Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 51
Found at i:3232273 original size:45 final size:45
Alignment explanation
Indices: 3232199--3232286 Score: 113
Period size: 45 Copynumber: 2.0 Consensus size: 45
3232189 AGCTGGTTCT
* * * *
3232199 GGTTCATTAATTTCAGGCTCACCTAGTTCTGGTTCATTAATTTTG
1 GGTTCACTAATTTCAGGCTCAACTAGTTCTGCTTCATCAATTTTG
* * *
3232244 GGTTCACTAATTTCTGGTTCAACTGGTTCTGCTTCATCAATTT
1 GGTTCACTAATTTCAGGCTCAACTAGTTCTGCTTCATCAATTT
3232287 CAGGTTGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (45 bp):
GGTTCACTAATTTCAGGCTCAACTAGTTCTGCTTCATCAATTTTG
Found at i:3233336 original size:28 final size:26
Alignment explanation
Indices: 3233305--3233452 Score: 97
Period size: 26 Copynumber: 5.5 Consensus size: 26
3233295 GAAAACCATT
3233305 TATACTAACAGTAAACCCACTAAACTCATA
1 TATACTAACA-TAAACCCACT-AA--CATA
* * *
3233335 TAAACTCATATAAACTCC-CTAACATA
1 TATACTAACATAAAC-CCACTAACATA
* *
3233361 TATACTAACATATA--TACTAACATA
1 TATACTAACATAAACCCACTAACATA
3233385 TATACTAACAGTAAACCCACTAAACTCATA
1 TATACTAACA-TAAACCCACT-AA--CATA
* * *
3233415 TAAACTCATATAAACTCC-CTAACATA
1 TATACTAACATAAAC-CCACTAACATA
*
3233441 TATATTAACATA
1 TATACTAACATA
3233453 TATACTAACA
Statistics
Matches: 92, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
24 18 0.20
25 3 0.03
26 26 0.28
27 3 0.03
28 6 0.07
29 14 0.15
30 22 0.24
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (26 bp):
TATACTAACATAAACCCACTAACATA
Found at i:3233340 original size:10 final size:10
Alignment explanation
Indices: 3233325--3233351 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3233315 GTAAACCCAC
3233325 TAAACTCATA
1 TAAACTCATA
3233335 TAAACTCATA
1 TAAACTCATA
3233345 TAAACTC
1 TAAACTC
3233352 CCTAACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAACTCATA
Found at i:3233377 original size:68 final size:71
Alignment explanation
Indices: 3233305--3233489 Score: 250
Period size: 68 Copynumber: 2.5 Consensus size: 71
3233295 GAAAACCATT
3233305 TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACTCCCTAACATATATACTAAC
1 TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACT-CC--AC------ACTAAC
3233370 ATATATACTAACATA
57 ATATATACTAACATA
*
3233385 TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACT-C-C-CTAACATATATATT
1 TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACTCCACACTAACATATATACT
3233447 AACATA
66 AACATA
*
3233453 TATACTAACAATAAACCCACTAAACTCATATAAACTC
1 TATACTAACAGTAAACCCACTAAACTCATATAAACTC
3233490 CCTAACATAT
Statistics
Matches: 103, Mismatches: 2, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
68 55 0.53
75 1 0.01
78 1 0.01
80 46 0.45
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.27
Consensus pattern (71 bp):
TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACTCCACACTAACATATATACT
AACATA
Found at i:3233387 original size:14 final size:12
Alignment explanation
Indices: 3233353--3233394 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
3233343 TATAAACTCC
3233353 CTAACATATATA
1 CTAACATATATA
3233365 CTAACATATATA
1 CTAACATATATA
3233377 CTAACATATATA
1 CTAACATATATA
3233389 CTAACA
1 CTAACA
3233395 GTAAACCCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (12 bp):
CTAACATATATA
Found at i:3233399 original size:80 final size:80
Alignment explanation
Indices: 3233305--3233462 Score: 307
Period size: 80 Copynumber: 2.0 Consensus size: 80
3233295 GAAAACCATT
3233305 TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACTCCCTAACATATATACTAAC
1 TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACTCCCTAACATATATACTAAC
3233370 ATATATACTAACATA
66 ATATATACTAACATA
*
3233385 TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACTCCCTAACATATATATTAAC
1 TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACTCCCTAACATATATACTAAC
3233450 ATATATACTAACA
66 ATATATACTAACA
3233463 ATAAACCCAC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.28
Consensus pattern (80 bp):
TATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACTCCCTAACATATATACTAAC
ATATATACTAACATA
Found at i:3233420 original size:10 final size:10
Alignment explanation
Indices: 3233405--3233431 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3233395 GTAAACCCAC
3233405 TAAACTCATA
1 TAAACTCATA
3233415 TAAACTCATA
1 TAAACTCATA
3233425 TAAACTC
1 TAAACTC
3233432 CCTAACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAACTCATA
Found at i:3233451 original size:12 final size:12
Alignment explanation
Indices: 3233433--3233462 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3233423 TATAAACTCC
3233433 CTAACATATATA
1 CTAACATATATA
*
3233445 TTAACATATATA
1 CTAACATATATA
3233457 CTAACA
1 CTAACA
3233463 ATAAACCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (12 bp):
CTAACATATATA
Found at i:3233453 original size:28 final size:28
Alignment explanation
Indices: 3233341--3233508 Score: 104
Period size: 28 Copynumber: 6.1 Consensus size: 28
3233331 CATATAAACT
3233341 CATATAAACTCCCTAACATATATACTAA
1 CATATAAACTCCCTAACATATATACTAA
*
3233369 CATAT--A-T-ACTAACATATATACTAA
1 CATATAAACTCCCTAACATATATACTAA
* *
3233393 CA-GTAAAC-CCACTAAACTCATATAAACT--
1 CATATAAACTCC-CT-AA--CATATATACTAA
*
3233421 CATATAAACTCCCTAACATATATATTAA
1 CATATAAACTCCCTAACATATATACTAA
* ** ** *
3233449 CATATATACTAACAATAAACCCACTAAACT--
1 CATATAAACT--CCCT-AACATA-TATACTAA
3233479 CATATAAACTCCCTAACATATATACTAA
1 CATATAAACTCCCTAACATATATACTAA
3233507 CA
1 CA
3233509 GTAAACCCAC
Statistics
Matches: 102, Mismatches: 20, Indels: 36
0.65 0.13 0.23
Matches are distributed among these distances:
23 1 0.01
24 18 0.18
25 2 0.02
26 14 0.14
27 6 0.06
28 24 0.24
29 7 0.07
30 22 0.22
31 4 0.04
32 4 0.04
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.27
Consensus pattern (28 bp):
CATATAAACTCCCTAACATATATACTAA
Found at i:3233542 original size:58 final size:55
Alignment explanation
Indices: 3233377--3233540 Score: 215
Period size: 58 Copynumber: 2.9 Consensus size: 55
3233367 AACATATATA
3233377 CTAACATATATACTAACAGTAAACCCACTAAACTCATATAAACTCATATAAACTCC
1 CTAACATATATACTAACAGTAAACCCACTAAACTCATAT-AACTCATATAAACTCC
* * * *
3233433 CTAACATATATATTAACA-TATATACTAACAATAAACCCACTA-AACTCATATAAACTCC
1 CTAACATATATACTAACAGTA-A-AC--CCACTAAACTCA-TATAACTCATATAAACTCC
3233491 CTAACATATATACTAACAGTAAACCCACTAAACTCATATAATCTCATATA
1 CTAACATATATACTAACAGTAAACCCACTAAACTCATATAA-CTCATATA
3233541 TACTATTCTC
Statistics
Matches: 92, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
54 2 0.02
55 13 0.14
56 26 0.28
57 4 0.04
58 34 0.37
59 11 0.12
60 2 0.02
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (55 bp):
CTAACATATATACTAACAGTAAACCCACTAAACTCATATAACTCATATAAACTCC
Found at i:3237524 original size:29 final size:29
Alignment explanation
Indices: 3237492--3237568 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
3237482 TAAAGTTCAC
*
3237492 AAATGTTCTATTGACTATTAAAAGTTATA
1 AAATGATCTATTGACTATTAAAAGTTATA
* * *
3237521 AAATGATCTCTTAATTATTAAAAGTTATA
1 AAATGATCTATTGACTATTAAAAGTTATA
3237550 AAATGATC-ATTTGACTATT
1 AAATGATCTA-TTGACTATT
3237569 CATATATTCG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (29 bp):
AAATGATCTATTGACTATTAAAAGTTATA
Found at i:3240309 original size:17 final size:19
Alignment explanation
Indices: 3240289--3240324 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
3240279 AATTCGATAC
3240289 AAATAAT-ATAC-TTTAAG
1 AAATAATAATACATTTAAG
3240306 AAATAATAATACATTTAAG
1 AAATAATAATACATTTAAG
3240325 CCTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 4 0.24
19 6 0.35
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (19 bp):
AAATAATAATACATTTAAG
Found at i:3241537 original size:215 final size:215
Alignment explanation
Indices: 3240877--3241803 Score: 1687
Period size: 215 Copynumber: 4.3 Consensus size: 215
3240867 TAATATATAT
*
3240877 AAAACATAATTTTTTTTAACGATTTCAGTTAATTAACCGATTTCAAACCAAATTAATCAATACCA
1 AAAACATAA-TTTTTTTAACGATTTCGGTTAATTAACCGATTTCAAACCAAATTAATCAATACCA
3240942 AACTTTAAAAGTTTTCTTAACCATTAACCGAGTTAACATCTAATTAACTAATCGATTTATTGAAC
65 AACTTTAAAAGTTTTCTTAACCATTAACCGAGTTAACATCTAATTAACTAATCGATTTATTGAAC
* *
3241007 TAAATTTTAATTCGATCAATTAATTCAGTTAAAACCGAACAATAAACACATCCTTAAACCGAAAG
130 TAAATTTCAATTCGATCAATTAATTCAGTTAAAACCAAACAATAAACACATCCTTAAACCGAAAG
3241072 TCTCTAAAACAAAACAGATGC
195 TCTCTAAAACAAAACAGATGC
3241093 AAAACATAA-TTTTTTAACGATTTCGGTTAATTAACCGATTTCAAACCAAATTAATCAATACCAA
1 AAAACATAATTTTTTTAACGATTTCGGTTAATTAACCGATTTCAAACCAAATTAATCAATACCAA
3241157 ACTTTAAAAGTTTTCTTAACCATTAA-CGAGTTAACATCTAATTAACTAATCGATTTATTGAACT
66 ACTTTAAAAGTTTTCTTAACCATTAACCGAGTTAACATCTAATTAACTAATCGATTTATTGAACT
* *
3241221 AAATTTTAATTCGATCAATTAATTCAGTTAAAACCGAACAATAAACACATCCTTAAACCGAAAGT
131 AAATTTCAATTCGATCAATTAATTCAGTTAAAACCAAACAATAAACACATCCTTAAACCGAAAGT
3241286 CTCTAAAACAAAACAGATGC
196 CTCTAAAACAAAACAGATGC
* *
3241306 AAAACATAATTTTTTTTAACGATTTCGGTTAATTAACCGATTTCAAACTAAAATAATCAATACCA
1 AAAACATAA-TTTTTTTAACGATTTCGGTTAATTAACCGATTTCAAACCAAATTAATCAATACCA
*
3241371 AACTTTAAAAGTTTTCTTAACCATTAACCGAGTTAACATCTAATTAACTAATTGATTTATTGAAC
65 AACTTTAAAAGTTTTCTTAACCATTAACCGAGTTAACATCTAATTAACTAATCGATTTATTGAAC
*
3241436 TAAATTTCAATTCGATCAATTAATTCAGTTAAAACCAAACGATAAACACATCCTTAAACCGAAAG
130 TAAATTTCAATTCGATCAATTAATTCAGTTAAAACCAAACAATAAACACATCCTTAAACCGAAAG
3241501 TCTCTAAAACAAAACAGATGC
195 TCTCTAAAACAAAACAGATGC
* * *
3241522 AAAAGATAATTTTTTTAACGATTTCGGTTAATTAACCGATTTCAAACTAAAATAATCAATACCAA
1 AAAACATAATTTTTTTAACGATTTCGGTTAATTAACCGATTTCAAACCAAATTAATCAATACCAA
*
3241587 ACTTTAAAAGTTTTCTTAACCATTAACCGAGTTAACATCTAATTAACTAATTGATTTATTGAACT
66 ACTTTAAAAGTTTTCTTAACCATTAACCGAGTTAACATCTAATTAACTAATCGATTTATTGAACT
3241652 AAATTTCAATTCGATCAATTAATTCAGTTAAAACCAAACAATAAACACATCCTTAAACCGAAAGT
131 AAATTTCAATTCGATCAATTAATTCAGTTAAAACCAAACAATAAACACATCCTTAAACCGAAAGT
3241717 CTCTAAAACAAAACAGATGC
196 CTCTAAAACAAAACAGATGC
* *
3241737 AAAACATAAATTTTTTAACGATTTCGGTTAATTAATCGATTTCAAACCAAATTAATCAATACCAA
1 AAAACATAATTTTTTTAACGATTTCGGTTAATTAACCGATTTCAAACCAAATTAATCAATACCAA
3241802 AC
66 AC
3241804 ATAAATAGAC
Statistics
Matches: 694, Mismatches: 14, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
213 132 0.19
214 80 0.12
215 346 0.50
216 136 0.20
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (215 bp):
AAAACATAATTTTTTTAACGATTTCGGTTAATTAACCGATTTCAAACCAAATTAATCAATACCAA
ACTTTAAAAGTTTTCTTAACCATTAACCGAGTTAACATCTAATTAACTAATCGATTTATTGAACT
AAATTTCAATTCGATCAATTAATTCAGTTAAAACCAAACAATAAACACATCCTTAAACCGAAAGT
CTCTAAAACAAAACAGATGC
Found at i:3242122 original size:19 final size:20
Alignment explanation
Indices: 3242082--3242121 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3242072 GCCTTTAGAA
3242082 TTAGATGAGAAATAATTATT
1 TTAGATGAGAAATAATTATT
*
3242102 TTAGA-GAGATATAA-TATT
1 TTAGATGAGAAATAATTATT
3242120 TT
1 TT
3242122 TGTGATCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 8 0.42
20 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (20 bp):
TTAGATGAGAAATAATTATT
Found at i:3252020 original size:216 final size:209
Alignment explanation
Indices: 3251626--3252050 Score: 721
Period size: 216 Copynumber: 2.0 Consensus size: 209
3251616 AATTTTAAAC
*
3251626 CCAGATTTTGACATATACGCCCAGAACCTGCGTGTTTTTAAAGAAAATGGGGTAAACTACCCTTT
1 CCAGATTTTGACACATACGCCCAGAACCTGCGTGTTTTTAAAGAAAATGGGGTAAACTACCCTTT
3251691 TGGGCCCTCGCTGCTTTAAAGTTATTTTGACCGAATTGCTTTTGAATTGGTCTCTAATTCTGATT
66 TGGGCCCTCGCTGCTTTAAAGTTATTTTGACCGAATTGCTTTTGAATTGGTCTCTAATTCTGATT
3251756 TTTCTTTCAATTAGCCACTTAACTTGTTTTGATTCAATTTACTACTTATACTAACCTTTTTTATT
131 TTTCTTTCAATTAGCCACTTAACTTGTTTTGATTCAATTTACTACTTATACTAACC--TTTTATT
3251821 TATTCCATATCATGTA
194 TATTCCATATCATGTA
3251837 CCAGATTTTGACACATACGCCCCAGAACCTGCGTGTTTTTAAAGAAAATGGGG-AAACTACCCTT
1 CCAGATTTTGACACATACG-CCCAGAACCTGCGTGTTTTTAAAGAAAATGGGGTAAACTACCCTT
*
3251901 TTGGTCCCTCGCTGCTTTAAAGAGTTATTTTGACCCCGAATTTGCTTTTGAATTGGTCTCTAATT
65 TTGGGCCCTCGCTGCTTT-AA-AGTTATTTTGA--CCGAA-TTGCTTTTGAATTGGTCTCTAATT
3251966 CTGA-TTTTCTTTCAATTTAGCCACTTAACTTGTTTTTGATTCAATTTA-TACTTATACTAACCT
125 CTGATTTTTCTTTCAA-TTAGCCACTTAACTTG-TTTTGATTCAATTTACTACTTATACTAACCT
3252029 TTTATTTATTCCATATCATGTA
188 TTTATTTATTCCATATCATGTA
3252051 ATTAGATATA
Statistics
Matches: 204, Mismatches: 2, Indels: 13
0.93 0.01 0.06
Matches are distributed among these distances:
211 46 0.23
212 35 0.17
213 11 0.05
214 23 0.11
215 16 0.08
216 58 0.28
217 15 0.07
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (209 bp):
CCAGATTTTGACACATACGCCCAGAACCTGCGTGTTTTTAAAGAAAATGGGGTAAACTACCCTTT
TGGGCCCTCGCTGCTTTAAAGTTATTTTGACCGAATTGCTTTTGAATTGGTCTCTAATTCTGATT
TTTCTTTCAATTAGCCACTTAACTTGTTTTGATTCAATTTACTACTTATACTAACCTTTTATTTA
TTCCATATCATGTA
Found at i:3252261 original size:2 final size:2
Alignment explanation
Indices: 3252256--3252292 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3252246 TGTATTTATG
*
3252256 TA TA TA CA 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 TA T
3252293 TCATTTTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3252398 original size:21 final size:21
Alignment explanation
Indices: 3252361--3252404 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3252351 CATTAATTAA
*
3252361 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
3252381 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
3252403 TT
1 TT
3252405 TACTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:3252457 original size:20 final size:20
Alignment explanation
Indices: 3252408--3252461 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 20
3252398 TACTTTTTAC
3252408 TATTATTATTATTTATTTATT
1 TATTATTA-TATTTATTTATT
3252429 TATGCTATTATATTATATTT-TT
1 TAT--TATTATATT-TATTTATT
3252451 TATTATTATAT
1 TATTATTATAT
3252462 ACGCATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 8 0.27
21 3 0.10
22 9 0.30
23 10 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTATTATATTTATTTATT
Found at i:3252462 original size:17 final size:18
Alignment explanation
Indices: 3252410--3252462 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
3252400 CTTTTTACTA
*
3252410 TTATTATTATTTATTTAT
1 TTATTATTATATATTTAT
*
3252428 TTATGCTATTATATTATATTTT
1 TTAT--TATTATA-TAT-TTAT
3252450 TTATTATTATATA
1 TTATTATTATATA
3252463 CGCATATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 13 0.45
21 3 0.10
22 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTATTATTATATATTTAT
Found at i:3263163 original size:53 final size:53
Alignment explanation
Indices: 3263081--3263182 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
3263071 AATACTTCGC
* * ** *
3263081 TTAGGATGAAAACCCGAGAGGTCGTCCTAAGTTGAAAAAAAAAAAAAGAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAAGAACGT
* *
3263134 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAAAGA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAAGA
3263183 GGAAAAAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.15
Consensus pattern (53 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAAGAACGT
Found at i:3264140 original size:105 final size:105
Alignment explanation
Indices: 3263958--3264935 Score: 1872
Period size: 105 Copynumber: 9.3 Consensus size: 105
3263948 AGGTTTTACC
* *
3263958 CAGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCCCGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3264023 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
3264063 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
3264128 ACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
3264168 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3264233 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
3264273 CAGAGCCAATTT-AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3264337 ACGAAGGGACCGCTGGTTGTCAACAAACA-TT-TCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
3264375 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3264440 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
3264480 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3264545 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
3264585 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3264650 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
3264690 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3264755 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
3264795 CAGAGCCAATTTCAACTTCACAACAAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
3264860 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
3264900 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3264936 GCTCGGAACA
Statistics
Matches: 860, Mismatches: 10, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
102 19 0.02
103 83 0.10
104 83 0.10
105 675 0.78
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:3266821 original size:2 final size:2
Alignment explanation
Indices: 3266816--3266846 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3266806 TTTATGTATG
*
3266816 TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3266847 TCATTTTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3266954 original size:21 final size:21
Alignment explanation
Indices: 3266917--3266961 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3266907 CATTAATTAA
*
3266917 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
3266937 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
3266959 TTA
1 TTA
3266962 CTATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:3266979 original size:25 final size:24
Alignment explanation
Indices: 3266951--3267006 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
3266941 TTATTTCCCC
3266951 TTTTACTTT-TACTATTATTATTATT
1 TTTTA-TTTATACTATTATTA-TATT
*
3266976 TTTTATTTATGCTATTATTATATT
1 TTTTATTTATACTATTATTATATT
3267000 TTTTATT
1 TTTTATT
3267007 ATTATATACG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTATTTATACTATTATTATATT
Found at i:3267096 original size:27 final size:26
Alignment explanation
Indices: 3267042--3267102 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
3267032 TTTTTTTTAC
* * * *
3267042 TTTTTATTTCTATATATCTTTATGTA
1 TTTTTATTTCTACATATATATATATA
3267068 TTTTTATATTCTACATATATATATATA
1 TTTTTAT-TTCTACATATATATATATA
3267095 -TTTTATTT
1 TTTTTATTT
3267103 ATTATTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.07
26 13 0.43
27 15 0.50
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTTATTTCTACATATATATATATA
Found at i:3268290 original size:23 final size:23
Alignment explanation
Indices: 3268241--3268291 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3268231 GATGAGTATA
* * *
3268241 TAAATGAACATGTTCATGAACGT
1 TAAATGAACATATTCACGAACGC
* *
3268264 TAAATGAACATATTTACGAATGC
1 TAAATGAACATATTCACGAACGC
3268287 TAAAT
1 TAAAT
3268292 AAACTGAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (23 bp):
TAAATGAACATATTCACGAACGC
Found at i:3268456 original size:16 final size:16
Alignment explanation
Indices: 3268435--3268467 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3268425 TTACACCTGT
3268435 ACTCCCCCCAAAAAAA
1 ACTCCCCCCAAAAAAA
3268451 ACTCCCCCCAAAAAAA
1 ACTCCCCCCAAAAAAA
3268467 A
1 A
3268468 GTAAAAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.42, G:0.00, T:0.06
Consensus pattern (16 bp):
ACTCCCCCCAAAAAAA
Found at i:3279254 original size:2 final size:2
Alignment explanation
Indices: 3279247--3279295 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
3279237 TCAAGCAAGC
3279247 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3279288 AT AT AT AT
1 AT AT AT AT
3279296 TATTTACAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3281342 original size:23 final size:23
Alignment explanation
Indices: 3281314--3281373 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
3281304 TATAAAATTT
3281314 TCCCAAAGGACCACGTAGAAATG
1 TCCCAAAGGACCACGTAGAAATG
3281337 TCCCAAAGGACCACGTAGAAATG
1 TCCCAAAGGACCACGTAGAAATG
3281360 TCCCAAAGGACCAC
1 TCCCAAAGGACCAC
3281374 ATATATGTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.30, G:0.20, T:0.12
Consensus pattern (23 bp):
TCCCAAAGGACCACGTAGAAATG
Found at i:3281383 original size:21 final size:21
Alignment explanation
Indices: 3281314--3281483 Score: 97
Period size: 21 Copynumber: 7.8 Consensus size: 21
3281304 TATAAAATTT
* *
3281314 TCCCAAAGGACCACGTAGAAATG
1 TCCCAAAGGACCAC--ATATATG
* *
3281337 TCCCAAAGGACCACGTAGAAATG
1 TCCCAAAGGACCAC--ATATATG
3281360 TCCCAAAGGACCACATATATG
1 TCCCAAAGGACCACATATATG
* * * * *
3281381 TCCCGAATGACCATATAGAAATC
1 TCCCAAAGGACCACAT--ATATG
** *
3281404 TCCTTAAGGACCACATATATA
1 TCCCAAAGGACCACATATATG
* * * *
3281425 TTCCAAAGAACCAAATATGTG
1 TCCCAAAGGACCACATATATG
* * **
3281446 TCTCAAAGAACTGCATATATG
1 TCCCAAAGGACCACATATATG
*
3281467 TCCCGAAGGACCACATA
1 TCCCAAAGGACCACATA
3281484 GAACCCTCGA
Statistics
Matches: 114, Mismatches: 31, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
21 62 0.54
23 52 0.46
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (21 bp):
TCCCAAAGGACCACATATATG
Found at i:3281400 original size:44 final size:44
Alignment explanation
Indices: 3281314--3281486 Score: 127
Period size: 44 Copynumber: 3.9 Consensus size: 44
3281304 TATAAAATTT
* * * *
3281314 TCCCAAAGGACCACGTAGAAATGTCCCAAAGGACCACGTAGAAATG
1 TCCCAAAGGACCAC--ATATATGTCCCAAAGGACCACATAGAAATC
* * *
3281360 TCCCAAAGGACCACATATATGTCCCGAATGACCATATAGAAATC
1 TCCCAAAGGACCACATATATGTCCCAAAGGACCACATAGAAATC
** * * * * *
3281404 TCCTTAAGGACCACATATATATTCCAAAGAACCAAATATG---TG
1 TCCCAAAGGACCACATATATGTCCCAAAGGACCACATA-GAAATC
* * ** *
3281446 TCTCAAAGAACTGCATATATGTCCCGAAGGACCACATAGAA
1 TCCCAAAGGACCACATATATGTCCCAAAGGACCACATAGAA
3281487 CCCTCGACTC
Statistics
Matches: 97, Mismatches: 27, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
41 1 0.01
42 28 0.29
44 53 0.55
45 1 0.01
46 14 0.14
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (44 bp):
TCCCAAAGGACCACATATATGTCCCAAAGGACCACATAGAAATC
Found at i:3285943 original size:21 final size:21
Alignment explanation
Indices: 3285917--3286064 Score: 107
Period size: 21 Copynumber: 7.0 Consensus size: 21
3285907 CCACGTAGAA
*
3285917 ATGTCCCGAAGGACCACATAT
1 ATGTCCCAAAGGACCACATAT
* *
3285938 ATGTCCCAAATGACCACATAG
1 ATGTCCCAAAGGACCACATAT
** *
3285959 AAATCTCATTAAGGACCACATAT
1 ATGTCCCA--AAGGACCACATAT
* * * *
3285982 ATATTCCAAAGAACCAAATAT
1 ATGTCCCAAAGGACCACATAT
* *
3286003 GTGTCCCAAAGAACCACATAT
1 ATGTCCCAAAGGACCACATAT
* * * * **
3286024 ATATTCTAAAAGATTACATAT
1 ATGTCCCAAAGGACCACATAT
*
3286045 ATATCCCAAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
3286065 GAACCCTATA
Statistics
Matches: 95, Mismatches: 30, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
21 79 0.83
23 16 0.17
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.23
Consensus pattern (21 bp):
ATGTCCCAAAGGACCACATAT
Found at i:3285953 original size:44 final size:44
Alignment explanation
Indices: 3285895--3285997 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
3285885 CATATAAAAT
* * * *
3285895 TGTCCCGAAGGACCACGTAGAAATGTCCCGAAGGACCACATATA
1 TGTCCCAAAGGACCACATAGAAATCTCACGAAGGACCACATATA
* **
3285939 TGTCCCAAATGACCACATAGAAATCTCATTAAGGACCACATATA
1 TGTCCCAAAGGACCACATAGAAATCTCACGAAGGACCACATATA
* * *
3285983 TATTCCAAAGAACCA
1 TGTCCCAAAGGACCA
3285998 AATATGTGTC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (44 bp):
TGTCCCAAAGGACCACATAGAAATCTCACGAAGGACCACATATA
Found at i:3286439 original size:2 final size:2
Alignment explanation
Indices: 3286432--3286463 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3286422 TGCACTTAAC
3286432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3286464 GCATATACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3286947 original size:35 final size:35
Alignment explanation
Indices: 3286900--3286969 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
3286890 CATCACAAGA
*
3286900 ATGGTACCGATACT-TCCACATT-GGTATCGATACCC
1 ATGGTACCGATACTAT-CAC-TTCAGTATCGATACCC
*
3286935 ATGGTACTGATACTATCACTTCAGTATCGATACCC
1 ATGGTACCGATACTATCACTTCAGTATCGATACCC
3286970 CATGAAGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 2 0.06
35 28 0.90
36 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (35 bp):
ATGGTACCGATACTATCACTTCAGTATCGATACCC
Found at i:3291530 original size:51 final size:51
Alignment explanation
Indices: 3291457--3291611 Score: 265
Period size: 51 Copynumber: 3.0 Consensus size: 51
3291447 AAAGAGATAA
* *
3291457 ATCATAGAAATGGATTTTGATATATATAAAGTGTCAAGGTGAGTGTATCTT
1 ATCATAGAAATGGATTTGGATATATATAAAGTGTCAAGGTGAGTGCATCTT
* *
3291508 ATCAAAGAATTGGATTTGGATATATATAAAGTGTCAAGGTGAGTGCATCTT
1 ATCATAGAAATGGATTTGGATATATATAAAGTGTCAAGGTGAGTGCATCTT
*
3291559 ATCATAGAAGTGGATTTGGATATATATAAAGTGTCAAGGTGAGTGCATCTT
1 ATCATAGAAATGGATTTGGATATATATAAAGTGTCAAGGTGAGTGCATCTT
3291610 AT
1 AT
3291612 TTTTATAGAA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 98 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (51 bp):
ATCATAGAAATGGATTTGGATATATATAAAGTGTCAAGGTGAGTGCATCTT
Found at i:3292395 original size:32 final size:32
Alignment explanation
Indices: 3292354--3292509 Score: 210
Period size: 32 Copynumber: 4.9 Consensus size: 32
3292344 GAGTCGAGGG
3292354 TTACCTATGTCTTTCGGGACATATGGACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACAGGA
* *
3292386 TTACCTATGTCTTTCGGGATATATGAACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACAGGA
* *
3292418 TTACCTATGTCGTTCGGGACATATGGACATGA
1 TTACCTATGTCTTTCGGGACATATGGACAGGA
*
3292450 TTACCTATGT-TCTTCGGGACATATGGACA-AA
1 TTACCTATGTCT-TTCGGGACATATGGACAGGA
* *
3292481 TTACCTATTTTCTTT-GGTACATATGGACA
1 TTACCTA-TGTCTTTCGGGACATATGGACA
3292510 AATTATTATA
Statistics
Matches: 111, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
31 21 0.19
32 89 0.80
33 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGGA
Found at i:3293750 original size:3 final size:3
Alignment explanation
Indices: 3293738--3293791 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
3293728 TTGGACCTAC
3293738 ATA A-A 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
3293785 ATA ATA A
1 ATA ATA A
3293792 CCCAGACAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3301730 original size:17 final size:16
Alignment explanation
Indices: 3301689--3301730 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
3301679 AAATACAATT
3301689 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
3301705 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
3301722 TAAAA-AATT
1 TAAAATAATT
3301731 ATATGCGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:3305092 original size:19 final size:19
Alignment explanation
Indices: 3305070--3305113 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
3305060 GATCATGAAC
3305070 TATGTAAATAACAATGACT
1 TATGTAAATAACAATGACT
3305089 TATGTAAATAACAATGACT
1 TATGTAAATAACAATGACT
3305108 TATGTA
1 TATGTA
3305114 GTAACAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (19 bp):
TATGTAAATAACAATGACT
Found at i:3305582 original size:2 final size:2
Alignment explanation
Indices: 3305575--3305613 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3305565 AGTTGTATGG
*
3305575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3305614 GAAACCATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3306817 original size:3 final size:3
Alignment explanation
Indices: 3306805--3306871 Score: 109
Period size: 3 Copynumber: 22.3 Consensus size: 3
3306795 TTGGACCTAC
3306805 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
*
3306850 ATA ATA ATA ATA ATA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
3306872 CCCAGACAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3308247 original size:76 final size:75
Alignment explanation
Indices: 3308152--3308382 Score: 286
Period size: 76 Copynumber: 3.1 Consensus size: 75
3308142 CATAATACAT
* * * * *
3308152 TTCATATCACCCAATATTGTTTTTCTTAAAACAATATTTGTCTCACTTGAGACAATTTTTACTCG
1 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTATCTCACTTGAGA-AATTTTTACTCG
3308217 AAACAAGAAGA
65 AAACAAGAAGA
* * *
3308228 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGATAGTTTTTACTCG
1 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTATCTCACTTGAGA-AATTTTTACTCG
*
3308293 AAACAAGATA-T
65 AAACAAGA-AGA
* * * **
3308304 TTCATTTCACTCCAGATTGTTTTTCTTAAAACAAGATTTATTTCACTTGAGATAGGTTTACTCGA
1 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTATCTCACTTGAGAAATTTTTACTCGA
*
3308369 AA-TAGAAGA
66 AACAAGAAGA
3308378 TTCAT
1 TTCAT
3308383 CTCGCTTGAG
Statistics
Matches: 133, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
73 1 0.01
74 8 0.06
75 11 0.08
76 112 0.84
77 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (75 bp):
TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTATCTCACTTGAGAAATTTTTACTCGA
AACAAGAAGA
Found at i:3308251 original size:40 final size:40
Alignment explanation
Indices: 3308207--3308327 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 40
3308197 CTTGAGACAA
3308207 TTTTTACTCGAAACAAGAAGATTCATTTCACTCAAGATTG
1 TTTTTACTCGAAACAAGAAGATTCATTTCACTCAAGATTG
* * * * ** *
3308247 TTTTT-CT--TAA-AACAAGATTCATCTCGCTTGAGATAG
1 TTTTTACTCGAAACAAGAAGATTCATTTCACTCAAGATTG
* *
3308283 TTTTTACTCGAAACAAGATA-TTTCATTTCACTCCAGATTG
1 TTTTTACTCGAAACAAGA-AGATTCATTTCACTCAAGATTG
3308323 TTTTT
1 TTTTT
3308328 CTTAAAACAA
Statistics
Matches: 61, Mismatches: 15, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
36 25 0.41
37 4 0.07
39 4 0.07
40 27 0.44
41 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (40 bp):
TTTTTACTCGAAACAAGAAGATTCATTTCACTCAAGATTG
Found at i:3308471 original size:39 final size:39
Alignment explanation
Indices: 3308336--3308801 Score: 616
Period size: 39 Copynumber: 11.9 Consensus size: 39
3308326 TTCTTAAAAC
* * *
3308336 AAGA-TTTATTTCACTTGAGATAGGTTT-ACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATA-GTTTCACTCGAAACAG
* * *
3308374 AAGA-TTCATCTCGCTTGAGATAGTTTCACTCAAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
3308412 AAGATTTTTATCTCGCTTGAGATAGTTTCACTTGAAATAG
1 AAGA-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
3308452 AAGATTTTATCTCGCTTGAGATAATTTCACTCGAAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
3308491 AAGATTTTTATCTCGCTTGAGATAGTTTCACTCGAAA-AGG
1 AAGA-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACA-G
* * *
3308531 AATATTTTATCTCGCTTGAGATAGTTTAACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
3308570 AAGATTTTTATCTCGCTTGAGATAGTTTCACTCGAAACAA
1 AAGA-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
3308610 AAGATTTTATCTCACTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
3308649 AAGATTTTATCTCACTTGAGATAGTTTCACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
** * *
3308688 AAGATTTCGTCTTGCTTGAGATATTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
3308727 AAAATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * *
3308766 AAGATTTTGTCTCGTTTAAGATAGTTTCACTCGAAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAA
3308802 TTCTCACTTG
Statistics
Matches: 376, Mismatches: 45, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
37 4 0.01
38 31 0.08
39 237 0.63
40 104 0.28
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
Found at i:3308489 original size:79 final size:79
Alignment explanation
Indices: 3308340--3308801 Score: 637
Period size: 79 Copynumber: 5.9 Consensus size: 79
3308330 TAAAACAAGA
* * *
3308340 TTTATTTCACTTGAGATAGGTTT-ACTCGAAATAGAAGA-TTCATCTCGCTTGAGATAGTTTCAC
1 TTTATCTCGCTTGAGATA-GTTTCACTCGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCAC
* *
3308403 TCAAAACATAAGATT
65 TCGAAACAGAAGATT
* *
3308418 TTTATCTCGCTTGAGATAGTTTCACTTGAAATAGAAGATTTTATCTCGCTTGAGATAATTTCACT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACT
*
3308483 CGAAACATAAGATT
66 CGAAACAGAAGATT
* *
3308497 TTTATCTCGCTTGAGATAGTTTCACTCGAAA-AGGAATATTTTATCTCGCTTGAGATAGTTTAAC
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAATA-GAAGATTTTATCTCGCTTGAGATAGTTTCAC
*
3308561 TTGAAACAGAAGATT
65 TCGAAACAGAAGATT
* * * *
3308576 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTTATCTCACTTGAGATTGTTTCACT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACT
3308641 CGAAACAGAAGA-T
66 CGAAACAGAAGATT
* ** * *
3308654 TTTATCTCACTTGAGATAGTTTCACTCGAAATAGAAGATTTCGTCTTGCTTGAGATATTTTCACT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACT
*
3308719 CGAAACAGAA-AAT
66 CGAAACAGAAGATT
* * * * *
3308732 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTTGTCTCGTTTAAGATAGTTTCACT
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACT
3308797 CGAAA
66 CGAAA
3308802 TTCTCACTTG
Statistics
Matches: 344, Mismatches: 35, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
77 5 0.01
78 161 0.47
79 177 0.51
80 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (79 bp):
TTTATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACT
CGAAACAGAAGATT
Found at i:3309069 original size:21 final size:21
Alignment explanation
Indices: 3309015--3309071 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
3309005 CAGGTCATCT
* *
3309015 ATAAGTCTTTCGAGCAAGATG
1 ATAAGTCCTTCGGGCAAGATG
3309036 ATAAGTCCTTCGGGCAAGATG
1 ATAAGTCCTTCGGGCAAGATG
3309057 ATAAGTCCTTCGGGC
1 ATAAGTCCTTCGGGC
3309072 CATCCATAAG
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:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
ATAAGTCCTTCGGGCAAGATG
Found at i:3314111 original size:22 final size:22
Alignment explanation
Indices: 3314083--3314124 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3314073 AGTCTGGACT
*
3314083 AAGCCACCCGATTGAGCCGACC
1 AAGCCACCCGATCGAGCCGACC
3314105 AAGCCACCCGATCGAGCCGA
1 AAGCCACCCGATCGAGCCGA
3314125 GCTGACCCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.40, G:0.24, T:0.07
Consensus pattern (22 bp):
AAGCCACCCGATCGAGCCGACC
Found at i:3316973 original size:2 final size:2
Alignment explanation
Indices: 3316966--3317042 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
3316956 ACCTAATTGA
3316966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3317006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3317043 GATTGCATTA
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 69 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3318181 original size:201 final size:205
Alignment explanation
Indices: 3317773--3318188 Score: 777
Period size: 201 Copynumber: 2.0 Consensus size: 205
3317763 TTATATTCAT
3317773 AAACCAAACAAAACATAAGTCTATGATTTTCAAAGTTTATACTGACAATAGAAAGTTATAACTAA
1 AAACC-AACAAAACATAAGTCTATGATTTTCAAAGTTTATACTGACAATAGAAAGTTATAACTAA
3317838 AATTAGATCAAAATATGAAGATTATAAAACCATAAAAATGAATTAATTCATAAAATAATAATAAA
65 AATTAGATCAAAATATGAAGATTATAAAACCATAAAAATGAATTAATTC--AAAATAATAATAAA
3317903 AATAATTGATTCTCAGTTATTCAAGACGAGGCACTGATGTCACTTGTTAGAACCGAATCATAATA
128 AATAATTGATTCTCAGTTATTCAAGACGAGGCACTGATGTCACTTGTTAGAACCGAATCATAATA
3317968 AATATGAAATAAA
193 AATATGAAATAAA
3317981 AAACCAACAAAACATAAGTCTATGATTTTCAAAGTTTATACTGACAATAGAAAGTTATAACTAAA
1 AAACCAACAAAACATAAGTCTATGATTTTCAAAGTTTATACTGACAATAGAAAGTTATAACTAAA
3318046 ATTAGATCAAAATAT-AAGATTATAAAACCATAAAAATGAATTAATTC-AAATAATAAT-AAAA-
66 ATTAGATCAAAATATGAAGATTATAAAACCATAAAAATGAATTAATTCAAAATAATAATAAAAAT
3318107 AATTGATTCTCAGTTATTCAAGACGAGGCACTGATGTCACTTGTTAGAACCGAATCATAATAAAT
131 AATTGATTCTCAGTTATTCAAGACGAGGCACTGATGTCACTTGTTAGAACCGAATCATAATAAAT
3318172 ATGAAATAAA
196 ATGAAATAAA
3318182 AAACCAA
1 AAACCAA
3318189 AGATCTATCA
Statistics
Matches: 208, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
201 82 0.39
202 4 0.02
203 10 0.05
206 32 0.15
207 75 0.36
208 5 0.02
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (205 bp):
AAACCAACAAAACATAAGTCTATGATTTTCAAAGTTTATACTGACAATAGAAAGTTATAACTAAA
ATTAGATCAAAATATGAAGATTATAAAACCATAAAAATGAATTAATTCAAAATAATAATAAAAAT
AATTGATTCTCAGTTATTCAAGACGAGGCACTGATGTCACTTGTTAGAACCGAATCATAATAAAT
ATGAAATAAA
Found at i:3320932 original size:16 final size:17
Alignment explanation
Indices: 3320901--3320936 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3320891 ATAACAACAT
*
3320901 TTTAAAGATTATATATA
1 TTTAAAGATTAAATATA
3320918 TTTAAA-ATTAAATATA
1 TTTAAAGATTAAATATA
3320934 TTT
1 TTT
3320937 TTGAATTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAGATTAAATATA
Found at i:3322454 original size:4 final size:4
Alignment explanation
Indices: 3322445--3322472 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3322435 GATAAGGATA
3322445 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3322473 TTAAAGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:3323963 original size:7 final size:7
Alignment explanation
Indices: 3323951--3323976 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3323941 TTTTATGGTT
3323951 TGTGGAG
1 TGTGGAG
3323958 TGTGGAG
1 TGTGGAG
3323965 TGTGGAG
1 TGTGGAG
3323972 TGTGG
1 TGTGG
3323977 TGGTCTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.58, T:0.31
Consensus pattern (7 bp):
TGTGGAG
Found at i:3327529 original size:20 final size:20
Alignment explanation
Indices: 3327504--3327542 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3327494 TCATCGCCTC
*
3327504 GTCGGCTGCTATTGATCGGT
1 GTCGGCCGCTATTGATCGGT
*
3327524 GTCGGCCGCTGTTGATCGG
1 GTCGGCCGCTATTGATCGG
3327543 CGCCGGTCGC
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:0.08, C:0.23, G:0.38, T:0.31
Consensus pattern (20 bp):
GTCGGCCGCTATTGATCGGT
Found at i:3329327 original size:32 final size:31
Alignment explanation
Indices: 3329261--3329333 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
3329251 GTTCCTTAGA
* *
3329261 ACATAGGTAAAATGTTCATATATCCCGAAGG
1 ACATAGGTAAAATGTCCATATATCCCGAAAG
* * *
3329292 ACATAGGTAATCATGTCCATATGTCTCGAAAG
1 ACATAGGTAA-AATGTCCATATATCCCGAAAG
3329324 ACATAGGTAA
1 ACATAGGTAA
3329334 CCTTCGACTC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 10 0.28
32 26 0.72
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (31 bp):
ACATAGGTAAAATGTCCATATATCCCGAAAG
Found at i:3331379 original size:2 final size:2
Alignment explanation
Indices: 3331372--3331417 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3331362 AATGATGATA
*
3331372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3331414 AT AT
1 AT AT
3331418 GCTCCTAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3333138 original size:7 final size:7
Alignment explanation
Indices: 3333116--3333161 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
3333106 ACCCACATTC
3333116 TTTTC-T
1 TTTTCTT
3333122 TTTTCTTT
1 TTTTC-TT
*
3333130 TTTTATT
1 TTTTCTT
3333137 TTTTCTT
1 TTTTCTT
3333144 TTTTCTT
1 TTTTCTT
3333151 TTCTT-TT
1 TT-TTCTT
3333158 TTTT
1 TTTT
3333162 TTCAATTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 7 0.20
7 21 0.60
8 7 0.20
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:3333145 original size:12 final size:11
Alignment explanation
Indices: 3333116--3333164 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
3333106 ACCCACATTC
*
3333116 TTTTCTTTTTC
1 TTTTCTTTTTT
*
3333127 TTTT-TTTATT
1 TTTTCTTTTTT
3333137 TTTTCTTTTTT
1 TTTTCTTTTTT
3333148 CTTTTCTTTTTT
1 -TTTTCTTTTTT
3333160 TTTTC
1 TTTTC
3333165 AATTTAGGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 8 0.24
11 14 0.42
12 11 0.33
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:3333160 original size:15 final size:15
Alignment explanation
Indices: 3333113--3333162 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
3333103 TAAACCCACA
3333113 TTCTTTTCTTTTTCTT
1 TTCTTTTCTTTTT-TT
* *
3333129 TTTTTATTTTTTCTTTT
1 TTCTT-TTCTTT-TTTT
3333146 TTCTTTTCTTTTTTT
1 TTCTTTTCTTTTTTT
3333161 TT
1 TT
3333163 TCAATTTAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 11 0.39
18 2 0.07
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (15 bp):
TTCTTTTCTTTTTTT
Found at i:3333221 original size:17 final size:17
Alignment explanation
Indices: 3333201--3333234 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3333191 ACCCTATACG
3333201 TTTTTTCTCTTTTTCTT
1 TTTTTTCTCTTTTTCTT
*
3333218 TTTTTTCTTTTTTTCTT
1 TTTTTTCTCTTTTTCTT
3333235 CGACTTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTCTCTTTTTCTT
Found at i:3337191 original size:13 final size:13
Alignment explanation
Indices: 3337173--3337197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3337163 ATGAACCGTA
3337173 CCGTGAACAGTGC
1 CCGTGAACAGTGC
3337186 CCGTGAACAGTG
1 CCGTGAACAGTG
3337198 AACAGTACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (13 bp):
CCGTGAACAGTGC
Found at i:3337944 original size:58 final size:58
Alignment explanation
Indices: 3337863--3338160 Score: 270
Period size: 58 Copynumber: 5.1 Consensus size: 58
3337853 TTGTTACCAT
* *
3337863 TTTAGCA-CATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTTAGCACCAT-ATATGCCTTATCTGGAAATCCATACTTTCAATATGATTTCCTTATCA
* * ** * * *
3337921 TTTAGCACCCT-TAGTGCCTTATCTGGAAACCCATACACTCAGTATGATTCCCTTACCA
1 TTTAGCACCATATA-TGCCTTATCTGGAAATCCATACTTTCAATATGATTTCCTTATCA
*
3337979 TTTTAGCA-CATAATATG-CTCTATCTGGAAATCCAT-TTTTCAATATGATTTCCTTATCA
1 -TTTAGCACCAT-ATATGCCT-TATCTGGAAATCCATACTTTCAATATGATTTCCTTATCA
* ** * * *
3338037 TTTAGCACCCT-TAGTGCCTTATCTGGAAA-CCATACACTCAGTATGATTCCCTTACCA
1 TTTAGCACCATATA-TGCCTTATCTGGAAATCCATACTTTCAATATGATTTCCTTATCA
* ** * * *
3338094 TTTTAGCA-CATAATATGCCATATCTAAAAATCCATAATTTCAATTTGATTTCCTTATGA
1 -TTTAGCACCAT-ATATGCCTTATCTGGAAATCCATACTTTCAATATGATTTCCTTATCA
3338153 TTTAGCAC
1 TTTAGCAC
3338161 ACACAGTGCT
Statistics
Matches: 189, Mismatches: 36, Indels: 29
0.74 0.14 0.11
Matches are distributed among these distances:
56 6 0.03
57 40 0.21
58 94 0.50
59 47 0.25
60 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (58 bp):
TTTAGCACCATATATGCCTTATCTGGAAATCCATACTTTCAATATGATTTCCTTATCA
Found at i:3338231 original size:117 final size:116
Alignment explanation
Indices: 3337856--3338220 Score: 547
Period size: 116 Copynumber: 3.1 Consensus size: 116
3337846 TATGATTTTG
*
3337856 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCATATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
3337921 TTTAGCACCCTTAGTGCCTTATCTGGAAACCCATACACTCAGTATGATTCCC
66 TTTAGCACCCTTAGTGCCTTATCTGGAAA-CCATACACTCAGTATGATTCCC
3337973 TTACCATTTTAGCACATAATATGCTC-TATCTGGAAATCCAT-TTTTCAATATGATTTCCTTATC
1 TTACCATTTTAGCACATAATATGC-CATATCTGGAAATCCATATTTTCAATATGATTTCCTTATC
3338036 ATTTAGCACCCTTAGTGCCTTATCTGGAAACCATACACTCAGTATGATTCCC
65 ATTTAGCACCCTTAGTGCCTTATCTGGAAACCATACACTCAGTATGATTCCC
** * * *
3338088 TTACCATTTTAGCACATAATATGCCATATCTAAAAATCCATAATTTCAATTTGATTTCCTTATGA
1 TTACCATTTTAGCACATAATATGCCATATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
* ** * * * *
3338153 TTTAGCACACACAGTG-CTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACCCTTAGTGCCT-TATCTGGAAA-CCATACACTCAGTATGATTCCC
*
3338205 TTAACATTTTAGCACA
1 TTACCATTTTAGCACA
3338221 CAAAGTGCCA
Statistics
Matches: 230, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
114 1 0.00
115 61 0.27
116 93 0.40
117 74 0.32
118 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (116 bp):
TTACCATTTTAGCACATAATATGCCATATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
TTTAGCACCCTTAGTGCCTTATCTGGAAACCATACACTCAGTATGATTCCC
Found at i:3344373 original size:22 final size:22
Alignment explanation
Indices: 3344321--3344373 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
3344311 AAGATTTTTA
* *
3344321 TGAATAGTAATGAACAGTACCG
1 TGAAAAGTGATGAACAGTACCG
3344343 TGAAAAGTGATGAACAGTACCG
1 TGAAAAGTGATGAACAGTACCG
*
3344365 TGAACAGTG
1 TGAAAAGTG
3344374 CATCGCTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (22 bp):
TGAAAAGTGATGAACAGTACCG
Found at i:3344399 original size:12 final size:12
Alignment explanation
Indices: 3344382--3344416 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
3344372 TGCATCGCTA
3344382 TGCTACAGTAAC
1 TGCTACAGTAAC
3344394 TGCTACAGTAAC
1 TGCTACAGTAAC
*
3344406 TGCTATAGTAA
1 TGCTACAGTAA
3344417 TTTCAGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (12 bp):
TGCTACAGTAAC
Found at i:3345026 original size:59 final size:58
Alignment explanation
Indices: 3344963--3345280 Score: 324
Period size: 59 Copynumber: 5.4 Consensus size: 58
3344953 ATACTATTAG
**
3344963 TATGATTTTGTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAA
1 TATGATTTCCTTACCA-TTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAA
* * * * *** *
3345022 TATGATTTCCTTATCATTTAGCACCCT--TAGTGCCTTATCTGGAAACCCATACACTCAG
1 TATGATTTCCTTACCATTTAGCA-CATAATA-TGCCCTATCTGGAAATCCATATTTTCAA
* *
3345080 TATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTAGAAATCCATATTTTCAA
1 TATGATTTCCTTACCA-TTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAA
* * * ** *
3345139 TATGATTTCCTTATCATTTAGCACCCT--TAGTGCCTTATCTGGAAA-CTCAT-TCACTCAG
1 TATGATTTCCTTACCATTTAGCA-CATAATA-TGCCCTATCTGGAAATC-CATAT-TTTCAA
* *
3345197 TATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAA
1 TATGATTTCCTTACCA-TTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAA
*
3345256 TATGATTTCCTTATCATTTAGCACA
1 TATGATTTCCTTACCATTTAGCACA
3345281 CTCAGTGCTC
Statistics
Matches: 207, Mismatches: 38, Indels: 29
0.76 0.14 0.11
Matches are distributed among these distances:
57 6 0.03
58 96 0.46
59 100 0.48
60 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (58 bp):
TATGATTTCCTTACCATTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAA
Found at i:3345061 original size:58 final size:58
Alignment explanation
Indices: 3344994--3345338 Score: 310
Period size: 58 Copynumber: 5.9 Consensus size: 58
3344984 GCACATAATA
**
3344994 TGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACCCTTAG
1 TGCCCTATCTGGAAATCCATATACTCAATATGATTTCCTTATCATTTAGCACCCTTAG
* * * * * * *
3345052 TGCCTTATCTGGAAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCA-CATAATA-
1 TGCCCTATCTGGAAATCCATATACTCAATATGATTTCCTTATCA-TTTAGCACCCT--TAG
* **
3345111 TGCCCTATCTAGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACCCTTAG
1 TGCCCTATCTGGAAATCCATATACTCAATATGATTTCCTTATCATTTAGCACCCTTAG
* * * * *
3345169 TGCCTTATCTGGAAA-CTCAT-TCACTCAGTATGATTCCCTTACCATTTTAGCA-CATAATA-
1 TGCCCTATCTGGAAATC-CATAT-ACTCAATATGATTTCCTTATCA-TTTAGCACCCT--TAG
* * *
3345228 TGCCCTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCATTTAGCACACTCAG
1 TGCCCTATCTGGAAATCCATATA-CTCAATATGATTTCCTTATCATTTAGCACCCTTAG
* * * * *
3345286 TGCTCC-ATATGGAAATCTATACACTCAGTATGATTTCCTTAACATTTAAGCAC
1 TGC-CCTATCTGGAAATCCATATACTCAATATGATTTCCTTATCATTT-AGCAC
3345339 ACAAAGTGCC
Statistics
Matches: 229, Mismatches: 40, Indels: 35
0.75 0.13 0.12
Matches are distributed among these distances:
57 5 0.02
58 125 0.55
59 94 0.41
60 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (58 bp):
TGCCCTATCTGGAAATCCATATACTCAATATGATTTCCTTATCATTTAGCACCCTTAG
Found at i:3345082 original size:117 final size:117
Alignment explanation
Indices: 3344973--3345339 Score: 601
Period size: 117 Copynumber: 3.1 Consensus size: 117
3344963 TATGATTTTG
3344973 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
3345038 TTTAGCACCCTTAGTGCCTTATCTGGAAACCCATACACTCAGTATGATTCCC
66 TTTAGCACCCTTAGTGCCTTATCTGGAAACCCATACACTCAGTATGATTCCC
*
3345090 TTACCATTTTAGCACATAATATGCCCTATCTAGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
* *
3345155 TTTAGCACCCTTAGTGCCTTATCTGGAAACTCATTCACTCAGTATGATTCCC
66 TTTAGCACCCTTAGTGCCTTATCTGGAAACCCATACACTCAGTATGATTCCC
*
3345207 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
* * * * * * *
3345272 TTTAGCACACTCAGTG-CTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACCCTTAGTGCCT-TATCTGGAAACCCATACACTCAGTATGATTCCC
* *
3345324 TTAACATTTAAGCACA
1 TTACCATTTTAGCACA
3345340 CAAAGTGCCA
Statistics
Matches: 233, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
116 2 0.01
117 231 0.99
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (117 bp):
TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
TTTAGCACCCTTAGTGCCTTATCTGGAAACCCATACACTCAGTATGATTCCC
Found at i:3345367 original size:59 final size:57
Alignment explanation
Indices: 3344880--3345348 Score: 211
Period size: 59 Copynumber: 8.0 Consensus size: 57
3344870 TAACAGTGAT
* * **
3344880 CCATTTGGAAAATC-ATACACTTAGTAT-ATTTCCCTTTTCATTTTAGCACACAAAGTGC
1 CCATATGG-AAATCTATACACTCAGTATGATTT-CCTTAACA-TTTAGCACACAAAGTGC
* * ** * *
3344938 CC-TATTCGAAAAT-TCATACTA-TTAGTATGATTTTGTTACCATTTTAGCACATAATA-TGC
1 CCATA-T-GGAAATCT-ATAC-ACTCAGTATGATTTCCTTAACA-TTTAGCACACAA-AGTGC
* * *** * * * **
3344997 CCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGC
1 CC-ATATGGAAATCTATACACTCAGTATGATTTCCTTAACATTTAGCACACAAAGTGC
* * * * * * *
3345055 CTTATCTGGAAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAATA-TGC
1 C-CATATGGAAATCTATACACTCAGTATGATTTCCTTAACA-TTTAGCACACAA-AGTGC
* * * *** * * * **
3345114 CCTATCTAGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGC
1 CC-ATATGGAAATCTATACACTCAGTATGATTTCCTTAACATTTAGCACACAAAGTGC
* * * * * *
3345172 CTTATCTGGAAA-CTCATTCACTCAGTATGATTCCCTTACCATTTTAGCACATAATA-TGC
1 C-CATATGGAAATCT-ATACACTCAGTATGATTTCCTTAACA-TTTAGCACACAA-AGTGC
* * * * * **
3345231 CCTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGC
1 CC-ATATGGAAATCTATACA-CTCAGTATGATTTCCTTAACATTTAGCACACAAAGTGC
3345289 TCCATATGGAAATCTATACACTCAGTATGATTTCCTTAACATTTAAGCACACAAAGTGC
1 -CCATATGGAAATCTATACACTCAGTATGATTTCCTTAACATTT-AGCACACAAAGTGC
3345348 C
1 C
3345349 ATTCGGTAAT
Statistics
Matches: 306, Mismatches: 77, Indels: 56
0.70 0.18 0.13
Matches are distributed among these distances:
57 5 0.02
58 137 0.45
59 153 0.50
60 10 0.03
61 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (57 bp):
CCATATGGAAATCTATACACTCAGTATGATTTCCTTAACATTTAGCACACAAAGTGC
Found at i:3350713 original size:17 final size:17
Alignment explanation
Indices: 3350691--3350734 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
3350681 AAAACACCTT
3350691 CTTCCATGACTCAACTA
1 CTTCCATGACTCAACTA
*
3350708 CTTCCATGACTCGACTA
1 CTTCCATGACTCAACTA
*
3350725 CTTCCTTGAC
1 CTTCCATGAC
3350735 CCTTTTCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.36, G:0.09, T:0.32
Consensus pattern (17 bp):
CTTCCATGACTCAACTA
Found at i:3353138 original size:5 final size:5
Alignment explanation
Indices: 3353111--3353326 Score: 78
Period size: 5 Copynumber: 43.0 Consensus size: 5
3353101 CAACATGAGG
* * * *
3353111 TAAAG TAAAA T-AAA T-AAA T-AAA TAAAA T--AA TAAAA CAAAG TGAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
* * *
3353156 TAAAA TAGAAA TAAAA TAAGAA AAAAA TGAAAAA TTAAA TCAAA TAACAA
1 TAAAA TA-AAA TAAAA TAA-AA TAAAA T--AAAA TAAAA TAAAA TAA-AA
* * *
3353206 CAGAAA CAAAA -AAAA CACAAA -AACAA -AAAA TAAAA TAAAA TAAATA
1 TA-AAA TAAAA TAAAA TA-AAA TAA-AA TAAAA TAAAA TAAAA TAAA-A
* * * * *
3353252 TAAAAA CAAAA CT-ACA TTACA TATAA -AAAA TAAAA -AAAA TAAAA TAAAA
1 T-AAAA TAAAA -TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
* *
3353301 TAATAA GAAAA TTAAGA -AAAA TAAAA
1 TAA-AA TAAAA -TAAAA TAAAA TAAAA
3353327 ATCTATATAT
Statistics
Matches: 165, Mismatches: 24, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
3 3 0.02
4 30 0.18
5 94 0.57
6 29 0.18
7 9 0.05
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:3353404 original size:2 final size:2
Alignment explanation
Indices: 3353399--3353427 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3353389 AAAAGAAAAA
3353399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3353428 AATAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3353501 original size:18 final size:17
Alignment explanation
Indices: 3353480--3353513 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3353470 AATTAAGAAT
3353480 AATAAAAATATATATATG
1 AATAAAAATAT-TATATG
*
3353498 AATAAATATATTATAT
1 AATAAAAATATTATAT
3353514 CAAATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AATAAAAATATTATATG
Found at i:3357868 original size:35 final size:35
Alignment explanation
Indices: 3357802--3357869 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
3357792 TTGCGATTCA
* * *
3357802 ATCATATATATATATTAATATATATAATATTTTAT
1 ATCATATATACATATCAATAAATATAATATTTTAT
* * *
3357837 ATCATATATACATATCATTAAATTTATTATTTT
1 ATCATATATACATATCAATAAATATAATATTTT
3357870 TACAAGAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (35 bp):
ATCATATATACATATCAATAAATATAATATTTTAT
Found at i:3358200 original size:29 final size:30
Alignment explanation
Indices: 3358142--3358202 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
3358132 ATATCTGTTG
* *
3358142 CAATATTATATATTATAAATTTAATTTATA
1 CAATATTATATAATATAAATTTAATATATA
*
3358172 CAATATATATATAATAT-ATTTTAA-ATATA
1 CAATAT-TATATAATATAAATTTAATATATA
3358201 CA
1 CA
3358203 TAACAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.22
30 12 0.44
31 9 0.33
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (30 bp):
CAATATTATATAATATAAATTTAATATATA
Found at i:3358847 original size:34 final size:35
Alignment explanation
Indices: 3358784--3358852 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
3358774 AAGCAAAGAC
*
3358784 AGTGCCACTAGACATCGTTAAAAATATAATTTTAT
1 AGTGCCACTAGACATAGTTAAAAATATAATTTTAT
3358819 AGTGCCACTAGACATAGTT-AAAATATAATTTTAT
1 AGTGCCACTAGACATAGTTAAAAATATAATTTTAT
3358853 TACATCTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 15 0.45
35 18 0.55
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (35 bp):
AGTGCCACTAGACATAGTTAAAAATATAATTTTAT
Found at i:3361483 original size:36 final size:33
Alignment explanation
Indices: 3361442--3361538 Score: 113
Period size: 35 Copynumber: 2.8 Consensus size: 33
3361432 AATGGATTAT
*
3361442 GAATTTAGGGTTAGGCATGTAATTAAAGTATTTTTG
1 GAATTTAGGGTTA-GAATGTAATTAAA-TA-TTTTG
*
3361478 GAATTTGAGGTTTAGAATGTAATTTAAATATTTTG
1 GAATTT-AGGGTTAGAATGTAA-TTAAATATTTTG
*
3361513 GAATTTGGGGTTTAGAATGTAATTAA
1 GAATTTAGGG-TTAGAATGTAATTAA
3361539 TGACTATATT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
34 6 0.11
35 22 0.41
36 15 0.28
37 11 0.20
ACGTcount: A:0.33, C:0.01, G:0.24, T:0.42
Consensus pattern (33 bp):
GAATTTAGGGTTAGAATGTAATTAAATATTTTG
Found at i:3361519 original size:35 final size:37
Alignment explanation
Indices: 3361458--3361536 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
3361448 AGGGTTAGGC
3361458 ATGTAA-TTAAAGTATTTTTGGAATTTGAGGTTTAGA
1 ATGTAATTTAAAGTATTTTTGGAATTTGAGGTTTAGA
*
3361494 ATGTAATTTAAA-TA-TTTTGGAATTTGGGGTTTAGA
1 ATGTAATTTAAAGTATTTTTGGAATTTGAGGTTTAGA
3361529 ATGTAATT
1 ATGTAATT
3361537 AATGACTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 28 0.68
36 8 0.20
37 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.46
Consensus pattern (37 bp):
ATGTAATTTAAAGTATTTTTGGAATTTGAGGTTTAGA
Found at i:3372314 original size:81 final size:81
Alignment explanation
Indices: 3371821--3372298 Score: 635
Period size: 81 Copynumber: 6.0 Consensus size: 81
3371811 TGTTTTAAAA
* * *
3371821 TAAAAGATTAAATGTCTAGTTGTGCATTTGGAAGAAAGGTGTCAATCATACAAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
*
3371886 GCTAATTGCCTTTGAG
66 GCTAAATGCCTTTGAG
** *
3371902 TAAAAGATTAAACACCTAGTTGTGCATTTGGCAGAAAAGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
3371967 GC---AT--CTTTGAG
66 GCTAAATGCCTTTGAG
* * * *
3371978 TAAAATATTAAACGCCTAGTTGTGCATTTGGCAGAAAGGTGCCAATCACGCAAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
* * *
3372043 ACTATATGCCTTTGAA
66 GCTAAATGCCTTTGAG
** * *
3372059 TAAAAGATTAAACACCTAGCTGTGCATTTGGCAGAAAGGT-TCCAATCATGCAAGTTAAATGAAA
1 TAAAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGT-CAATCATGCAAGTTAGATGAAA
** *
3372123 AACTATATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* * * * *
3372140 TAAAAGATTAAATGCCTAGCTGTACATTTGGTAGAAAGGTGCCAACCATGCAAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
*
3372205 GCTAAATGCATTTGAG
66 GCTAAATGCCTTTGAG
* * *
3372221 TAAAAGATTAAATGCCTAGTTATGAATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAATG
1 TAAAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
3372286 GCTAAATGCCTTT
66 GCTAAATGCCTTT
3372299 AAAATAAAGA
Statistics
Matches: 348, Mismatches: 42, Indels: 14
0.86 0.10 0.03
Matches are distributed among these distances:
76 68 0.20
78 1 0.00
79 2 0.01
81 277 0.80
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (81 bp):
TAAAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Found at i:3376253 original size:63 final size:62
Alignment explanation
Indices: 3376164--3376296 Score: 175
Period size: 63 Copynumber: 2.1 Consensus size: 62
3376154 TTTAAACAGA
* * *
3376164 TAATA-ATATATTTTAATTTTAAATATTCCAAAG-ATTTAATCT-TCTTTTACTATTCAAA-CT
1 TAATAGATATATTTTAATTTGAAATATT-CAAAGTATATAAT-TATCTTTTAATATTCAAAGCT
3376224 TAAATAGATATTATTTTAATTTGAAATATTCAAAGTATATAATTATCTTTTAATATTCAAAGCT
1 T-AATAGATA-TATTTTAATTTGAAATATTCAAAGTATATAATTATCTTTTAATATTCAAAGCT
3376288 TAATAGATA
1 TAATAGATA
3376297 ATAAATACAT
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
60 1 0.02
61 4 0.06
62 9 0.14
63 47 0.73
64 3 0.05
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (62 bp):
TAATAGATATATTTTAATTTGAAATATTCAAAGTATATAATTATCTTTTAATATTCAAAGCT
Found at i:3376769 original size:14 final size:14
Alignment explanation
Indices: 3376750--3376781 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3376740 CGTTCGTGAA
*
3376750 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
3376764 CGTTCGATTATGTT
1 CGTTCGATTATGTT
3376778 CGTT
1 CGTT
3376782 TATGTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:3376778 original size:24 final size:24
Alignment explanation
Indices: 3376751--3376801 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3376741 GTTCGTGAAC
*
3376751 GTTCGGTTATGTTCGTTCGA-TTAT
1 GTTCGGTTATGTTCATTC-ATTTAT
*
3376775 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCATTTAT
3376799 GTT
1 GTT
3376802 TAACCCAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCATTTAT
Found at i:3377675 original size:12 final size:12
Alignment explanation
Indices: 3377651--3377727 Score: 106
Period size: 12 Copynumber: 6.7 Consensus size: 12
3377641 TGGGGCAATG
3377651 TCGAGCT-TGAA
1 TCGAGCTCTGAA
3377662 TCGAGCTCTGAA
1 TCGAGCTCTGAA
*
3377674 TCGAGCTCAGAA
1 TCGAGCTCTGAA
*
3377686 TTGAGCT-TGAA
1 TCGAGCTCTGAA
*
3377697 TCGAGCTCAGAA
1 TCGAGCTCTGAA
3377709 TCGAGCT-TGAA
1 TCGAGCTCTGAA
3377720 TCGAGCTC
1 TCGAGCTC
3377728 GAGTCTCGAG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
11 26 0.46
12 31 0.54
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (12 bp):
TCGAGCTCTGAA
Found at i:3377696 original size:23 final size:23
Alignment explanation
Indices: 3377651--3377775 Score: 126
Period size: 24 Copynumber: 5.3 Consensus size: 23
3377641 TGGGGCAATG
*
3377651 TCGAGCT-TGAATCGAGCTCTGAA
1 TCGAGCTCAGAATCGAGCT-TGAA
*
3377674 TCGAGCTCAGAATTGAGCTTGAA
1 TCGAGCTCAGAATCGAGCTTGAA
3377697 TCGAGCTCAGAATCGAGCTTGAA
1 TCGAGCTCAGAATCGAGCTTGAA
** * *
3377720 TCGAGCTCGAGTCTCGAGTTTTAA
1 TCGAGCTC-AGAATCGAGCTTGAA
** * *
3377744 TCGAGCTCGAGTCTCGAGTTTTAA
1 TCGAGCTC-AGAATCGAGCTTGAA
3377768 TCGAGCTC
1 TCGAGCTC
3377776 TTAAATTTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
23 41 0.44
24 52 0.56
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (23 bp):
TCGAGCTCAGAATCGAGCTTGAA
Found at i:3378002 original size:16 final size:16
Alignment explanation
Indices: 3377981--3378031 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
3377971 ATCTCCAACG
3377981 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
3377997 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
3378013 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
3378027 TTTAT
1 TTTAT
3378032 TAAATGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.15
15 2 0.06
16 26 0.79
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:3378292 original size:23 final size:21
Alignment explanation
Indices: 3378264--3378305 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
3378254 TAATAATTTA
3378264 TAGTTTATATTATATATATTTTT
1 TAGTTT-T-TTATATATATTTTT
*
3378287 TAGTTTTTTATATTTATTT
1 TAGTTTTTTATATATATTT
3378306 ATTCTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
TAGTTTTTTATATATATTTTT
Found at i:3378383 original size:14 final size:15
Alignment explanation
Indices: 3378366--3378398 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3378356 TTTTTTTAGT
3378366 TTTA-TTTTTATTTA
1 TTTATTTTTTATTTA
*
3378380 TTTATTTTTTATTTG
1 TTTATTTTTTATTTA
3378395 TTTA
1 TTTA
3378399 AAAACAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTATTTTTTATTTA
Found at i:3379469 original size:32 final size:32
Alignment explanation
Indices: 3379433--3379494 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
3379423 ATATAACAAG
* *
3379433 TCATCAATTTAAGTAACATGACATATATTATA
1 TCATCAATTTAAATAACATGACAGATATTATA
* * *
3379465 TCATCATTTTAAATGACGTGACAGATATTA
1 TCATCAATTTAAATAACATGACAGATATTA
3379495 CGTCAATACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (32 bp):
TCATCAATTTAAATAACATGACAGATATTATA
Found at i:3381263 original size:3 final size:3
Alignment explanation
Indices: 3381255--3381307 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
3381245 CTTTTATTCA
* * *
3381255 AAT AAT AAT AAT AAT AAT AAT AAT AAG CAT AAT CAAT ATT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
*
3381300 GAT AAT AA
1 AAT AAT AA
3381308 GATATGATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3381521 original size:14 final size:15
Alignment explanation
Indices: 3381493--3381522 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3381483 CTAAAAAAAC
3381493 TTCATATTATTTTTG
1 TTCATATTATTTTTG
3381508 TTCATATT-TTTTTG
1 TTCATATTATTTTTG
3381522 T
1 T
3381523 CTCCTTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (15 bp):
TTCATATTATTTTTG
Found at i:3382890 original size:32 final size:31
Alignment explanation
Indices: 3382825--3382928 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
3382815 GGGCCTGAGA
* * * * **
3382825 GCCTACCCAAGATAGATTTCGGGGCCGTGGG
1 GCCTACCTAAGAAACATTTCAGGGCCGCAGG
3382856 GCCTACCTAAGAACACATCTT-AGGGCCGCAGG
1 GCCTACCTAAGAA-ACAT-TTCAGGGCCGCAGG
** ** *
3382888 GCCTACCCGAGAATGATTTCAGGGCCGCAGA
1 GCCTACCTAAGAAACATTTCAGGGCCGCAGG
3382919 GCCTACCTAA
1 GCCTACCTAA
3382929 AAGTCACATT
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
30 2 0.04
31 31 0.54
32 22 0.39
33 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (31 bp):
GCCTACCTAAGAAACATTTCAGGGCCGCAGG
Found at i:3382906 original size:63 final size:63
Alignment explanation
Indices: 3382807--3382928 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
3382797 TCCTAAGGGA
* ** *
3382807 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
3382870 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATTTCAGGGCCGCAGAGCCTACCTAA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATTTCAGGGCCGCAGAGCCTACCTAA
3382929 AAGTCACATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:3383883 original size:27 final size:29
Alignment explanation
Indices: 3383817--3383947 Score: 153
Period size: 28 Copynumber: 4.6 Consensus size: 29
3383807 AACATTCGAA
* *
3383817 AATTACCAAAATGTCACCTTTTT-AAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
*
3383845 AATTCCCAGAATGTCACCTTTTTCACAA-
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
*
3383873 AATTCCC-GAATGTCACATTTTTCACAAA-
1 AATTCCCAGAATGTCACCTTTTTCA-AAAT
* **
3383901 AATTCCCAAAATACCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
*
3383930 AATTCCCAGAATGCCACC
1 AATTCCCAGAATGTCACC
3383948 GGGTCGGGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.18
28 40 0.45
29 32 0.36
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (29 bp):
AATTCCCAGAATGTCACCTTTTTCAAAAT
Found at i:3384006 original size:19 final size:19
Alignment explanation
Indices: 3383982--3384060 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
3383972 GTCAGACCGA
*
3383982 TCAACCCGGTTCGGACTTG
1 TCAACCCGGTTCGGACTGG
3384001 TCAACCCGGTTCGGACTGG
1 TCAACCCGGTTCGGACTGG
* * *
3384020 TCAGA-CCGGTTCAGACCGA
1 TCA-ACCCGGTTCGGACTGG
* * *
3384039 TCAAACCGGTTCAGACCGG
1 TCAACCCGGTTCGGACTGG
3384058 TCA
1 TCA
3384061 GGACGATCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
18 1 0.02
19 51 0.96
20 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.20
Consensus pattern (19 bp):
TCAACCCGGTTCGGACTGG
Found at i:3384035 original size:10 final size:10
Alignment explanation
Indices: 3384006--3384058 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
3383996 ACTTGTCAAC
*
3384006 CCGGTTCGGA
1 CCGGTTCAGA
*
3384016 CTGG-TCAGA
1 CCGGTTCAGA
3384025 CCGGTTCAGA
1 CCGGTTCAGA
* *
3384035 CC-GATCAAA
1 CCGGTTCAGA
3384044 CCGGTTCAGA
1 CCGGTTCAGA
3384054 CCGGT
1 CCGGT
3384059 CAGGACGATC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
9 14 0.41
10 20 0.59
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (10 bp):
CCGGTTCAGA
Found at i:3385897 original size:18 final size:19
Alignment explanation
Indices: 3385862--3385904 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
3385852 TTAAGTTATA
3385862 CTTTTCTTTCATTTTTTTT
1 CTTTTCTTTCATTTTTTTT
3385881 CTTTTCTTTCA-TTTTTTT
1 CTTTTCTTTCATTTTTTTT
3385899 CTTTTC
1 CTTTTC
3385905 ATAATGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (19 bp):
CTTTTCTTTCATTTTTTTT
Found at i:3386696 original size:21 final size:21
Alignment explanation
Indices: 3386672--3386711 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3386662 TTTTATTTTA
*
3386672 TTTAATTAATTGAGAATTAGG
1 TTTAATTAATTGAAAATTAGG
* *
3386693 TTTATTTATTTGAAAATTA
1 TTTAATTAATTGAAAATTA
3386712 CAACACTTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
TTTAATTAATTGAAAATTAGG
Found at i:3389899 original size:9 final size:8
Alignment explanation
Indices: 3389887--3389936 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
3389877 GCAATACAAT
3389887 TAATAAACA
1 TAATAAA-A
3389896 TAATTAAAA
1 TAA-TAAAA
3389905 TAATAAAA
1 TAATAAAA
*
3389913 T-A-ACAA
1 TAATAAAA
3389919 TAATAAAA
1 TAATAAAA
3389927 -AATAAAA
1 TAATAAAA
3389934 TAA
1 TAA
3389937 AATAAAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
6 4 0.11
7 9 0.26
8 11 0.31
9 7 0.20
10 4 0.11
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (8 bp):
TAATAAAA
Found at i:3389923 original size:17 final size:16
Alignment explanation
Indices: 3389903--3389943 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
3389893 ACATAATTAA
3389903 AATAATAAAATAACAAT
1 AATAATAAAATAA-AAT
3389920 AATAA-AAAATAAAAT
1 AATAATAAAATAAAAT
3389935 AA-AATAAAA
1 AATAATAAAA
3389944 AAGCAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.09
15 9 0.39
16 7 0.30
17 5 0.22
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AATAATAAAATAAAAT
Found at i:3389933 original size:5 final size:5
Alignment explanation
Indices: 3389906--3389943 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
3389896 TAATTAAAAT
3389906 AATAA AATAA CAATAA TAA-AA AATAA AATAA AATAA AA
1 AATAA AATAA -AATAA -AATAA AATAA AATAA AATAA AA
3389944 AAGCAAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 2 0.07
5 21 0.70
6 7 0.23
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:3389944 original size:17 final size:18
Alignment explanation
Indices: 3389900--3389945 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
3389890 TAAACATAAT
3389900 TAAAATAATAAAATAACAA
1 TAAAATAA-AAAATAACAA
3389919 T--AATAAAAAATAA-AA
1 TAAAATAAAAAATAACAA
3389934 TAAAATAAAAAA
1 TAAAATAAAAAA
3389946 GCAAAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.12
16 7 0.28
17 14 0.56
19 1 0.04
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (18 bp):
TAAAATAAAAAATAACAA
Found at i:3389980 original size:25 final size:24
Alignment explanation
Indices: 3389906--3389969 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
3389896 TAATTAAAAT
** *
3389906 AATAAAATAACAATAATAAAAAATAA
1 AATAAAATAA-AA-AAGCAAAAACAA
3389932 AATAAAATAAAAAAGCAAAAACAA
1 AATAAAATAAAAAAGCAAAAACAA
*
3389956 AATAGAATAAAAAA
1 AATAAAATAAAAAA
3389970 CATAAGTACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 22 0.65
25 2 0.06
26 10 0.29
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (24 bp):
AATAAAATAAAAAAGCAAAAACAA
Found at i:3391783 original size:19 final size:20
Alignment explanation
Indices: 3391749--3391788 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
3391739 TATCTAACCT
3391749 TTATTCATTTGGTTAA-TTG
1 TTATTCATTTGGTTAACTTG
3391768 TTATTCA-TTGGATTAACTTG
1 TTATTCATTTGG-TTAACTTG
3391788 T
1 T
3391789 CACTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 11 0.58
20 4 0.21
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.55
Consensus pattern (20 bp):
TTATTCATTTGGTTAACTTG
Found at i:3392453 original size:19 final size:18
Alignment explanation
Indices: 3392429--3392471 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
3392419 TTAAGTTATA
3392429 CTTTTCTTTCATCT-TTTT
1 CTTTTCTTTCAT-TATTTT
3392447 GCTTTTCTTTCATTATTTT
1 -CTTTTCTTTCATTATTTT
3392466 CTTTTC
1 CTTTTC
3392472 ATAATGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.07, C:0.21, G:0.02, T:0.70
Consensus pattern (18 bp):
CTTTTCTTTCATTATTTT
Found at i:3395290 original size:21 final size:21
Alignment explanation
Indices: 3395264--3395311 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3395254 ATAAATTGAA
*
3395264 ATTTTTAGTAATTTTATTTTT
1 ATTTTTAGTAATTTTATATTT
*
3395285 ATTTTTAGTATTTTTATATTT
1 ATTTTTAGTAATTTTATATTT
*
3395306 AATTTT
1 ATTTTT
3395312 CTTATATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
ATTTTTAGTAATTTTATATTT
Found at i:3395296 original size:15 final size:15
Alignment explanation
Indices: 3395278--3395324 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3395268 TTAGTAATTT
*
3395278 TATTTTTATTTTTAG
1 TATTTTTATATTTAG
*
3395293 TATTTTTATATTTAA
1 TATTTTTATATTTAG
3395308 T-TTTCTTATATTT-G
1 TATTT-TTATATTTAG
3395322 TAT
1 TAT
3395325 AGTCTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (15 bp):
TATTTTTATATTTAG
Found at i:3396633 original size:2 final size:2
Alignment explanation
Indices: 3396628--3396661 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3396618 ACACACACAC
3396628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3396662 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3399634 original size:29 final size:29
Alignment explanation
Indices: 3399592--3399653 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
3399582 AGAACATATG
*
3399592 AATAGTCAGGTGATCATTTTGAAACTTTT
1 AATAGTCAGGTGATAATTTTGAAACTTTT
3399621 AATAGTC-GAGTGATAATTTTGAAACTTTT
1 AATAGTCAG-GTGATAATTTTGAAACTTTT
3399650 AATA
1 AATA
3399654 ATTGAGATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.40
Consensus pattern (29 bp):
AATAGTCAGGTGATAATTTTGAAACTTTT
Found at i:3402138 original size:89 final size:91
Alignment explanation
Indices: 3401984--3402163 Score: 219
Period size: 89 Copynumber: 2.0 Consensus size: 91
3401974 CAGAATTGCG
* * * *
3401984 TCCATAGGGCTTACCCTAAGCACATAGCAAAAAGGGAGCCAACCTAAGGATACTCATTGGGGCCT
1 TCCATAGGGCTTACCCTAAGCACA-AGCAAAAAGGAAACCAACCAAAGGATACTCATTGAGGCCT
3402049 AT-GGTCCTAT-CCAAGGGTATCCTTAGA
65 ATGGGT-CT-TCCCAAGGGTATCCTTAGA
* *
3402076 TCCATAGGG-TTACCTTAAGCAC-A-CAACAAAGGAAACCAACCAAAGGATA-TGCCTTGAGGCC
1 TCCATAGGGCTTACCCTAAGCACAAGCAA-AAAGGAAACCAACCAAAGGATACT-CATTGAGGCC
3402137 TATGGGTCTTCCCAAGGGTATCCTTAG
64 TATGGGTCTTCCCAAGGGTATCCTTAG
3402164 GTTCGTAAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
88 5 0.06
89 49 0.63
90 3 0.04
91 12 0.15
92 9 0.12
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (91 bp):
TCCATAGGGCTTACCCTAAGCACAAGCAAAAAGGAAACCAACCAAAGGATACTCATTGAGGCCTA
TGGGTCTTCCCAAGGGTATCCTTAGA
Found at i:3405671 original size:16 final size:17
Alignment explanation
Indices: 3405635--3405668 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3405625 TATTTTATTA
3405635 GAAAATAAAAAACGTTG
1 GAAAATAAAAAACGTTG
3405652 GAAAATAAAAAACGTTG
1 GAAAATAAAAAACGTTG
3405669 AAAGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
GAAAATAAAAAACGTTG
Found at i:3407448 original size:36 final size:37
Alignment explanation
Indices: 3407389--3407460 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
3407379 TTTTTCGTCA
3407389 TACTAGGATTCAAACTCTCAAAAATAGGATAGAATTC
1 TACTAGGATTCAAACTCTCAAAAATAGGATAGAATTC
*
3407426 TACTAGGATTC-AACTC-CTAAAAATATGATAGAATT
1 TACTAGGATTCAAACTCTC-AAAAATAGGATAGAATT
3407461 TTGCTATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 1 0.03
36 21 0.64
37 11 0.33
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (37 bp):
TACTAGGATTCAAACTCTCAAAAATAGGATAGAATTC
Found at i:3411615 original size:20 final size:20
Alignment explanation
Indices: 3411563--3411632 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
3411553 CAAAAAGAGC
*
3411563 AAAAAGAAAAAAGAAAAGAAGCTA
1 AAAAAG-AAAAA-ACAAGAA-C-A
*
3411587 AAAAGGAAAAAACAAGAACA
1 AAAAAGAAAAAACAAGAACA
* * *
3411607 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
3411627 AAAAAG
1 AAAAAG
3411633 GGAACAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 23 0.57
21 1 0.03
22 6 0.15
23 5 0.12
24 5 0.12
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:3413224 original size:37 final size:37
Alignment explanation
Indices: 3413130--3413239 Score: 161
Period size: 36 Copynumber: 3.0 Consensus size: 37
3413120 GTGCTCACCA
3413130 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
3413166 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* *
3413203 TTTTCTCCCTTGAGACAGTTTCTCC-TGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTC-CCTTGAAACA-AAAC
3413240 ATTGAAAACA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
36 31 0.46
37 31 0.46
38 5 0.07
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:3413279 original size:102 final size:102
Alignment explanation
Indices: 3413148--3413641 Score: 801
Period size: 102 Copynumber: 4.9 Consensus size: 102
3413138 CTTGAGACAG
** * * *
3413148 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
3413213 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
3413250 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
3413315 TGAGACAGTTTCTCTTGAAACATAATCATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* ** *
3413352 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
3413417 TGAGACAGTTTCTCTTGAATCATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
3413454 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
3413519 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAATA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
3413556 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
3413620 TGAGACAGTTTCTATTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
3413642 CAAAACCTTT
Statistics
Matches: 366, Mismatches: 26, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
101 35 0.10
102 331 0.90
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:3413325 original size:37 final size:37
Alignment explanation
Indices: 3413266--3413336 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
3413256 TTGAAATGAG
* *
3413266 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
* *
3413303 TTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
3413337 TAATCATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:3413521 original size:37 final size:37
Alignment explanation
Indices: 3413454--3413540 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
3413444 ATTGGAAACA
** * *
3413454 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3413490 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3413527 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
3413541 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:3413602 original size:36 final size:36
Alignment explanation
Indices: 3413555--3413624 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
3413545 CATTGAAAAT
** *
3413555 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGATA
*
3413591 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
3413625 CAGTTTCTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGATA
Found at i:3413638 original size:36 final size:36
Alignment explanation
Indices: 3413555--3413641 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
3413545 CATTGAAAAT
* ** * *
3413555 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCATTGAAACAAATTTCGTCTCCCTTGAGACA
* *
3413591 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCATTGAAACAAATTTCGTCTCCCTTGAGACA
* *
3413627 GTTTCTATTGAAACA
1 ATTTCCATTGAAACA
3413642 CAAAACCTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCATTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:3413732 original size:67 final size:67
Alignment explanation
Indices: 3413583--3413741 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
3413573 TTCGTCTCTC
** *
3413583 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTATTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTATTGAAACACAAAAC
3413648 CT
66 CT
* * *
3413650 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTATTGAAACACAAAAC
3413715 CT
66 CT
*
3413717 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
3413742 ATTTCGTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTATTGAAACACAAAAC
CT
Found at i:3414509 original size:109 final size:107
Alignment explanation
Indices: 3414318--3414684 Score: 399
Period size: 109 Copynumber: 3.4 Consensus size: 107
3414308 TTTTAGCTAG
* * ** *
3414318 ACACAAGTTCAACTTCATAACGAAGGGATGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAA
1 ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAATTTC--AA
* * *
3414383 C-TGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGAAA
64 CGCGATTTCAACTCCACGACGGAGGATATCGTGC-ACTCGAGACA
* * *
3414427 ACACAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCATCC
1 ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAATTTCA-AC
*
3414492 GCGATTTCAACTCCACGACGGAGGATATCGTTCCACTCGAGACA
65 GCGATTTCAACTCCACGACGGAGGATATCG-TGCACTCGAGACA
* * * *
3414536 ATACAAGTTCAACTTCACAATGAAGGGACAGCTGGTTGTCAAC-AA-ATATTTTTCAAATTTCAG
1 ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACA-ACTTTTC-AATTTCA-
* * *
3414599 A-GCCAATTTCAACTTCAC-AGCGAAGGATAT--TAG-ACTCGAGACA
63 ACG-CGATTTCAACTCCACGA-CGGAGGATATCGT-GCACTCGAGACA
*
3414642 ACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC
1 ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
3414685 AAGATTTCGT
Statistics
Matches: 222, Mismatches: 28, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
106 50 0.23
107 2 0.01
108 11 0.05
109 157 0.71
110 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (107 bp):
ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAATTTCAACG
CGATTTCAACTCCACGACGGAGGATATCGTGCACTCGAGACA
Done.