Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004345.1 Hibiscus syriacus cultivar Beakdansim tig00009518_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: 85137
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5426 original size:2 final size:2
Alignment explanation
Indices: 5419--5453 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5409 TACATTCTTT
5419 TA TA TA TA TA 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 TA TA TA TA TA T
5454 TAATGACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9340 original size:49 final size:49
Alignment explanation
Indices: 9283--9376 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
9273 GGCACTTATG
** *
9283 GAGGGGTTGCTTGGGATACCCCGGGCACCATGGAGGTCCACCCCTGGAT
1 GAGGGGTTGCCCGGGATACCCCGGACACCATGGAGGTCCACCCCTGGAT
* *
9332 GAGGGGTTGCCCGGGATACCCCGGACTCCATGGAGGTCCGCCCCT
1 GAGGGGTTGCCCGGGATACCCCGGACACCATGGAGGTCCACCCCT
9377 TAGAGGTGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.15, C:0.32, G:0.36, T:0.17
Consensus pattern (49 bp):
GAGGGGTTGCCCGGGATACCCCGGACACCATGGAGGTCCACCCCTGGAT
Found at i:10552 original size:15 final size:16
Alignment explanation
Indices: 10517--10561 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
10507 CTAATATTAA
* *
10517 TTATACATTGAATTCT
1 TTATAAATTAAATTCT
*
10533 TTATAATTTAAATT-T
1 TTATAAATTAAATTCT
10548 TTATAAATTAAATT
1 TTATAAATTAAATT
10562 AATAATATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (16 bp):
TTATAAATTAAATTCT
Found at i:10823 original size:19 final size:20
Alignment explanation
Indices: 10791--10829 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
10781 ATATTAATTT
10791 TTTAAAATAACATA-TATAA
1 TTTAAAATAACATATTATAA
**
10810 TTTAAAATTTCATATTATAA
1 TTTAAAATAACATATTATAA
10830 AATAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAAAATAACATATTATAA
Found at i:21198 original size:21 final size:21
Alignment explanation
Indices: 21173--21221 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
21163 TTATACAGAT
*
21173 TTTATATTTTAAAATTTATTA
1 TTTATATTTAAAAATTTATTA
*
21194 TTTATAATTAAAAATTTATTA
1 TTTATATTTAAAAATTTATTA
*
21215 TATATAT
1 TTTATAT
21222 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATATTTAAAAATTTATTA
Found at i:21798 original size:25 final size:26
Alignment explanation
Indices: 21712--21833 Score: 81
Period size: 25 Copynumber: 4.7 Consensus size: 26
21702 AAAATAAATT
* * *
21712 TTAACATAATAT-ATATATTTTTAAA
1 TTAAGATAATATAAAATATATTTAAA
* * * *
21737 TGAAAATAAAATAAAATAATTTTTAAA
1 TTAAGATAATATAAAAT-ATATTTAAA
*
21764 TTAAGTTAATCATAAAATATATTT-AA
1 TTAAGATAAT-ATAAAATATATTTAAA
* *
21790 -TAAGATAATATAAAAATATTTTTAAG
1 TTAAGATAATAT-AAAATATATTTAAA
* *
21816 TTAATAT-TTATAAAATAT
1 TTAAGATAATATAAAATAT
21834 TATGAATTTG
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
24 2 0.03
25 34 0.44
26 9 0.12
27 25 0.32
28 7 0.09
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (26 bp):
TTAAGATAATATAAAATATATTTAAA
Found at i:23621 original size:5 final size:5
Alignment explanation
Indices: 23611--23641 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
23601 TTAAGGTTTC
23611 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
23642 ATATATGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:31302 original size:24 final size:24
Alignment explanation
Indices: 31275--31331 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
31265 ACTCTTTGAA
31275 CTTCATAAAAGTCTATAAATTTTC
1 CTTCATAAAAGTCTATAAATTTTC
*
31299 CTTCATAAAAGTCTCTAAATTTTC
1 CTTCATAAAAGTCTATAAATTTTC
31323 CTTCATAAA
1 CTTCATAAA
31332 GTAAACCCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (24 bp):
CTTCATAAAAGTCTATAAATTTTC
Found at i:51859 original size:21 final size:21
Alignment explanation
Indices: 51835--51883 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
51825 GTTTTTTTCA
51835 ATGATGATGTGGTATTTCTTT
1 ATGATGATGTGGTATTTCTTT
*
51856 ATGATAATGTGGTATTTCTTT
1 ATGATGATGTGGTATTTCTTT
51877 ATGATGA
1 ATGATGA
51884 CTTGTTACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.49
Consensus pattern (21 bp):
ATGATGATGTGGTATTTCTTT
Found at i:53824 original size:20 final size:20
Alignment explanation
Indices: 53799--53851 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
53789 AATCATTCAT
53799 TGAGTATCGATACCAGGGCA
1 TGAGTATCGATACCAGGGCA
53819 TGAGTATCGATACCAGGGCA
1 TGAGTATCGATACCAGGGCA
*
53839 GGAGTATCGATAC
1 TGAGTATCGATAC
53852 TCCCCTAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (20 bp):
TGAGTATCGATACCAGGGCA
Found at i:54050 original size:20 final size:20
Alignment explanation
Indices: 54027--54077 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
54017 CAACAGGTGG
* *
54027 GTATCGATACCAAAGGTTTA
1 GTATCGATACCAAAGGGTCA
*
54047 GTATCGATACTAAAGGGTCA
1 GTATCGATACCAAAGGGTCA
*
54067 GTATCGGTACC
1 GTATCGATACC
54078 CACGAACATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (20 bp):
GTATCGATACCAAAGGGTCA
Found at i:54983 original size:23 final size:23
Alignment explanation
Indices: 54947--55006 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
54937 CAGCTTGTAT
54947 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
54970 AATTGCACCTAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
54993 AAATGCACCGAAGT
1 AAATGCACCGAAGT
55007 ACCATATAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:56582 original size:24 final size:20
Alignment explanation
Indices: 56525--56562 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
56515 TTCCCCTTGA
56525 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
56545 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
56563 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:57886 original size:31 final size:31
Alignment explanation
Indices: 57850--57908 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
57840 AACTTAAAAG
*
57850 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
57881 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
57909 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:57957 original size:22 final size:22
Alignment explanation
Indices: 57932--58629 Score: 895
Period size: 22 Copynumber: 31.5 Consensus size: 22
57922 ATAATAAATT
57932 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
57954 TTTTAAAATAAATCAATACATA
1 TTTTAAAATAAATCAATCCATA
**
57976 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
***
57998 TTTTAAAATAAAATTTTTTCCATA
1 TTTTAAAAT-AAA-TCAATCCATA
58022 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
58044 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
58066 TTTTAAAATAAATCTATCCATA
1 TTTTAAAATAAATCAATCCATA
58088 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
58110 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
58132 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* ***
58154 TTTTAAAATAATTTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
58176 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
58198 TTTTAAAATAAAAT-TTTCTATA
1 TTTTAAAAT-AAATCAATCCATA
*
58220 CTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
58242 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
58264 TTTTTAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *
58286 TTTTAAAATAAGTCAATCAATA
1 TTTTAAAATAAATCAATCCATA
58308 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
58330 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
58352 TTTTAAAAATAAATCAATCCATA
1 TTTT-AAAATAAATCAATCCATA
**
58375 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
58397 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
58419 TTTTAAAATAATTTTTTTTCATA
1 TTTTAAAATAA-ATCAATCCATA
*
58442 TTTTAAAATAAATCAATGCATA
1 TTTTAAAATAAATCAATCCATA
58464 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
58486 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
58508 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
58530 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
58552 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
58574 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
58596 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
58618 TTTTAAAATAAA
1 TTTTAAAATAAA
58630 ATTTTAAAAT
Statistics
Matches: 591, Mismatches: 70, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
21 16 0.03
22 497 0.84
23 61 0.10
24 17 0.03
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:60242 original size:2 final size:2
Alignment explanation
Indices: 60237--60264 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60227 CAACGTTTTA
60237 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
60265 GCGTAGAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60506 original size:21 final size:20
Alignment explanation
Indices: 60479--60577 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
60469 AATCAGTTTC
60479 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
60500 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
60521 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
60541 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
60562 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
60578 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:60639 original size:20 final size:20
Alignment explanation
Indices: 60545--60737 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
60535 GATTTTCCAG
* ** *
60545 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
60565 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
60585 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
60605 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
60625 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
60645 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
60665 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
60685 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
60706 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
60726 AATCGCAACGCG
1 AATCGCAACGCG
60738 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 129 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:61155 original size:33 final size:33
Alignment explanation
Indices: 61116--61186 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
61106 TTCACTTAGA
*
61116 TTTCATTTCGTGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
61149 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
61182 TTTCA
1 TTTCA
61187 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:61334 original size:21 final size:21
Alignment explanation
Indices: 61266--61339 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
61256 TGCAGAAGAG
*
61266 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAAAAATGAAAA
* * **
61287 TCACAACGTG-AAAATGACTA
1 TCGCAACGAGAAAAATGAAAA
61307 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAAAAATGAAAA
61329 TCGCAACGAGA
1 TCGCAACGAGA
61340 GAATCGCAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 9 0.21
21 23 0.55
22 10 0.24
ACGTcount: A:0.49, C:0.18, G:0.19, T:0.15
Consensus pattern (21 bp):
TCGCAACGAGAAAAATGAAAA
Found at i:61365 original size:19 final size:19
Alignment explanation
Indices: 61278--61385 Score: 73
Period size: 19 Copynumber: 5.7 Consensus size: 19
61268 GCAACGAGAT
* *
61278 AAATGAAAATCACAACGTG
1 AAATGAAAATCGCAACGCG
** *
61297 AAAATGACTATCTGCAACGAG
1 -AAATGAAAATC-GCAACGCG
61318 AAAAATGAAAATCGCAA--CG
1 --AAATGAAAATCGCAACGCG
*
61337 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
61353 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
**
61372 AAACCAAAATCGCA
1 AAATGAAAATCGCA
61386 TTGCGATTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
18 1 0.01
19 27 0.39
20 9 0.13
21 10 0.14
22 10 0.14
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:61403 original size:19 final size:19
Alignment explanation
Indices: 61381--61508 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
61371 GAAACCAAAA
*
61381 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
61400 TCGCGTTGCGA--TT-A--
1 TCGCGTTGCGATTTTCATT
*
61414 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
61433 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
61447 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
61467 CTCTCGTTGCGACAATCATT
1 -TCGCGTTGCGATTTTCATT
*
61487 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
61507 TC
1 TC
61509 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:61422 original size:14 final size:14
Alignment explanation
Indices: 61403--61459 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
61393 TTTCATTTCG
61403 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
61417 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
61436 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
61450 CGTTGCGATT
1 CGTTGCGATT
61460 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:61428 original size:33 final size:33
Alignment explanation
Indices: 61386--61467 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
61376 CAAAATCGCA
61386 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
*
61419 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
61452 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
61468 TCTCGTTGCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
Found at i:61470 original size:21 final size:21
Alignment explanation
Indices: 61444--61508 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
61434 CGCGTTGCGA
61444 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
61465 TTCTCTCGTTGCGACAATCA-
1 TTCTCTCGTTGCGATTTTCAT
61485 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
61506 TTC
1 TTC
61509 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:61505 original size:20 final size:20
Alignment explanation
Indices: 61443--61506 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
61433 TCGCGTTGCG
61443 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
61463 ATTTCTCTCGTTGCGACAATC
1 A-TTCTCTCGTTGCGATTTTC
61484 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
61504 ATT
1 ATT
61507 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:63229 original size:19 final size:19
Alignment explanation
Indices: 63205--63289 Score: 116
Period size: 19 Copynumber: 4.4 Consensus size: 19
63195 TAAATTTACT
63205 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
63224 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTCATTTCG
*
63243 CGTTGCGATTCTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
63262 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
63282 TGTTGCGA
1 CGTTGCGA
63290 AAGTAAACTA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 45 0.79
20 12 0.21
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:63247 original size:38 final size:39
Alignment explanation
Indices: 63205--63289 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 39
63195 TAAATTTACT
* *
63205 CGTTGCGATTTTCATTTCGCGTTGCGATTTT-GGTTTCG
1 CGTTGCGATTCTCATTTCGCGTTGCGATTTTAAGTTTCG
63243 CGTTGCGATTCTCATTTCGCGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTCTCATTTCGCGTTGCGATTTTAAGTTTCG
*
63282 TGTTGCGA
1 CGTTGCGA
63290 AAGTAAACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
38 30 0.70
39 13 0.30
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
CGTTGCGATTCTCATTTCGCGTTGCGATTTTAAGTTTCG
Found at i:63804 original size:21 final size:21
Alignment explanation
Indices: 63744--63810 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
63734 TCATTCCTCG
* *
63744 AGAGTTCCCTCCCACCGTTCA
1 AGAGGTCCCTCCCACCATTCA
** * *
63765 AGAGG-CCACTGTCATCATTGA
1 AGAGGTCC-CTCCCACCATTCA
63786 AGAGGTCCCTCCCACCATTCA
1 AGAGGTCCCTCCCACCATTCA
63807 AGAG
1 AGAG
63811 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 2 0.06
21 30 0.88
22 2 0.06
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGGTCCCTCCCACCATTCA
Found at i:65229 original size:14 final size:14
Alignment explanation
Indices: 65210--65245 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
65200 ATTGTTTAAT
65210 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
65224 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
65238 TGATTTGT
1 TGATTTGT
65246 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:65420 original size:20 final size:19
Alignment explanation
Indices: 65352--65435 Score: 106
Period size: 19 Copynumber: 4.6 Consensus size: 19
65342 AAAAATGACT
65352 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
65371 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
65385 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
65404 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
65424 ATCGCAACGCGA
1 ATCGCAATGCGA
65436 GAATCGCAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 22 0.39
20 18 0.32
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:65467 original size:19 final size:19
Alignment explanation
Indices: 65439--65680 Score: 272
Period size: 19 Copynumber: 13.7 Consensus size: 19
65429 AACGCGAGAA
*
65439 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
65458 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
65474 TCG--TTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
65491 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
65510 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
65526 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
65543 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
65562 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
65579 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
65596 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
65615 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
65634 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
65652 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
65668 TCGCATTGCGATT
1 TCGCATTGCGATT
65681 CTCTCGTTGC
Statistics
Matches: 190, Mismatches: 11, Indels: 44
0.78 0.04 0.18
Matches are distributed among these distances:
14 29 0.15
16 20 0.11
17 21 0.11
18 4 0.02
19 90 0.47
20 26 0.14
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:65568 original size:105 final size:106
Alignment explanation
Indices: 65438--65702 Score: 391
Period size: 105 Copynumber: 2.5 Consensus size: 106
65428 CAACGCGAGA
*
65438 ATCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTTCGCATTGCGAT
1 ATCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTTCGCATTGCGAT
65503 TTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTC
66 TTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTC
*
65540 ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 A--TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTAATTTCGCATTGC
*
65605 GATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
63 GATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTGCGATTTTC
* *
65651 AT-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTC
1 ATCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTTC
65703 CGTGTTGCGA
Statistics
Matches: 148, Mismatches: 6, Indels: 15
0.88 0.04 0.09
Matches are distributed among these distances:
102 1 0.01
104 19 0.13
105 93 0.63
106 14 0.09
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.08
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (106 bp):
ATCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATTTCGCATTGCGAT
TTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTC
Found at i:65605 original size:72 final size:71
Alignment explanation
Indices: 65445--65680 Score: 283
Period size: 72 Copynumber: 3.4 Consensus size: 71
65435 AGAATCGCAA
* *
65445 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTAATTT-CGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
*
65504 T-TCAT
66 TCTCGT
* * * *
65509 TTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
65573 ATTCTCTCGT
63 ATT-TCTCGT
65583 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
65648 T-TCATGT
66 TCTC--GT
*
65655 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
65681 CTCTCGTTGC
Statistics
Matches: 146, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
64 6 0.04
65 4 0.03
66 9 0.06
68 3 0.02
69 4 0.03
70 2 0.01
71 15 0.10
72 89 0.61
73 5 0.03
74 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (71 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
TCTCGT
Found at i:65702 original size:33 final size:33
Alignment explanation
Indices: 65445--65694 Score: 238
Period size: 33 Copynumber: 7.2 Consensus size: 33
65435 AGAATCGCAA
65445 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* *
65478 TGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
65516 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
65549 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
65583 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
*
65621 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
65655 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
65688 TGCGATT
1 TGCGATT
65695 GTAATTTCCG
Statistics
Matches: 177, Mismatches: 20, Indels: 40
0.75 0.08 0.17
Matches are distributed among these distances:
31 4 0.02
32 7 0.04
33 67 0.38
34 32 0.18
35 8 0.05
36 10 0.06
37 5 0.03
38 23 0.13
39 13 0.07
40 8 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:65709 original size:53 final size:52
Alignment explanation
Indices: 65439--65702 Score: 367
Period size: 52 Copynumber: 5.0 Consensus size: 52
65429 AACGCGAGAA
*
65439 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATT
*
65491 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATT
*
65543 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTAATT
* *
65596 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTAATT
* *
65652 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATT
65701 TC
1 TC
65703 CGTGTTGCGA
Statistics
Matches: 195, Mismatches: 7, Indels: 22
0.87 0.03 0.10
Matches are distributed among these distances:
47 10 0.05
49 3 0.02
50 2 0.01
51 3 0.02
52 80 0.41
53 76 0.39
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.06
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTAATT
Found at i:68207 original size:24 final size:24
Alignment explanation
Indices: 68173--68219 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
68163 CTGAAACATC
68173 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
68197 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
68220 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:68802 original size:21 final size:21
Alignment explanation
Indices: 68774--68813 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
68764 ACCTGTTGCC
68774 GGATTAGGAA-GGATGTCGTT
1 GGATTAGGAACGGATGTCGTT
68794 GGATATAGGAACGGATGTCG
1 GGAT-TAGGAACGGATGTCG
68814 CCGGAGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.28, C:0.07, G:0.40, T:0.25
Consensus pattern (21 bp):
GGATTAGGAACGGATGTCGTT
Found at i:68939 original size:20 final size:20
Alignment explanation
Indices: 68911--69139 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
68901 AAATTTCAGT
* * *
68911 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
68931 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
68951 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
68971 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
68991 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
69011 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
69031 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
69051 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
69071 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
69091 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
69111 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
69131 GTTGCGATT
1 GTTGCGATT
69140 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:69192 original size:21 final size:20
Alignment explanation
Indices: 69107--69204 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
69097 ATTTATGTGT
* *
69107 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
69127 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
69148 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
69169 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
69190 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
69205 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:69200 original size:42 final size:43
Alignment explanation
Indices: 69107--69205 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
69097 ATTTATGTGT
* *
69107 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
69148 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
69190 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
69206 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:70471 original size:3 final size:3
Alignment explanation
Indices: 70463--70491 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
70453 CGAGCAAATA
70463 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
70492 CTGAGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:70752 original size:3 final size:3
Alignment explanation
Indices: 70744--70816 Score: 103
Period size: 3 Copynumber: 23.7 Consensus size: 3
70734 GATTTGACAA
70744 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CCTT C-T CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT
*
70789 CCTT CTTT CTT CTC CTT CTT CTT CTT CT
1 -CTT C-TT CTT CTT CTT CTT CTT CTT CT
70817 CACACACTCT
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.03
3 53 0.83
4 9 0.14
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:72299 original size:6 final size:6
Alignment explanation
Indices: 72288--72348 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
72278 GACACGTATT
* *
72288 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
72336 ACCACG ACCACG A
1 ACCACG ACCACG A
72349 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:72356 original size:5 final size:5
Alignment explanation
Indices: 72346--72394 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
72336 ACCACGACCA
* * * * *
72346 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGTGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
72395 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.14, C:0.37, G:0.41, T:0.08
Consensus pattern (5 bp):
CGAGC
Found at i:72366 original size:15 final size:15
Alignment explanation
Indices: 72346--72394 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
72336 ACCACGACCA
*
72346 CGAGCCGAGCCGAGC
1 CGAGCCGTGCCGAGC
*
72361 CGAGCCGTGCCGTGC
1 CGAGCCGTGCCGAGC
* *
72376 CGTGCCGTGCCGAGA
1 CGAGCCGTGCCGAGC
72391 CGAG
1 CGAG
72395 ACGGACGGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.14, C:0.37, G:0.41, T:0.08
Consensus pattern (15 bp):
CGAGCCGTGCCGAGC
Found at i:78234 original size:6 final size:6
Alignment explanation
Indices: 78223--78281 Score: 100
Period size: 6 Copynumber: 9.8 Consensus size: 6
78213 ACGTGTCGAA
* *
78223 CACGAC CACGAC CACGAC CACGAC CACGAC CTCGAC CTCGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
78271 CACGAC CACGA
1 CACGAC CACGA
78282 GCCGAGCCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.31, C:0.49, G:0.17, T:0.03
Consensus pattern (6 bp):
CACGAC
Found at i:78289 original size:5 final size:5
Alignment explanation
Indices: 78279--78327 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
78269 ACCACGACCA
* * * * *
78279 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGTGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
78328 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.14, C:0.37, G:0.41, T:0.08
Consensus pattern (5 bp):
CGAGC
Found at i:78299 original size:15 final size:15
Alignment explanation
Indices: 78279--78327 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
78269 ACCACGACCA
*
78279 CGAGCCGAGCCGAGC
1 CGAGCCGTGCCGAGC
*
78294 CGAGCCGTGCCGTGC
1 CGAGCCGTGCCGAGC
* *
78309 CGTGCCGTGCCGAGA
1 CGAGCCGTGCCGAGC
78324 CGAG
1 CGAG
78328 ACGGACGGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.14, C:0.37, G:0.41, T:0.08
Consensus pattern (15 bp):
CGAGCCGTGCCGAGC
Found at i:79163 original size:3 final size:3
Alignment explanation
Indices: 79155--79291 Score: 240
Period size: 3 Copynumber: 45.7 Consensus size: 3
79145 AAAGTGTGTG
79155 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
79203 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
79251 AGA AGG AGA AGA AGA AGA AGA A-A AGGA TGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AG
79292 CTGCCACACC
Statistics
Matches: 128, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.02
3 125 0.98
4 1 0.01
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:84864 original size:20 final size:21
Alignment explanation
Indices: 84835--84873 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
84825 GAGCAATTCG
*
84835 AAAGTTCAGTGAG-AAAATTA
1 AAAGTACAGTGAGTAAAATTA
84855 AAAGTACAGTGAGTAAAAT
1 AAAGTACAGTGAGTAAAAT
84874 AGGTGCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.23
Consensus pattern (21 bp):
AAAGTACAGTGAGTAAAATTA
Done.