Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 23
Found at i:1976211 original size:2 final size:2
Alignment explanation
Indices: 1976204--1976250 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1976194 TTAATATGTG
1976204 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
1976246 TA TA T
1 TA TA T
1976251 TGGTATTATG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1981845 original size:21 final size:22
Alignment explanation
Indices: 1981805--1981846 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1981795 ACAAGACAGG
*
1981805 ACCAAGGATAGTGATGATGATT
1 ACCAAGGATAGGGATGATGATT
*
1981827 ACCAA-GATAGGGATTATGAT
1 ACCAAGGATAGGGATGATGAT
1981847 GTTACAGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (22 bp):
ACCAAGGATAGGGATGATGATT
Found at i:1985246 original size:19 final size:17
Alignment explanation
Indices: 1985222--1985265 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
1985212 TCAGCTACAA
1985222 TCGGGTTGAATCTTGGG
1 TCGGGTTGAATCTTGGG
* *
1985239 CTTCGGGTCGGATCTTGGG
1 --TCGGGTTGAATCTTGGG
1985258 TCGGGTTG
1 TCGGGTTG
1985266 GTTTGTTGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
19 15 0.68
ACGTcount: A:0.07, C:0.16, G:0.43, T:0.34
Consensus pattern (17 bp):
TCGGGTTGAATCTTGGG
Found at i:1985326 original size:3 final size:3
Alignment explanation
Indices: 1985318--1985389 Score: 119
Period size: 3 Copynumber: 24.3 Consensus size: 3
1985308 AATGTAAAAG
1985318 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1985366 ATA ATA ACA A-A AAA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1985390 ATGAGAGCCC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1985923 original size:99 final size:100
Alignment explanation
Indices: 1985784--1986008 Score: 321
Period size: 99 Copynumber: 2.3 Consensus size: 100
1985774 TCAGGTCGGT
* * *
1985784 GGATGACATTGTTCCT--ATGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGGAGACAACA
1 GGATGACACTGCTCCTACATGATGAGGACGTCTAACCATCTTTAGGGATAATTTGGGAGACAACA
*
1985847 CGATTCCTACATGATGA-AAAGTCTGGTTATCTAA
66 CGATTCCTACATGATGACAAAGTATGGTTATCTAA
* * * *
1985881 GGATGACACTGCTCCTACATGATGAGGATGTCTAACCGTCTTTAGTGATAATTTGGGAGATAACA
1 GGATGACACTGCTCCTACATGATGAGGACGTCTAACCATCTTTAGGGATAATTTGGGAGACAACA
* * *
1985946 CGGTTCCTACGTGATGACAAAGTATGGTTATCTAT
66 CGATTCCTACATGATGACAAAGTATGGTTATCTAA
*
1985981 GGATGACACTGCTCCTACGTGATGAGGA
1 GGATGACACTGCTCCTACATGATGAGGA
1986009 GATATGTTCG
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
97 14 0.12
99 57 0.50
100 42 0.37
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (100 bp):
GGATGACACTGCTCCTACATGATGAGGACGTCTAACCATCTTTAGGGATAATTTGGGAGACAACA
CGATTCCTACATGATGACAAAGTATGGTTATCTAA
Found at i:1986195 original size:37 final size:36
Alignment explanation
Indices: 1986142--1986353 Score: 167
Period size: 37 Copynumber: 6.1 Consensus size: 36
1986132 TTATTAATGT
*
1986142 TTCAAG-GAAAACTGTCTCAAGAGACACAAAACTTTG
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAACTTTG
* *
1986178 CTTCAAGAGAAATTGTCTCAAGCGAGACAAAACTTTG
1 -TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
* *
1986215 TTTCAAGGGAAACTGTCTCAAGTGAGACAAAA-TTTG
1 -TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
** ** *** *
1986251 TTCAAG-GTAAACAATCTC-A-ATTG--TTTA-TGT-
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAACTTTG
1986281 TTCAAGAG-AACTGTCTCAAGAGAGACAAAAC-TTG
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
* *
1986315 TTTAAAGAGAAACTGTCTCAAGCGAGACAAAACTTTG
1 -TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
1986352 TT
1 TT
1986354 TCGTGAGAAA
Statistics
Matches: 137, Mismatches: 26, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
29 7 0.05
30 7 0.05
31 6 0.04
33 3 0.02
34 2 0.01
35 21 0.15
36 28 0.20
37 62 0.45
38 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
Found at i:1986324 original size:35 final size:37
Alignment explanation
Indices: 1986278--1986354 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
1986268 CAATTGTTTA
*
1986278 TGTTTCAAGAG-AACTGTCTCAAGAGAGACAAAAC-T
1 TGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAACTT
*
1986313 TGTTTAAAGAGAAACTGTCTCAAGCGAGACAAAACTT
1 TGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1986350 TGTTT
1 TGTTT
1986355 CGTGAGAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 10 0.26
36 22 0.58
37 6 0.16
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (37 bp):
TGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:1986362 original size:37 final size:36
Alignment explanation
Indices: 1986278--1986377 Score: 121
Period size: 37 Copynumber: 2.8 Consensus size: 36
1986268 CAATTGTTTA
* *
1986278 TGTTTCAAGAG-AACTGTCTCAAGAGAGACAAAACT
1 TGTTTAAAGAGAAACTGTCTCAAGCGAGACAAAACT
1986313 TGTTTAAAGAGAAACTGTCTCAAGCGAGACAAAACTT
1 TGTTTAAAGAGAAACTGTCTCAAGCGAGACAAAAC-T
*** * *
1986350 TGTTTCGTGAGAAACTATATCAAGCGAG
1 TGTTTAAAGAGAAACTGTCTCAAGCGAG
1986378 TCGAAATTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 10 0.18
36 22 0.39
37 24 0.43
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (36 bp):
TGTTTAAAGAGAAACTGTCTCAAGCGAGACAAAACT
Found at i:1986533 original size:100 final size:101
Alignment explanation
Indices: 1986369--1986695 Score: 301
Period size: 100 Copynumber: 3.2 Consensus size: 101
1986359 AGAAACTATA
* * * ** *
1986369 TCAAGCGAGTCGAAATTTTTTTTGAGAGAAACAATCTCAAAGAT-TTATCAATTTTGTTTCAAGT
1 TCAAGTGAGACGAAATTTGTTTTGA-AGAAACAATCTC-AAG-TGAGATAAATTTTGTTTCAAGT
1986433 GAAACAATTTTAGAATTTGTGTTCCGAAGAAAAAAATGTC
63 GAAACAATTTTAGAATTTGTGTTCCGAAG-AAAAAATGTC
*
1986473 TCAAGTGAGACGAAATTTGTTTTG-AG-AAGAATCTCAAGTGAGATAAATTTTGTTTCAAGTGAA
1 TCAAGTGAGACGAAATTTGTTTTGAAGAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGTGAA
** * * *
1986536 ACAATTTTCA-AATTCTGTGTT-TTAAGGAAATATTATC
66 ACAATTTT-AGAATT-TGTGTTCCGAA-GAAAAAATGTC
* ** * * * *
1986573 TCCAGCAAGATG-AATTTGTTTTGAAAGAAACAATCTCAAGTGAGATTAATTTTATTTCAAGTAA
1 TCAAGTGAGACGAAATTTGTTTTG-AAGAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGTGA
* ** *
1986637 AACAACTTT-GAAATTTGTGTTCCG-AGGGAAACTGTC
65 AACAATTTTAG-AATTTGTGTTCCGAAGAAAAAATGTC
*
1986673 TCAAGTGAGACGAAATTTATTTT
1 TCAAGTGAGACGAAATTTGTTTT
1986696 TAGGAAAAAT
Statistics
Matches: 179, Mismatches: 33, Indels: 25
0.76 0.14 0.11
Matches are distributed among these distances:
99 12 0.07
100 66 0.37
101 34 0.19
102 46 0.26
104 21 0.12
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (101 bp):
TCAAGTGAGACGAAATTTGTTTTGAAGAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGTGAA
ACAATTTTAGAATTTGTGTTCCGAAGAAAAAATGTC
Found at i:1986917 original size:66 final size:67
Alignment explanation
Indices: 1986826--1986953 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 67
1986816 AATTTACATC
* * * * * *
1986826 TCAAAGGAAAATTGTCTCAAACGAGACGAAATTTGTTTTGAGAGAAACAATCTTAAAGGCTTGTG
1 TCAAAAGAAAATTGTCCCAAACGAGACAAAATGTGTTTTGAGAAAAACAATCTCAAAGGCTTGTG
1986891 TT
66 TT
* * *
1986893 TCAAAAGAAAA-TGTCCCAAGCGAGATAAAATGTGTTTTGTGAAAAACAATCTCAAAGGCTT
1 TCAAAAGAAAATTGTCCCAAACGAGACAAAATGTGTTTTGAGAAAAACAATCTCAAAGGCTT
1986954 ATAGACTGTC
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
66 42 0.81
67 10 0.19
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (67 bp):
TCAAAAGAAAATTGTCCCAAACGAGACAAAATGTGTTTTGAGAAAAACAATCTCAAAGGCTTGTG
TT
Found at i:1989509 original size:4 final size:4
Alignment explanation
Indices: 1989495--1989570 Score: 75
Period size: 4 Copynumber: 18.8 Consensus size: 4
1989485 CTTGTCTTCT
* * *
1989495 TTTC TTTTC TTTC TTCC TTTC -TTC TTCC TTTC TTTC TTCC TTTC TTTC
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
1989543 TTT- TTTC TTTGC TTTT TTCTC TTTC TTT
1 TTTC TTTC TTT-C TTTC TT-TC TTTC TTT
1989571 TTCACTTTGC
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
3 6 0.10
4 42 0.71
5 11 0.19
ACGTcount: A:0.00, C:0.26, G:0.01, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:1989514 original size:8 final size:8
Alignment explanation
Indices: 1989489--1989545 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
1989479 GTGCTTCTTG
*
1989489 TCTTCTTT
1 TCTTCCTT
*
1989497 TCTTTTCTT
1 TC-TTCCTT
1989506 TCTTCCTT
1 TCTTCCTT
1989514 TCTT-CTT
1 TCTTCCTT
* *
1989521 CCTTTCTT
1 TCTTCCTT
1989529 TCTTCCTT
1 TCTTCCTT
*
1989537 TCTTTCTT
1 TCTTCCTT
1989545 T
1 T
1989546 TTTCTTTGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
7 6 0.15
8 28 0.70
9 6 0.15
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (8 bp):
TCTTCCTT
Found at i:1989517 original size:12 final size:12
Alignment explanation
Indices: 1989500--1989544 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
1989490 CTTCTTTTCT
1989500 TTTCTTTCTTCC
1 TTTCTTTCTTCC
1989512 TTTC-TTCTTCC
1 TTTCTTTCTTCC
1989523 TTTCTTTCTTCC
1 TTTCTTTCTTCC
1989535 TTTCTTTCTT
1 TTTCTTTCTT
1989545 TTTTCTTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.34
12 21 0.66
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCTTTCTTCC
Found at i:1989530 original size:23 final size:22
Alignment explanation
Indices: 1989491--1989596 Score: 84
Period size: 23 Copynumber: 4.9 Consensus size: 22
1989481 GCTTCTTGTC
*
1989491 TTCTTTTCTTTTCTTTCTTCCT
1 TTCTTTTCCTTTCTTTCTTCCT
1989513 TTCTTCTTCCTTTCTTTCTTCCT
1 TTCTT-TTCCTTTCTTTCTTCCT
*
1989536 TTC-TTT-CTTT-TTTCTTTGC-
1 TTCTTTTCCTTTCTTTC-TTCCT
1989555 TT-TTTTCTCTTTCTTT-TTCACT
1 TTCTTTTC-CTTTCTTTCTTC-CT
1989577 TTGCTTTT--TTTCTTTGCTTC
1 TT-CTTTTCCTTTCTTT-CTTC
1989597 TTTTACATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 23
0.73 0.03 0.24
Matches are distributed among these distances:
19 9 0.13
20 9 0.13
21 14 0.20
22 11 0.16
23 22 0.32
24 4 0.06
ACGTcount: A:0.01, C:0.25, G:0.03, T:0.71
Consensus pattern (22 bp):
TTCTTTTCCTTTCTTTCTTCCT
Found at i:1989557 original size:12 final size:12
Alignment explanation
Indices: 1989535--1989600 Score: 71
Period size: 13 Copynumber: 5.2 Consensus size: 12
1989525 TCTTTCTTCC
1989535 TTTCTTT-CTTT
1 TTTCTTTGCTTT
1989546 TTTCTTTGCTTT
1 TTTCTTTGCTTT
*
1989558 TTTCTCTTTCTTT
1 TTTCT-TTGCTTT
*
1989571 TTCACTTTGCTTTT
1 TT-TCTTTGC-TTT
1989585 TTTCTTTGCTTCT
1 TTTCTTTGCTT-T
1989598 TTT
1 TTT
1989601 ACATTTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 7 0.15
12 11 0.24
13 21 0.46
14 7 0.15
ACGTcount: A:0.02, C:0.20, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTCTTTGCTTT
Found at i:1989579 original size:26 final size:24
Alignment explanation
Indices: 1989535--1989591 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 24
1989525 TCTTTCTTCC
*
1989535 TTTCTTTCTTTTTTCTTTGCTTTT
1 TTTCTTTCTTTTTACTTTGCTTTT
1989559 TTCTCTTTCTTTTTCACTTTGCTTTT
1 TT-TCTTTCTTTTT-ACTTTGCTTTT
1989585 TTTCTTT
1 TTTCTTT
1989592 GCTTCTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 2 0.07
25 16 0.53
26 12 0.40
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTCTTTCTTTTTACTTTGCTTTT
Found at i:1992359 original size:21 final size:20
Alignment explanation
Indices: 1992324--1992362 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1992314 TAATGGATGG
1992324 TTGTTTTTATATGATGTTGT
1 TTGTTTTTATATGATGTTGT
*
1992344 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TATATGATGTT
1992363 TAGTGCCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.13, C:0.00, G:0.21, T:0.67
Consensus pattern (20 bp):
TTGTTTTTATATGATGTTGT
Found at i:2001647 original size:20 final size:20
Alignment explanation
Indices: 2001618--2001656 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2001608 AGAGCCCATA
*
2001618 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
2001638 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
2001657 GAGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:2004695 original size:55 final size:55
Alignment explanation
Indices: 2004611--2004925 Score: 447
Period size: 55 Copynumber: 5.7 Consensus size: 55
2004601 CCCACTACCA
* * * * *
2004611 ATACAGAAATTTATACA-TATAGTATGAATTTC-TAAGTTTTGCATATCAAGTGCCC
1 ATACAGAAATTCATCCACT-TAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCC
2004666 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
2004721 ATAC-GAAAATTCATTCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACAG-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* *
2004776 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAATTTTACACATAAAGTGCAC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* * * * * *
2004831 ATACGGAAGTTCATCCACTTAGTATGAATTTCTTAAGTTCACATATATAGTGACC
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
2004886 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
1 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
2004926 TTGCGCACTT
Statistics
Matches: 237, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
54 1 0.00
55 230 0.97
56 6 0.03
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (55 bp):
ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
Found at i:2005309 original size:22 final size:18
Alignment explanation
Indices: 2005282--2005335 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 18
2005272 TACCCTTACC
2005282 ATGGTATCGATACTACTATACT
1 ATGGTA-CGATACT-CTAT--T
2005304 ATGGTACTGATACTCTATT
1 ATGGTAC-GATACTCTATT
2005323 ATGGTACCGATAC
1 ATGGTA-CGATAC
2005336 CATTTTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 12 0.40
20 1 0.03
21 5 0.17
22 12 0.40
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (18 bp):
ATGGTACGATACTCTATT
Found at i:2005384 original size:20 final size:20
Alignment explanation
Indices: 2005359--2005409 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
2005349 TGTTTTGAAT
2005359 GGTATCGATACCTTCCCTTC
1 GGTATCGATACCTTCCCTTC
2005379 GGTATCGATACCTTCCCTTC
1 GGTATCGATACCTTCCCTTC
2005399 GGTATCGATAC
1 GGTATCGATAC
2005410 TGATTGCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (20 bp):
GGTATCGATACCTTCCCTTC
Found at i:2008879 original size:108 final size:105
Alignment explanation
Indices: 2008619--2009030 Score: 477
Period size: 105 Copynumber: 3.9 Consensus size: 105
2008609 CCCACTACCA
* * * * * * *
2008619 ATACGGAAATTTATACACTT-GCTATGAATTTCCT-AGTTTTTCATATAAAGTGTCCATACAGCA
1 ATACGAAAATTCATCCACTTAG-TATGAATTTCTTAAG-TTTACACATAAAGTG-CCATACAGAA
*
2008682 ATTCATCCACTTAGTATGAA-TTCTTAAG-TTACACATAAAGGCC
63 ATTCATCCACTTAGTATGAATTTCTTAAGTTTACAC--AAAGTCC
* * *
2008725 ATACGAAAATT-ATCCACTAAGTATGAATTTCTTAAGTTTACTCATAAAGTACCTATACAGAAAT
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCC-ATACAGAAAT
2008789 TCATCCACTTAGTATGAATTTCTTAAGTTTACACAAAGTCTGC
65 TCATCCACTTAGTATGAATTTCTTAAGTTTACACAAAGTC--C
*
2008832 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAG-GCCCATAC-GGAA
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACAT-AAAGTG-CCATACAGAAA
* *
2008895 TTCATCCACTTTGTATGAATTTCTTAATTTTACACATAAGTACCC
64 TTCATCCACTTAGTATGAATTTCTTAAGTTTACACA-AAGT--CC
* *
2008940 ATACGGAAATTCATCCACTTAGTATGAATTTC-TAAG-TTAAACATAAAGTGCCATA-AGAAAAT
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCATACAG-AAAT
2009002 TCATCCAC-TAGTATGAATTTCTTAAGTTT
65 TCATCCACTTAGTATGAATTTCTTAAGTTT
2009031 TTCACACTTA
Statistics
Matches: 269, Mismatches: 21, Indels: 33
0.83 0.07 0.10
Matches are distributed among these distances:
104 2 0.01
105 89 0.33
106 40 0.15
107 59 0.22
108 72 0.27
109 6 0.02
110 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (105 bp):
ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCATACAGAAATT
CATCCACTTAGTATGAATTTCTTAAGTTTACACAAAGTCC
Found at i:2008921 original size:54 final size:54
Alignment explanation
Indices: 2008619--2009030 Score: 451
Period size: 54 Copynumber: 7.7 Consensus size: 54
2008609 CCCACTACCA
* * * * * *
2008619 ATACGGAAATTTATACACTT-GCTATGAATTTCCT-AGTTTTTCATATAAAGTGTCC
1 ATAC-GAAATTCATCCACTTAG-TATGAATTTCTTAAG-TTTACACATAAAGTGCCC
*
2008674 ATACAGCAATTCATCCACTTAGTATGAA-TTCTTAAG-TTACACATAAAG-G-CC
1 ATAC-GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* * * *
2008725 ATACGAAAATT-ATCCACTAAGTATGAATTTCTTAAGTTTACTCATAAAGTACCT
1 ATACG-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
2008779 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACAC--AAAGT-CTGC
1 ATAC-GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGC-CC
2008832 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAG-GCCC
1 ATACG-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACAT-AAAGTGCCC
* * * *
2008887 ATACGGAATTCATCCACTTTGTATGAATTTCTTAATTTTACACAT-AAGTACCC
1 ATACGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
2008940 ATACGGAAATTCATCCACTTAGTATGAATTTC-TAAG-TTAAACATAAAGTG-CC
1 ATAC-GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
2008992 ATAAGAAAATTCATCCAC-TAGTATGAATTTCTTAAGTTT
1 ATACG-AAATTCATCCACTTAGTATGAATTTCTTAAGTTT
2009031 TTCACACTTA
Statistics
Matches: 309, Mismatches: 27, Indels: 44
0.81 0.07 0.12
Matches are distributed among these distances:
50 16 0.05
51 32 0.10
52 45 0.15
53 73 0.24
54 76 0.25
55 61 0.20
56 6 0.02
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (54 bp):
ATACGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
Found at i:2012767 original size:3 final size:3
Alignment explanation
Indices: 2012761--2012809 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
2012751 AATATATTAT
* * *
2012761 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA CAA AAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
2012807 TAA
1 TAA
2012810 ATGAGTACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2015720 original size:20 final size:20
Alignment explanation
Indices: 2015695--2015739 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
2015685 TCTCTTTGAA
2015695 TTTCTCTGGTTTTTGGGTTT
1 TTTCTCTGGTTTTTGGGTTT
2015715 TTTCTCTGGTTTTTGGGTTT
1 TTTCTCTGGTTTTTGGGTTT
2015735 TTTCT
1 TTTCT
2015740 TTCTCCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.00, C:0.11, G:0.22, T:0.67
Consensus pattern (20 bp):
TTTCTCTGGTTTTTGGGTTT
Found at i:2018097 original size:13 final size:12
Alignment explanation
Indices: 2018070--2018104 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2018060 TTAAACAATT
2018070 AAAATAACTAAA
1 AAAATAACTAAA
*
2018082 AAAATTACTAAA
1 AAAATAACTAAA
2018094 AAAAT-ACTAAA
1 AAAATAACTAAA
2018105 TATAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAATAACTAAA
Found at i:2019316 original size:21 final size:21
Alignment explanation
Indices: 2019269--2019364 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
2019259 GATGCACCTA
**
2019269 TCATCATTCAAGAGGCGACTC
1 TCATCATTCAAGAGGCCCCTC
2019290 -CTATCATTCAAGAGGCCCCTC
1 TC-ATCATTCAAGAGGCCCCTC
*
2019311 TCATCA-TCGAAGAAGCCCCTC
1 TCATCATTC-AAGAGGCCCCTC
* * * * *
2019332 CCACCGTTCAAGAGGCTCCTG
1 TCATCATTCAAGAGGCCCCTC
2019353 TCATCATTCAAG
1 TCATCATTCAAG
2019365 TGGTCCCGCC
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:2019316 original size:42 final size:42
Alignment explanation
Indices: 2019269--2019364 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
2019259 GATGCACCTA
* * * *
2019269 TCATCATTCAAGAGGCGACTCCTATCATTCAAGAGGCCCCTC
1 TCATCATTCAAGAAGCCACTCCCACCATTCAAGAGGCCCCTC
* * * *
2019311 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCTCCTG
1 TCATCATTC-AAGAAGCCACTCCCACCATTCAAGAGGCCCCTC
2019353 TCATCATTCAAG
1 TCATCATTCAAG
2019365 TGGTCCCGCC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 2 0.05
42 40 0.91
43 2 0.05
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAAGCCACTCCCACCATTCAAGAGGCCCCTC
Found at i:2020193 original size:14 final size:14
Alignment explanation
Indices: 2020174--2020213 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2020164 TTTTGATTAA
2020174 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
2020188 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
2020202 TTGATTTGTAAA
1 TTGATTTGTAAA
2020214 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2020206 original size:60 final size:63
Alignment explanation
Indices: 2020124--2020262 Score: 162
Period size: 65 Copynumber: 2.2 Consensus size: 63
2020114 TTTTACATTG
2020124 AAAGTTGATTTG-TTACAATTGATGAGGAAAT-AA-TATTTATTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAATTATTT-TTTCTTGATTAATTGATTTGTA
* ** * *
2020184 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAAT-A-AATTATTTTTT-CTTGATTAATTGATTTGT
2020248 A
63 A
2020249 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
2020263 GTTTCTAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
60 23 0.34
61 3 0.04
63 5 0.07
64 5 0.07
65 31 0.46
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.50
Consensus pattern (63 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAATTATTTTTTCTTGATTAATTGATTTGTA
Found at i:2020338 original size:20 final size:20
Alignment explanation
Indices: 2020313--2020350 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2020303 GTTGAAGGTA
*
2020313 CAAATTTGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
2020333 CAAATTCGCAACGCGAAA
1 CAAATTCGCAACGCGAAA
2020351 TAAGCGTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:2020675 original size:39 final size:39
Alignment explanation
Indices: 2020621--2020707 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
2020611 TCAAGTTGTA
*
2020621 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
*
2020660 GATTTTGATTTCCTTTTGCTTGACACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
2020699 GATTTTGAT
1 GATTTTGAT
2020708 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
Found at i:2021043 original size:6 final size:6
Alignment explanation
Indices: 2021022--2021078 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
2021012 ATTTATATTG
* * * * * *
2021022 AAATTC AAACTC AAATTG AAATTT AAATTC AAACTC AAATTG AAATTT
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC
2021070 AAATTC AAA
1 AAATTC AAA
2021079 ATCCAATTAC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.32
Consensus pattern (6 bp):
AAATTC
Found at i:2021086 original size:24 final size:24
Alignment explanation
Indices: 2021022--2021078 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
2021012 ATTTATATTG
2021022 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAATTT
2021046 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAATTT
2021070 AAATTCAAA
1 AAATTCAAA
2021079 ATCCAATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATTCAAACTCAAATTGAAATTT
Found at i:2021491 original size:25 final size:25
Alignment explanation
Indices: 2021463--2021514 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
2021453 ACATTATTTT
*
2021463 TTCAAATAATGTACCCATAACAATG
1 TTCAAATAATGTACCCACAACAATG
2021488 TTCAAATAATGTACCCACAACAATG
1 TTCAAATAATGTACCCACAACAATG
2021513 TT
1 TT
2021515 TAATTGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (25 bp):
TTCAAATAATGTACCCACAACAATG
Found at i:2021659 original size:20 final size:20
Alignment explanation
Indices: 2021630--2021723 Score: 152
Period size: 20 Copynumber: 4.7 Consensus size: 20
2021620 GCGTTGAGAT
2021630 AGTCAAATTCGCAACGTGAA
1 AGTCAAATTCGCAACGTGAA
*
2021650 AGTTAAATTCGCAACGTGAA
1 AGTCAAATTCGCAACGTGAA
2021670 AGTCAAATTCGCAACGTGAA
1 AGTCAAATTCGCAACGTGAA
* * *
2021690 AGTCAAATTCGCTACGCGAT
1 AGTCAAATTCGCAACGTGAA
2021710 AGTCAAATTCGCAA
1 AGTCAAATTCGCAA
2021724 TGCTTATTTC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (20 bp):
AGTCAAATTCGCAACGTGAA
Found at i:2024339 original size:24 final size:24
Alignment explanation
Indices: 2024305--2024358 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2024295 CCATCACATC
*
2024305 ATCAAAATCCGAGTATTTACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2024329 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2024353 ATCAAA
1 ATCAAA
2024359 TTTTGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2024505 original size:12 final size:12
Alignment explanation
Indices: 2024484--2024517 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2024474 GGTTGTGGGT
*
2024484 TTTGAGATTGTG
1 TTTGATATTGTG
2024496 TTTGATATTGTG
1 TTTGATATTGTG
*
2024508 TTTGGTATTG
1 TTTGATATTG
2024518 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2025382 original size:20 final size:20
Alignment explanation
Indices: 2025262--2025386 Score: 91
Period size: 19 Copynumber: 6.4 Consensus size: 20
2025252 ACTAAAACCT
2025262 GTTGCGAAA-TGAAATTCGC
1 GTTGCGAAATTGAAATTCGC
* * *
2025281 GTTACGAATTTGAAATTC-A
1 GTTGCGAAATTGAAATTCGC
* *
2025300 GTTGCGAATTTGAAATTC-A
1 GTTGCGAAATTGAAATTCGC
*
2025319 GTTGCG--ATTTACATATTCGC
1 GTTGCGAAATTGA-A-ATTCGC
* * *
2025339 TTTGCGAAATTAGAAACT-GT
1 GTTGCGAAATT-GAAATTCGC
*
2025359 GTTGCGAAATTGGAATTCGC
1 GTTGCGAAATTGAAATTCGC
2025379 GTTGCGAA
1 GTTGCGAA
2025387 TTTGTTGGTC
Statistics
Matches: 83, Mismatches: 15, Indels: 15
0.73 0.13 0.13
Matches are distributed among these distances:
17 3 0.04
18 1 0.01
19 39 0.47
20 33 0.40
21 2 0.02
22 4 0.05
23 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (20 bp):
GTTGCGAAATTGAAATTCGC
Found at i:2026046 original size:4 final size:4
Alignment explanation
Indices: 2026037--2026184 Score: 60
Period size: 4 Copynumber: 35.8 Consensus size: 4
2026027 ATGAAAGTAC
* * *
2026037 ATAA ATAA ATAA ATAAA ATAA ATAA ATAA GTAAA ATGAGA TTAA AAAA
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA AT-AA AT-A-A ATAA ATAA
* *
2026085 ATAA AGTAAA GATAA A-AA A-AA GT-A ATAAA ATAA ATAAA ATAA AGAA
1 ATAA A-T-AA -ATAA ATAA ATAA ATAA AT-AA ATAA AT-AA ATAA ATAA
* *
2026131 CAT-A AT-A AT-A ATATA ATAA ATAA A-ATA A-AA ATAA ATAA AGAA ACAAA
1 -ATAA ATAA ATAA ATA-A ATAA ATAA ATA-A ATAA ATAA ATAA ATAA A-TAA
2026178 ATAA ATA
1 ATAA ATA
2026185 TAAAGCGAAT
Statistics
Matches: 114, Mismatches: 14, Indels: 32
0.71 0.09 0.20
Matches are distributed among these distances:
3 18 0.16
4 63 0.55
5 27 0.24
6 5 0.04
7 1 0.01
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:2026057 original size:9 final size:9
Alignment explanation
Indices: 2026037--2026284 Score: 90
Period size: 9 Copynumber: 27.1 Consensus size: 9
2026027 ATGAAAGTAC
2026037 ATAAAT-AA
1 ATAAATAAA
2026045 ATAAATAAA
1 ATAAATAAA
2026054 ATAAAT-AA
1 ATAAATAAA
*
2026062 ATAAGTAAA
1 ATAAATAAA
*
2026071 ATGAGATTAAA
1 AT-A-AATAAA
2026082 A-AAATAAA
1 ATAAATAAA
* * *
2026090 GTAAAGATA
1 ATAAATAAA
2026099 A-AAA-AAA
1 ATAAATAAA
*
2026106 GT-AATAAA
1 ATAAATAAA
2026114 ATAAATAAA
1 ATAAATAAA
* *
2026123 ATAAAGAAC
1 ATAAATAAA
2026132 AT-AATAATA
1 ATAAATAA-A
2026141 ATATAAT-AA
1 ATA-AATAAA
2026150 ATAAAATAAAA
1 AT-AAAT-AAA
2026161 ATAAAT-AA
1 ATAAATAAA
* *
2026169 AGAAACAAA
1 ATAAATAAA
2026178 ATAAATATAA
1 ATAAATA-AA
**
2026188 AGCGAATAACAA
1 A-TAAAT-A-AA
*
2026200 ATAAGTAAA
1 ATAAATAAA
*
2026209 GATAAAGAAAA
1 -ATAAA-TAAA
2026220 TATAAATATAA
1 -ATAAATA-AA
2026231 ACTACAA-AAA
1 A-TA-AATAAA
*
2026241 ATAAAGAAA
1 ATAAATAAA
*
2026250 ATGAATGAAA
1 ATAAAT-AAA
*
2026260 A-AAAGAAA
1 ATAAATAAA
*
2026268 A-AAA-ACA
1 ATAAATAAA
2026275 ATAAATAAA
1 ATAAATAAA
2026284 A
1 A
2026285 AATAATAATG
Statistics
Matches: 179, Mismatches: 34, Indels: 53
0.67 0.13 0.20
Matches are distributed among these distances:
7 7 0.04
8 47 0.26
9 64 0.36
10 24 0.13
11 31 0.17
12 6 0.03
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.19
Consensus pattern (9 bp):
ATAAATAAA
Found at i:2026143 original size:23 final size:22
Alignment explanation
Indices: 2026039--2026184 Score: 88
Period size: 23 Copynumber: 6.6 Consensus size: 22
2026029 GAAAGTACAT
*
2026039 AAAT-AAATAAATAAAATAAAT
1 AAATAAAATAAATAAAATAAAG
* * * *
2026060 AAAT-AAGTAAAATGAGATTAAAA
1 AAATAAAAT-AAAT-AAAATAAAG
* *
2026083 AAATAAAGTAAAGATAAAAAAAAG
1 AAATAAAAT-AA-ATAAAATAAAG
*
2026107 TAATAAAATAAATAAAATAAAG
1 AAATAAAATAAATAAAATAAAG
* *
2026129 AACAT--AAT-AATAATAT-AAT
1 AA-ATAAAATAAATAAAATAAAG
*
2026148 AAATAAAATAAAAATAAATAAAG
1 AAATAAAATAAATA-AAATAAAG
*
2026171 AAACAAAATAAATA
1 AAATAAAATAAATA
2026185 TAAAGCGAAT
Statistics
Matches: 96, Mismatches: 19, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 10 0.10
21 13 0.14
22 18 0.19
23 28 0.29
24 19 0.20
25 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (22 bp):
AAATAAAATAAATAAAATAAAG
Found at i:2026152 original size:15 final size:15
Alignment explanation
Indices: 2026081--2026184 Score: 74
Period size: 17 Copynumber: 6.7 Consensus size: 15
2026071 ATGAGATTAA
2026081 AAAAATAAAGTAAAGAT
1 AAAAATAAA-TAAA-AT
2026098 AAAAA-AAAGT--AAT
1 AAAAATAAA-TAAAAT
2026111 -AAAATAAATAAAAT
1 AAAAATAAATAAAAT
*
2026125 AAAGAACATAATAATAAT
1 AAA-AATA-AATAA-AAT
*
2026143 -ATAATAAATAAAAT
1 AAAAATAAATAAAAT
*
2026157 AAAAATAAATAAAGAA
1 AAAAATAAATAAA-AT
2026173 ACAAAATAAATA
1 A-AAAATAAATA
2026185 TAAAGCGAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
12 5 0.07
13 5 0.07
14 7 0.10
15 18 0.25
16 13 0.18
17 21 0.29
18 3 0.04
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (15 bp):
AAAAATAAATAAAAT
Found at i:2026298 original size:13 final size:13
Alignment explanation
Indices: 2026268--2026313 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
2026258 AAAAAAGAAA
* *
2026268 AAAAACAATAAATA
1 AAAAATAAT-AATG
2026282 AAAAATAATAATG
1 AAAAATAATAATG
2026295 AAAAATAATAATG
1 AAAAATAATAATG
2026308 AAAAAT
1 AAAAAT
2026314 TAAAAACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 22 0.73
14 8 0.27
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (13 bp):
AAAAATAATAATG
Found at i:2026356 original size:11 final size:11
Alignment explanation
Indices: 2026342--2026372 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2026332 ACTATTATAT
*
2026342 AAAAAATAGTA
1 AAAAAATAATA
2026353 AAAAAATAATA
1 AAAAAATAATA
2026364 AAAAAATAA
1 AAAAAATAA
2026373 AACAATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:2027082 original size:12 final size:12
Alignment explanation
Indices: 2027057--2027107 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2027047 CCAAAAATAA
2027057 AAATATAGAAAAT
1 AAATATA-AAAAT
2027070 AAATATAAAAAT
1 AAATATAAAAAT
*
2027082 ATAAT-TAAATAT
1 A-AATATAAAAAT
* *
2027094 ATATATAATAAT
1 AAATATAAAAAT
2027106 AA
1 AA
2027108 GGGTTAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.06
12 19 0.61
13 10 0.32
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:2027155 original size:3 final size:3
Alignment explanation
Indices: 2027142--2027198 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
2027132 TAACAAAATA
2027142 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2027188 AAT AAT AAT AA
1 AAT AAT AAT AA
2027199 AATGATTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2029030 original size:84 final size:83
Alignment explanation
Indices: 2028933--2029121 Score: 252
Period size: 84 Copynumber: 2.3 Consensus size: 83
2028923 TGAAAAATAC
* * *
2028933 CCCTTCTCGCCTTGAGCTATGCTGAAAATAATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAG
1 CCCTTATCGCCTTGAGTTATGCTGAAAATAATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAG
* *
2028998 GTCTTTTGTTGGCAGATAG
66 GTC-TTTGTTGACAGATAA
* ** * * *
2029017 CCCTTATTGCCTTGAGTTAAACTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTATCGCCTTGAGTTATGCTGAAAATAATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAG
2029082 GTCTTTGTTGACAGATAA
66 GTCTTTGTTGACAGATAA
*
2029100 CTCTTATCGCCTTTGAGTTATG
1 CCCTTATCGCC-TTGAGTTATG
2029122 ATGTACTTGG
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
83 22 0.25
84 67 0.75
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (83 bp):
CCCTTATCGCCTTGAGTTATGCTGAAAATAATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAG
GTCTTTGTTGACAGATAA
Found at i:2029403 original size:120 final size:121
Alignment explanation
Indices: 2029190--2029425 Score: 393
Period size: 120 Copynumber: 2.0 Consensus size: 121
2029180 GTATAACTAT
* *
2029190 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGAT
1 TGGGCACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGAGAT
* *
2029255 TTGAATTGGATATCCTTTATCGTGAAGTTG-AATCCAAGGGTTGCATTGCTACTTG
66 TTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAAGGTTGCATTGCTACTTG
* *
2029310 TGGGCACGATATCATTCGTCGTGAAGTTGAAATTGTGGATGGCTCATTCATTGTGAAGTTGAGCT
1 TGGGCACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGAGAT
* *
2029375 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAAAGGTTGCATTGCT
66 TTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAAGGTTGCATTGCT
2029426 TCGAGTCCAA
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
120 88 0.82
121 19 0.18
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.35
Consensus pattern (121 bp):
TGGGCACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCATTGTGAAGTTGAGAT
TTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAAGGTTGCATTGCTACTTG
Found at i:2029507 original size:64 final size:64
Alignment explanation
Indices: 2029428--2029594 Score: 307
Period size: 64 Copynumber: 2.6 Consensus size: 64
2029418 GCATTGCTTC
* * *
2029428 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAATTGGAAAGTTGTTTTTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
2029492 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
2029556 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
2029595 AAAAGCTGCA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 100 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:2030939 original size:26 final size:25
Alignment explanation
Indices: 2030905--2030963 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
2030895 TTTCCTATGT
*
2030905 TTTTGTTTCTCTTT-TTATTCTCTTTGC
1 TTTT-TTTC-CTTTATTATTCTCTCT-C
*
2030932 TTTTTTTCCTTTATTTTTCTCTCTC
1 TTTTTTTCCTTTATTATTCTCTCTC
2030957 TTTTTTT
1 TTTTTTT
2030964 TTTTTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 12 0.41
26 13 0.45
27 4 0.14
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (25 bp):
TTTTTTTCCTTTATTATTCTCTCTC
Found at i:2030939 original size:41 final size:41
Alignment explanation
Indices: 2030893--2030979 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
2030883 TCTTGTCTTC
* * *
2030893 TTTTTCCTATGTTTTTGTTTCTCTTTTTATTCTCTTTGCTT
1 TTTTTCCTATATTTTTCTCTCTCTTTTTATTCTCTTTGCTT
* * * * *
2030934 TTTTTCCTTTATTTTTCTCTCTCTTTTTTTTTTTTTTTCTT
1 TTTTTCCTATATTTTTCTCTCTCTTTTTATTCTCTTTGCTT
2030975 TTTTT
1 TTTTT
2030980 TATTGGATCT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (41 bp):
TTTTTCCTATATTTTTCTCTCTCTTTTTATTCTCTTTGCTT
Found at i:2034084 original size:23 final size:24
Alignment explanation
Indices: 2034051--2034199 Score: 72
Period size: 23 Copynumber: 6.5 Consensus size: 24
2034041 ATGAGATAAA
* *
2034051 AATAAAGTAAAGATAAAA-AAA-TT
1 AATAAAATAAA-ATAAAATAAAGAT
2034074 AATAAAAT-AAATAAAATAAAGAT
1 AATAAAATAAAATAAAATAAAGAT
*
2034097 AATAAAATAAAA-GAAATAAA-AGT
1 AATAAAATAAAATAAAATAAAGA-T
*
2034120 AA-AAATAAATAAATAAAATAAAGA-
1 AATAAA-ATA-AAATAAAATAAAGAT
* *
2034144 ACAT--AATAATAATATAATAAATA-
1 A-ATAAAATAA-AATAAAATAAAGAT
* *
2034167 AAT-AAAT-AAAT-AAATAAACAA
1 AATAAAATAAAATAAAATAAAGAT
2034188 AATAAATATAAA
1 AATAAA-ATAAA
2034200 GGGAATAGAA
Statistics
Matches: 100, Mismatches: 10, Indels: 31
0.71 0.07 0.22
Matches are distributed among these distances:
20 7 0.07
21 12 0.12
22 15 0.15
23 47 0.47
24 10 0.10
25 8 0.08
26 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (24 bp):
AATAAAATAAAATAAAATAAAGAT
Found at i:2034087 original size:4 final size:4
Alignment explanation
Indices: 2034063--2034195 Score: 78
Period size: 4 Copynumber: 31.8 Consensus size: 4
2034053 TAAAGTAAAG
* * * *
2034063 ATAA AAAA ATTA ATAAA ATAA ATAAA ATAA AGATA ATAAA ATAAA AGAA
1 ATAA ATAA ATAA AT-AA ATAA AT-AA ATAA ATA-A AT-AA AT-AA ATAA
*
2034112 ATAA A-AGTA A-AA ATAA ATAA ATAAA ATAA AGAA CAT-A AT-A AT-A
1 ATAA ATA--A ATAA ATAA ATAA AT-AA ATAA ATAA -ATAA ATAA ATAA
*
2034155 ATATA ATAA ATAA ATAA ATAA ATAA ATAA ACAAA ATAA ATA
1 ATA-A ATAA ATAA ATAA ATAA ATAA ATAA A-TAA ATAA ATA
2034196 TAAAGGGAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
3 11 0.10
4 62 0.59
5 31 0.30
6 1 0.01
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:2034102 original size:52 final size:50
Alignment explanation
Indices: 2034046--2034233 Score: 136
Period size: 48 Copynumber: 3.6 Consensus size: 50
2034036 GTAAAATGAG
2034046 ATAAAAATAAAGTAAAGATAAAAAAATTAATAAAATAAATAAAATAAAGATA
1 ATAAAAATAAA-TAAAGATAAAAAAA-TAATAAAATAAATAAAATAAAGATA
2034098 AT-AAAATAAA-AGAA-ATAAAAGTAAA-AAT-AAATAAATAAAATAAAGAACATA
1 ATAAAAATAAATA-AAGATAAAA--AAATAATAAAATAAATAAAATAAAG---ATA
* * * **
2034149 ATAATAATATAATAAATAAATAAATAAATAAATAAACA-AAATAAATATAAAGGGA
1 ATAAAAATA-AAT-AA-AGATAAAAAAAT-AATAAA-ATAAATAAA-ATAAAGATA
*
2034204 ATAGAAAATAAGTAAAGATAAAGAAAATAA
1 ATA-AAAATAAATAAAGATAAA-AAAATAA
2034234 AAATGAAAAT
Statistics
Matches: 109, Mismatches: 8, Indels: 37
0.71 0.05 0.24
Matches are distributed among these distances:
48 17 0.16
49 10 0.09
50 2 0.02
51 16 0.15
52 7 0.06
53 10 0.09
54 10 0.09
55 8 0.07
56 13 0.12
57 9 0.08
58 7 0.06
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (50 bp):
ATAAAAATAAATAAAGATAAAAAAATAATAAAATAAATAAAATAAAGATA
Found at i:2034130 original size:48 final size:49
Alignment explanation
Indices: 2034063--2034198 Score: 143
Period size: 52 Copynumber: 2.7 Consensus size: 49
2034053 TAAAGTAAAG
* *
2034063 ATAAAAAAATTAATAAAATAAATAAAATAAAGATAATAA-AATAAAAGAA
1 ATAAATAAATAAAT-AAATAAATAAAATAAAGATAATAATAATAAAAGAA
* *
2034112 ATAAA-AGTAA-AAATAAATAAATAAAATAAAGAACATAATAATAATATAATAA
1 ATAAATA--AATAAATAAATAAATAAAATAAAG---ATAATAATAATAAAAGAA
* *
2034164 ATAAATAAATAAATAAATAAACAAAATAAATATAA
1 ATAAATAAATAAATAAATAAATAAAATAAAGATAA
2034199 AGGGAATAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
48 18 0.24
49 12 0.16
50 2 0.03
51 9 0.12
52 32 0.43
53 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (49 bp):
ATAAATAAATAAATAAATAAATAAAATAAAGATAATAATAATAAAAGAA
Found at i:2034274 original size:10 final size:9
Alignment explanation
Indices: 2034049--2034281 Score: 77
Period size: 9 Copynumber: 24.9 Consensus size: 9
2034039 AAATGAGATA
2034049 AAAATAAAG
1 AAAATAAAG
2034058 TAAAGATAAA-
1 -AAA-ATAAAG
* *
2034068 AAAATTAAT
1 AAAATAAAG
*
2034077 AAAATAAAT
1 AAAATAAAG
2034086 AAAATAAAG
1 AAAATAAAG
* *
2034095 ATAATAAAAT
1 AAAAT-AAAG
* *
2034105 AAAAGAAAT
1 AAAATAAAG
*
2034114 AAAAGTAAAA
1 AAAA-TAAAG
*
2034124 ATAAATAAAT
1 A-AAATAAAG
2034134 AAAATAAAG
1 AAAATAAAG
*
2034143 AACATAATA-
1 AAAATAA-AG
*
2034152 ATAATATAA-
1 AAAATA-AAG
*
2034161 TAAATAAA-
1 AAAATAAAG
*
2034169 TAAATAAA-
1 AAAATAAAG
* *
2034177 TAAATAAAC
1 AAAATAAAG
*
2034186 AAAATAAAT
1 AAAATAAAG
*
2034195 ATAAAGGGAATAG
1 A-AAA--TAA-AG
2034208 AAAAT-AAG
1 AAAATAAAG
2034216 TAAAGATAAAG
1 -AAA-ATAAAG
2034227 AAAATAAAAATG
1 AAAAT--AAA-G
*
2034239 AAAATATA-
1 AAAATAAAG
* *
2034247 AAACTACAG
1 AAAATAAAG
2034256 AAAATAAAG
1 AAAATAAAG
2034265 AAAATGAAAG
1 AAAAT-AAAG
2034275 -AAATAAA
1 AAAATAAA
2034282 AAGGAAAAAT
Statistics
Matches: 177, Mismatches: 26, Indels: 42
0.72 0.11 0.17
Matches are distributed among these distances:
8 33 0.19
9 83 0.47
10 34 0.19
11 14 0.08
12 11 0.06
13 2 0.01
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.19
Consensus pattern (9 bp):
AAAATAAAG
Found at i:2034354 original size:27 final size:22
Alignment explanation
Indices: 2034286--2034337 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
2034276 AATAAAAAGG
*
2034286 AAAAA-TAATAAATAAAAAAACT
1 AAAAATTAAT-AATGAAAAAACT
2034308 AAAAATTAATAATG-AAAAACT
1 AAAAATTAATAATGAAAAAACT
2034329 AAAAATTAA
1 AAAAATTAA
2034338 AATATATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 16 0.57
22 8 0.29
23 4 0.14
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAATTAATAATGAAAAAACT
Found at i:2034637 original size:20 final size:20
Alignment explanation
Indices: 2034612--2034848 Score: 146
Period size: 20 Copynumber: 11.7 Consensus size: 20
2034602 AAATGACCAA
2034612 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
2034632 CAAATTCGCAACGCG-AACT
1 CAAATTCGCAACGCGAAAGT
* * **
2034651 CCAATTTCGCAAC-CCAATTT
1 -CAAATTCGCAACGCGAAAGT
*
2034671 CCAATTTCGCAACGCGAATACGT
1 -CAAATTCGCAACGCGAA-A-GT
** ***
2034694 -AAATTCGCATTGCGATTTT
1 CAAATTCGCAACGCGAAAGT
* *
2034713 CCAAATTCGTAACGCGAATCTGT
1 -CAAATTCGCAACGCGAA--AGT
*
2034736 -AAATT-GCAACAC-ATAAGT
1 CAAATTCGCAACGCGA-AAGT
2034754 CAAATTCGCAACGC-AATAGT
1 CAAATTCGCAACGCGAA-AGT
* *
2034774 CAAATTCGTAACGCGAAATTT
1 CAAATTCGCAACGCGAAA-GT
*
2034795 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
2034815 CAAATTCGCAACGTGAATAGT
1 CAAATTCGCAACGCGAA-AGT
* *
2034836 AAAAATCGCAACG
1 CAAATTCGCAACG
2034849 TGAATAGTAA
Statistics
Matches: 169, Mismatches: 32, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
18 2 0.01
19 12 0.07
20 87 0.51
21 65 0.38
23 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:2034702 original size:21 final size:21
Alignment explanation
Indices: 2034612--2034930 Score: 184
Period size: 21 Copynumber: 15.6 Consensus size: 21
2034602 AAATGACCAA
2034612 CAAATTCGCAACGCGAA-AGT
1 CAAATTCGCAACGCGAATAGT
*
2034632 CAAATTCGCAACGCGAACT--C
1 CAAATTCGCAACGCGAA-TAGT
* * *
2034652 CAATTTCGCAAC-CCAAT-TT
1 CAAATTCGCAACGCGAATAGT
*
2034671 CCAATTTCGCAACGCGAATACGT
1 -CAAATTCGCAACGCGAATA-GT
** **
2034694 -AAATTCGCATTGCG-ATTTT
1 CAAATTCGCAACGCGAATAGT
* *
2034713 CCAAATTCGTAACGCGAATCTGT
1 -CAAATTCGCAACGCGAAT-AGT
*
2034736 -AAATT-GCAACAC--ATAAGT
1 CAAATTCGCAACGCGAAT-AGT
2034754 CAAATTCGCAACGC-AATAGT
1 CAAATTCGCAACGCGAATAGT
* *
2034774 CAAATTCGTAACGCGAA-ATTT
1 CAAATTCGCAACGCGAATA-GT
2034795 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAATAGT
*
2034815 CAAATTCGCAACGTGAATAGT
1 CAAATTCGCAACGCGAATAGT
* * *
2034836 AAAAATCGCAACGTGAATAGT
1 CAAATTCGCAACGCGAATAGT
* * * * *
2034857 AAAAATCACAATGTGAATAGT
1 CAAATTCGCAACGCGAATAGT
* * * *
2034878 AAAAATCGTAACGTGAATAGT
1 CAAATTCGCAACGCGAATAGT
* * *
2034899 TAAA-TCTCAACGTGAATAGT
1 CAAATTCGCAACGCGAATAGT
*
2034919 -AAAATCGCAACG
1 CAAATTCGCAACG
2034931 AATCTATATG
Statistics
Matches: 244, Mismatches: 36, Indels: 38
0.77 0.11 0.12
Matches are distributed among these distances:
18 5 0.02
19 12 0.05
20 107 0.44
21 115 0.47
22 2 0.01
23 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (21 bp):
CAAATTCGCAACGCGAATAGT
Found at i:2034759 original size:61 final size:61
Alignment explanation
Indices: 2034714--2034827 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
2034704 TGCGATTTTC
2034714 CAAATTCGTAACGCG-AATCTGT-AAATT-GCAACAC-ATAAGTCAAATTCGCAACGCAATAGT
1 CAAATTCGTAACGCGAAAT-T-TCAAATTCGCAACACGAT-AGTCAAATTCGCAACGCAATAGT
*
2034774 CAAATTCGTAACGCGAAATTTCAAATTCGCAACGCGATAGTCAAATTCGCAACG
1 CAAATTCGTAACGCGAAATTTCAAATTCGCAACACGATAGTCAAATTCGCAACG
2034828 TGAATAGTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
59 1 0.02
60 21 0.43
61 25 0.51
62 2 0.04
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (61 bp):
CAAATTCGTAACGCGAAATTTCAAATTCGCAACACGATAGTCAAATTCGCAACGCAATAGT
Found at i:2034826 original size:81 final size:83
Alignment explanation
Indices: 2034612--2034826 Score: 205
Period size: 81 Copynumber: 2.6 Consensus size: 83
2034602 AAATGACCAA
* * * * **
2034612 CAAATTCGCAACGCGAAA-GTCAAATTCGCAACGCGA-ACTCCAATTTCGCAACCCAATTTCCAA
1 CAAATTCGCAACGCGAAATTTCAAATTCGCAACGCGATAGT-CAAATTCGCAACACAAAGTCCAA
*
2034675 TTTCGCAACGCGAATACGT
65 ATTCGCAACGCGAATACGT
** * * *
2034694 -AAATTCGCATTGCG-ATTTTCCAAATTCGTAACGCGAATCTGT-AAATT-GCAACACATAAGT-
1 CAAATTCGCAACGCGAAATTT-CAAATTCGCAACGCG-AT-AGTCAAATTCGCAACACA-AAGTC
2034754 CAAATTCGCAACGC-AATA-GT
62 CAAATTCGCAACGCGAATACGT
*
2034774 CAAATTCGTAACGCGAAATTTCAAATTCGCAACGCGATAGTCAAATTCGCAAC
1 CAAATTCGCAACGCGAAATTTCAAATTCGCAACGCGATAGTCAAATTCGCAAC
2034827 GTGAATAGTA
Statistics
Matches: 105, Mismatches: 18, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
79 2 0.02
80 10 0.10
81 47 0.45
82 38 0.36
83 7 0.07
85 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (83 bp):
CAAATTCGCAACGCGAAATTTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAGTCCAAA
TTCGCAACGCGAATACGT
Found at i:2034845 original size:41 final size:42
Alignment explanation
Indices: 2034759--2034930 Score: 174
Period size: 41 Copynumber: 4.2 Consensus size: 42
2034749 TAAGTCAAAT
* * * * *
2034759 TCGCAACGC-AATAGTCAAATTCGTAACGCGAA-ATTTCAAAT
1 TCGCAACGCGAATAGTCAAATTCGCAACGTGAATA-GTAAAAA
2034800 TCGCAACGCG-ATAGTCAAATTCGCAACGTGAATAGTAAAAA
1 TCGCAACGCGAATAGTCAAATTCGCAACGTGAATAGTAAAAA
* * * * *
2034841 TCGCAACGTGAATAGTAAAAATCACAATGTGAATAGTAAAAA
1 TCGCAACGCGAATAGTCAAATTCGCAACGTGAATAGTAAAAA
* * * *
2034883 TCGTAACGTGAATAGTTAAA-TCTCAACGTGAATAGT-AAAA
1 TCGCAACGCGAATAGTCAAATTCGCAACGTGAATAGTAAAAA
2034923 TCGCAACG
1 TCGCAACG
2034931 AATCTATATG
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
40 11 0.10
41 56 0.50
42 46 0.41
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (42 bp):
TCGCAACGCGAATAGTCAAATTCGCAACGTGAATAGTAAAAA
Found at i:2035309 original size:21 final size:20
Alignment explanation
Indices: 2035283--2035329 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2035273 ATGCGATTGT
2035283 GATTTTCTAAATTCGCGTTGC
1 GATTTTC-AAATTCGCGTTGC
* *
2035304 GATTTTCCAATTTGCGTTGC
1 GATTTTCAAATTCGCGTTGC
2035324 GATTTT
1 GATTTT
2035330 ACTATTCACG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (20 bp):
GATTTTCAAATTCGCGTTGC
Found at i:2035320 original size:20 final size:20
Alignment explanation
Indices: 2035292--2035389 Score: 79
Period size: 20 Copynumber: 4.9 Consensus size: 20
2035282 TGATTTTCTA
2035292 AATTCGCGTTGCGATTTTCC
1 AATTCGCGTTGCGATTTTCC
* *
2035312 AATTTGCGTTGCGATTTTAC
1 AATTCGCGTTGCGATTTTCC
* * * *
2035332 TATTCACGTTACGATTTTAC
1 AATTCGCGTTGCGATTTTCC
* * * *
2035352 TATTCACGTTACGATTTTAC
1 AATTCGCGTTGCGATTTTCC
* **
2035372 TATTCATGTTGCGATTTT
1 AATTCGCGTTGCGATTTT
2035390 TACTATTCAC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.46
Consensus pattern (20 bp):
AATTCGCGTTGCGATTTTCC
Found at i:2035348 original size:40 final size:40
Alignment explanation
Indices: 2035293--2035402 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
2035283 GATTTTCTAA
* * ** *
2035293 ATTCGCGTTGCGATTTTCCAATTTGCGTTGCGATTTTACT
1 ATTCACGTTGCGATTTTACAATTCACGTTACGATTTTACT
* *
2035333 ATTCACGTTACGATTTTACTATTCACGTTACGATTTTACT
1 ATTCACGTTGCGATTTTACAATTCACGTTACGATTTTACT
* *
2035373 ATTCATGTTGCGATTTTTACTATTCACGTT
1 ATTCACGTTGCGA-TTTTACAATTCACGTT
2035403 GCGAAATTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 44 0.73
41 16 0.27
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (40 bp):
ATTCACGTTGCGATTTTACAATTCACGTTACGATTTTACT
Found at i:2035593 original size:3 final size:3
Alignment explanation
Indices: 2035585--2035813 Score: 115
Period size: 3 Copynumber: 75.7 Consensus size: 3
2035575 AGTAAAGTAA
*
2035585 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAGT AA- AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
* * * * *
2035629 -AT AAAT AAAT AAA AACC AAA AAT AAA AAT -AT AGAA AAT AA- ATAT
1 AAT -AAT -AAT AAT AA-T AAT AAT AAT AAT AAT A-AT AAT AAT A-AT
* * ** ** *
2035673 AAA AAT -AT AAT TA- AAT -AT ATAT ATAT AAT AAT AAT AGG GGT TA-
1 AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT
2035716 AAT AA- AAT AAT AAT AA- AAT AAAT ACAT ATAT AAT AA- AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT A-AT A-AT AAT AAT AAT -AAT AAT
2035762 AAAT AAT AA- AGCAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 -AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2035809 AAT AA
1 AAT AA
2035814 CAAAAGGATT
Statistics
Matches: 179, Mismatches: 22, Indels: 50
0.71 0.09 0.20
Matches are distributed among these distances:
2 22 0.12
3 120 0.67
4 36 0.20
5 1 0.01
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2035641 original size:20 final size:20
Alignment explanation
Indices: 2035594--2035769 Score: 68
Period size: 20 Copynumber: 8.7 Consensus size: 20
2035584 AAATAATAAT
2035594 AATAATAATAATAATAATAAA-A
1 AATAA-AAT-ATAAT-ATAAATA
*
2035616 AGTAAAATATAATATAAATA
1 AATAAAATATAATATAAATA
**
2035636 AATAAAA-ACCA-A-AAATA
1 AATAAAATATAATATAAATA
* * *
2035653 AA-AATATAGAAAATAAATA
1 AATAAAATATAATATAAATA
*
2035672 TA-AAAATATAAT-TAAATA
1 AATAAAATATAATATAAATA
* *
2035690 TAT-ATATATAATAATAATAGGGGTTA
1 AATAAAATATAAT-ATAA-A-----TA
2035716 AATAAAATAATAATA-AAATA
1 AATAAAAT-ATAATATAAATA
*
2035736 AATACATATATAATA-AAATA
1 AATA-AAATATAATATAAATA
2035756 AATAATAA-ATAATA
1 AATAA-AATATAATA
2035770 AAGCATAATA
Statistics
Matches: 121, Mismatches: 16, Indels: 37
0.70 0.09 0.21
Matches are distributed among these distances:
16 3 0.02
17 9 0.07
18 18 0.15
19 27 0.22
20 37 0.31
21 7 0.06
22 4 0.03
25 1 0.01
26 6 0.05
27 4 0.03
28 5 0.04
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (20 bp):
AATAAAATATAATATAAATA
Found at i:2038101 original size:7 final size:7
Alignment explanation
Indices: 2038089--2038164 Score: 152
Period size: 7 Copynumber: 10.9 Consensus size: 7
2038079 TGTATGTATG
2038089 CATGCAA
1 CATGCAA
2038096 CATGCAA
1 CATGCAA
2038103 CATGCAA
1 CATGCAA
2038110 CATGCAA
1 CATGCAA
2038117 CATGCAA
1 CATGCAA
2038124 CATGCAA
1 CATGCAA
2038131 CATGCAA
1 CATGCAA
2038138 CATGCAA
1 CATGCAA
2038145 CATGCAA
1 CATGCAA
2038152 CATGCAA
1 CATGCAA
2038159 CATGCA
1 CATGCA
2038165 TTCCATGGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 69 1.00
ACGTcount: A:0.42, C:0.29, G:0.14, T:0.14
Consensus pattern (7 bp):
CATGCAA
Found at i:2044911 original size:4 final size:4
Alignment explanation
Indices: 2044904--2044950 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
2044894 TTGGTTGTTA
* *
2044904 CATG CATG CATG CAT- C-TG TATA CATG CATG CATCG CATG CATG CATG
1 CATG CATG CATG CATG CATG CATG CATG CATG CAT-G CATG CATG CATG
2044951 AATTGATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 1 0.03
3 1 0.03
4 30 0.83
5 4 0.11
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (4 bp):
CATG
Found at i:2044931 original size:18 final size:17
Alignment explanation
Indices: 2044908--2044950 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
2044898 TTGTTACATG
*
2044908 CATGCATGCATCTGTATA
1 CATGCATGCATC-GCATA
*
2044926 CATGCATGCATCGCATG
1 CATGCATGCATCGCATA
2044943 CATGCATG
1 CATGCATG
2044951 AATTGATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (17 bp):
CATGCATGCATCGCATA
Found at i:2047382 original size:12 final size:11
Alignment explanation
Indices: 2047363--2047397 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2047353 AATTTTCAAC
2047363 ATAAAATATAT
1 ATAAAATATAT
2047374 ATAAAAATATAT
1 AT-AAAATATAT
*
2047386 GTAAAATATAT
1 ATAAAATATAT
2047397 A
1 A
2047398 GTAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
ATAAAATATAT
Found at i:2047401 original size:12 final size:12
Alignment explanation
Indices: 2047364--2047401 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2047354 ATTTTCAACA
2047364 TAAAATATATA-
1 TAAAATATATAG
2047375 TAAAA-ATATATG
1 TAAAATATATA-G
2047387 TAAAATATATAG
1 TAAAATATATAG
2047399 TAA
1 TAA
2047402 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.21
11 5 0.21
12 9 0.38
13 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (12 bp):
TAAAATATATAG
Found at i:2047561 original size:15 final size:16
Alignment explanation
Indices: 2047541--2047570 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2047531 TTTATACATG
2047541 AAAATT-AAAGAGAAT
1 AAAATTGAAAGAGAAT
2047556 AAAATTGAAAGAGAA
1 AAAATTGAAAGAGAA
2047571 ACTAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
AAAATTGAAAGAGAAT
Found at i:2050299 original size:18 final size:18
Alignment explanation
Indices: 2050243--2050293 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
2050233 TAATATAAGT
2050243 TTATCGGCGGGAATAGTA
1 TTATCGGCGGGAATAGTA
2050261 TTATCGGCGGGAATAGTA
1 TTATCGGCGGGAATAGTA
*
2050279 TTACCGGCGGGAATA
1 TTATCGGCGGGAATA
2050294 AGATTATTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.25
Consensus pattern (18 bp):
TTATCGGCGGGAATAGTA
Found at i:2050974 original size:18 final size:19
Alignment explanation
Indices: 2050939--2050975 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2050929 CACGGAATGT
2050939 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2050959 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2050976 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2055614 original size:40 final size:40
Alignment explanation
Indices: 2055554--2055648 Score: 145
Period size: 40 Copynumber: 2.4 Consensus size: 40
2055544 ATTTGGCACT
* * * *
2055554 TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
1 TTAATATTATGGTTTATTTATGAATTTTATTATTCTAGAC
2055594 TTAATATTATGGTTTATTTATGAATTTTATTATTCTAGAC
1 TTAATATTATGGTTTATTTATGAATTTTATTATTCTAGAC
*
2055634 TTAATATTGTGGTTT
1 TTAATATTATGGTTT
2055649 GAATTTTGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (40 bp):
TTAATATTATGGTTTATTTATGAATTTTATTATTCTAGAC
Found at i:2060811 original size:19 final size:19
Alignment explanation
Indices: 2060789--2060830 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2060779 AAACAGATGC
*
2060789 ATGAGTT-ATATATGTTTAT
1 ATGAGTTGATACATG-TTAT
*
2060808 ATGATTTGATACATGTTAT
1 ATGAGTTGATACATGTTAT
2060827 ATGA
1 ATGA
2060831 TTCATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (19 bp):
ATGAGTTGATACATGTTAT
Found at i:2073034 original size:22 final size:22
Alignment explanation
Indices: 2073002--2073046 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2072992 CCCCACCATA
*
2073002 TGCACTGGGTATCATTTAGTGC
1 TGCACTAGGTATCATTTAGTGC
*
2073024 TGCACTAGGTATCCTTTAGTGC
1 TGCACTAGGTATCATTTAGTGC
2073046 T
1 T
2073047 AAACCAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (22 bp):
TGCACTAGGTATCATTTAGTGC
Found at i:2074489 original size:18 final size:20
Alignment explanation
Indices: 2074466--2074508 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2074456 AAAATGGTTC
*
2074466 AATTTC-AAATTCTAACA-T
1 AATTTCAAAACTCTAACATT
2074484 AATTTCAAAACTCTAACATT
1 AATTTCAAAACTCTAACATT
2074504 AATTT
1 AATTT
2074509 TCAGCATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 10 0.45
20 6 0.27
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTTCAAAACTCTAACATT
Found at i:2085297 original size:10 final size:10
Alignment explanation
Indices: 2085256--2085297 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
2085246 ACTAAGAGGT
2085256 CATATAGAT-
1 CATATAGATG
2085265 CATATAGATG
1 CATATAGATG
* *
2085275 CATTTAGAAG
1 CATATAGATG
*
2085285 CATATAGTTG
1 CATATAGATG
2085295 CAT
1 CAT
2085298 GTGGTGGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (10 bp):
CATATAGATG
Found at i:2094385 original size:22 final size:22
Alignment explanation
Indices: 2094357--2094402 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2094347 CTGCAAGGAT
2094357 GATAGATTCTCTTTTCAAAGAA
1 GATAGATTCTCTTTTCAAAGAA
2094379 GATAGATTCTCTTTTCAAAGAA
1 GATAGATTCTCTTTTCAAAGAA
2094401 GA
1 GA
2094403 AAGCTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
GATAGATTCTCTTTTCAAAGAA
Found at i:2095364 original size:87 final size:90
Alignment explanation
Indices: 2095195--2095364 Score: 220
Period size: 87 Copynumber: 1.9 Consensus size: 90
2095185 TGATTTCGAG
* * * ***
2095195 TCAGTCTTCACGAAAGAGTAGTGAAGCAATAGCGAAAGCAATATCAAAATTTTCTCTCCACGGAA
1 TCAGCCTTCACAAAAGAGTAGTGAAG--ATA-CGAAAGCAAGATCAAAATTCGATCTCCACGGAA
*
2095260 GAGTAGTGGAATAGATTTTTCAGCAAGT
63 GAGTAGTGGAACAGATTTTTCAGCAAGT
2095288 TCAGCCTTCACAAAAGAGTAGTGAAG-TA-GAAA-CAAGATCAAAATTCGATCTCCACGGAAGAG
1 TCAGCCTTCACAAAAGAGTAGTGAAGATACGAAAGCAAGATCAAAATTCGATCTCCACGGAAGAG
*
2095350 TAGTGGAACGGATTT
66 TAGTGGAACAGATTT
2095365 CCAAGCAAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
87 39 0.57
88 4 0.06
90 2 0.03
93 24 0.35
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (90 bp):
TCAGCCTTCACAAAAGAGTAGTGAAGATACGAAAGCAAGATCAAAATTCGATCTCCACGGAAGAG
TAGTGGAACAGATTTTTCAGCAAGT
Found at i:2098707 original size:34 final size:33
Alignment explanation
Indices: 2098668--2098738 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
2098658 TTTTGTAAAG
*
2098668 GGGAAAGGTTCTAGGTAAGCCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGGTAAGCCCGTG-AAAAACTA
* * *
2098702 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGGTAAGCCCGTGAAAAACTA
2098735 GGGA
1 GGGA
2098739 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGGTAAGCCCGTGAAAAACTA
Found at i:2100265 original size:20 final size:21
Alignment explanation
Indices: 2100227--2100267 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2100217 TAGTACTGTG
2100227 AATAGTGAGGGTATCGGTACC
1 AATAGTGAGGGTATCGGTACC
* *
2100248 AATAGT-AGTGTATTGGTACC
1 AATAGTGAGGGTATCGGTACC
2100268 CTTGAAGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (21 bp):
AATAGTGAGGGTATCGGTACC
Found at i:2105122 original size:18 final size:18
Alignment explanation
Indices: 2105096--2105130 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2105086 ACGAAATCCT
2105096 GAACCTTGAGTACCCACC
1 GAACCTTGAGTACCCACC
*
2105114 GAACTTTGAGTACCCAC
1 GAACCTTGAGTACCCAC
2105131 GAAGCTGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
GAACCTTGAGTACCCACC
Found at i:2111172 original size:21 final size:21
Alignment explanation
Indices: 2111143--2111198 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
2111133 TTAAAACTTG
*
2111143 TCCCGAAGGACCACATATATA
1 TCCCGAAGGACCACATAAATA
* *
2111164 TCCCTAAGGACCACATAAATG
1 TCCCGAAGGACCACATAAATA
2111185 TCCCGAAGGACCAC
1 TCCCGAAGGACCAC
2111199 TCCTTAAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (21 bp):
TCCCGAAGGACCACATAAATA
Found at i:2113071 original size:21 final size:21
Alignment explanation
Indices: 2112977--2113072 Score: 66
Period size: 21 Copynumber: 4.6 Consensus size: 21
2112967 TCGAGGGTTC
* *
2112977 TATGTGGTCCTTCGGGATATA
1 TATGTGGTCCTTCGGAACATA
** *
2112998 TATGTAATCCTTTGGAACATA
1 TATGTGGTCCTTCGGAACATA
** * * *
2113019 TATACGGTTCTTCGGGACACA
1 TATGTGGTCCTTCGGAACATA
* * *
2113040 TATTTGGTCCTTTGGAATATA
1 TATGTGGTCCTTCGGAACATA
*
2113061 TATGTGATCCTT
1 TATGTGGTCCTT
2113073 AAGGAGTGGT
Statistics
Matches: 53, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (21 bp):
TATGTGGTCCTTCGGAACATA
Found at i:2113104 original size:21 final size:21
Alignment explanation
Indices: 2113078--2113122 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2113068 TCCTTAAGGA
* *
2113078 GTGGTCATTCGAGACATTTAT
1 GTGGTCATTAGAGACATATAT
* *
2113099 GTGGTCCTTAGGGACATATAT
1 GTGGTCATTAGAGACATATAT
2113120 GTG
1 GTG
2113123 TGGTCCTTCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (21 bp):
GTGGTCATTAGAGACATATAT
Found at i:2113985 original size:18 final size:18
Alignment explanation
Indices: 2113962--2113997 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2113952 CAGGTTTTGT
2113962 GTTTTCAAGAGCTGAGAG
1 GTTTTCAAGAGCTGAGAG
2113980 GTTTTCAAGAGCTGAGAG
1 GTTTTCAAGAGCTGAGAG
2113998 TTATTCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (18 bp):
GTTTTCAAGAGCTGAGAG
Found at i:2120061 original size:23 final size:23
Alignment explanation
Indices: 2120014--2120062 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2120004 CGAGTTTGAG
**
2120014 ATACAACATCATCACCATCTTCC
1 ATACAACATCATCACCATCAACC
2120037 ATACAACATCCA-CACCATCAACC
1 ATACAACAT-CATCACCATCAACC
2120060 ATA
1 ATA
2120063 TTCCATCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (23 bp):
ATACAACATCATCACCATCAACC
Found at i:2126756 original size:20 final size:20
Alignment explanation
Indices: 2126731--2126789 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
2126721 CATTGAATTT
*
2126731 ATTCAAAGTTTTTAAAACTA
1 ATTCAAAGTCTTTAAAACTA
*
2126751 ATTCAAAGTCTTCAAAACTA
1 ATTCAAAGTCTTTAAAACTA
*
2126771 ATTCAAAGTCTATAAAACT
1 ATTCAAAGTCTTTAAAACT
2126790 TGAATTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (20 bp):
ATTCAAAGTCTTTAAAACTA
Found at i:2135407 original size:32 final size:32
Alignment explanation
Indices: 2135318--2135432 Score: 87
Period size: 32 Copynumber: 3.6 Consensus size: 32
2135308 AACTGCTTTA
*
2135318 CATTATCTAAAT-ATGACACTAACA-TTATTGTG
1 CATTATCTGAATGA-GACACTAACACTTA-TGTG
* * * *
2135350 CATTATTTGAATGCA-ATATTGACACTTATGTG
1 CATTATCTGAATG-AGACACTAACACTTATGTG
2135382 CATTATCTGAATGAGACACTAACACTGT-TGTG
1 CATTATCTGAATGAGACACTAACACT-TATGTG
* *
2135414 -AGTTATATGAATGTGACAC
1 CA-TTATCTGAATGAGACAC
2135433 ACTACTTGTG
Statistics
Matches: 66, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
31 2 0.03
32 59 0.89
33 4 0.06
34 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (32 bp):
CATTATCTGAATGAGACACTAACACTTATGTG
Found at i:2143485 original size:18 final size:18
Alignment explanation
Indices: 2143444--2143487 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2143434 GTCTCCAGCA
*
2143444 TTCTTCTTTTTCTCCGTC
1 TTCTTCTTTGTCTCCGTC
*
2143462 TCCTTCTTTGTCT-CGTCC
1 TTCTTCTTTGTCTCCGT-C
2143480 TTCTTCTT
1 TTCTTCTT
2143488 GAGGTCTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.00, C:0.34, G:0.07, T:0.59
Consensus pattern (18 bp):
TTCTTCTTTGTCTCCGTC
Found at i:2144838 original size:21 final size:21
Alignment explanation
Indices: 2144812--2144868 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2144802 TTGGGAGCAT
*
2144812 ATGGGTATCGGTACCCCTTCA
1 ATGGGTATCGATACCCCTTCA
*
2144833 ATGGGTATCGATACCCCTTTA
1 ATGGGTATCGATACCCCTTCA
2144854 ATGGGTATCGATACC
1 ATGGGTATCGATACC
2144869 ACCTGCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (21 bp):
ATGGGTATCGATACCCCTTCA
Found at i:2146443 original size:11 final size:10
Alignment explanation
Indices: 2146427--2146460 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
2146417 TTTTAATTCC
2146427 TTTATCTTTT
1 TTTATCTTTT
2146437 GTTTATCTTATT
1 -TTTATCTT-TT
2146449 TTTATCTTTT
1 TTTATCTTTT
2146459 TT
1 TT
2146461 CTTTTCTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTATCTTTT
Found at i:2146814 original size:7 final size:7
Alignment explanation
Indices: 2146802--2146839 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
2146792 TTTTTTTCAA
2146802 AAAAAAC
1 AAAAAAC
2146809 AAAAAAC
1 AAAAAAC
2146816 AAAAAA-
1 AAAAAAC
2146822 AACAAAA-
1 AA-AAAAC
2146829 AAAAAAC
1 AAAAAAC
2146836 AAAA
1 AAAA
2146840 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:2146820 original size:16 final size:16
Alignment explanation
Indices: 2146799--2146839 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
2146789 CTATTTTTTT
2146799 CAAAAAAAACAAAAAA
1 CAAAAAAAACAAAAAA
2146815 CAAAAAAAACAAAAAA
1 CAAAAAAAACAAAAAA
2146831 -AAAACAAAA
1 CAAAA-AAAA
2146840 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
CAAAAAAAACAAAAAA
Found at i:2146839 original size:9 final size:9
Alignment explanation
Indices: 2146799--2146832 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
2146789 CTATTTTTTT
2146799 CAAAAAAAA
1 CAAAAAAAA
2146808 C--AAAAAA
1 CAAAAAAAA
2146815 CAAAAAAAA
1 CAAAAAAAA
2146824 CAAAAAAAA
1 CAAAAAAAA
2146833 AACAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
9 16 0.70
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:2155896 original size:20 final size:20
Alignment explanation
Indices: 2155871--2155910 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2155861 GAAAATGCAT
* *
2155871 ACTTTTGATGAAGATTTATG
1 ACTTTTAATGAAGAATTATG
*
2155891 ACTTTTAATGGAGAATTATG
1 ACTTTTAATGAAGAATTATG
2155911 CCTTAGGTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (20 bp):
ACTTTTAATGAAGAATTATG
Found at i:2156405 original size:18 final size:18
Alignment explanation
Indices: 2156382--2156423 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2156372 AAGCTCAATC
2156382 CAGCTATGAGCACAAGTA
1 CAGCTATGAGCACAAGTA
*
2156400 CAGCTATGAGCACAAGTG
1 CAGCTATGAGCACAAGTA
2156418 CAGCTA
1 CAGCTA
2156424 ACAACTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (18 bp):
CAGCTATGAGCACAAGTA
Found at i:2159003 original size:16 final size:17
Alignment explanation
Indices: 2158958--2159010 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
2158948 TCTTAAAGGT
2158958 ATAATTTT-TTAA--TA
1 ATAATTTTATTAATTTA
* *
2158972 ATAATTTTGTTTATTTA
1 ATAATTTTATTAATTTA
2158989 AT-ATTTTATTAATTTA
1 ATAATTTTATTAATTTA
*
2159005 TTAATT
1 ATAATT
2159011 AATTATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 13 0.42
17 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATAATTTTATTAATTTA
Found at i:2162027 original size:27 final size:27
Alignment explanation
Indices: 2161997--2162051 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
2161987 TGTTTTTATC
*
2161997 TCCTTAATGTAATGTTTTATGGTTTGT
1 TCCTTAATGTAATGTTTTATAGTTTGT
2162024 TCCTTAATGTAATGTTTTATAGTTTGT
1 TCCTTAATGTAATGTTTTATAGTTTGT
2162051 T
1 T
2162052 GTTTTTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.07, G:0.16, T:0.56
Consensus pattern (27 bp):
TCCTTAATGTAATGTTTTATAGTTTGT
Found at i:2163360 original size:168 final size:171
Alignment explanation
Indices: 2162854--2163360 Score: 599
Period size: 173 Copynumber: 3.0 Consensus size: 171
2162844 ATGATATAAA
* * * * * *
2162854 AAAAGGAAAGGCTTGTCCCATAAGAAGAT-CTTTCACCTTTTCCAGAGAACCTCTGACATGTCAT
1 AAAAGGAAAGGCTCGTCCCACAAAAAG-TGCTTTCACCTTTTTCAGAGAATCTCTAACATGTCA-
* * * ** *
2162918 AGTGTCTCTTCTCATCAAATAGAACATTGGGTTAACGGGAATAGTTCCTCCACCGCAAACATCAC
64 AGTGTCTCATCTCATCAAACAGAACATTGGGTTAACGGGAATAGTTCCCCCACCGGGAACAT-AT
*
2162983 ATGCTTCATATAATTGACTAAAATATGTATAGATAATCTGACAG
128 ATGCTTCATATAATTGACTAAAATATGCATAGATAATCTGACAG
* * * * * * * * *
2163027 AAAAGAAAAGGCTCATCCCAGAATAAGCGATTTCACCTTTTTCATAGAATCTCTTATATGTCATA
1 AAAAGGAAAGGCTCGTCCCACAAAAAGTGCTTTCACCTTTTTCAGAGAATCTCTAACATGTCA-A
* * * * * **
2163092 ATGTCTCATCTCATCAAACAGGAGATTGGGTTAATGGGAATAGTTCCCCCGCTAGGAACATCATA
65 GTGTCTCATCTCATCAAACAGAACATTGGGTTAACGGGAATAGTTCCCCCACCGGGAACAT-ATA
2163157 TGCTTCATATAATTGACTAAAATATGCATAGATAATCTGACAG
129 TGCTTCATATAATTGACTAAAATATGCATAGATAATCTGACAG
* *
2163200 AAAAGGAAAGGCTCGTCCCACAAAAAGTGCTTTCACCTTTTTTAGAGAATATCTAACATGTC-AG
1 AAAAGGAAAGGCTCGTCCCACAAAAAGTGCTTTCACCTTTTTCAGAGAATCTCTAACATGTCAAG
* * * * *
2163264 TGTC-CATCTCATCAAACAGAATATTGGATTTACAGAAATAGTTCCCCCACCGGGAACAT-TATG
66 TGTCTCATCTCATCAAACAGAACATTGGGTTAACGGGAATAGTTCCCCCACCGGGAACATATATG
* *
2163327 CTTCACATAATTGACTAAAATATGCAGAGATAAT
131 CTTCATATAATTGACTAAAATATGCATAGATAAT
2163361 TAGGGGTGTT
Statistics
Matches: 283, Mismatches: 50, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
168 36 0.13
170 45 0.16
171 5 0.02
173 197 0.70
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (171 bp):
AAAAGGAAAGGCTCGTCCCACAAAAAGTGCTTTCACCTTTTTCAGAGAATCTCTAACATGTCAAG
TGTCTCATCTCATCAAACAGAACATTGGGTTAACGGGAATAGTTCCCCCACCGGGAACATATATG
CTTCATATAATTGACTAAAATATGCATAGATAATCTGACAG
Found at i:2164481 original size:24 final size:23
Alignment explanation
Indices: 2164441--2164488 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
2164431 AAATATCAAG
2164441 TTTTATTAATGGTAATTTTGAAAT
1 TTTTATTAATGGTAATTTT-AAAT
*
2164465 TTTTCATTAATTG-AATTTTAAAT
1 TTTT-ATTAATGGTAATTTTAAAT
2164488 T
1 T
2164489 CAATTGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 10 0.45
25 7 0.32
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTTATTAATGGTAATTTTAAAT
Found at i:2167774 original size:16 final size:16
Alignment explanation
Indices: 2167731--2167778 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
2167721 CAAAAATCCT
* *
2167731 AAAGTATCAGACTCTG
1 AAAGTATCAAACTCTC
*
2167747 AAACTCAT-AAACTCTC
1 AAAGT-ATCAAACTCTC
2167763 AAAGTATCAAACTCTC
1 AAAGTATCAAACTCTC
2167779 GCTCTTATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (16 bp):
AAAGTATCAAACTCTC
Found at i:2170831 original size:31 final size:31
Alignment explanation
Indices: 2170770--2170831 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
2170760 CTTATATTTC
*
2170770 AATTTATGTGATTCGATTTTCTTGTTTTTTA
1 AATTTATGTGATTCGATTTACTTGTTTTTTA
* **
2170801 AATTTATTTGATTTTATTTACTT-TTCTTTTA
1 AATTTATGTGATTCGATTTACTTGTT-TTTTA
2170832 CAAGATGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.21, C:0.06, G:0.08, T:0.65
Consensus pattern (31 bp):
AATTTATGTGATTCGATTTACTTGTTTTTTA
Found at i:2182189 original size:25 final size:28
Alignment explanation
Indices: 2182141--2182209 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 28
2182131 ACTATATATA
*
2182141 TTAACTTAAAAAT-TTTT-TTAATTAAC
1 TTAATTTAAAAATATTTTATTAATTAAC
*
2182167 TT-A-TTAAATATATTTTATT-ATTAAC
1 TTAATTTAAAAATATTTTATTAATTAAC
2182192 TTAATTTAAAAATATTTT
1 TTAATTTAAAAATATTTT
2182210 TTTTATTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
24 7 0.19
25 13 0.35
26 5 0.14
27 12 0.32
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAATTTAAAAATATTTTATTAATTAAC
Found at i:2182190 original size:29 final size:28
Alignment explanation
Indices: 2182148--2182216 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 28
2182138 ATATTAACTT
2182148 AAAA-ATTTTT-TTAATTAACTT-A-TTA
1 AAAATATTTTTATT-ATTAACTTAACTTA
* *
2182173 AATATA-TTTTATTATTAACTTAATTTA
1 AAAATATTTTTATTATTAACTTAACTTA
*
2182200 AAAATATTTTTTTTATT
1 AAAATATTTTTATTATT
2182217 TTCATATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
25 15 0.42
26 4 0.11
27 8 0.22
28 9 0.25
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
AAAATATTTTTATTATTAACTTAACTTA
Found at i:2195596 original size:25 final size:25
Alignment explanation
Indices: 2195567--2195629 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
2195557 TTAAGGAGTG
2195567 GCGAGCTAGGCGCCGAGAGGAGCTA
1 GCGAGCTAGGCGCCGAGAGGAGCTA
*
2195592 GCGAGCTAGGCGCCGAGGGGAGCTA
1 GCGAGCTAGGCGCCGAGAGGAGCTA
2195617 GCGAGCTAAGGCG
1 GCGAGCT-AGGCG
2195630 GTTCGTGGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 31 0.86
26 5 0.14
ACGTcount: A:0.22, C:0.24, G:0.46, T:0.08
Consensus pattern (25 bp):
GCGAGCTAGGCGCCGAGAGGAGCTA
Found at i:2201844 original size:12 final size:12
Alignment explanation
Indices: 2201827--2201855 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2201817 CTGGAGAGAG
2201827 CCGCCATAAGAC
1 CCGCCATAAGAC
2201839 CCGCCATAAGAC
1 CCGCCATAAGAC
2201851 CCGCC
1 CCGCC
2201856 TTGCTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.48, G:0.17, T:0.07
Consensus pattern (12 bp):
CCGCCATAAGAC
Found at i:2205319 original size:108 final size:108
Alignment explanation
Indices: 2205102--2205335 Score: 407
Period size: 109 Copynumber: 2.2 Consensus size: 108
2205092 AGAGGCATTG
* *
2205102 AAAAGTAAAATAGAAGGGGGTTTTTAATGTCCGTTGAGATACTTTTTTATTTTGACGGTTATAGA
1 AAAAGTAAAATAGAAGGGGGGTTTTAATGTCCATTGAGATACTTTTTTATTTTGACGGTTATAGA
* *
2205167 GGGGTTTTTTAATGAGACATTGAGACTTCTCTTTCTTATAAAA
66 GAGATTTTTTAATGAGACATTGAGACTTCTCTTTCTTATAAAA
2205210 AAAAGTAAAATAGAAGGGGGGTTTTAATGTCCATTGAGATACTTTTTTTATTTTGACGGTTATAG
1 AAAAGTAAAATAGAAGGGGGGTTTTAATGTCCATTGAGATAC-TTTTTTATTTTGACGGTTATAG
2205275 AGAGATTTTTTAATGAGACATTGAGACTTC-CTTTTCTTATAAAA
65 AGAGATTTTTTAATGAGACATTGAGACTTCTC-TTTCTTATAAAA
2205319 AAAAGTAAAATAGAAGG
1 AAAAGTAAAATAGAAGG
2205336 AACACCAACC
Statistics
Matches: 120, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
108 41 0.34
109 79 0.66
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.38
Consensus pattern (108 bp):
AAAAGTAAAATAGAAGGGGGGTTTTAATGTCCATTGAGATACTTTTTTATTTTGACGGTTATAGA
GAGATTTTTTAATGAGACATTGAGACTTCTCTTTCTTATAAAA
Found at i:2211406 original size:21 final size:22
Alignment explanation
Indices: 2211380--2211428 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2211370 TATTATTTTT
*
2211380 AATTTATAT-ATTTTATTTA-AA
1 AATTTATATAATTGT-TTTACAA
2211401 AATTTATATAATTGTTTTACAA
1 AATTTATATAATTGTTTTACAA
2211423 AATTTA
1 AATTTA
2211429 AAAGATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTATATAATTGTTTTACAA
Found at i:2213549 original size:63 final size:67
Alignment explanation
Indices: 2213472--2213624 Score: 174
Period size: 63 Copynumber: 2.3 Consensus size: 67
2213462 CATTTATTTC
* *
2213472 TATTTAATTTTGAATATTAAAGATGAT-TATATA-CTTTTGAATATTTCAAATT-AAA-ATAATA
1 TATTTAAATTTGAATATTAAA-ATGATGTATATATCTTTTCAATATTTCAAATTAAAAGATAATA
2213533 -TA
65 TTA
* * * * *
2213535 TATTTAAGTTTGAATAGT-GAATGGTGTATATATCTTTTCAATATTTCAAATTAAAAGATATTAT
1 TATTTAAATTTGAATATTAAAATGATGTATATATCTTTTCAATATTTCAAATTAAAAGATAATAT
2213599 TA
66 TA
2213601 TCAGTTTAAATTTGAATATTAAAA
1 T-A-TTTAAATTTGAATATTAAAA
2213625 GTTATTTGAT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
61 4 0.05
62 7 0.10
63 34 0.47
64 3 0.04
65 5 0.07
66 3 0.04
67 1 0.01
68 14 0.19
69 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (67 bp):
TATTTAAATTTGAATATTAAAATGATGTATATATCTTTTCAATATTTCAAATTAAAAGATAATAT
TA
Found at i:2218849 original size:16 final size:17
Alignment explanation
Indices: 2218822--2218853 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2218812 CGAAGTTCGG
2218822 GGACTAAAAAGGTCAAA
1 GGACTAAAAAGGTCAAA
2218839 GGACT-AAAAGGTCAA
1 GGACTAAAAAGGTCAA
2218854 GTTCTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (17 bp):
GGACTAAAAAGGTCAAA
Found at i:2219226 original size:23 final size:25
Alignment explanation
Indices: 2219182--2219234 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
2219172 AACCTAATTA
* *
2219182 AAAAAATAAAACAATAAAAT-AAAT
1 AAAAAACAAAACAACAAAATAAAAT
*
2219206 AAAAAACAAAA-AACAACATAAAAT
1 AAAAAACAAAACAACAAAATAAAAT
2219230 AAAAA
1 AAAAA
2219235 TAAAATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (25 bp):
AAAAAACAAAACAACAAAATAAAAT
Found at i:2219239 original size:23 final size:24
Alignment explanation
Indices: 2219182--2219239 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
2219172 AACCTAATTA
*
2219182 AAAAAATAAAACAATAAAATAAAT
1 AAAAAATAAAACAACAAAATAAAT
* *
2219206 AAAAAACAAAA-AACAACATAAA-
1 AAAAAATAAAACAACAAAATAAAT
2219228 ATAAAAATAAAA
1 A-AAAAATAAAA
2219240 TAAACCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.03
23 18 0.62
24 10 0.34
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (24 bp):
AAAAAATAAAACAACAAAATAAAT
Found at i:2221344 original size:39 final size:39
Alignment explanation
Indices: 2221237--2222043 Score: 1159
Period size: 39 Copynumber: 20.6 Consensus size: 39
2221227 AGAAAAAATA
* *
2221237 ATCTCAAGTGAGAT-AAATATTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
2221275 ATCTCAAGCGAGATAAAAATATTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* * *
2221315 ATCTCAAGCTAGATAAAATCTTATGTTTCGGGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
2221354 ATCTCAAGCGAGATAAAAATCTTATGTTTCGAGTGAAAGT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* *
2221394 ATCTCAAGCGAGATAAAATCTTTTGTTTCGAGTGAAAGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * * *
2221433 ATCTAAAGCGAGATAAAATCTTCTGTTTTGACTGCAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
2221472 ATCTCAAGCGAGATAAAAATATTTTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
*
2221512 ATCTCAAGCGAGATAAAATCTTCTCTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
2221551 ATCTCAAGAGAGATAAAAATCTTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
2221591 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
2221630 ATCTCAAGCGGGATAAAATATTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
2221669 ATCTCAAGCGAGATAAAAATCTTATGTTTCAAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* * *
2221709 ATCTTAAGCAAGATAAAATCTTCTATTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
2221748 ATCTCAAGCCAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
2221787 ATCTCAAGCGAGAT-AGATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* ** * * *
2221825 ATCTTAATTGAGATAAAAATCTTTTGTTTTGAGTGAAATT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* * *
2221865 ATCTCAAGCGAGATAAAATCTTTTATTTCGAGTAAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
2221904 ATCTCAAGCGAGATAAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* *
2221944 ATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTGAAATT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * *
2221983 ATCTCAAGTGAGATAAAATCTTATGTTTCAAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
2222022 ATCTCAAGCGAGATAAAATCTT
1 ATCTCAAGCGAGATAAAATCTT
2222044 GTTTTAAAAA
Statistics
Matches: 690, Mismatches: 70, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
38 47 0.07
39 398 0.58
40 245 0.36
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (39 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
Found at i:2221350 original size:79 final size:78
Alignment explanation
Indices: 2221237--2222043 Score: 1159
Period size: 79 Copynumber: 10.3 Consensus size: 78
2221227 AGAAAAAATA
* * *
2221237 ATCTCAAGTGAGAT-AAATATTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAATATTCTG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
2221301 TTTCGAGTGAAACT
65 TTTCGAGTGAAACT
* * * *
2221315 ATCTCAAGCTAGATAAAATCTTATGTTTCGGGTGAAACTATCTCAAGCGAGATAAAAATCTTATG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
*
2221380 TTTCGAGTGAAAGT
65 TTTCGAGTGAAACT
* * *
2221394 ATCTCAAGCGAGATAAAATCTTTTGTTTCGAGTGAAAGTATCTAAAGCGAGATAAAATCTTCTGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
* * *
2221459 TTTGACTGCAACT
66 TTCGAGTGAAACT
* * *
2221472 ATCTCAAGCGAGATAAAAATATTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTC
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
2221537 TTTCGAGTGAAACT
65 TTTCGAGTGAAACT
* *
2221551 ATCTCAAGAGAGATAAAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
2221616 TTTCGAGTGAAACT
65 TTTCGAGTGAAACT
* * *
2221630 ATCTCAAGCGGGATAAAATATTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAATCTTATG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
*
2221695 TTTCAAGTGAAACT
65 TTTCGAGTGAAACT
* * * *
2221709 ATCTTAAGCAAGATAAAATCTTCTATTTCGAGTGAAACTATCTCAAGCCAGATAAAATCTTCTGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
2221774 TTCGAGTGAAACT
66 TTCGAGTGAAACT
* * ** *
2221787 ATCTCAAGCGAGAT-AGATCTTCTGTTTCGAGTGAAACTATCTTAATTGAGATAAAAATCTTTTG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
* *
2221851 TTTTGAGTGAAATT
65 TTTCGAGTGAAACT
* * *
2221865 ATCTCAAGCGAGATAAAATCTTTTATTTCGAGTAAAACTATCTCAAGCGAGATAAAAATCTTCTG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
2221930 TTTCGAGTGAAACT
65 TTTCGAGTGAAACT
* * * *
2221944 ATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTGAAATTATCTCAAGTGAGATAAAATCTTATGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
*
2222009 TTCAAGTGAAACT
66 TTCGAGTGAAACT
2222022 ATCTCAAGCGAGATAAAATCTT
1 ATCTCAAGCGAGATAAAATCTT
2222044 GTTTTAAAAA
Statistics
Matches: 652, Mismatches: 72, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
77 32 0.05
78 199 0.31
79 421 0.65
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (78 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
TTCGAGTGAAACT
Found at i:2221397 original size:22 final size:22
Alignment explanation
Indices: 2221372--2221436 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
2221362 CGAGATAAAA
2221372 ATCTTATGTTTCGAGTGAAAGT
1 ATCTTATGTTTCGAGTGAAAGT
* *
2221394 ATCTCAAG---CGAGAT-AAA--
1 ATCTTATGTTTCGAG-TGAAAGT
*
2221411 ATCTTTTGTTTCGAGTGAAAGT
1 ATCTTATGTTTCGAGTGAAAGT
2221433 ATCT
1 ATCT
2221437 AAAGCGAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 14
0.62 0.10 0.28
Matches are distributed among these distances:
17 5 0.16
19 8 0.26
20 8 0.26
22 10 0.32
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (22 bp):
ATCTTATGTTTCGAGTGAAAGT
Done.