Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004507.1 Hibiscus syriacus cultivar Beakdansim tig00009942_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: 1776135
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:158085 original size:22 final size:22
Alignment explanation
Indices: 158037--158087 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
158027 TTCATTTTAT
* **
158037 TTTATTATTATTTATTATATTA
1 TTTATTATTATTTATTAAAAAA
158059 TTTATTATTA-TTATTAAAAAA
1 TTTATTATTATTTATTAAAAAA
158080 TATTATTA
1 T-TTATTA
158088 CAAACAGGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTATTATTATTTATTAAAAAA
Found at i:158087 original size:3 final size:3
Alignment explanation
Indices: 158033--158074 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
158023 TCATTTCATT
158033 TTA TT- TTA TTA TTA TTTA TTA -TA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA
158075 AAAAATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.11
3 25 0.71
4 6 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:159310 original size:13 final size:14
Alignment explanation
Indices: 159292--159338 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
159282 CACTGTTTAG
159292 TTATAT-TTTAATT
1 TTATATATTTAATT
*
159305 TTATATATTTATTT
1 TTATATATTTAATT
159319 TTAATATATTTAATT
1 TT-ATATATTTAATT
159334 ATTAT
1 -TTAT
159339 TGTTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.21
14 8 0.28
15 13 0.45
16 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:159442 original size:15 final size:15
Alignment explanation
Indices: 159424--159453 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
159414 TAATCTTATT
159424 TATAAATTAATTTTA
1 TATAAATTAATTTTA
*
159439 TATAAATTACTTTTA
1 TATAAATTAATTTTA
159454 AGAAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TATAAATTAATTTTA
Found at i:160633 original size:35 final size:35
Alignment explanation
Indices: 160563--160633 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
160553 TATTTTAAGG
*
160563 TAAATTAAACCCCATGATGATTTAATTATGGGAGA
1 TAAATTAAACCCCATGATGATTTAATTATGAGAGA
* *
160598 TAAATTAAACCCCATGATGGTTTAATTATTAGAGA
1 TAAATTAAACCCCATGATGATTTAATTATGAGAGA
160633 T
1 T
160634 TTTAGTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (35 bp):
TAAATTAAACCCCATGATGATTTAATTATGAGAGA
Found at i:175411 original size:2 final size:2
Alignment explanation
Indices: 175404--175428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
175394 TAAAAGAACT
175404 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 T
175429 GGGCAGCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:175766 original size:19 final size:20
Alignment explanation
Indices: 175742--175792 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
175732 AATGACCAAT
175742 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* * *
175761 AAAATCGCAACACGATTTAG
1 AAAATCGCAACGCGATATAC
175781 AAAATCGCAACG
1 AAAATCGCAACG
175793 TTAAAAAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:175821 original size:18 final size:19
Alignment explanation
Indices: 175779--175830 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
175769 AACACGATTT
*
175779 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGT-AAA
*
175799 AGAAAATCGCAACGGT-CA
1 AGAAAATCGCAACGGTAAA
175817 AGAAAATCGCAACG
1 AGAAAATCGCAACG
175831 CGAGCTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.50
20 15 0.50
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (19 bp):
AGAAAATCGCAACGGTAAA
Found at i:175890 original size:20 final size:20
Alignment explanation
Indices: 175865--176035 Score: 207
Period size: 20 Copynumber: 8.4 Consensus size: 20
175855 TTTAGAAGAA
*
175865 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
* *
175885 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
175905 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
175925 AGTCGCAACGCGATCTAGAAGAA
1 AATCGCAATGCGAT-T-G-AGAG
*
175948 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
175968 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
175988 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * * *
176008 AATTGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
176028 AATCGCAA
1 AATCGCAA
176036 CGTTAAAAAG
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
20 114 0.86
21 2 0.02
22 2 0.02
23 14 0.11
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:175918 original size:40 final size:40
Alignment explanation
Indices: 175844--176035 Score: 231
Period size: 40 Copynumber: 4.7 Consensus size: 40
175834 GCTTCCAAGT
*
175844 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
175887 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
175927 TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
175970 TCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
176010 TTGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAGAATCGCAA
176036 CGTTAAAAAG
Statistics
Matches: 127, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 75 0.59
41 2 0.02
42 4 0.03
43 46 0.36
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:175947 original size:83 final size:83
Alignment explanation
Indices: 175844--176027 Score: 296
Period size: 83 Copynumber: 2.2 Consensus size: 83
175834 GCTTCCAAGT
* * * * *
175844 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
*
175909 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAA
*
175927 TCGCAACGCGATCTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
175992 GCAATGCGATTGAGAGAA
66 GCAATGCGATTGAGAGAA
*
176010 TTGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
176028 AATCGCAACG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.20
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGAGAGAA
Found at i:176036 original size:20 final size:20
Alignment explanation
Indices: 175742--176037 Score: 157
Period size: 20 Copynumber: 14.6 Consensus size: 20
175732 AATGACCAAT
* *
175742 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
175761 AAAATCGCAACACGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
175781 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
175801 AAAATCGCAACG-G-TCAAG
1 AAAATCGCAACGCGATTTAG
* **
175819 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
175840 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
175863 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
175883 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
175903 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
175923 AGAGTCGCAACGCGATCTAGAAG
1 AAAATCGCAACGCGAT-T--TAG
* * *
175946 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
175966 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
175986 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
176006 AGAATTGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
176026 AAAATCGCAACG
1 AAAATCGCAACG
176038 TTAAAAAGAA
Statistics
Matches: 221, Mismatches: 46, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
18 15 0.07
19 17 0.08
20 146 0.66
21 14 0.06
22 1 0.00
23 28 0.13
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:176047 original size:20 final size:20
Alignment explanation
Indices: 176024--176087 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
176014 AACGCGATTT
* *
176024 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTCAAA
176044 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTCAAA
176064 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTCAAA
176084 AGAA
1 AGAA
176088 TAGTTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.53, C:0.17, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTCAAA
Found at i:176176 original size:6 final size:6
Alignment explanation
Indices: 176165--176303 Score: 222
Period size: 6 Copynumber: 24.5 Consensus size: 6
176155 GACACGTATT
176165 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
176213 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
176261 ACCA-G ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
176301 ACC
1 ACC
176304 CGAGACGAGA
Statistics
Matches: 132, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
5 38 0.29
6 94 0.71
ACGTcount: A:0.30, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:176987 original size:6 final size:6
Alignment explanation
Indices: 176971--177008 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
176961 TCTCGTCTCG
176971 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
177009 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:177111 original size:20 final size:20
Alignment explanation
Indices: 177086--177149 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
177076 TTTTTAACTA
177086 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGACCGTTGCGATT
177106 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGACCGTTGCGATT
* *
177126 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGACCGTTGCGATT
177146 TTCT
1 TTCT
177150 AAATCGCGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.11, C:0.19, G:0.17, T:0.53
Consensus pattern (20 bp):
TTCTTTTGACCGTTGCGATT
Found at i:177159 original size:20 final size:20
Alignment explanation
Indices: 177136--177431 Score: 157
Period size: 20 Copynumber: 14.6 Consensus size: 20
177126 TTCTTTTTAA
177136 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
177156 CGTTGCAATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
177176 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
177196 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* *
177216 CATTGCGATTTTCTTCTAGATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
177239 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
177259 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
177279 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
177299 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
177322 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
**
177343 CGTTGCGATTTTCTTGA-C-
1 CGTTGCGATTTTCTAAATCG
*** **
177361 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTAAATCG
177381 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
177401 TGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
177420 CGTTGCGATTTT
1 CGTTGCGATTTT
177432 ATTGGTCATT
Statistics
Matches: 219, Mismatches: 48, Indels: 19
0.77 0.17 0.07
Matches are distributed among these distances:
18 15 0.07
19 17 0.08
20 142 0.65
21 14 0.06
22 4 0.02
23 27 0.12
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:177182 original size:40 final size:40
Alignment explanation
Indices: 177138--177329 Score: 222
Period size: 40 Copynumber: 4.7 Consensus size: 40
177128 CTTTTTAACG
*
177138 TTGCGATTTTCTAAATCGCGTTGCAATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * *
177178 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* *
177218 TTGCGATTTTCTTCTAGATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
177261 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
177301 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
177330 ACTTGGAAGC
Statistics
Matches: 124, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
40 72 0.58
41 2 0.02
42 4 0.03
43 46 0.37
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.37
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:177260 original size:83 final size:83
Alignment explanation
Indices: 177146--177329 Score: 296
Period size: 83 Copynumber: 2.2 Consensus size: 83
177136 CGTTGCGATT
* * * * * *
177146 TTCTAAATCGCGTTGCAATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
*
177211 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
*
177229 TTCTAGATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
177294 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
177312 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
177330 ACTTGGAAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.36
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:188419 original size:19 final size:18
Alignment explanation
Indices: 188395--188433 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
188385 ACCCGAACCG
*
188395 GGATTCCGATAAGGGATTT
1 GGATTCC-AGAAGGGATTT
*
188414 GGATTCCAGAGGGGATTT
1 GGATTCCAGAAGGGATTT
188432 GG
1 GG
188434 GTACCAAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.23, C:0.10, G:0.38, T:0.28
Consensus pattern (18 bp):
GGATTCCAGAAGGGATTT
Found at i:200992 original size:21 final size:21
Alignment explanation
Indices: 200968--201011 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
200958 TTTTGAAAGC
200968 TCTAAATCATTTTTCAAAATT
1 TCTAAATCATTTTTCAAAATT
200989 TCTAAATCATTTTTCAAAATT
1 TCTAAATCATTTTTCAAAATT
201010 TC
1 TC
201012 ATTTTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (21 bp):
TCTAAATCATTTTTCAAAATT
Found at i:207752 original size:20 final size:20
Alignment explanation
Indices: 207727--207764 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
207717 CACATGTTAA
*
207727 AGAATGCATCGATGCACTAT
1 AGAATGCACCGATGCACTAT
*
207747 AGAATGTACCGATGCACT
1 AGAATGCACCGATGCACT
207765 TCAATGGGGA
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:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAATGCACCGATGCACTAT
Found at i:209049 original size:16 final size:15
Alignment explanation
Indices: 209028--209069 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
209018 AAAAGTGATC
209028 TATGTGATCATATGT
1 TATGTGATCATATGT
209043 ATATGTGATACA-ATGT
1 -TATGTGAT-CATATGT
209059 TATGTGA-CATA
1 TATGTGATCATA
209070 AGATACGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 1 0.04
15 7 0.29
16 12 0.50
17 2 0.08
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (15 bp):
TATGTGATCATATGT
Found at i:209399 original size:23 final size:23
Alignment explanation
Indices: 209373--209431 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
209363 TGGCACTACG
*
209373 GTGCATTTCTACGCGACACTTCA
1 GTGCATTTCTACGCGACACTCCA
* * * *
209396 GTGCAATTCTACGTGGCACTCCG
1 GTGCATTTCTACGCGACACTCCA
*
209419 GTGCATTTATACG
1 GTGCATTTCTACG
209432 AGTTGTGGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (23 bp):
GTGCATTTCTACGCGACACTCCA
Found at i:216289 original size:23 final size:21
Alignment explanation
Indices: 216184--216289 Score: 79
Period size: 23 Copynumber: 4.8 Consensus size: 21
216174 AGAAATTGCA
216184 CCGAAGTG-CCACATAGAATGTC
1 CCGAAG-GACCACATAG-ATGTC
*
216206 CCGAAGGACCACATATATGTC
1 CCGAAGGACCACATAGATGTC
* * * *
216227 CCGAAAGACCGCGTGAAAATGTC
1 CCGAAGGACCACAT--AGATGTC
* *
216250 TCGAAGGACCACGTAGAGTTGTC
1 CCGAAGGACCACATAGA--TGTC
*
216273 CCGAAGGACCGCATAGA
1 CCGAAGGACCACATAGA
216290 ACCCTCGACT
Statistics
Matches: 67, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
21 19 0.28
22 13 0.19
23 35 0.52
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.16
Consensus pattern (21 bp):
CCGAAGGACCACATAGATGTC
Found at i:218390 original size:27 final size:29
Alignment explanation
Indices: 218355--218420 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 29
218345 ATTATAAATT
*
218355 ACAAGAAAT-TAAAATGTATAAAA-ATAA
1 ACAAAAAATGTAAAATGTATAAAATATAA
* *
218382 ACAAAAAATGTACAATTTATAAAATATAA
1 ACAAAAAATGTAAAATGTATAAAATATAA
*
218411 A-AAAACATGT
1 ACAAAAAATGT
218421 TCAAATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 8 0.24
28 20 0.61
29 5 0.15
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (29 bp):
ACAAAAAATGTAAAATGTATAAAATATAA
Found at i:218427 original size:29 final size:29
Alignment explanation
Indices: 218366--218427 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
218356 CAAGAAATTA
*
218366 AAATGTATAAAAATAAACAAAAAATGTAC
1 AAATTTATAAAAATAAACAAAAAATGTAC
* *
218395 -AATTTATAAAATATAAA-AAAACATGTTC
1 AAATTTATAAAA-ATAAACAAAAAATGTAC
218423 AAATT
1 AAATT
218428 AAAATAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.61, C:0.06, G:0.05, T:0.27
Consensus pattern (29 bp):
AAATTTATAAAAATAAACAAAAAATGTAC
Found at i:219688 original size:65 final size:64
Alignment explanation
Indices: 219560--219716 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 64
219550 CACACCCATT
* * **
219560 TCGAAT-ACAATTTATGCACCGATGCACAACCATGCATCGATGCACTATGGATTTTATTAAAACA
1 TCGAATCA-AATTTGTGCACCGATGCACAACCATGCATCGATGCACCAACGATTTTATTAAAACA
** * *
219624 TCGAATTGATTTTGTGCACCGATGCACAAGCCATGCATCGATGCACCCCAACTATTTT-TT-AAA
1 TCGAATCAAATTTGTGCACCGATGCACAA-CCATGCATCGATGCA--CCAACGATTTTATTAAAA
219687 CA
63 CA
219689 TCGAATCAAATTTGTGCACCGATGCACA
1 TCGAATCAAATTTGTGCACCGATGCACA
219717 CCCTAGTGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
64 25 0.32
65 45 0.57
66 2 0.03
67 7 0.09
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (64 bp):
TCGAATCAAATTTGTGCACCGATGCACAACCATGCATCGATGCACCAACGATTTTATTAAAACA
Found at i:230538 original size:6 final size:6
Alignment explanation
Indices: 230521--230573 Score: 79
Period size: 6 Copynumber: 8.5 Consensus size: 6
230511 TTTTTCCTAT
*
230521 TTTTTC TTTTTT TCTTTTC TTTTTC TTTTTC TTTTTC TTTTTTC TTTTTC
1 TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC
230571 TTT
1 TTT
230574 AATGAACTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 32 0.74
7 11 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:230540 original size:13 final size:12
Alignment explanation
Indices: 230520--230569 Score: 73
Period size: 13 Copynumber: 4.0 Consensus size: 12
230510 TTTTTTCCTA
230520 TTTTTTCTTTTT
1 TTTTTTCTTTTT
230532 TTCTTTTCTTTTT
1 TT-TTTTCTTTTT
*
230545 CTTTTTCTTTTT
1 TTTTTTCTTTTT
230557 CTTTTTTCTTTTT
1 -TTTTTTCTTTTT
230570 CTTTAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 12 0.35
13 22 0.65
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:230549 original size:25 final size:25
Alignment explanation
Indices: 230521--230573 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
230511 TTTTTCCTAT
230521 TTTTTCTTTTT-TTCTTTTCTTTTTC
1 TTTTTCTTTTTCTT-TTTTCTTTTTC
230546 TTTTTCTTTTTCTTTTTTCTTTTTC
1 TTTTTCTTTTTCTTTTTTCTTTTTC
230571 TTT
1 TTT
230574 AATGAACTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTTTCTTTTTCTTTTTTCTTTTTC
Found at i:235148 original size:35 final size:35
Alignment explanation
Indices: 235101--235186 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
235091 AAAACAGTCA
* * *
235101 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
235136 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
235171 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
235187 TACTTCAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:235199 original size:21 final size:21
Alignment explanation
Indices: 235155--235196 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
235145 TTCTAAACCC
235155 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
235176 TAAATTCT-AAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
235196 T
1 T
235197 TAAGGTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:235342 original size:16 final size:17
Alignment explanation
Indices: 235311--235343 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
235301 ATATTATGTA
235311 TGAATCATTATATTTTT
1 TGAATCATTATATTTTT
*
235328 TGAAT-ATTTTATTTTT
1 TGAATCATTATATTTTT
235344 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATCATTATATTTTT
Found at i:235991 original size:128 final size:126
Alignment explanation
Indices: 235797--236038 Score: 389
Period size: 128 Copynumber: 1.9 Consensus size: 126
235787 AATTTTCTTC
* *
235797 TAATTAGGAGGTGACATGTGTCACCAATAACATCATGATCATGTGTTAACACATGTCAGATCCTA
1 TAATTAGGAGGTAACATGTGTCACCAATAACATCATGATCATGTGCTAACACATGTCAGATCCTA
235862 ATTAAATGATTAATTTATTAAATTTT-TTTAATTTAGGACC-AATTGATAGCATATATAAA
66 ATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* *
235921 TAATTAGGTGGTAACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACATGTGTCACCAAT-A-AC--ATCATGATCATGTGCTAACACATGTCAGAT
*
235986 CCTAATTAAATGATTAATTTATTAATTTTTATTTAATTTAGGACCAAATTGAT
62 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
236039 TATATAAATA
Statistics
Matches: 107, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
124 26 0.24
125 1 0.01
126 2 0.02
128 57 0.53
129 14 0.13
130 7 0.07
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (126 bp):
TAATTAGGAGGTAACATGTGTCACCAATAACATCATGATCATGTGCTAACACATGTCAGATCCTA
ATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:256702 original size:2 final size:2
Alignment explanation
Indices: 256695--256741 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
256685 GCTTTAACTC
256695 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
256737 AT AT A
1 AT AT A
256742 AAAAGAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:269175 original size:21 final size:21
Alignment explanation
Indices: 269149--269326 Score: 236
Period size: 21 Copynumber: 8.6 Consensus size: 21
269139 GCGTTGCATT
*
269149 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
269170 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
269191 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
269212 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
269233 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
269254 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTGAAAA
** **
269274 TCGCGTTGCGATTTTTCG--TT
1 TCGCGTTGCGATAGTT-GAAAA
269294 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
269315 TCGCGTTGCGAT
1 TCGCGTTGCGAT
269327 TTTCCATTTC
Statistics
Matches: 141, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.01
20 30 0.21
21 110 0.78
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:269279 original size:20 final size:20
Alignment explanation
Indices: 269254--269346 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
269244 TAGTTGAAAA
269254 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
*
269274 TCGCGTTGCGATTTTTC-GTT
1 TCGCGTTGCGATTTTCCAG-T
* ** **
269294 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
*
269315 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
269335 TCGCGTTGCGAT
1 TCGCGTTGCGAT
269347 AGTCTACAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.02
20 44 0.75
21 14 0.24
ACGTcount: A:0.13, C:0.22, G:0.26, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:269328 original size:61 final size:61
Alignment explanation
Indices: 269148--269349 Score: 262
Period size: 63 Copynumber: 3.3 Consensus size: 61
269138 CGCGTTGCAT
* * **
269148 TTCGCGTTGCGATAATTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCAA
* *
269211 ATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAA
** ** *
269273 TTCGCGTTGCGATTTTTCG-TTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTT-GAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAA
269334 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
269350 CTACAATTGT
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
61 53 0.43
62 17 0.14
63 54 0.44
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (61 bp):
TTCGCGTTGCGATAGTTGAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAA
Found at i:269383 original size:41 final size:40
Alignment explanation
Indices: 269173--269386 Score: 155
Period size: 42 Copynumber: 5.2 Consensus size: 40
269163 TTGAAAATCG
* ** *
269173 CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATC
1 CGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCAATTC
* ** *
269214 GCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATC
1 -CGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCAATTC
* ** ** * **
269256 GCGTTGCGAT-TTTCCAGTTCGCGTTGCGATTTTTCGTTTC
1 -CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC
*
269296 GCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTC
1 -CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC
* *
269337 GCGTTGCGATAGTCT-ACAATTGTCGTTGCGATTTTCCAAATT-
1 -CGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTC
269379 CGTTGCGA
1 CGTTGCGA
269387 AAATTCGTTG
Statistics
Matches: 147, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
40 14 0.10
41 64 0.44
42 66 0.45
43 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC
Found at i:270150 original size:22 final size:22
Alignment explanation
Indices: 270122--270192 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
270112 ATTTGGAAAA
270122 TCGCAACGACAACTGTAGACTT
1 TCGCAACGACAACTGTAGACTT
270144 TCGCAACGACAACTGTAGACTT
1 TCGCAACGACAACTGTAGACTT
*
270166 TCGC-A--ACAACTGTAGACTA
1 TCGCAACGACAACTGTAGACTT
270185 TCGCAACG
1 TCGCAACG
270193 CGAAATGGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
19 17 0.38
20 1 0.02
21 1 0.02
22 26 0.58
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.21
Consensus pattern (22 bp):
TCGCAACGACAACTGTAGACTT
Found at i:270176 original size:19 final size:19
Alignment explanation
Indices: 270130--270191 Score: 88
Period size: 19 Copynumber: 3.1 Consensus size: 19
270120 AATCGCAACG
270130 ACAACTGTAGACTTTCGCAA
1 ACAACTGTAGACTTTCGC-A
270150 CGACAACTGTAGACTTTCGCA
1 --ACAACTGTAGACTTTCGCA
*
270171 ACAACTGTAGACTATCGCA
1 ACAACTGTAGACTTTCGCA
270190 AC
1 AC
270192 GCGAAATGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
19 20 0.51
21 1 0.03
22 18 0.46
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (19 bp):
ACAACTGTAGACTTTCGCA
Found at i:270226 original size:41 final size:41
Alignment explanation
Indices: 270181--270404 Score: 394
Period size: 41 Copynumber: 5.5 Consensus size: 41
270171 ACAACTGTAG
*
270181 ACTATCGCAACGCGAAATGGAAAATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
270222 ACTATCGCAACGCAAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
270263 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
**
270304 ACTATAACAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
270345 ACTATCGCAACGCGAAATGGAAAATCGCAACGCAATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
270386 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
270405 CAACGCGAAT
Statistics
Matches: 175, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 175 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:280368 original size:2 final size:2
Alignment explanation
Indices: 280361--280399 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
280351 ATTCACGTGA
280361 AT AT AT 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
280400 ATTTTCTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:287397 original size:25 final size:25
Alignment explanation
Indices: 287364--287411 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
287354 GTGGAAGACA
287364 TGGTGGATTTAGAGGATCTGAGGCG
1 TGGTGGATTTAGAGGATCTGAGGCG
287389 TGGTGGATTTAGAGGATCTGAGG
1 TGGTGGATTTAGAGGATCTGAGG
287412 AGAATGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.06, G:0.44, T:0.29
Consensus pattern (25 bp):
TGGTGGATTTAGAGGATCTGAGGCG
Found at i:287771 original size:12 final size:12
Alignment explanation
Indices: 287730--287775 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
287720 TTAATAATTC
287730 TTTTTAAAATAT
1 TTTTTAAAATAT
*
287742 TTTTCTAAATATTT
1 TTTT-TAAA-ATAT
*
287756 TTTTTAAAATAA
1 TTTTTAAAATAT
287768 TTTTTAAA
1 TTTTTAAA
287776 GTATATGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 14 0.48
13 8 0.28
14 7 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTTAAAATAT
Found at i:291722 original size:20 final size:21
Alignment explanation
Indices: 291697--291748 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
291687 TTTTCCCAAT
*
291697 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
291717 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
291738 TCGCAATGCGA
1 TCGCAATGCGA
291749 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:291762 original size:20 final size:20
Alignment explanation
Indices: 291737--291851 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
291727 AATTGGGAAA
*
291737 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
** * *
291757 ATCGCAATTCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
291778 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
291798 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
291818 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
291838 TTCGCAACGCGATA
1 ATCGCAACGCGATA
291852 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 65 0.80
21 12 0.15
22 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:292067 original size:22 final size:22
Alignment explanation
Indices: 292039--292082 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
292029 AACTCTCTCA
292039 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
292061 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
292083 TATCTCCATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:292399 original size:20 final size:20
Alignment explanation
Indices: 292345--292403 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
292335 GCGATTCTCT
**
292345 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
292365 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
292385 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
292404 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:293744 original size:18 final size:18
Alignment explanation
Indices: 293723--293767 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
293713 TCTACTTCGG
293723 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
293741 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
293759 GAGCCATCA
1 GAGCCATCA
293768 TCTGATCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:294274 original size:20 final size:20
Alignment explanation
Indices: 294249--294294 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
294239 TAGTTTACTT
294249 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
294269 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
294289 TCGCAA
1 TCGCAA
294295 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:294303 original size:19 final size:20
Alignment explanation
Indices: 294260--294304 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
294250 CGCAACACGA
294260 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
294280 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
294299 AAATGA
1 AAATGA
294305 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:294310 original size:19 final size:19
Alignment explanation
Indices: 294268--294383 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
294258 GAAAATGACT
***
294268 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
294288 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
294307 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
294321 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
294339 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
294353 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
294372 ATCGCAATGCGA
1 ATCGCAATGCGA
294384 TTTGTGTTTC
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 6 0.08
17 2 0.03
18 11 0.14
19 27 0.35
20 10 0.13
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:294323 original size:14 final size:14
Alignment explanation
Indices: 294304--294361 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
294294 ATGCGAAATG
294304 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
294318 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
294334 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
294350 AAAATCGCAACG
1 AAAATCGCAACG
294362 CGAAATGAAA
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:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:294346 original size:32 final size:33
Alignment explanation
Indices: 294288--294378 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
294278 GGAAATGGCT
294288 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
294321 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
294353 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
294379 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:294414 original size:14 final size:14
Alignment explanation
Indices: 294395--294452 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
294385 TTGTGTTTCG
294395 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
294409 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
294425 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
294441 CGTTGTGATTTT
1 CGTTGCGATTTT
294453 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:294429 original size:32 final size:33
Alignment explanation
Indices: 294390--294468 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
294380 GCGATTTGTG
294390 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
294422 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
294455 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
294469 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:294487 original size:20 final size:19
Alignment explanation
Indices: 294453--294508 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
294443 TTGTGATTTT
*
294453 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
294472 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
294492 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
294509 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:296392 original size:14 final size:14
Alignment explanation
Indices: 296373--296408 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
296363 ATTGTTTAAT
296373 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
296387 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
296401 TGATTTGT
1 TGATTTGT
296409 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:296564 original size:19 final size:18
Alignment explanation
Indices: 296495--296591 Score: 93
Period size: 19 Copynumber: 5.7 Consensus size: 18
296485 AAAACAGACT
**
296495 ATCGCAATGCGAAATGACT
1 ATCGCAATGCG-AATGAAA
296514 ATCGCAA--CG-A-GAAA
1 ATCGCAATGCGAATGAAA
296528 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCG-AATGAAA
296547 ATCGCAATGCGAATTGAAA
1 ATCGCAATGCGAA-TGAAA
296566 ATCGCAA--CG-A-GAAA
1 ATCGCAATGCGAATGAAA
296580 ATCGCAATGCGA
1 ATCGCAATGCGA
296592 TTTTCATTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 20
0.75 0.02 0.22
Matches are distributed among these distances:
14 20 0.30
15 1 0.01
16 5 0.07
17 4 0.06
18 3 0.04
19 34 0.51
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAATGAAA
Found at i:296635 original size:20 final size:20
Alignment explanation
Indices: 296610--296667 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
296600 TCGCATTGCG
*
296610 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
296630 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
296650 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
296668 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:296915 original size:19 final size:19
Alignment explanation
Indices: 296891--296951 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
296881 CTTAAGTGAG
296891 ATCGCAATGCGAAAAGAAA
1 ATCGCAATGCGAAAAGAAA
*
296910 ATCGCAA--CG---AGATA
1 ATCGCAATGCGAAAAGAAA
* *
296924 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAAAGAAA
296943 ATCGCAATG
1 ATCGCAATG
296952 ACAAAATCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 10 0.31
16 2 0.06
17 2 0.06
19 18 0.56
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAAAGAAA
Found at i:297018 original size:33 final size:33
Alignment explanation
Indices: 296963--297086 Score: 140
Period size: 33 Copynumber: 3.7 Consensus size: 33
296953 CAAAATCGCA
* * *
296963 ACGATTTTAATTTTCGCTTTGCGATTCCCTCGTT
1 ACGATTTTCA-TTTCGCATTGCGATTCTCTCGTT
296997 ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
* ** ** *
297030 GCCTTTTTCATTTCGCATTATGATTCTATCGTT
1 ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
* *
297063 GCGATTTGCATTTCGCATTGCGAT
1 ACGATTTTCATTTCGCATTGCGAT
297087 GGTCAAATGA
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
33 67 0.88
34 9 0.12
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (33 bp):
ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
Found at i:297888 original size:24 final size:24
Alignment explanation
Indices: 297861--297914 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
297851 GTATTCGAAA
* *
297861 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
297885 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
297909 TTTGAT
1 TTTGAT
297915 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:298103 original size:12 final size:12
Alignment explanation
Indices: 298086--298110 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
298076 ATATAATCCT
298086 GAAGAAGAAAAA
1 GAAGAAGAAAAA
298098 GAAGAAGAAAAA
1 GAAGAAGAAAAA
298110 G
1 G
298111 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:298378 original size:66 final size:66
Alignment explanation
Indices: 298301--298434 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
298291 TGGAAGATGG
298301 CTATCAACTAAAAGTTAACAAATCAAGCAAAGATCGTTTCGAAACAAGGTGTATGATTGACAAAA
1 CTATCAACTAAAAGTTAACAAATCAAGCAAAGATCGTTTCGAAACAAGGTGTATGATTGACAAAA
298366 A
66 A
298367 CTATCAACTAAAAGTTAACAAATCAAGCAAAGATCGTTTCGAAACAAGGTGTATGATTGACAAAA
1 CTATCAACTAAAAGTTAACAAATCAAGCAAAGATCGTTTCGAAACAAGGTGTATGATTGACAAAA
298432 A
66 A
298433 CT
1 CT
298435 GTACGTGGCG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (66 bp):
CTATCAACTAAAAGTTAACAAATCAAGCAAAGATCGTTTCGAAACAAGGTGTATGATTGACAAAA
A
Found at i:300473 original size:19 final size:19
Alignment explanation
Indices: 300451--300509 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
300441 GGAAATTACT
300451 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
300470 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
300484 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
300503 ATCGCAA
1 ATCGCAA
300510 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:300653 original size:14 final size:14
Alignment explanation
Indices: 300634--300670 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
300624 ACATCAATTA
300634 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
300648 ACAAATCACCTTTT
1 ACAAATCAACTTTT
300662 ACAAATCAA
1 ACAAATCAA
300671 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:302902 original size:166 final size:163
Alignment explanation
Indices: 302631--302948 Score: 609
Period size: 166 Copynumber: 1.9 Consensus size: 163
302621 AAGTGAAATT
302631 ACGAGTAAATTTATCATCAAGTTAAATGGAAAATCTAAACTTACCTCGTTGCGTAGAGTATGAAC
1 ACGAGTAAATTTATCATCAAGTTAAATGGAAAATCTAAACTTACCTCGTTGCGTAGAGTATGAAC
302696 CTCATTCTGCAACGATACTACCATCTCATGTAGAGCGGCAACCTCACCACGTAAAGTAGACACCT
66 CTCATTCTGCAACGATACTACCATCTCATGTAGAGCGGCAACCTCACCACGTAAAGTAGACACCT
302761 CCACACGCCATGCACCATCGTTTAATCTAAGTG
131 CCACACGCCATGCACCATCGTTTAATCTAAGTG
302794 ACGAGTAAATTTATCATCAAGTTAAATATGGAAAATCTTAAACTTACCTCGTTGCGTAGAGTATG
1 ACGAGTAAATTTATCATCAAGTT-AA-ATGGAAAATC-TAAACTTACCTCGTTGCGTAGAGTATG
302859 AACCTCATTCTGCAACGATACTACCATCTCATGTAGAGCGGCAACCTCACCACGTAAAGTAGACA
63 AACCTCATTCTGCAACGATACTACCATCTCATGTAGAGCGGCAACCTCACCACGTAAAGTAGACA
302924 CCTCCACACGCCATGCACCATCGTT
128 CCTCCACACGCCATGCACCATCGTT
302949 ATTGCGTAGA
Statistics
Matches: 152, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
163 23 0.15
164 2 0.01
165 10 0.07
166 117 0.77
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (163 bp):
ACGAGTAAATTTATCATCAAGTTAAATGGAAAATCTAAACTTACCTCGTTGCGTAGAGTATGAAC
CTCATTCTGCAACGATACTACCATCTCATGTAGAGCGGCAACCTCACCACGTAAAGTAGACACCT
CCACACGCCATGCACCATCGTTTAATCTAAGTG
Found at i:304518 original size:33 final size:33
Alignment explanation
Indices: 304461--304559 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
304451 ACGAGATAAT
304461 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
304495 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
304528 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
304560 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:304553 original size:19 final size:19
Alignment explanation
Indices: 304436--304581 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
304426 TCTTTTGGTT
*
304436 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
304455 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
304475 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
304493 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
304509 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
304526 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
304542 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
304561 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
304580 GA
1 GA
304582 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 43 0.43
20 27 0.27
21 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:304599 original size:19 final size:18
Alignment explanation
Indices: 304577--304643 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
304567 AAAATCGCAA
*
304577 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
*
304596 TGCGTTTTTTATTTCGCGT
1 TGCG-ATTTTATTTCGCGT
*
304615 TGCGATAATTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
304635 TGCGATTTT
1 TGCGATTTT
304644 CATTCTTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 24 0.60
20 15 0.38
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:305186 original size:20 final size:20
Alignment explanation
Indices: 305161--305213 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
305151 GCGCTATGTA
305161 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
305181 AATCGCGTTGCGAAAGTCAT
1 AATCGCGTTGCGAAAGTCAG
* *
305201 TATCTCGTTGCGA
1 AATCGCGTTGCGA
305214 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:305366 original size:21 final size:21
Alignment explanation
Indices: 305326--305366 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
305316 ATTGTAGACC
**
305326 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
305347 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
305367 GCGAATTTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:309634 original size:12 final size:12
Alignment explanation
Indices: 309614--309654 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
309604 TTCTAACTCC
*
309614 TCGTTGTCATCA
1 TCGTCGTCATCA
*
309626 TCGTCGTCATCG
1 TCGTCGTCATCA
*
309638 TCGTCGTCACCA
1 TCGTCGTCATCA
309650 TCGTC
1 TCGTC
309655 ATCGTCGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.34
Consensus pattern (12 bp):
TCGTCGTCATCA
Found at i:310024 original size:15 final size:15
Alignment explanation
Indices: 310006--310035 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
309996 ATGGCGGCAT
310006 CATATATGGCTGCGG
1 CATATATGGCTGCGG
310021 CATATATGGCTGCGG
1 CATATATGGCTGCGG
310036 TGGCTGCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (15 bp):
CATATATGGCTGCGG
Found at i:311678 original size:111 final size:111
Alignment explanation
Indices: 311545--311754 Score: 368
Period size: 111 Copynumber: 1.9 Consensus size: 111
311535 ATTACAAAAA
* * *
311545 TTAATTCTTAATCTAATAATCATGCAT-TAAATGAATCAACTAATTATTATTAATAATTTAAATT
1 TTAATTCTTAATCTAATAATCATGCATAT-AATAAATCAACTAAATATTACTAATAATTTAAATT
*
311609 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAATTATCGAGATAT
65 AAATTAAAACGTTAAAATGTTACCGCATCAGCAAATTATCGAGATAT
311656 TTAATTCTTAATCTAATAATCATGCATATAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATATAATAAATCAACTAAATATTACTAATAATTTAAATTA
311721 AATTAAAACGTTAAAATGTTACCGCATCAGCAAA
66 AATTAAAACGTTAAAATGTTACCGCATCAGCAAA
311755 GTGTAGAGAT
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
111 93 0.99
112 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATATAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGCATCAGCAAATTATCGAGATAT
Found at i:311904 original size:12 final size:10
Alignment explanation
Indices: 311890--311930 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
311880 AAATTAAAAA
*
311890 GAGAGTATTT
1 GAGAGAATTT
311900 GAGAGAAATTT
1 GAGAG-AATTT
311911 -AGAGAATTT
1 GAGAGAATTT
311920 GAGAGAATTT
1 GAGAGAATTT
311930 G
1 G
311931 GAGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:318673 original size:28 final size:28
Alignment explanation
Indices: 318633--318688 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
318623 TCAAGTTTTA
318633 GCTTCCTGATTCAAGTTGTGAAACCTTT
1 GCTTCCTGATTCAAGTTGTGAAACCTTT
*
318661 GCTTCTTGATTCAAGTTGTGAAACCTTT
1 GCTTCCTGATTCAAGTTGTGAAACCTTT
318689 CTGATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (28 bp):
GCTTCCTGATTCAAGTTGTGAAACCTTT
Found at i:326233 original size:14 final size:14
Alignment explanation
Indices: 326214--326241 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
326204 CATCCAAACA
326214 CTGAAAAATATTTT
1 CTGAAAAATATTTT
326228 CTGAAAAATATTTT
1 CTGAAAAATATTTT
326242 ACATTTCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
CTGAAAAATATTTT
Found at i:328262 original size:35 final size:34
Alignment explanation
Indices: 328210--328279 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
328200 ATTTTAACAG
328210 ATCAAAATTAACCTATTTAATCAAATTTAATTTA
1 ATCAAAATTAACCTATTTAATCAAATTTAATTTA
*
328244 ATCAAATATTAACTTATTTAATCAAATTTAATTTA
1 ATCAAA-ATTAACCTATTTAATCAAATTTAATTTA
328279 A
1 A
328280 AGATATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 6 0.18
35 28 0.82
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (34 bp):
ATCAAAATTAACCTATTTAATCAAATTTAATTTA
Found at i:328264 original size:20 final size:18
Alignment explanation
Indices: 328210--328274 Score: 73
Period size: 15 Copynumber: 3.6 Consensus size: 18
328200 ATTTTAACAG
*
328210 ATCAAAATTAACCTATTTA
1 ATCAAATTTAA-CTATTTA
328229 ATCAAATTT-A--ATTTA
1 ATCAAATTTAACTATTTA
328244 ATCAAATATTAACTTATTTA
1 ATCAAAT-TTAAC-TATTTA
328264 ATCAAATTTAA
1 ATCAAATTTAA
328275 TTTAAAGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 12 0.30
16 2 0.05
17 1 0.03
18 1 0.03
19 12 0.30
20 12 0.30
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.42
Consensus pattern (18 bp):
ATCAAATTTAACTATTTA
Found at i:330298 original size:51 final size:51
Alignment explanation
Indices: 330221--330318 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
330211 ATATCAACCG
330221 TCTATTTTCACTCATCAAATGATTTTAAATACATGTAAAACTTAAAAAACA
1 TCTATTTTCACTCATCAAATGATTTTAAATACATGTAAAACTTAAAAAACA
* * * * *
330272 TCTATTTTTACTCGTCAAATGGTTTTAATTATATGTAAAACTTAAAA
1 TCTATTTTCACTCATCAAATGATTTTAAATACATGTAAAACTTAAAA
330319 CGTTTTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (51 bp):
TCTATTTTCACTCATCAAATGATTTTAAATACATGTAAAACTTAAAAAACA
Found at i:331450 original size:2 final size:2
Alignment explanation
Indices: 331443--331468 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
331433 AGCCTTCAAA
331443 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
331469 CATAAATCTA
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:331579 original size:3 final size:3
Alignment explanation
Indices: 331571--331595 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
331561 GATTGATGCC
331571 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
331596 TAAAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:334463 original size:36 final size:36
Alignment explanation
Indices: 334416--334497 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 36
334406 TCGTCTCCCC
* *
334416 GAGACACTTTTTCT-TAAAAACAAATGCTGTCTCGCTT
1 GAGACA-TTTTTCTCTAAAAACAAAT-CTATCTCACTT
* *
334453 GAGACATTTTTCTCTTAAAACAAATTTATCTCACTT
1 GAGACATTTTTCTCTAAAAACAAATCTATCTCACTT
334489 GAGACATTT
1 GAGACATTT
334498 CCCCTCAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 24 0.60
37 16 0.40
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
GAGACATTTTTCTCTAAAAACAAATCTATCTCACTT
Found at i:334742 original size:66 final size:66
Alignment explanation
Indices: 334653--334863 Score: 316
Period size: 66 Copynumber: 3.2 Consensus size: 66
334643 ATTTATAATA
* ** * * *
334653 TTTGAGTTTGTTTGTCTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCTCATGAAACACTAAA
1 TTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACCAAT
334718 C
66 C
*
334719 TTTAAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACCAAT
1 TTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACCAAT
334784 C
66 C
* * *
334785 TTTGAG-TATGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAA
1 TTTGAGAT-TGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACCAA
334849 TC
65 TC
334851 TTTGAGATTGTTT
1 TTTGAGATTGTTT
334864 TTGTCACACC
Statistics
Matches: 132, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
65 1 0.01
66 130 0.98
67 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (66 bp):
TTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACCAAT
C
Found at i:336941 original size:22 final size:21
Alignment explanation
Indices: 336913--336956 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
336903 CAGTATCGAA
*
336913 TGCTACAGAAGTATCGATACCC
1 TGCTACAG-AGTACCGATACCC
*
336935 TGCTACAGTGTACCGATACCC
1 TGCTACAGAGTACCGATACCC
336956 T
1 T
336957 TACTACAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (21 bp):
TGCTACAGAGTACCGATACCC
Found at i:336953 original size:21 final size:22
Alignment explanation
Indices: 336913--336965 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
336903 CAGTATCGAA
* *
336913 TGCTACAGAAGTATCGATACCC-
1 TGCTACAG-TGTACCGATACCCT
336935 TGCTACAGTGTACCGATACCCT
1 TGCTACAGTGTACCGATACCCT
*
336957 TACTACAGT
1 TGCTACAGT
336966 AAATTCGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (22 bp):
TGCTACAGTGTACCGATACCCT
Found at i:337624 original size:22 final size:21
Alignment explanation
Indices: 337590--337650 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
337580 TGAAATTTTA
* * *
337590 TCCCAAAGGACCTGTGAATATG
1 TCCCGAAGAACCTATGAAT-TG
* *
337612 TTCCGAAGAACCTATGAGTTG
1 TCCCGAAGAACCTATGAATTG
* *
337633 TCCCGAAGGACCTTTGAA
1 TCCCGAAGAACCTATGAA
337651 ACCCTCGACT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
TCCCGAAGAACCTATGAATTG
Found at i:339724 original size:40 final size:40
Alignment explanation
Indices: 339669--339816 Score: 111
Period size: 40 Copynumber: 3.6 Consensus size: 40
339659 TGATCTATCA
*
339669 TCCTCATTACATAGGAACCGTGTCATCCACCAACCATACC
1 TCCTCATCACATAGGAACCGTGTCATCCACCAACCATACC
* *** **
339709 TCCTCATCACGTAGGAGTTGTGTCA-CC-CCTAGATAACTAACC
1 TCCTCATCACATAGGAACCGTGTCATCCACC-A-ACCA-T-ACC
* * * * *
339751 ATCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAGATC
1 -TCCTCATCACATAGGAACCGTGTCATCCACCAACCATACC
**
339792 TCCTCATCACATAGGAGTCGTGTCA
1 TCCTCATCACATAGGAACCGTGTCA
339817 CGTTTAGATG
Statistics
Matches: 81, Mismatches: 20, Indels: 14
0.70 0.17 0.12
Matches are distributed among these distances:
38 2 0.02
39 3 0.04
40 43 0.53
41 3 0.04
42 3 0.04
43 23 0.28
44 2 0.02
45 2 0.02
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (40 bp):
TCCTCATCACATAGGAACCGTGTCATCCACCAACCATACC
Found at i:339756 original size:131 final size:131
Alignment explanation
Indices: 339517--339768 Score: 328
Period size: 131 Copynumber: 1.9 Consensus size: 131
339507 CTTGAAATAA
* * * * *
339517 ATCCCTAAAGATGACCAGCTATCCTCATCGCGTAGGAATCGTGTTATCCACCGACCAGACCTCCT
1 ATCCCTAAAGATGACCAGCTATCCTCATCACATAGGAACCGTGTCATCCACCAACCAGACCTCCT
* * * *
339582 CATCACGTAGGAGTCGCGTCACTCTTAGATAACAAGCCTTCCTCATCACTTAGGAATCATGTTAT
66 CATCACGTAGGAGTCGCGTCACCCCTAGATAACAAGCCATCCTCATCACGTAGGAATCATGTTAT
339647 C
131 C
* * * *
339648 ATCCCTAAAGATGATCTATC-ATCCTCATTACATAGGAACCGTGTCATCCACCAACCATACCTCC
1 ATCCCTAAAGATGA-CCAGCTATCCTCATCACATAGGAACCGTGTCATCCACCAACCAGACCTCC
* * *
339712 TCATCACGTAGGAGTTGTGTCACCCCTAGATAACTAA-CCATCCTCATCGCGTAGGAA
65 TCATCACGTAGGAGTCGCGTCACCCCTAGATAAC-AAGCCATCCTCATCACGTAGGAA
339769 CCGTGTCATC
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
131 98 0.95
132 5 0.05
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.25
Consensus pattern (131 bp):
ATCCCTAAAGATGACCAGCTATCCTCATCACATAGGAACCGTGTCATCCACCAACCAGACCTCCT
CATCACGTAGGAGTCGCGTCACCCCTAGATAACAAGCCATCCTCATCACGTAGGAATCATGTTAT
C
Found at i:340029 original size:3 final size:3
Alignment explanation
Indices: 340023--340090 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
340013 TATTATTATT
* * * *
340023 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATT ATT ATT ATT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
340071 ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC AT
340091 TATTATTATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (3 bp):
ATC
Found at i:340632 original size:8 final size:8
Alignment explanation
Indices: 340592--340653 Score: 61
Period size: 8 Copynumber: 7.5 Consensus size: 8
340582 TGAAAGAAGA
340592 AAAAAAAG
1 AAAAAAAG
*
340600 AAAAATAGG
1 AAAAA-AAG
*
340609 GAAAAAAG
1 AAAAAAAG
***
340617 ATCGAAAG
1 AAAAAAAG
340625 AAAAAAAG
1 AAAAAAAG
340633 AAAAAAAG
1 AAAAAAAG
340641 AAAAAAGAG
1 AAAAAA-AG
340650 AAAA
1 AAAA
340654 TAAAAGAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
8 30 0.71
9 12 0.29
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:344818 original size:37 final size:38
Alignment explanation
Indices: 344756--344832 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 38
344746 AACCTAAGAG
344756 TTTGCTTAAGCGATATAAATATAATTTAACCTGAGACC
1 TTTGCTTAAGCGATATAAATATAATTTAACCTGAGACC
* *
344794 TTTGCTTAAGCTATATAAA-GTAATTTAACCTGAGACC
1 TTTGCTTAAGCGATATAAATATAATTTAACCTGAGACC
344831 TT
1 TT
344833 GAGAAAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
37 19 0.51
38 18 0.49
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (38 bp):
TTTGCTTAAGCGATATAAATATAATTTAACCTGAGACC
Found at i:346280 original size:23 final size:23
Alignment explanation
Indices: 346249--346309 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
346239 CTCGTGTAAA
*
346249 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
346272 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
346295 TGCACTGAAGTGCCA
1 TGCACCGAAGTGCCA
346310 TTTAAGTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:346808 original size:2 final size:2
Alignment explanation
Indices: 346790--346836 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
346780 TTACATAAAC
* *
346790 AT AT AT CAT AT CT -T AT AT AT AT AT AT CT -T AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
346831 AT AT AT
1 AT AT AT
346837 CCACAAATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 36 0.90
3 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:346817 original size:15 final size:15
Alignment explanation
Indices: 346790--346830 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
346780 TTACATAAAC
346790 ATATATCATATCTTAT
1 ATATAT-ATATCTTAT
346806 ATATATATATCTTAT
1 ATATATATATCTTAT
346821 ATATATATAT
1 ATATATATAT
346831 ATATATCCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATATCTTAT
Found at i:347793 original size:24 final size:22
Alignment explanation
Indices: 347742--347798 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
347732 TTCCCTTGAA
347742 GTGCATCGATACATTCTAAAAT
1 GTGCATCGATACATTCTAAAAT
* *
347764 GT--ATCGATGCATTCTTTAACAT
1 GTGCATCGATACATTC--TAAAAT
347786 GTGCATCGATACA
1 GTGCATCGATACA
347799 CTATCCATGC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 11 0.39
22 9 0.32
24 8 0.29
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (22 bp):
GTGCATCGATACATTCTAAAAT
Found at i:348799 original size:37 final size:38
Alignment explanation
Indices: 348731--348814 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 38
348721 ATGACTCGGA
*
348731 CTGAGA-CTTTGCTTAAGCGATATAAATATAATTTAAC
1 CTGAGACCTTTGCTTAAACGATATAAATATAATTTAAC
348768 CTGAGACCTTTGCTTAAACGATATAAA-ATAATTTAAC
1 CTGAGACCTTTGCTTAAACGATATAAATATAATTTAAC
348805 CTGAGACCTT
1 CTGAGACCTT
348815 GCCAAAGAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 26 0.58
38 19 0.42
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (38 bp):
CTGAGACCTTTGCTTAAACGATATAAATATAATTTAAC
Found at i:354139 original size:21 final size:22
Alignment explanation
Indices: 354113--354156 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
354103 TATTATAGAA
354113 AGGGTATCGATA-CACTGTAGC
1 AGGGTATCGATACCACTGTAGC
*
354134 AGGGTATCGATACCCCTGTAGC
1 AGGGTATCGATACCACTGTAGC
354156 A
1 A
354157 TCCTGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (22 bp):
AGGGTATCGATACCACTGTAGC
Found at i:359006 original size:34 final size:34
Alignment explanation
Indices: 358968--359036 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
358958 TATGAAGAAG
358968 AACCGATTCAAATTTTAGCTCATGAAATTAAGCA
1 AACCGATTCAAATTTTAGCTCATGAAATTAAGCA
359002 AACCGATTCAAATTTTAGCTCATGAAATTAAGCA
1 AACCGATTCAAATTTTAGCTCATGAAATTAAGCA
359036 A
1 A
359037 TTGAGGAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (34 bp):
AACCGATTCAAATTTTAGCTCATGAAATTAAGCA
Found at i:360552 original size:22 final size:22
Alignment explanation
Indices: 360522--360563 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
360512 AGTCAAGGGT
*
360522 TTCATAGGTCCTTCGGGACATA
1 TTCACAGGTCCTTCGGGACATA
*
360544 TTCACAGGTCTTTCGGGACA
1 TTCACAGGTCCTTCGGGACA
360564 AAATTTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (22 bp):
TTCACAGGTCCTTCGGGACATA
Found at i:361151 original size:21 final size:21
Alignment explanation
Indices: 361104--361155 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
361094 GGACAAAATT
*
361104 ACTGTAGCAAGGGTATCAGTAC
1 ACTGTAGC-AGGGTATCAATAC
*
361126 ACTGTAGCAGGGTATCAATCC
1 ACTGTAGCAGGGTATCAATAC
*
361147 TCTGTAGCA
1 ACTGTAGCA
361156 TTCTGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGGGTATCAATAC
Found at i:364393 original size:27 final size:28
Alignment explanation
Indices: 364355--364416 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
364345 TATAGAATTA
*
364355 CCCTAAAGTGTAAAATGACC-AAAATAC
1 CCCTAAAATGTAAAATGACCTAAAATAC
*
364382 CCCTAAAATGTAAAATGACCTAAAGTAC
1 CCCTAAAATGTAAAATGACCTAAAATAC
*
364410 CTCTAAA
1 CCCTAAA
364417 CCCTAGAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 19 0.61
28 12 0.39
ACGTcount: A:0.47, C:0.23, G:0.10, T:0.21
Consensus pattern (28 bp):
CCCTAAAATGTAAAATGACCTAAAATAC
Found at i:369308 original size:2 final size:2
Alignment explanation
Indices: 369301--369479 Score: 116
Period size: 2 Copynumber: 92.5 Consensus size: 2
369291 TACGTATAGT
*
369301 TA TA TA TA TA TA TA TA CT- TA TA TA TA TT TA TA -A GTA TA -A TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
369342 TA TG TT TA TA T- TA TA TA CT- TA TA -A GTA TA -A TG TA TA CT-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA
* *
369380 TA TA T- TA TA TA CT- TA TA -A GTA TA -A TA TA CA TT TA TA T- TA
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
369419 TA TA TA TA 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 TA TA TA TA
* *
369461 CTA TG TA -A TG TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA T
369480 TTGTTTTAAT
Statistics
Matches: 140, Mismatches: 15, Indels: 44
0.70 0.08 0.22
Matches are distributed among these distances:
1 14 0.10
2 117 0.84
3 9 0.06
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:369364 original size:32 final size:32
Alignment explanation
Indices: 369305--369456 Score: 170
Period size: 32 Copynumber: 4.8 Consensus size: 32
369295 TATAGTTATA
*
369305 TATATATATATACTTATA-TATAT--TTATAAG
1 TATA-ATATATATTTATATTATATACTTATAAG
*
369335 TATAATATATGTTTATATTATATACTTATAAG
1 TATAATATATATTTATATTATATACTTATAAG
* *
369367 TATAATGTATACTTATATTATATACTTATAAG
1 TATAATATATATTTATATTATATACTTATAAG
*
369399 TATAATATACATTTATATTATATA-TATATATA-
1 TATAATATATATTTATATTATATACT-TATA-AG
*
369431 TATATATATATATATATATATATATA
1 TATA-ATATATATTTATAT-TATATA
369457 TATACTATGT
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
29 11 0.10
30 9 0.09
31 1 0.01
32 65 0.62
33 13 0.12
34 6 0.06
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
TATAATATATATTTATATTATATACTTATAAG
Found at i:376475 original size:2 final size:2
Alignment explanation
Indices: 376468--376513 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
376458 AGAGGGATAC
*
376468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
376510 AT AT
1 AT AT
376514 TCTTTTATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:379173 original size:19 final size:19
Alignment explanation
Indices: 379149--379185 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
379139 TCATCTTCGG
*
379149 AGACCACAGTGGTGCCCAA
1 AGACCACAGTGGTCCCCAA
379168 AGACCACAGTGGTCCCCA
1 AGACCACAGTGGTCCCCA
379186 TATCAATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.35, G:0.24, T:0.11
Consensus pattern (19 bp):
AGACCACAGTGGTCCCCAA
Found at i:389561 original size:27 final size:26
Alignment explanation
Indices: 389497--389590 Score: 66
Period size: 30 Copynumber: 3.3 Consensus size: 26
389487 ATAAGCATTA
389497 AAAAAAATTATTTT-ATACA-TTTAAT
1 AAAAAAA-TATTTTAATACATTTTAAT
*
389522 ATTAAAATCATATTTTAATATCATTTTAAT
1 A--AAAA-AATATTTTAATA-CATTTTAAT
*
389552 AAAAAAATATTAATTAATAAAATATTTAAT
1 AAAAAAATATT--TTAAT-ACAT-TTTAAT
*
389582 ATAAAAATA
1 AAAAAAATA
389591 ATATAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
25 1 0.02
27 15 0.27
28 8 0.15
29 9 0.16
30 22 0.40
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAAAAATATTTTAATACATTTTAAT
Found at i:389608 original size:32 final size:31
Alignment explanation
Indices: 389533--389609 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
389523 TTAAAATCAT
*
389533 ATTTTAAT-ATCATTTTAATAAAAAAATATTA
1 ATTTTAATAAT-ATTTAAATAAAAAAATATTA
*
389564 ATTAATAA-AATATTTAATATAAAAATAATA-TA
1 ATT-TTAATAATATTTAA-ATAAAAA-AATATTA
389596 ATTTTAATAATATT
1 ATTTTAATAATATT
389610 ATATTTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
31 11 0.29
32 23 0.61
33 4 0.11
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (31 bp):
ATTTTAATAATATTTAAATAAAAAAATATTA
Found at i:389612 original size:17 final size:17
Alignment explanation
Indices: 389587--389621 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
389577 TTAATATAAA
389587 AATAATATAATTTTAAT
1 AATAATATAATTTTAAT
* *
389604 AATATTATATTTTTAAT
1 AATAATATAATTTTAAT
389621 A
1 A
389622 TTACATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATAATATAATTTTAAT
Found at i:389768 original size:19 final size:19
Alignment explanation
Indices: 389746--389785 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
389736 TAATAATGAG
389746 TAATATTAAT-TTATATATT
1 TAATATTAATATTATA-ATT
389765 TAATATTAATATTATAATT
1 TAATATTAATATTATAATT
389784 TA
1 TA
389786 TTTTTACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATTAATATTATAATT
Found at i:390088 original size:30 final size:30
Alignment explanation
Indices: 390052--390132 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
390042 TTCCCTAAAA
*
390052 ATGTAATTTATTTTACGTAAAATAATTTTC
1 ATGTAATTTATTTTACGTAAAACAATTTTC
* * *
390082 ATGTAATTCATTTTATGTAAAACAATTTTT
1 ATGTAATTTATTTTACGTAAAACAATTTTC
*
390112 AAGTAATATT-TTTTACGTAAA
1 ATGTAAT-TTATTTTACGTAAA
390133 TTATTTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 42 0.98
31 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.48
Consensus pattern (30 bp):
ATGTAATTTATTTTACGTAAAACAATTTTC
Found at i:394661 original size:51 final size:51
Alignment explanation
Indices: 394546--394741 Score: 234
Period size: 51 Copynumber: 3.8 Consensus size: 51
394536 TGATGGGTCT
* * *
394546 GCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAGCAATCTTCATA-AAACGGGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTC--G--ATCTTCA-ACAAACGTGTTC
** *
394601 GCTATCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACGTGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTGTTC
* * *
394652 GCTCCCTATTCCTTCAGAGAGTTTAAGACTTGATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTGTTC
*
394703 GCTCCCTATTCCTTTAGAGAGTATAAGACTCGATCTTCA
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCA
394742 TAAAATGAGT
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
50 1 0.01
51 97 0.78
53 1 0.01
55 24 0.19
56 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTGTTC
Found at i:394811 original size:37 final size:37
Alignment explanation
Indices: 394752--394861 Score: 166
Period size: 37 Copynumber: 3.0 Consensus size: 37
394742 TAAAATGAGT
* * *
394752 TTGCTTTACTACTCTTCCGTGAAGGCTTAAGATTGAA
1 TTGCTTCAATACTCTTTCGTGAAGGCTTAAGATTGAA
*
394789 TTTCTTCAATACTCTTTCGTGAAGGCTTAAGATTGAA
1 TTGCTTCAATACTCTTTCGTGAAGGCTTAAGATTGAA
* *
394826 TTGCTTCATTGCTCTTTCGTGAAGGCTTAAGATTGA
1 TTGCTTCAATACTCTTTCGTGAAGGCTTAAGATTGA
394862 CTTGTTTCGA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (37 bp):
TTGCTTCAATACTCTTTCGTGAAGGCTTAAGATTGAA
Found at i:396186 original size:33 final size:33
Alignment explanation
Indices: 396144--396308 Score: 124
Period size: 33 Copynumber: 4.8 Consensus size: 33
396134 CTTTTTTCTT
396144 TTTTCATTTTTCATTTTTCATTTTTCATTTTCA
1 TTTTCATTTTTCATTTTTCATTTTTCATTTTCA
* * *
396177 TTTTCATTTTTCATTTTTCTCTTTCTTCTTTTTCT
1 TTTTCATTTTTCATTTTTC-ATTT-TTCATTTTCA
*
396212 TTTTCATTTTTTTTCCATTTTTCCATTTTTCTTTTTTCTA
1 TTTTCA---TTTTT-CATTTTT-CATTTTTC-ATTTTC-A
*
396252 TTTT--TTTATT--TTTTCATCATTTTTCATTTT-T
1 TTTTCATTT-TTCATTTT--TCATTTTTCATTTTCA
*
396283 TTTTCATTTCTTCTTTTTTCATTTTT
1 TTTTCATTT-TTCATTTTTCATTTTT
396309 TTCTTCAAGC
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
31 4 0.04
33 40 0.37
34 11 0.10
35 22 0.20
36 2 0.02
38 8 0.07
39 16 0.15
40 5 0.05
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTCATTTTTCATTTTTCATTTTTCATTTTCA
Found at i:396187 original size:26 final size:26
Alignment explanation
Indices: 396130--396307 Score: 113
Period size: 26 Copynumber: 6.7 Consensus size: 26
396120 CCCCCTTTTA
* *
396130 TTTTCTTTTTTCTTTTTTCATTTTTCAT
1 TTTTCATTTTTC-ATTTTCA-TTTTCAT
396158 TTTTCATTTTTCATTTTCATTTTCAT
1 TTTTCATTTTTCATTTTCATTTTCAT
396184 TTTTCATTTTTC-TCTTTC---TTC-T
1 TTTTCATTTTTCAT-TTTCATTTTCAT
396206 TTTTC-TTTTTCATTTT--TTTTCCAT
1 TTTTCATTTTTCATTTTCATTTT-CAT
* *
396230 TTTTCCATTTTTCTTTTTTCTATTTTTTTATTT
1 TTTT-CATTTTTC-ATTTTC-A--TTTTCA--T
*
396263 TTTCATCATTTTTCATTTT-TTTTTCAT
1 TTT--TCATTTTTCATTTTCATTTTCAT
*
396290 TTCTTCTTTTTTCATTTT
1 TT-TTCATTTTTCATTTT
396308 TTTCTTCAAG
Statistics
Matches: 123, Mismatches: 8, Indels: 40
0.72 0.05 0.23
Matches are distributed among these distances:
21 9 0.07
22 9 0.07
23 4 0.03
24 5 0.04
25 2 0.02
26 42 0.34
27 13 0.11
28 12 0.10
29 5 0.04
31 1 0.01
32 4 0.03
33 8 0.07
34 8 0.07
35 1 0.01
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTCATTTTTCATTTTCATTTTCAT
Found at i:396274 original size:18 final size:18
Alignment explanation
Indices: 396253--396304 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
396243 TTTTTTCTAT
396253 TTTTTTATTTTTTCATCA
1 TTTTTTATTTTTTCATCA
* **
396271 TTTTTCATTTTTTTTTCA
1 TTTTTTATTTTTTCATCA
* *
396289 TTTCTTCTTTTTTCAT
1 TTTTTTATTTTTTCAT
396305 TTTTTTCTTC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTATTTTTTCATCA
Done.