGCAACAC
1 GAAAATGAAAATCGCAACAC
*
52756 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
52776 GAA
1 GAA
52779 TTTGACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:53084 original size:22 final size:22
Alignment explanation
Indices: 53057--53100 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53047 GATGGAGATA
53057 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
53079 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
53101 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:53318 original size:20 final size:20
Alignment explanation
Indices: 53293--53359 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
53283 GTATTATCTC
*
53293 GTTGCGAAAGTCAGTATTGA
1 GTTGCGAAAGTCAGTATCGA
* *
53313 GTTGCGAAATTAAGTATCGA
1 GTTGCGAAAGTCAGTATCGA
*
53333 GTTGCGAAAGTCAGTATCGG
1 GTTGCGAAAGTCAGTATCGA
53353 GTTGCGA
1 GTTGCGA
53360 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.28
Consensus pattern (20 bp):
GTTGCGAAAGTCAGTATCGA
Found at i:53386 original size:41 final size:41
Alignment explanation
Indices: 53273--53404 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
53263 GAAAATCGTA
* * *
53273 TTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATTGAG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGAG
** * * * *
53314 TTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGTATCGGG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGAG
* * *
53354 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTACCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGAG
*
53395 TTGAGATTTT
1 TTGCGATTTT
53405 CCAAATTCGC
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.44
41 40 0.56
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGAG
Found at i:53425 original size:21 final size:21
Alignment explanation
Indices: 53399--53462 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
53389 ACCGCGTTGA
53399 GATTTTCCAAATTCGCATTGC
1 GATTTTCCAAATTCGCATTGC
53420 GATTTTCCAAATTCGCATTGC
1 GATTTTCCAAATTCGCATTGC
* **
53441 GA-TTTACTTATTCGCATTGC
1 GATTTTCCAAATTCGCATTGC
53461 GA
1 GA
53463 ATTGGGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 17 0.43
21 23 0.57
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (21 bp):
GATTTTCCAAATTCGCATTGC
Found at i:56007 original size:18 final size:17
Alignment explanation
Indices: 55971--56011 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
55961 ATTTTTTATT
* *
55971 AAAAATTCTTATTTAAA
1 AAAAATTCTAAATTAAA
55988 AAAAATTCTAAATTATAA
1 AAAAATTCTAAATTA-AA
56006 AAAAAT
1 AAAAAT
56012 CGTATCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAAATTCTAAATTAAA
Found at i:56041 original size:18 final size:17
Alignment explanation
Indices: 55971--56045 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 17
55961 ATTTTTTATT
*
55971 AAAAATTCTTATTTAAA
1 AAAAATTCTTAATTAAA
*
55988 AAAAATTCTAAATTATAA
1 AAAAATTCTTAATTA-AA
56006 AAAAATCGTATCTT--TTAAA
1 AAAAA---T-TCTTAATTAAA
56025 AAAAATATCTTAATTAAA
1 AAAAAT-TCTTAATTAAA
56043 AAA
1 AAA
56046 TTCCTAACTT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
16 6 0.12
17 13 0.27
18 15 0.31
19 7 0.15
20 3 0.06
21 1 0.02
22 3 0.06
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (17 bp):
AAAAATTCTTAATTAAA
Found at i:56046 original size:16 final size:16
Alignment explanation
Indices: 56024--56063 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
56014 TATCTTTTAA
*
56024 AAAAAATATCTTAA-TT
1 AAAAAAT-TCCTAACTT
56040 AAAAAATTCCTAACTT
1 AAAAAATTCCTAACTT
56056 AAAAAATT
1 AAAAAATT
56064 ATTACAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAATTCCTAACTT
Found at i:56061 original size:18 final size:18
Alignment explanation
Indices: 55983--56061 Score: 51
Period size: 18 Copynumber: 4.4 Consensus size: 18
55973 AAATTCTTAT
*
55983 TTAAAAAAAATT-CTAAA
1 TTAAAAAAAATTCCTAAC
* *
56000 TTATAAAAAAA-TCGTATC
1 TTA-AAAAAAATTCCTAAC
*
56018 TTTTAAAAAAAATATCTTAA-
1 --TTAAAAAAAAT-TCCTAAC
56038 TT--AAAAAATTCCTAAC
1 TTAAAAAAAATTCCTAAC
56054 TTAAAAAA
1 TTAAAAAA
56062 TTATTACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 17
0.67 0.09 0.24
Matches are distributed among these distances:
15 5 0.11
16 9 0.19
17 4 0.09
18 15 0.32
19 7 0.15
20 3 0.06
21 4 0.09
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.33
Consensus pattern (18 bp):
TTAAAAAAAATTCCTAAC
Found at i:56433 original size:4 final size:4
Alignment explanation
Indices: 56424--56479 Score: 62
Period size: 4 Copynumber: 14.2 Consensus size: 4
56414 TTAGGAGGTA
* *
56424 TATT TATT TATT TA-T TAAT T-TT TATT TATT TATT TATT GATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
*
56470 ATTTT TATT T
1 -TATT TATT T
56480 TAATTTGAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
3 5 0.11
4 36 0.82
5 3 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:56449 original size:22 final size:23
Alignment explanation
Indices: 56424--56473 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
56414 TTAGGAGGTA
56424 TATTTATTTATTTATTAATTT-T
1 TATTTATTTATTTATTAATTTAT
*
56446 TATTTATTTATTTATTGATTTAT
1 TATTTATTTATTTATTAATTTAT
56469 TATTT
1 TATTT
56474 TTATTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (23 bp):
TATTTATTTATTTATTAATTTAT
Found at i:56481 original size:22 final size:21
Alignment explanation
Indices: 56430--56481 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
56420 GGTATATTTA
56430 TTTA-TTTATTAATTTTTATT
1 TTTATTTTATTAATTTTTATT
*
56450 TATT-TATTTATTGATTTATTATT
1 T-TTAT-TTTATTAATTT-TTATT
56473 TTTATTTTA
1 TTTATTTTA
56482 ATTTGAAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
20 1 0.04
21 2 0.08
22 16 0.62
23 7 0.27
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTATTTTATTAATTTTTATT
Found at i:61441 original size:200 final size:200
Alignment explanation
Indices: 60942--61461 Score: 597
Period size: 197 Copynumber: 2.6 Consensus size: 200
60932 TTTTAAATCA
* * * * *
60942 CTTATAATGTCTAGTGTGTACCGATATTAGCCTTAACTTAAAGATAAGTTCCAATACTATGCCTC
1 CTTATAATGTCTCGTATGTACCGATATTAGCCTCAACTTAAAGATAAGTTCCAATACTACGCCTT
61007 TAATCTTTTAAATTACA-AAAATTTTCCTATTAACTTCCTGGAAATACCCCTTGAACATGCATAT
66 TAATCTTTTAAATTA-AGAAAATTTTCCTATTAACTTCCTGGAAATACCCCTTGAACATGCATAT
* * * * *
61071 GAAGCTATTTTACATTGTTCTTTATGCACAAAACAAAGCTTTGGAATCATTTCAACGCAATTTTT
130 CAAGCTATTATACATTGTTCTTCATGCACAAAACAAAGCTCTGGAACCATTTCAACGCAATTTTT
*
61136 AACCCG
195 AACACG
* * ** * *
61142 CTTATAATGTCTCATATATATTGATA--A-CTTCAACTTAGAGATAAGTTCCAATACTACGCCTT
1 CTTATAATGTCTCGTATGTACCGATATTAGCCTCAACTTAAAGATAAGTTCCAATACTACGCCTT
* * * * * *
61204 TAATATTTTAAATTATGATAATTTTCTTATTAACTTCCTGGGAATACCCCTTGAACATGCCTATC
66 TAATCTTTTAAATTAAGAAAATTTTCCTATTAACTTCCTGGAAATACCCCTTGAACATGCATATC
* * **
61269 AAG-TCATTATAGC-TTGTTCTTCATGCACAAAACCAAGCTCTGGAACCATTTTCAATGTGATTT
131 AAGCT-ATTATA-CATTGTTCTTCATGCACAAAACAAAGCTCTGGAACCA-TTTCAACGCAATTT
*
61332 TTAACATG
193 TTAACACG
* * * *
61340 TTTATAATATCTCGTATGTA-CGATATTAGCCTCAACTTAAAGATAGGTTACAATACTACGCCTT
1 CTTATAATGTCTCGTATGTACCGATATTAGCCTCAACTTAAAGATAAGTTCCAATACTACGCCTT
* * * * * *
61404 TAACCTTTCT-AATTAAGAAAATTTTCCAATTAACTTCCCGAAAATACTCCTCGAACAT
66 TAATCTTT-TAAATTAAGAAAATTTTCCTATTAACTTCCTGGAAATACCCCTTGAACAT
61462 ACCTAACACT
Statistics
Matches: 264, Mismatches: 48, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
196 1 0.00
197 130 0.49
198 35 0.13
199 1 0.00
200 96 0.36
201 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (200 bp):
CTTATAATGTCTCGTATGTACCGATATTAGCCTCAACTTAAAGATAAGTTCCAATACTACGCCTT
TAATCTTTTAAATTAAGAAAATTTTCCTATTAACTTCCTGGAAATACCCCTTGAACATGCATATC
AAGCTATTATACATTGTTCTTCATGCACAAAACAAAGCTCTGGAACCATTTCAACGCAATTTTTA
ACACG
Found at i:61693 original size:25 final size:24
Alignment explanation
Indices: 61659--61729 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
61649 CACAGATAAG
61659 AATAATATTATTTTCATATATAAAA
1 AATAATATTATTTT-ATATATAAAA
* *
61684 AATATTATTATTTTATGAAATAAAA
1 AATAATATTATTTTAT-ATATAAAA
* *
61709 AA-AGTATTGTTTTAATATATA
1 AATAATATTATTTT-ATATATA
61730 TTCTTAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 15 0.38
25 24 0.62
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (24 bp):
AATAATATTATTTTATATATAAAA
Done.