Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005584.1 Hibiscus syriacus cultivar Beakdansim tig00012963_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: 57409
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3141 original size:18 final size:18
Alignment explanation
Indices: 3097--3142 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
3087 ATTCACCTGA
*
3097 ATTCGATTCTGATTCTGG
1 ATTCGATTATGATTCTGG
*
3115 ATTCAATTATGATTCTGG
1 ATTCGATTATGATTCTGG
*
3133 ATTTGATTAT
1 ATTCGATTAT
3143 TGTATCATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (18 bp):
ATTCGATTATGATTCTGG
Found at i:3494 original size:21 final size:22
Alignment explanation
Indices: 3469--3514 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
3459 GGTTTTGGTA
*
3469 AAAAGATG-TTTAAA-TAATAAT
1 AAAAG-TGATTTAAAGTAAAAAT
3490 AAAAGTGATTTAAAGTAAAAAT
1 AAAAGTGATTTAAAGTAAAAAT
3512 AAA
1 AAA
3515 GAAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 2 0.09
21 11 0.50
22 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (22 bp):
AAAAGTGATTTAAAGTAAAAAT
Found at i:20390 original size:135 final size:134
Alignment explanation
Indices: 20181--20484 Score: 369
Period size: 135 Copynumber: 2.3 Consensus size: 134
20171 TCAATAAATG
* * *
20181 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGAAAGACTTGTTCCATTGTTACCAAG
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGAAAGACTAGATCCACTGTTACCAAG
* * * * *
20246 GGAATATCAAATCTTGAAAGAGATG-ATTCTGATCCGC-TTGTTCTTGAGGGGAAAATCAGACAT
66 GGAAGATCAAATCTTGAAAGAAAAGAATT-TGATCCACGTT-TTCTT-AAGGGAAAATCAGACAT
*
20309 GGGGACA
128 AGGGACA
** **
20316 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTAGATCCACTGTTACTTAG
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGAAAGACTAGATCCACTGTTACCAAG
** * * *
20381 GGAAGATCAAATCTTGAATTAAAAGAATTTGTTCCACGTTTTCTTAAGGGAAAATTAGATATAGG
66 GGAAGATCAAATCTTGAAAGAAAAGAATTTGATCCACGTTTTCTTAAGGGAAAATCAGACATAGG
* *
20446 TACT
131 GACA
* *
20450 TTGATTCATTTCACTATTCTTCAGGGAAGATTGAA
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAA
20485 CCAAATTTGA
Statistics
Matches: 145, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
134 51 0.35
135 89 0.61
136 5 0.03
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32
Consensus pattern (134 bp):
TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGAAAGACTAGATCCACTGTTACCAAG
GGAAGATCAAATCTTGAAAGAAAAGAATTTGATCCACGTTTTCTTAAGGGAAAATCAGACATAGG
GACA
Found at i:21579 original size:41 final size:41
Alignment explanation
Indices: 21534--21635 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
21524 AATGTCTTAT
* * * *
21534 AGATGGCCCGAAGGACTTATCATCTTTCTCAAAAGACTGAC
1 AGATGACCCGAAGGACTTATCATCATGCTCAAAACACTGAC
** * *
21575 AGATGACCTAAAGGATTTAATCATCATGCTCAAAACACTTAC
1 AGATGACCCGAAGGACTT-ATCATCATGCTCAAAACACTGAC
*
21617 TGATGACCCGAAGGACTTA
1 AGATGACCCGAAGGACTTA
21636 CTTATTTTGA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
41 15 0.31
42 33 0.69
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (41 bp):
AGATGACCCGAAGGACTTATCATCATGCTCAAAACACTGAC
Found at i:21830 original size:259 final size:254
Alignment explanation
Indices: 21241--21830 Score: 644
Period size: 257 Copynumber: 2.3 Consensus size: 254
21231 ATCATTTAAA
* * * * **
21241 AAAAACATGTGAAAACATTATACCTGAAGGTCTTATGGATGGCTAGAAGGACTTATCATCTTGCT
1 AAAATCATGTGAAAACATCATACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCA---TGCT
* * ** * * * * *
21306 TGAAAGGCTTACAAATGACATGCATGATTTAATCATCATGCTCGAAAGACTTATTGATAGCCGGA
63 TGAAAGACTGACAAATGACATAAAGGATTTAATCATCATGCTCAAAACACTTACTGATAGCCCGA
* * * *
21371 AGGACTTACTAATTTTGGAAATATTTTACTAGAAGAAACTTTGGGAATCGCTTTCGTACTTTTCA
128 AGGACTTACTAATTTTGAAAATAGTTTACTAGAAGAAACTTTGGAAATCGATTTCGTACTTTTCA
* *
21436 AAAATTTCATTTTCTTAAAAGATTTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCG
193 AAAATTTCATTTTCTGAAAAGATTTAAATGAGAAACTTTGGAAACCGCTTTCTCATTTTTCG
* * * *
21498 AATATCATGTGGAAACATCATGCCCGAATGTCTTATAGATGGCCCGAAGGACTTATCAT-CTTTC
1 AAAATCATGTGAAAACATCATACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATGC--T-
* * *
21562 TCAAAAGACTGACAGATGACCTAAAGGATTTAATCATCATGCTCAAAACACTTACTGAT-GACCC
63 T-GAAAGACTGACAAATGACATAAAGGATTTAATCATCATGCTCAAAACACTTACTGATAG-CCC
* * * * * * ** *
21626 GAAGGACTTACTTATTTTGAAAATAGTTTATTGGGTAATAAATTTTTGAAATCGATTTTTTTCTT
126 GAAGGACTTACTAATTTTGAAAATAGTTTACT-AG-AAGAAACTTTGGAAATCGATTTCGTACTT
* * *
21691 TTCAAAAATTTTATTTTCTGAAAAGTTTTAAATGAGAAACTTTGTAAACCGCTTTCTCAATTTTT
189 TTCAAAAATTTCATTTTCTGAAAAGATTTAAATGAGAAACTTTGGAAACCGCTTTCTC-A--TTT
*
21756 TTTG
251 TTCG
* * * *
21760 AAAATCATGTAAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAAGACTTATCATGCTTGA
1 AAAATCATGTGAAAACATCATACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATGCTTGA
21825 AAGACT
66 AAGACT
21831 TACTGATGGC
Statistics
Matches: 272, Mismatches: 50, Indels: 20
0.80 0.15 0.06
Matches are distributed among these distances:
253 1 0.00
254 1 0.00
255 1 0.00
256 2 0.01
257 124 0.46
258 1 0.00
259 81 0.30
260 2 0.01
261 1 0.00
262 57 0.21
263 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (254 bp):
AAAATCATGTGAAAACATCATACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATGCTTGA
AAGACTGACAAATGACATAAAGGATTTAATCATCATGCTCAAAACACTTACTGATAGCCCGAAGG
ACTTACTAATTTTGAAAATAGTTTACTAGAAGAAACTTTGGAAATCGATTTCGTACTTTTCAAAA
ATTTCATTTTCTGAAAAGATTTAAATGAGAAACTTTGGAAACCGCTTTCTCATTTTTCG
Found at i:21854 original size:20 final size:20
Alignment explanation
Indices: 21791--21854 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
21781 ACCCGAAGGT
* *
21791 CTTACAGATGGCCCGAAAGA
1 CTTACTGATGGCTCGAAAGA
* *
21811 CTTA-TCAT-GCTTGAAAGA
1 CTTACTGATGGCTCGAAAGA
*
21829 CTTACTGATGGCTCGAAGGA
1 CTTACTGATGGCTCGAAAGA
21849 CTTACT
1 CTTACT
21855 AATTTTGGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
18 12 0.34
19 5 0.14
20 18 0.51
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (20 bp):
CTTACTGATGGCTCGAAAGA
Found at i:21974 original size:217 final size:215
Alignment explanation
Indices: 21597--22066 Score: 636
Period size: 217 Copynumber: 2.2 Consensus size: 215
21587 GGATTTAATC
*
21597 ATCATGCTCAAAACACTTACTGATGACCCGAAGGACTTACTTATTTTGAAAATAGTTTATTGGGT
1 ATCATGCTCAAAACACTTACTGATGACCCGAAGGACTTACTAATTTTGAAAATAGTTTATTGGGT
* * * * * * * *
21662 AATAAATTTTTGAAATCGATTTTTTTCTTTTCAAAAATTTTATTTTCTGAAAAGTTTTAAATGAG
66 AAGAAACTTTGGAAATCGATTTCTTACTTTTAAAAAATTTCATTTTCTGAAAAGATTTAAATGAG
* * *
21727 AAACTTTGTAAACCGCTTTCTCAATTTTTTTTGAAAATCATGTAAAAACATCCTACCCGAAGGTC
131 AAACTTTGGAAACCACTTTCTC-ATTTTTTTTGAAAATCATGTAAAAACATCCTACCCAAAGGTC
21792 TTACAGATGGCCCGAAAGACTT
195 TTA-AGATGGCCCGAAAGACTT
** * * * *
21814 ATCATGCTTGAAAGACTTACTGATGGCTCGAAGGACTTACTAATTTTGGAAATAGTTTATTGGGT
1 ATCATGCTCAAAACACTTACTGATGACCCGAAGGACTTACTAATTTTGAAAATAGTTTATTGGGT
*
21879 AAGAAACTTTGGAAATCGCTTTCTTACTTTTAAAAAATTTCATTTTCT-AAAATGATTTAAATGA
66 AAGAAACTTTGGAAATCGATTTCTTACTTTTAAAAAATTTCATTTTCTGAAAA-GATTTAAATGA
* *
21943 GAAACTTTGGAAATCACTTTCTCATTTTTTTTGAAAATCATGTTAAAACATCCTACCCAAAGGTC
130 GAAACTTTGGAAACCACTTTCTCATTTTTTTTGAAAATCATGTAAAAACATCCTACCCAAAGGTC
* *
22008 TTAAGATTGCCCGAACGACTT
195 TTAAGATGGCCCGAAAGACTT
* * * *
22029 ATCATATTGGTCGAAAGACTTACAGATGACCCGAAGGA
1 ATC--A-TGCTCAAAACACTTACTGATGACCCGAAGGA
22067 TTTAATTATC
Statistics
Matches: 221, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
215 19 0.09
216 47 0.21
217 129 0.58
218 26 0.12
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (215 bp):
ATCATGCTCAAAACACTTACTGATGACCCGAAGGACTTACTAATTTTGAAAATAGTTTATTGGGT
AAGAAACTTTGGAAATCGATTTCTTACTTTTAAAAAATTTCATTTTCTGAAAAGATTTAAATGAG
AAACTTTGGAAACCACTTTCTCATTTTTTTTGAAAATCATGTAAAAACATCCTACCCAAAGGTCT
TAAGATGGCCCGAAAGACTT
Found at i:22111 original size:20 final size:20
Alignment explanation
Indices: 22083--22133 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
22073 TATCATGCAT
*
22083 CGAAAGACTTACTGATTGCC
1 CGAAGGACTTACTGATTGCC
22103 CGAAGGACTTACTGATTGCC
1 CGAAGGACTTACTGATTGCC
*
22123 TGAAGGACTTA
1 CGAAGGACTTA
22134 ATAAATAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (20 bp):
CGAAGGACTTACTGATTGCC
Found at i:22232 original size:478 final size:474
Alignment explanation
Indices: 21340--22232 Score: 1181
Period size: 478 Copynumber: 1.9 Consensus size: 474
21330 TGATTTAATC
* *
21340 ATCATGCTCGAAAGACTTATTGATAGCCGGAAGGACTTACTAATTTTGGAAATATTTTACTAGAA
1 ATCATGCTCGAAAGACTTACTGATAGCCGGAAGGACTTACTAATTTTGGAAATAGTTTACTAGAA
* *
21405 GAAACTTTGGGAATCGCTTTCGTACTTTTCAAAAATTTCATTTTCTTAAAAGATTTAAATGAGAA
66 GAAACTTTGGAAATCGCTTTCGTACTTTTAAAAAATTTCATTTTCTTAAAAGATTTAAATGAGAA
* * * * * *
21470 ACTTTGGAAATCGCTTTCTCATTTTTCGAATATCATGTGGAAACATCATGCCCGAATGTCTTATA
131 ACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATACCCAAAGGTCTTATA
* * * *
21535 GATGGCCCGAAGGACTTATCATCTTTCTCAAAAGACTGACAGATGACCTAAAGGATTTAATCATC
196 GATGGCCCGAACGACTTATCATATTGCTCAAAAGACTGACAGATGACCCAAAGGATTTAATCATC
* * * * * *** *
21600 ATGCTCAAAACACTTACTGATGACCCGAAGGACTTACTTATTTTGAAAATAGTTTATTGGGTAAT
261 ATGCTCAAAACACTTACTGATGACCCGAAGGACTTACTGATTCTGAAAAGAGCTTAATAAATAAG
* * * * *
21665 AAATTTTTGAAATCGATTTTTTTCTTTTCAAAAATTTTATTTTCTGAAAAGTTTTAAATGAGAAA
326 AAACTTTGGAAATCGATTTTTTTCTTTTCAAAAATTTCATTTTCAGAAAAGATTTAAATGAGAAA
* * *
21730 CTTTGTAAACCGCTTTCTCAATTTTTTTTGAAAATCATGTAAAAACATCCTACCCGAAGGTCTTA
391 CTTCGGAAACCACTTTCTCAATTTTTTTTGAAAATCATGTAAAAACATCCTACCCGAAGGTCTTA
21795 CAGATGGCCCGAAAGACTT
456 CAGATGGCCCGAAAGACTT
* * * *
21814 ATCATGCTTGAAAGACTTACTGATGGCTC-GAAGGACTTACTAATTTTGGAAATAGTTTATTGGG
1 ATCATGCTCGAAAGACTTACTGATAGC-CGGAAGGACTTACTAATTTTGGAAATAGTTTACT-AG
*
21878 TAAGAAACTTTGGAAATCGCTTTCTTACTTTTAAAAAATTTCATTTTC-TAAAATGATTTAAATG
64 -AAGAAACTTTGGAAATCGCTTTCGTACTTTTAAAAAATTTCATTTTCTTAAAA-GATTTAAATG
* * *
21942 AGAAACTTTGGAAATCACTTTCTCATTTTTTTTGAAAATCATGTTAAAACATCCTACCCAAAGGT
127 AGAAACTTTGGAAATCACTTTCTCA--TTTTTCGAAAATCATGTGAAAACATCATACCCAAAGGT
* * * * *
22007 CTTA-AGATTGCCCGAACGACTTATCATATTGGTCGAAAGACTTACAGATGACCCGAAGGATTTA
190 CTTATAGATGGCCCGAACGACTTATCATATTGCTCAAAAGACTGACAGATGACCCAAAGGATTTA
* * * *
22071 ATTATCATGCATCGAAAGACTTACTGATTG-CCCGAAGGACTTACTGATTGCCTG-AAGGA-CTT
255 ATCATCATGC-TCAAAACACTTACTGA-TGACCCGAAGGACTTACTGATT--CTGAAAAGAGCTT
22133 AATAAATAAGAAACTTTGGAAATCG-TTTTCTTAT-TTTTCAAAAATTTCATTTTCAGAAAAGAT
316 AATAAATAAGAAACTTTGGAAATCGATTTT-TT-TCTTTTCAAAAATTTCATTTTCAGAAAAGAT
*
22196 TTAAATGAGAAACTTCGGAAATCACTTTCTCAATTTT
379 TTAAATGAGAAACTTCGGAAACCACTTTCTCAATTTT
22233 CAAAAGAACT
Statistics
Matches: 358, Mismatches: 49, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
474 54 0.15
475 7 0.02
476 78 0.22
477 64 0.18
478 147 0.41
479 6 0.02
480 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (474 bp):
ATCATGCTCGAAAGACTTACTGATAGCCGGAAGGACTTACTAATTTTGGAAATAGTTTACTAGAA
GAAACTTTGGAAATCGCTTTCGTACTTTTAAAAAATTTCATTTTCTTAAAAGATTTAAATGAGAA
ACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATACCCAAAGGTCTTATA
GATGGCCCGAACGACTTATCATATTGCTCAAAAGACTGACAGATGACCCAAAGGATTTAATCATC
ATGCTCAAAACACTTACTGATGACCCGAAGGACTTACTGATTCTGAAAAGAGCTTAATAAATAAG
AAACTTTGGAAATCGATTTTTTTCTTTTCAAAAATTTCATTTTCAGAAAAGATTTAAATGAGAAA
CTTCGGAAACCACTTTCTCAATTTTTTTTGAAAATCATGTAAAAACATCCTACCCGAAGGTCTTA
CAGATGGCCCGAAAGACTT
Found at i:22837 original size:3 final size:3
Alignment explanation
Indices: 22831--22904 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
22821 TCATTTAAAT
** * *
22831 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22879 TTA TTA TTA TTA TATA TTA TTTA TTA
1 TTA TTA TTA TTA T-TA TTA -TTA TTA
22905 AATATTACAA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:23734 original size:8 final size:8
Alignment explanation
Indices: 23723--23747 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
23713 AGAGAAGAAG
23723 AGAAATGA
1 AGAAATGA
23731 AGAAATGA
1 AGAAATGA
23739 AGAAATGA
1 AGAAATGA
23747 A
1 A
23748 AGGTTGGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (8 bp):
AGAAATGA
Found at i:24221 original size:12 final size:12
Alignment explanation
Indices: 24191--24228 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
24181 ATTACTTTTA
24191 TATTTTAATTAT
1 TATTTTAATTAT
**
24203 TGCTTTAATTAT
1 TATTTTAATTAT
24215 TATTTT-ATTAT
1 TATTTTAATTAT
24226 TAT
1 TAT
24229 CTTAGTCACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:24249 original size:2 final size:2
Alignment explanation
Indices: 24242--24277 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24232 AGTCACATAA
24242 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
24278 TTAAATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24386 original size:22 final size:22
Alignment explanation
Indices: 24361--24406 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
24351 GGTATTTTAA
24361 ATAATTAAATATTATAAAAATT
1 ATAATTAAATATTATAAAAATT
* * * *
24383 ATAATTTAGTTTTATTAAAATT
1 ATAATTAAATATTATAAAAATT
24405 AT
1 AT
24407 TAAAATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATAATTAAATATTATAAAAATT
Found at i:24412 original size:31 final size:32
Alignment explanation
Indices: 24364--24429 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
24354 ATTTTAAATA
*
24364 ATTAAATATTATAAAAATTATAATTTAGTTTT
1 ATTAAATATTATAAAAATTATAATATAGTTTT
* * *
24396 ATTAAA-ATTATTAAAATTTTAATATATTTTT
1 ATTAAATATTATAAAAATTATAATATAGTTTT
24427 ATT
1 ATT
24430 TATTAATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (32 bp):
ATTAAATATTATAAAAATTATAATATAGTTTT
Found at i:24541 original size:17 final size:18
Alignment explanation
Indices: 24509--24543 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
24499 TCTTACTATA
*
24509 TTAAAATAAATTTTTGTC
1 TTAAAATAAATGTTTGTC
24527 TTAAAA-AAATGTTTGTC
1 TTAAAATAAATGTTTGTC
24544 ATTTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (18 bp):
TTAAAATAAATGTTTGTC
Found at i:25719 original size:75 final size:73
Alignment explanation
Indices: 25624--25798 Score: 181
Period size: 74 Copynumber: 2.4 Consensus size: 73
25614 ATAGGATAAT
* * * *
25624 ATGGGCTTTCAACATGCCCCAATATTGGCTAATACAAGTGTTCAAAATGCATCAACAGTTCTGAT
1 ATGGGTTTTCAGCATGCCCCAATATTGGCTAATA-AA-TATTCAAAATACATCAACAGTTCTGAT
*
25689 TTTGATTGAA
64 TCTGATTGAA
* * * ** *
25699 ATGGGTTTTCAGCATGCCCCAGCAT-TTTGCTGATAAATATTCAGAATATTTCAACATTTCTGAT
1 ATGGGTTTTCAGCATGCCCCA--ATATTGGCTAATAAATATTCAAAATACATCAACAGTTCTGAT
*
25763 TCTGTTTGAA
64 TCTGATTGAA
* *
25773 AAGGGTATTCAGCATGCCCCAATATT
1 ATGGGTTTTCAGCATGCCCCAATATT
25799 TGCTTCTTGT
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
72 2 0.02
73 2 0.02
74 48 0.58
75 21 0.25
76 8 0.10
77 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (73 bp):
ATGGGTTTTCAGCATGCCCCAATATTGGCTAATAAATATTCAAAATACATCAACAGTTCTGATTC
TGATTGAA
Found at i:29777 original size:3 final size:3
Alignment explanation
Indices: 29771--29838 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
29761 TCATTTAAAT
** * *
29771 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29819 TTA TTA TATA TTA TTTA TTA
1 TTA TTA T-TA TTA -TTA TTA
29839 AATATTACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:30637 original size:31 final size:31
Alignment explanation
Indices: 30537--30644 Score: 89
Period size: 31 Copynumber: 3.4 Consensus size: 31
30527 CTTCAGTGCA
30537 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
* ***
30568 TGATATTTCTCACATCAGTAAGTCCTTC---AG-TGCA
1 TGATGTTTC-CA-A--A--AAG-CCTTCGGGAGCTTTT
30602 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
30633 TGATGTTTCCAA
1 TGATGTTTCCAA
30645 GCCTTCGGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 22
0.66 0.09 0.25
Matches are distributed among these distances:
27 5 0.09
28 3 0.05
30 3 0.05
31 21 0.36
32 3 0.05
33 3 0.05
34 9 0.16
35 3 0.05
37 3 0.05
38 5 0.09
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
Found at i:30919 original size:76 final size:76
Alignment explanation
Indices: 30580--31815 Score: 1968
Period size: 76 Copynumber: 16.4 Consensus size: 76
30570 ATATTTCTCA
* *
30580 CATCAGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30644 AGCCTTCGGGT
66 AGCCTTCGGGT
*
30655 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30719 AGCCTTCGGGT
66 AGCCTTCGGGT
*
30730 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30794 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
30805 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30870 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
30881 CATCTGTAAGTCCTTCAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
30945 AGCCTTCGGGT
66 AGCCTTCGGGT
*
30956 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31021 AGCCTTCGGGT
66 AGCCTTCGGGT
31032 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31097 AGCCTTCGGGT
66 AGCCTTCGGGT
* * *
31108 CATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAAACCTTAGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTC-CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
31173 AAACCTTCGGGT
65 AAGCCTTCGGGT
*
31185 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGC----T--T-TTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
31243 AAGCCTTAGGGT
65 AAGCCTTCGGGT
* *
31255 CATCTGTAAGTCCTTCAGTGCATGTTGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
31320 AAGCCTTAGGGT
65 AAGCCTTCGGGT
* * * *
31332 CGTCTATAAGTTCTTCAGTGCGTGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31397 AGCCTTCGGGT
66 AGCCTTCGGGT
*
31408 CATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGC----T--T-TTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
31466 AAGCCTTAGGGT
65 AAGCCTTCGGGT
31478 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
31543 AAGCCTTAGGGT
65 AAGCCTTCGGGT
* *
31555 CATCTATAAGTCCTTCAGTGCGTGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
31620 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
31631 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
31696 AACCTTCGGGT
66 AGCCTTCGGGT
*
31707 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
31772 AAAAACCTTCGGGT
64 -AAAGCCTTCGGGT
* *
31786 CATCTGTAAGCCCTTCAGTGCCTGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
31816 TCAACATTTC
Statistics
Matches: 1088, Mismatches: 49, Indels: 44
0.92 0.04 0.04
Matches are distributed among these distances:
69 33 0.03
70 94 0.09
71 2 0.00
73 4 0.00
75 279 0.26
76 357 0.33
77 247 0.23
78 30 0.03
79 42 0.04
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:31301 original size:223 final size:224
Alignment explanation
Indices: 30519--31815 Score: 1944
Period size: 223 Copynumber: 5.8 Consensus size: 224
30509 GGGTGGGTTT
* *** *
30519 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC--T-TTTTGATATTTCTCA-
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTATTTTCA-AAGCCTTAG
*
30580 ---CATCAGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTT
65 GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
*
30641 C-CAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCT
130 CAAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCT
*
30705 TTTTGATG-TTTCCAAGCCTTCGGGTCATC
195 TTTTGATGTTTTCAAAGCCTTCGGGTCATC
*
30734 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCCAAGCCT
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC--TTT-AT-TTTCAAAGCCT
* * *
30799 TCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGTTTTTTGATGT
62 TAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
*
30864 TTTC-AAAGCCTTCGGGTCATCTGTAAGTCCTTCAATGCATGATGTTTCCAAAAAGCCTTCGGGA
127 TTTCAAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGA
*
30928 GCTTTTTGATG-TTTCCAAGCCTTCGGGTCATC
192 GCTTTTTGATGTTTTCAAAGCCTTCGGGTCATC
*
30960 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC--TTT-A--TTTTCAAAGCC
*
31025 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
61 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
* * *
31090 TTTTC-AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCAAAAAAAACCTTAGG
126 TTTTCAAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC-CAAAAAGCCTTCGG
*
31154 GAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATC
190 GAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATC
*
31189 TGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGC-TT-TTTTCAAAGCCTTAG
1 TGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTATTTTCAAAGCCTTAG
* *
31252 GGTCATCTGTAAGTCCTTCAGTGCATGTTGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTT
65 GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
* * * * *
31317 CAAAAGCCTTAGGGTCGTCTATAAGTTCTTCAGTGCGTGATGTTTCCAAAAAGCCTTCGGGAGCT
130 CAAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCT
31382 TTTTGATGTTTTCAAAGCCTTCGGGTCATC
195 TTTTGATGTTTTCAAAGCCTTCGGGTCATC
*
31412 TGTAAATCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGC-TT-TTTTCAAAGCCTTAG
1 TGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTATTTTCAAAGCCTTAG
31475 GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
65 GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
* * *
31540 CAAAAGCCTTAGGGTCATCTATAAGTCCTTCAGTGCGTGATGTTTCCAAAAAGCCTTCGGGAGCT
130 CAAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCT
31605 TTTTGATGTTTTCAAAGCCTTCGGGTCATC
195 TTTTGATGTTTTCAAAGCCTTCGGGTCATC
* *
31635 TGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC---TT--TATTTTCAAAGCC
* *
31700 TTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGA
61 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGA
* * *
31765 TGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCCTGATGTTT
124 TGTTTTCAAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
31816 TCAACATTTC
Statistics
Matches: 1003, Mismatches: 52, Indels: 38
0.92 0.05 0.03
Matches are distributed among these distances:
215 45 0.04
219 1 0.00
221 4 0.00
222 20 0.02
223 366 0.36
224 39 0.04
225 55 0.05
226 146 0.15
227 122 0.12
228 26 0.03
229 93 0.09
230 16 0.02
231 70 0.07
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (224 bp):
TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTATTTTCAAAGCCTTAGG
GTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
AAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTT
TTTGATGTTTTCAAAGCCTTCGGGTCATC
Found at i:31953 original size:3 final size:3
Alignment explanation
Indices: 31947--31998 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
31937 TCATTTAAAT
** * *
31947 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31995 TTA T
1 TTA T
31999 ATATATTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:33315 original size:12 final size:12
Alignment explanation
Indices: 33285--33322 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
33275 ATTACTTTTA
33285 TATTTTAATTAT
1 TATTTTAATTAT
**
33297 TGCTTTAATTAT
1 TATTTTAATTAT
33309 TATTTT-ATTAT
1 TATTTTAATTAT
33320 TAT
1 TAT
33323 CTTAGTCACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:33463 original size:22 final size:22
Alignment explanation
Indices: 33438--33483 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
33428 GGTATTTTAA
33438 ATAATTAAATATTATAAAAATT
1 ATAATTAAATATTATAAAAATT
* * * *
33460 ATAATTTAGTTTTATTAAAATT
1 ATAATTAAATATTATAAAAATT
33482 AT
1 AT
33484 TAAAATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATAATTAAATATTATAAAAATT
Found at i:33489 original size:31 final size:32
Alignment explanation
Indices: 33441--33506 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
33431 ATTTTAAATA
*
33441 ATTAAATATTATAAAAATTATAATTTAGTTTT
1 ATTAAATATTATAAAAATTATAATATAGTTTT
* * *
33473 ATTAAA-ATTATTAAAATTTTAATATATTTTT
1 ATTAAATATTATAAAAATTATAATATAGTTTT
33504 ATT
1 ATT
33507 TATTAATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (32 bp):
ATTAAATATTATAAAAATTATAATATAGTTTT
Found at i:43080 original size:54 final size:54
Alignment explanation
Indices: 42993--43108 Score: 196
Period size: 54 Copynumber: 2.1 Consensus size: 54
42983 ACTTCAATGA
* * *
42993 TTACGAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTATTGTCAAATGTT
1 TTACAAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTT
*
43047 TTACAAACATCTGAGCAGAAGCCACAGAAAAGGATGAATGCACTGTCAAATGTT
1 TTACAAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTT
43101 TTACAAAC
1 TTACAAAC
43109 CTGTTATTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.22
Consensus pattern (54 bp):
TTACAAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTT
Found at i:43507 original size:22 final size:22
Alignment explanation
Indices: 43476--43530 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
43466 ATCTACACTC
*
43476 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
43498 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
43520 TTCAAAGATGA
1 TTCAAAGATGA
43531 AAACTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:44588 original size:77 final size:77
Alignment explanation
Indices: 44456--45034 Score: 903
Period size: 76 Copynumber: 7.6 Consensus size: 77
44446 TCGGGAGCTT
44456 TTTTC-AAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1 TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
*
44520 AGTTTTTTGATG
66 AGCTTTTTGATG
* * * *
44532 TTTTCAAAAGCCTTAGGGTCGTCTGTAAGTTCTTCAGTGCGTAATGTTTCCAAAAAGCCTTCGGG
1 TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
44597 AGCTTTTTGATG
66 AGCTTTTTGATG
*
44609 TTTTC-AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGG
1 TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGG
44673 GAGC----T--T-
65 GAGCTTTTTGATG
44679 TTTTCAAAA-CCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1 TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
44743 AGCTTTTTGATG
66 AGCTTTTTGATG
*
44755 TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCGTGATGTTTCCAAAAAGCCTTCGGG
1 TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
44820 AGCTTTTTGATG
66 AGCTTTTTGATG
* *
44832 TTTTC-AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1 TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
*
44896 AGCTTTTTGATA
66 AGCTTTTTGATG
* *
44908 TTTTCAAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCG
1 TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCG
44972 GGAGCTTTTTGATG
64 GGAGCTTTTTGATG
* * * *
44986 TTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCCTGATGTTT
1 TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
45035 TCAACATTTC
Statistics
Matches: 470, Mismatches: 18, Indels: 27
0.91 0.03 0.05
Matches are distributed among these distances:
69 17 0.04
70 45 0.10
71 4 0.01
73 2 0.00
75 1 0.00
76 167 0.36
77 162 0.34
78 34 0.07
79 38 0.08
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (77 bp):
TTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
AGCTTTTTGATG
Found at i:44792 original size:223 final size:223
Alignment explanation
Indices: 44404--45034 Score: 1057
Period size: 223 Copynumber: 2.8 Consensus size: 223
44394 ATATTTCTCA
* *
44404 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCATTCGGGAGCTTTTTTCAAAGCCTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTTCAAAACCTT
*
44469 AGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTT
66 AGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
* * *
44534 TTCAAAAGCCTTAGGGTCGTCTGTAAGTTCTTCAGTGCGTAATGTTTCCAAAAAGCCTTCGGGAG
131 TTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCGTGATGTTTCCAAAAAGCCTTCGGGAG
44599 CTTTTTGATGTTTTCAAAGCCTTCGGGT
196 CTTTTTGATGTTTTCAAAGCCTTCGGGT
*
44627 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTTCAAAACCTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTTCAAAACCTT
44692 AGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
66 AGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
44757 TTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCGTGATGTTTCCAAAAAGCCTTCGGGAG
131 TTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCGTGATGTTTCCAAAAAGCCTTCGGGAG
44822 CTTTTTGATGTTTTCAAAGCCTTCGGGT
196 CTTTTTGATGTTTTCAAAGCCTTCGGGT
44850 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATATTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGC----T--T-TTTTCA
* *
44914 AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTT
59 AAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTT
* * * *
44979 TTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCCTGATGTTT
122 TTTGATGTTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCGTGATGTTT
45035 TCAACATTTC
Statistics
Matches: 385, Mismatches: 14, Indels: 10
0.94 0.03 0.02
Matches are distributed among these distances:
222 17 0.04
223 247 0.64
226 1 0.00
228 1 0.00
229 48 0.12
231 71 0.18
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (223 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTTCAAAACCTT
AGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
TTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCGTGATGTTTCCAAAAAGCCTTCGGGAG
CTTTTTGATGTTTTCAAAGCCTTCGGGT
Found at i:45172 original size:3 final size:3
Alignment explanation
Indices: 45166--45233 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
45156 TCATTTAAAT
** * *
45166 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45214 TTA TTA TATA TTA TTTA TTA
1 TTA TTA T-TA TTA -TTA TTA
45234 AATATTATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:45186 original size:15 final size:14
Alignment explanation
Indices: 45168--45241 Score: 70
Period size: 15 Copynumber: 5.6 Consensus size: 14
45158 ATTTAAATTT
45168 ATTATTATTATTAAA
1 ATTATTATTATT-AA
45183 ATTATTATTATT--
1 ATTATTATTATTAA
*
45195 AGTATTATTATTATA
1 ATTATTATTATTA-A
*
45210 ATTATTATTA-TAT
1 ATTATTATTATTAA
45223 ATTA-T-TTATTAA
1 ATTATTATTATTAA
45235 A-TATTAT
1 ATTATTAT
45242 AAAGCCCAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
11 5 0.10
12 16 0.33
13 5 0.10
14 2 0.04
15 21 0.43
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (14 bp):
ATTATTATTATTAA
Found at i:45188 original size:12 final size:12
Alignment explanation
Indices: 45171--45241 Score: 61
Period size: 12 Copynumber: 5.4 Consensus size: 12
45161 TAAATTTATT
45171 ATTATTATTAAA
1 ATTATTATTAAA
*
45183 ATTATTATTATTAGT
1 ATTATTATTA--A-A
*
45198 ATTATTATTATA
1 ATTATTATTAAA
*
45210 ATTATTATTATAT
1 ATTATTATTA-AA
45223 ATTATTTATTAAA
1 ATTA-TTATTAAA
45236 TATTAT
1 -ATTAT
45242 AAAGCCCAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
12 20 0.43
13 6 0.13
14 11 0.23
15 10 0.21
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (12 bp):
ATTATTATTAAA
Found at i:46505 original size:12 final size:12
Alignment explanation
Indices: 46475--46512 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
46465 ATTACTTTTA
46475 TATTTTAATTAT
1 TATTTTAATTAT
**
46487 TGCTTTAATTAT
1 TATTTTAATTAT
46499 TATTTT-ATTAT
1 TATTTTAATTAT
46510 TAT
1 TAT
46513 CTTAGTCACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:46661 original size:22 final size:22
Alignment explanation
Indices: 46636--46681 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
46626 GGTATTTTAA
46636 ATAATTAAATATTATAAAAATT
1 ATAATTAAATATTATAAAAATT
* * * *
46658 ATAATTTAGTTTTATTAAAATT
1 ATAATTAAATATTATAAAAATT
46680 AT
1 AT
46682 TAAAATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATAATTAAATATTATAAAAATT
Found at i:46687 original size:31 final size:32
Alignment explanation
Indices: 46639--46704 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
46629 ATTTTAAATA
*
46639 ATTAAATATTATAAAAATTATAATTTAGTTTT
1 ATTAAATATTATAAAAATTATAATATAGTTTT
* * *
46671 ATTAAA-ATTATTAAAATTTTAATATATTTTT
1 ATTAAATATTATAAAAATTATAATATAGTTTT
46702 ATT
1 ATT
46705 TATTAATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (32 bp):
ATTAAATATTATAAAAATTATAATATAGTTTT
Found at i:46816 original size:17 final size:18
Alignment explanation
Indices: 46784--46818 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
46774 TCTTACTATA
*
46784 TTAAAATAAATTTTTGTC
1 TTAAAATAAATGTTTGTC
46802 TTAAAA-AAATGTTTGTC
1 TTAAAATAAATGTTTGTC
46819 ATTTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (18 bp):
TTAAAATAAATGTTTGTC
Done.