Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003917.1 Hibiscus syriacus cultivar Beakdansim tig00008468_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: 67566
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1151 original size:20 final size:20
Alignment explanation
Indices: 1108--1152 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1098 ATTCACGATA
*
1108 GTATCAATACTCCTCATTGC
1 GTATCAATACTCCTCAATGC
*
1128 GTATCAGTACTCCTCTAATG-
1 GTATCAATACTCCTC-AATGC
1148 GTATC
1 GTATC
1153 GATAATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (20 bp):
GTATCAATACTCCTCAATGC
Found at i:9056 original size:54 final size:54
Alignment explanation
Indices: 8847--9045 Score: 337
Period size: 54 Copynumber: 3.7 Consensus size: 54
8837 ATGAATGCTA
*
8847 TATGATTTAGTTTTATTTTTGATCAAGATTAACCCTGATGGCCTCTTATTATAT
1 TATGATTTAGTTTTATTTTTGATCAAGATTAACCCTGATGGCCTCTTATTCTAT
*
8901 TATGATTTAGTTTTATTTTTTTATCAAGATTAACCCTGAT-GCCTCTTATTCTAT
1 TATGATTTAGTTTTA-TTTTTGATCAAGATTAACCCTGATGGCCTCTTATTCTAT
* *
8955 TATGATTTAGTTTTATTTTTGATCAAGATTAGCCTTGATGGCCTCTTATTCTAT
1 TATGATTTAGTTTTATTTTTGATCAAGATTAACCCTGATGGCCTCTTATTCTAT
*
9009 TATGATTTAGTTTTATTTTTTATCAAGATTAACCCTG
1 TATGATTTAGTTTTATTTTTGATCAAGATTAACCCTG
9046 TTGCTCTCTT
Statistics
Matches: 135, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
53 21 0.16
54 91 0.67
55 23 0.17
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (54 bp):
TATGATTTAGTTTTATTTTTGATCAAGATTAACCCTGATGGCCTCTTATTCTAT
Found at i:10733 original size:31 final size:29
Alignment explanation
Indices: 10662--10737 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
10652 TTACCCTTAT
* *
10662 ATTTTAGAT-AAATAATAATTTAACTCTAA
1 ATTTTAGATAAAAT-ATAATCTAACCCTAA
* *
10691 ACTTTAAATAAAATATCAATCTAACCCCTAA
1 ATTTTAGATAAAATAT-AATCTAA-CCCTAA
10722 ATTTTAGATAAAATAT
1 ATTTTAGATAAAATAT
10738 TTTATATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 9 0.24
30 10 0.26
31 19 0.50
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.37
Consensus pattern (29 bp):
ATTTTAGATAAAATATAATCTAACCCTAA
Found at i:10768 original size:31 final size:30
Alignment explanation
Indices: 10733--10799 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
10723 TTTTAGATAA
10733 AATATTTTATATATA-GTTTAGGGGTTAAATT
1 AATATTTTATATA-ACGTTTA-GGGTTAAATT
* *
10764 AATATTTTATCTAACTTTTAGGGTTAAATT
1 AATATTTTATATAACGTTTAGGGTTAAATT
*
10794 AGTATT
1 AATATT
10800 CTATTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.49
Consensus pattern (30 bp):
AATATTTTATATAACGTTTAGGGTTAAATT
Found at i:10821 original size:31 final size:30
Alignment explanation
Indices: 10749--10821 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
10739 TTATATATAG
* * *
10749 TTTAGGGGTTAAATTAATATTTTATCTAAC
1 TTTAAGGGTTAAATTAATATTCTATCTAAA
* * *
10779 TTTTAGGGTTAAATTAGTATTCTATTTAAAA
1 TTTAAGGGTTAAATTAATATTCTATCT-AAA
10810 TTTAAGGGTTAA
1 TTTAAGGGTTAA
10822 TGTAACCCCC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 22 0.63
31 13 0.37
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (30 bp):
TTTAAGGGTTAAATTAATATTCTATCTAAA
Found at i:18596 original size:13 final size:13
Alignment explanation
Indices: 18578--18618 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
18568 ACTTTTTTTT
*
18578 GTCAAAGTCAACG
1 GTCAAAGTCAACA
18591 GTCAAAG-CTAACA
1 GTCAAAGTC-AACA
18604 GTCAAAGTCAACA
1 GTCAAAGTCAACA
18617 GT
1 GT
18619 TTGACTCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (13 bp):
GTCAAAGTCAACA
Found at i:20891 original size:66 final size:66
Alignment explanation
Indices: 20799--20932 Score: 207
Period size: 66 Copynumber: 2.0 Consensus size: 66
20789 AAAGTAGTAT
*
20799 ATGTTCTAAGTACTCTCAACTATTTGACAATGAACGCTCAATCACCTGATTCCTTTAA-CTACTA
1 ATGTTCTAAGTACTCTCAACCATTTGACAATGAACGCTCAATCACCTGATTCCTTTAATC-ACTA
20863 GG
65 GG
* * * *
20865 ATGTTCTAAGTATTCTTAACCGTTTGACAATGAACGTTCAATCACCTGATTCCTTTAATCACTAG
1 ATGTTCTAAGTACTCTCAACCATTTGACAATGAACGCTCAATCACCTGATTCCTTTAATCACTAG
20930 G
66 G
20931 AT
1 AT
20933 AAGTTTATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 61 0.98
67 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (66 bp):
ATGTTCTAAGTACTCTCAACCATTTGACAATGAACGCTCAATCACCTGATTCCTTTAATCACTAG
G
Found at i:22410 original size:21 final size:20
Alignment explanation
Indices: 22381--22433 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
22371 ATTGTGAGGT
*
22381 GAGTGTCGATACCCCATCAAG
1 GAGTATCGATACCCCA-CAAG
* *
22402 GAGTATCGATACTCCACATG
1 GAGTATCGATACCCCACAAG
*
22422 AAGTATCGATAC
1 GAGTATCGATAC
22434 TCGAGGACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (20 bp):
GAGTATCGATACCCCACAAG
Found at i:23804 original size:22 final size:23
Alignment explanation
Indices: 23779--23825 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
23769 TTTCTTTGTG
*
23779 ATTTTTTTTACTACGT-TTTTGA
1 ATTTTTCTTACTACGTGTTTTGA
* *
23801 ATTTTTCTTGCTTCGTGTTTTGA
1 ATTTTTCTTACTACGTGTTTTGA
23824 AT
1 AT
23826 GGTTTTGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.62
Consensus pattern (23 bp):
ATTTTTCTTACTACGTGTTTTGA
Found at i:24283 original size:13 final size:12
Alignment explanation
Indices: 24253--24333 Score: 51
Period size: 13 Copynumber: 6.5 Consensus size: 12
24243 CAAAAAAAAT
*
24253 TAAATATATAAA
1 TAAATAAATAAA
24265 -ATAATACAATAAA
1 TA-AATA-AATAAA
*
24278 TAAATATATAATA
1 TAAATAAATAA-A
24291 TAAATAGTAAT-AA
1 TAAATA--AATAAA
*
24304 TAAATATAATATA
1 TAAATA-AATAAA
*
24317 T-AATAAATATA
1 TAAATAAATAAA
24328 TAAATA
1 TAAATA
24334 TAAATATAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
11 8 0.14
12 20 0.35
13 25 0.44
14 2 0.04
15 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (12 bp):
TAAATAAATAAA
Found at i:24288 original size:12 final size:12
Alignment explanation
Indices: 24253--24436 Score: 91
Period size: 12 Copynumber: 14.9 Consensus size: 12
24243 CAAAAAAAAT
24253 TAAATATATAAA
1 TAAATATATAAA
*
24265 -ATAATACAATAAA
1 TA-AATA-TATAAA
24278 TAAATATATAATA
1 TAAATATATAA-A
24291 TAAATAGTA-ATAA
1 TAAATA-TATA-AA
24304 TAAATATAATATATAA
1 T-AA-AT-ATATA-AA
24320 TAAATATATAAA
1 TAAATATATAAA
24332 TATAA-ATAT-AA
1 TA-AATATATAAA
* *
24343 TATATA-ACTATA
1 TAAATATA-TAAA
*
24355 TAACTATAT-AA
1 TAAATATATAAA
24366 T-AATATAT-AA
1 TAAATATATAAA
* *
24376 TATATAT-TATA
1 TAAATATATAAA
24387 TATAATATATAACTA
1 TA-AATATATAA--A
*
24402 TAAATATATATA
1 TAAATATATAAA
*
24414 TATATATAT-AA
1 TAAATATATAAA
24425 TATAATATATAA
1 TA-AATATATAA
24437 CTATAGAAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 45
0.69 0.08 0.23
Matches are distributed among these distances:
10 12 0.09
11 19 0.14
12 41 0.31
13 30 0.23
14 16 0.12
15 9 0.07
16 6 0.05
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (12 bp):
TAAATATATAAA
Found at i:24292 original size:7 final size:7
Alignment explanation
Indices: 24255--24550 Score: 204
Period size: 7 Copynumber: 43.4 Consensus size: 7
24245 AAAAAAATTA
24255 AATATAT
1 AATATAT
24262 AA-A-AT
1 AATATAT
*
24267 AATACAAT
1 AATA-TAT
24275 AA-ATA-
1 AATATAT
24280 AATATAT
1 AATATAT
24287 AATATA-
1 AATATAT
*
24293 AATA-GT
1 AATATAT
24299 AATA-AT
1 AATATAT
24305 AA-ATAT
1 AATATAT
24311 AATATAT
1 AATATAT
24318 -A-ATA-
1 AATATAT
24322 AATATAT
1 AATATAT
24329 AA-ATAT
1 AATATAT
24335 AA-ATAT
1 AATATAT
24341 AATATAT
1 AATATAT
24348 AACTATAT
1 AA-TATAT
24356 AACTATAT
1 AA-TATAT
24364 AATA-AT
1 AATATAT
24370 -ATATA-
1 AATATAT
24375 ATATATAT
1 A-ATATAT
*
24383 TATATAT
1 AATATAT
24390 AATATAT
1 AATATAT
24397 AACTATA-
1 AA-TATAT
24404 AATATAT
1 AATATAT
24411 ATATATAT
1 A-ATATAT
24419 ATATAATAT
1 A-AT-ATAT
24428 AATATAT
1 AATATAT
*
24435 AACTATAG
1 AA-TATAT
*
24443 AAAATAT
1 AATATAT
24450 AAT-TAT
1 AATATAT
*
24456 AATA-AC
1 AATATAT
* *
24462 AAAACAT
1 AATATAT
24469 ACATATAT
1 A-ATATAT
*
24477 AAAATAT
1 AATATAT
24484 AATATAT
1 AATATAT
24491 ATACTATAT
1 A-A-TATAT
24500 AATATA-
1 AATATAT
24506 ATATATAT
1 A-ATATAT
*
24514 ACTATAT
1 AATATAT
24521 AATATACT
1 AATATA-T
*
24529 TATA-AT
1 AATATAT
24535 -ATATAT
1 AATATAT
*
24541 ACTATAT
1 AATATAT
24548 AAT
1 AAT
24551 GTATTTCATC
Statistics
Matches: 236, Mismatches: 21, Indels: 64
0.74 0.07 0.20
Matches are distributed among these distances:
5 17 0.07
6 58 0.25
7 97 0.41
8 53 0.22
9 11 0.05
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (7 bp):
AATATAT
Found at i:24328 original size:2 final size:2
Alignment explanation
Indices: 24281--24548 Score: 128
Period size: 2 Copynumber: 144.5 Consensus size: 2
24271 CAATAAATAA
* *
24281 AT AT AT A- AT AT AA AT AGT A- AT A- AT AA AT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * *
24319 AT AA AT AT AT AA AT AT AA AT AT A- AT AT AT A- ACT AT AT A- ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T
24360 AT AT A- AT A- AT AT AT A- AT AT AT AT -T AT AT AT A- 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
*
24397 A- ACT AT AA AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT A-
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
24436 ACT AT AG A- AA AT AT A- AT -T AT A- AT A- AC A- AA AC AT AC AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
24473 AT AT A- AA AT AT A- AT AT AT AT ACT AT AT A- AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
24512 AT ACT AT AT A- AT AT ACT -T AT A- AT AT AT AT ACT AT AT A
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A
24549 ATGTATTTCA
Statistics
Matches: 208, Mismatches: 19, Indels: 78
0.68 0.06 0.26
Matches are distributed among these distances:
1 30 0.14
2 165 0.79
3 13 0.06
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:28953 original size:42 final size:39
Alignment explanation
Indices: 28907--29000 Score: 98
Period size: 42 Copynumber: 2.3 Consensus size: 39
28897 TTAAATTAAG
*
28907 AAAATAAAAAAGGTAAAAATAAAAATGTTAAAAGAGAAAAAT
1 AAAATAAAAAA-GAAAAAATAAAAAT-TTAAAAGA-AAAAAT
* * * *
28949 AAAATAAGATGAAGAAAAAATTAAACTTTAAAAGACAAAAT
1 AAAATAA-A-AAAGAAAAAATAAAAATTTAAAAGAAAAAAT
28990 AAAATAAAAAA
1 AAAATAAAAAA
29001 AATGCATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
39 2 0.05
40 1 0.02
41 12 0.27
42 15 0.34
43 12 0.27
44 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (39 bp):
AAAATAAAAAAGAAAAAATAAAAATTTAAAAGAAAAAAT
Found at i:29045 original size:50 final size:52
Alignment explanation
Indices: 28985--29103 Score: 147
Period size: 52 Copynumber: 2.3 Consensus size: 52
28975 TTTAAAAGAC
* *
28985 AAAATAAAATAAAAAAAATGCA-TAAATGTTA-AATTTT-AAAAGAAAT-AA
1 AAAATAAAATAAAAAAAATGAAGAAAATGTTATAATTTTCAAAAGAAATAAA
**
29033 AAAATAAGAAATAAGAAAAAATGAAGAAAATGTTATTTTTTTCAAAAGAAATAAA
1 AAAAT-A-AAATAA-AAAAAATGAAGAAAATGTTATAATTTTCAAAAGAAATAAA
29088 AAAATAAAATAAAAAA
1 AAAATAAAATAAAAAA
29104 TGTTAAATGT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
48 5 0.08
49 1 0.02
50 6 0.10
51 9 0.15
52 12 0.20
53 10 0.17
54 10 0.17
55 7 0.12
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (52 bp):
AAAATAAAATAAAAAAAATGAAGAAAATGTTATAATTTTCAAAAGAAATAAA
Found at i:30285 original size:5 final size:4
Alignment explanation
Indices: 30263--30356 Score: 52
Period size: 4 Copynumber: 22.5 Consensus size: 4
30253 CAAAAAAAAT
* *
30263 TAAA TATA TAAA -ATAA TACAA TAAA TATA TAATA TAAA TAGTAA T-AA
1 TAAA TAAA TAAA TA-AA TA-AA TAAA TAAA TAA-A TAAA TA--AA TAAA
* *
30310 TAAA TATAA TAATA TATAA TAAA TATA TAAA T-AA T-AA TATA TAAA TA
1 TAAA TA-AA TAA-A TA-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
30357 TAATTATAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
3 10 0.14
4 38 0.54
5 19 0.27
6 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (4 bp):
TAAA
Found at i:30296 original size:19 final size:18
Alignment explanation
Indices: 30263--30384 Score: 76
Period size: 19 Copynumber: 6.6 Consensus size: 18
30253 CAAAAAAAAT
30263 TAAATATATAAAATAATACAA
1 TAAATATAT--AATAATA-AA
30284 TAAATATATAAT-ATAAA
1 TAAATATATAATAATAAA
*
30301 T-AGTA-ATAATAAATATAA
1 TAAATATATAAT-AATA-AA
*
30319 T-AATATATAATAAATATA
1 TAAATATATAAT-AATAAA
30337 TAAATA-ATAATATATAAA
1 TAAATATATAATA-ATAAA
*
30355 TATAAT-TATAACTATATATA
1 TA-AATATATAA-TA-ATAAA
*
30375 TATATATATA
1 TAAATATATA
30385 TATATATTAA
Statistics
Matches: 85, Mismatches: 6, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
15 5 0.06
16 3 0.04
17 7 0.08
18 22 0.26
19 26 0.31
20 13 0.15
21 9 0.11
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.37
Consensus pattern (18 bp):
TAAATATATAATAATAAA
Found at i:30311 original size:22 final size:21
Alignment explanation
Indices: 30265--30493 Score: 85
Period size: 22 Copynumber: 11.0 Consensus size: 21
30255 AAAAAAATTA
* *
30265 AATATATAAAAT-AATACAAT
1 AATATATAATATAAATATAAT
30285 AAATATATAATATAAATAGTAAT
1 -AATATATAATATAAATA-TAAT
*
30308 AATAAAT-ATA-ATAATAT-AT
1 AATATATAATATA-AATATAAT
*
30327 AATAAAT-ATAT-AA-ATAAT
1 AATATATAATATAAATATAAT
*
30345 AATATATAAATATAATTATAACT
1 AATATAT-AATATAAATATAA-T
*
30368 -ATATAT-ATATATATAT-AT
1 AATATATAATATAAATATAAT
*
30386 -ATATATTAAGTTATATATATAACT
1 AATATA-TAA--TATAAATATAA-T
* * *
30410 -ATATAAAATATAATTGTAAT
1 AATATATAATATAAATATAAT
* *
30430 AACA-A-AACATACATATATAAT
1 AATATATAATATA-A-ATATAAT
*
30451 -ATATATACTATATAATATAAT
1 AATATATAATATA-AATATAAT
* *
30472 TATA-ATATATATACTATATAAT
1 AATATATA-ATATA-AATATAAT
30494 GTATTATATA
Statistics
Matches: 163, Mismatches: 22, Indels: 45
0.71 0.10 0.20
Matches are distributed among these distances:
17 2 0.01
18 16 0.10
19 19 0.12
20 20 0.12
21 45 0.28
22 48 0.29
23 7 0.04
24 6 0.04
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (21 bp):
AATATATAATATAAATATAAT
Found at i:30312 original size:34 final size:33
Alignment explanation
Indices: 30263--30372 Score: 104
Period size: 34 Copynumber: 3.3 Consensus size: 33
30253 CAAAAAAAAT
30263 TAAATATAT-AA-AATAATACAATAAATATATAA
1 TAAATATATAAATAATAATA-AATAAATATATAA
30295 TATAA-ATAGT-AATAATAAATATAAT-AATATATAA
1 TA-AATATA-TAAATAAT-AATA-AATAAATATATAA
* *
30329 TAAATATATAAATAATAATATATAAATATAATTA
1 TAAATATATAAATAATAATAAATAAATAT-ATAA
*
30363 TAACTATATA
1 TAAATATATA
30373 TATATATATA
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
32 7 0.11
33 17 0.26
34 35 0.53
35 7 0.11
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (33 bp):
TAAATATATAAATAATAATAAATAAATATATAA
Found at i:30337 original size:2 final size:2
Alignment explanation
Indices: 30287--30503 Score: 76
Period size: 2 Copynumber: 119.5 Consensus size: 2
30277 AATACAATAA
* *
30287 AT AT AT A- AT AT AA AT AGT A- AT A- AT AA AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * *
30325 AT A- AT AA AT AT AT AA AT A- AT A- AT AT AT AA AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30362 AT A- ACT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AGT -T AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * *
30402 AT AT A- ACT AT AT A- AA AT AT A- AT -T GT A- AT A- AC A- AA AC
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
30438 AT AC AT AT AT A- AT AT AT AT ACT AT AT A- AT AT A- AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
30476 AT AT AT AT ACT AT AT A- AT GT AT -T AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A
30504 CTAAAAAAAA
Statistics
Matches: 163, Mismatches: 18, Indels: 68
0.65 0.07 0.27
Matches are distributed among these distances:
1 28 0.17
2 127 0.78
3 8 0.05
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:30456 original size:9 final size:9
Alignment explanation
Indices: 30442--30491 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
30432 CAAAACATAC
30442 ATATATAAT
1 ATATATAAT
30451 ATATAT-A-
1 ATATATAAT
*
30458 CTATATAAT
1 ATATATAAT
30467 ATAATTATAAT
1 AT-A-TATAAT
*
30478 ATATATACT
1 ATATATAAT
30487 ATATA
1 ATATA
30492 ATGTATTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 17 0.50
10 2 0.06
11 8 0.24
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATATAAT
Found at i:30480 original size:34 final size:33
Alignment explanation
Indices: 30287--30503 Score: 106
Period size: 32 Copynumber: 7.2 Consensus size: 33
30277 AATACAATAA
*
30287 ATATATAATATAAATAGTAATA-ATAA-ATATA-
1 ATATATAATATAATTA-TAATATATAATATATAT
30318 ATA-AT-ATATAA-TA-AATATATAAATA-ATAAT
1 ATATATAATATAATTATAATATAT-AATATAT-AT
30348 ATATA-AATATAATTATAACTATAT-ATATATAT
1 ATATATAATATAATTATAA-TATATAATATATAT
*
30380 ATATAT-ATAT-ATTA-AGT-TAT-ATATATAACT
1 ATATATAATATAATTATAATATATAATATAT-A-T
* * * * * *
30410 ATATAAAATATAATTGTAATA-ACAAAACATAC
1 ATATATAATATAATTATAATATATAATATATAT
*
30442 ATATATAATAT-A-TATACTATATAATA--TA-
1 ATATATAATATAATTATAATATATAATATATAT
* *
30470 AT-TATAATAT-A-TATACTATATAATGTAT-T
1 ATATATAATATAATTATAATATATAATATATAT
30499 ATATA
1 ATATA
30504 CTAAAAAAAA
Statistics
Matches: 148, Mismatches: 14, Indels: 49
0.70 0.07 0.23
Matches are distributed among these distances:
26 4 0.03
27 24 0.16
28 17 0.11
29 15 0.10
30 19 0.13
31 23 0.16
32 29 0.20
33 8 0.05
34 9 0.06
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (33 bp):
ATATATAATATAATTATAATATATAATATATAT
Found at i:33844 original size:57 final size:57
Alignment explanation
Indices: 33780--33893 Score: 158
Period size: 57 Copynumber: 2.0 Consensus size: 57
33770 TATAGTACCT
*
33780 ACGTAACTTCAATTAATATTTTCAAAAAAAGTGCTCTAT-TCGAAATTTAATCCTCAA
1 ACGTAACTTCAATTAATATTTTCAAAAAAAGTGCTCTATCT-GAAACTTAATCCTCAA
**** *
33837 ACGTAACTTCAATTAATATTTTTTTTAAAATTGCTCTATCTGAAACTTAATCCTCAA
1 ACGTAACTTCAATTAATATTTTCAAAAAAAGTGCTCTATCTGAAACTTAATCCTCAA
33894 TTTTATAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
57 49 0.98
58 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.39
Consensus pattern (57 bp):
ACGTAACTTCAATTAATATTTTCAAAAAAAGTGCTCTATCTGAAACTTAATCCTCAA
Found at i:37197 original size:21 final size:21
Alignment explanation
Indices: 37173--37223 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
37163 AAGCAGAGAA
* * * *
37173 AGAAGTAGTGGCATCACTGAG
1 AGAAGCAGCGGCAACACAGAG
37194 AGAAGCAGCGGCAACACAGAG
1 AGAAGCAGCGGCAACACAGAG
37215 AGAAGCAGC
1 AGAAGCAGC
37224 ATATCAGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.33, T:0.08
Consensus pattern (21 bp):
AGAAGCAGCGGCAACACAGAG
Found at i:37632 original size:44 final size:44
Alignment explanation
Indices: 37538--37663 Score: 159
Period size: 44 Copynumber: 2.9 Consensus size: 44
37528 AATTCTGTGT
*
37538 TATACCATACATTTAGCGGCGTTTGTA-A-AAAAAACGCCGCAA
1 TATACCATACATTTAGCGGCGTTTGTATACAAGAAACGCCGCAA
* **
37580 TATACCATACATTTAGCGGCGTTTGTATACTAGAAACGTTGCAA
1 TATACCATACATTTAGCGGCGTTTGTATACAAGAAACGCCGCAA
* * *
37624 TCA-ACCATATATTTAGCGGCATTTGTATACCAGAAACGCC
1 T-ATACCATACATTTAGCGGCGTTTGTATACAAGAAACGCC
37664 ACTAATTCTC
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
42 27 0.38
43 1 0.01
44 43 0.60
45 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (44 bp):
TATACCATACATTTAGCGGCGTTTGTATACAAGAAACGCCGCAA
Found at i:37747 original size:43 final size:43
Alignment explanation
Indices: 37700--37927 Score: 174
Period size: 43 Copynumber: 5.3 Consensus size: 43
37690 TTTTCGATAT
* * * * *
37700 AAACGCCGCTAAATCTGAAAACCTACTGTGACGTTTGTGGGGA
1 AAACGCCGCTAAATCTCAAAACCTACTGCGACATTTGTAGGAA
** * * * *
37743 AAACGCCGCTAAAAT-T-ATCACCTACTGTGGCGTTTGTGGGAA
1 AAACGCCGCT-AAATCTCAAAACCTACTGCGACATTTGTAGGAA
* * * * * *
37785 AAACGCCGCAAAATATCAAAACCTACTGCAACATTTTTAAGTA
1 AAACGCCGCTAAATCTCAAAACCTACTGCGACATTTGTAGGAA
* *
37828 AAACGCCGCTAAATCTCAATACCTACTGCGACATTTTTAGGAA
1 AAACGCCGCTAAATCTCAAAACCTACTGCGACATTTGTAGGAA
* * * * * **
37871 AAACGCCGCT-AAGCATCAACACCTATTGCGACGTTTTTCTGAA
1 AAACGCCGCTAAATC-TCAAAACCTACTGCGACATTTGTAGGAA
*
37914 AAACGCCACTAAAT
1 AAACGCCGCTAAAT
37928 AACAACACCT
Statistics
Matches: 151, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
41 4 0.03
42 35 0.23
43 106 0.70
44 6 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAATCTCAAAACCTACTGCGACATTTGTAGGAA
Found at i:37798 original size:41 final size:41
Alignment explanation
Indices: 37720--37802 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
37710 AAATCTGAAA
*
37720 ACCTACTGTGACGTTTGTGGGGAAAACGCCGCTAAAATTATC
1 ACCTACTGTGACGTTTGTGGGAAAAACGCCGCTAAAA-TATC
*
37762 ACCTACTGTGGCGTTTGTGGGAAAAACGCCGC-AAAATATC
1 ACCTACTGTGACGTTTGTGGGAAAAACGCCGCTAAAATATC
37802 A
1 A
37803 AAACCTACTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 5 0.13
41 4 0.10
42 30 0.77
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (41 bp):
ACCTACTGTGACGTTTGTGGGAAAAACGCCGCTAAAATATC
Found at i:37934 original size:43 final size:43
Alignment explanation
Indices: 37782--37985 Score: 210
Period size: 43 Copynumber: 4.7 Consensus size: 43
37772 GCGTTTGTGG
* * * * *
37782 GAAAAACGCCGCAAAATATCAAAACCTACTGCAACATTTTTAA
1 GAAAAACGCCGCTAAATATCAACACCTATTGCGACATTTTTAT
* * * * *
37825 GTAAAACGCCGCTAAATCTCAATACCTACTGCGACATTTTTAG
1 GAAAAACGCCGCTAAATATCAACACCTATTGCGACATTTTTAT
** * *
37868 GAAAAACGCCGCTAAGCATCAACACCTATTGCGACGTTTTTCT
1 GAAAAACGCCGCTAAATATCAACACCTATTGCGACATTTTTAT
* * * * *
37911 GAAAAACGCCACTAAATAACAACACCTATTGCGGCGTTTTTCT
1 GAAAAACGCCGCTAAATATCAACACCTATTGCGACATTTTTAT
* *
37954 GAAAAAACGTCGCTAAATAACAACACCTATTG
1 G-AAAAACGCCGCTAAATATCAACACCTATTG
37986 TGGCGTTTGT
Statistics
Matches: 138, Mismatches: 22, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
43 110 0.80
44 28 0.20
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (43 bp):
GAAAAACGCCGCTAAATATCAACACCTATTGCGACATTTTTAT
Found at i:37975 original size:44 final size:43
Alignment explanation
Indices: 37742--37993 Score: 191
Period size: 43 Copynumber: 5.9 Consensus size: 43
37732 GTTTGTGGGG
** * * * * **
37742 AAAACGCCGCTAAA-ATTATCACCTACTGTGGCGTTTGTGGGA
1 AAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTCTGA
* * * * ** * ** *
37784 AAAACGCCGCAAAATATCAAAACCTACTGCAACATTTTTAAGT
1 AAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTCTGA
** * * * * **
37827 AAAACGCCGCTAAATCTCAATACCTACTGCGACATTTTTAGGA
1 AAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTCTGA
** * *
37870 AAAACGCCGCTAAGCATCAACACCTATTGCGACGTTTTTCTGA
1 AAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTCTGA
*
37913 AAAACGCCACTAAATAACAACACCTATTGCGGCGTTTTTCTGAA
1 AAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTCTG-A
* *
37957 AAAACGTCGCTAAATAACAACACCTATTGTGGCGTTT
1 AAAACGCCGCTAAATAACAACACCTATTGCGGCGTTT
37994 GTGGAACAAA
Statistics
Matches: 174, Mismatches: 34, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 13 0.07
43 126 0.72
44 35 0.20
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.25
Consensus pattern (43 bp):
AAAACGCCGCTAAATAACAACACCTATTGCGGCGTTTTTCTGA
Found at i:38081 original size:15 final size:15
Alignment explanation
Indices: 38063--38096 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38053 CGCTAACTTT
38063 AGCGGCGCTATTTT-C
1 AGCGGCGCT-TTTTGC
38078 AGCGGCGCTTTTTGC
1 AGCGGCGCTTTTTGC
38093 AGCG
1 AGCG
38097 TTTATCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.12, C:0.26, G:0.32, T:0.29
Consensus pattern (15 bp):
AGCGGCGCTTTTTGC
Found at i:39347 original size:42 final size:42
Alignment explanation
Indices: 39288--39373 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
39278 GCCTGGGGTA
* *
39288 TCCCAGGCAACCCCTCAAAATTGTAACTTGGTGTTAATTTTT
1 TCCCAGACAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
*
39330 TCCCAGACAACCCCTCAAAATTGTAACTTAGTTTTAATTTTT
1 TCCCAGACAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
39372 TC
1 TC
39374 TATTTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.37
Consensus pattern (42 bp):
TCCCAGACAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
Found at i:43161 original size:43 final size:43
Alignment explanation
Indices: 42952--43160 Score: 213
Period size: 43 Copynumber: 4.9 Consensus size: 43
42942 GGCATTTGTA
* * * * *
42952 GTTGAGTTTTAGCGGCATTTTTCCGACAAACACCACAATAGGT
1 GTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGT
* *
42995 GTTGAGATTTAGCGGCG-TTTTCTCACAAACGTCGCAATAGGT
1 GTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGT
* * * *
43037 GTTGAGATTTAGCGGTGTTTTTCACATAAATGCCGCAATAGGT
1 GTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGT
* * *** ** ** * *
43080 TTTGATATTTAGCAATGTTTTTATCGTAAACGCCGCAAAAGGA
1 GTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGT
43123 GTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAA
1 GTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAA
43161 ATGCTTATGT
Statistics
Matches: 134, Mismatches: 31, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
42 36 0.27
43 98 0.73
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (43 bp):
GTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGT
Found at i:43604 original size:21 final size:21
Alignment explanation
Indices: 43580--43665 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
43570 CTGCTGATAT
*
43580 GCTGCTTCTCTCTCTGCTTCC
1 GCTGCTGCTCTCTCTGCTTCC
* *
43601 GCTGCTGCTCTCACTGCTTCT
1 GCTGCTGCTCTCTCTGCTTCC
* *
43622 TCTGCTGCTTCCGCTGCTGCTTCC
1 GCTGCTGC-T-CTCT-CTGCTTCC
* *
43646 ACTGCTGCTCTCTATGCTTC
1 GCTGCTGCTCTCTCTGCTTC
43666 TCTTGCTTCA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
21 31 0.60
22 4 0.08
23 3 0.06
24 14 0.27
ACGTcount: A:0.03, C:0.40, G:0.17, T:0.40
Consensus pattern (21 bp):
GCTGCTGCTCTCTCTGCTTCC
Found at i:43619 original size:33 final size:33
Alignment explanation
Indices: 43581--43665 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
43571 TGCTGATATG
43581 CTGCTTCTCTCTCTGCTTCCGCTGCTGC-TCTCA
1 CTGCTTCTCTCTCTGCTTCCGCTGCTGCTTC-CA
43614 CTGCTTCT-TCTGCTGCTTCCGCTGCTGCTTCCA
1 CTGCTTCTCTCT-CTGCTTCCGCTGCTGCTTCCA
* *
43647 CTGCTGCTCTCTATGCTTC
1 CTGCTTCTCTCTCTGCTTC
43666 TCTTGCTTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
32 3 0.06
33 39 0.83
34 5 0.11
ACGTcount: A:0.04, C:0.40, G:0.16, T:0.40
Consensus pattern (33 bp):
CTGCTTCTCTCTCTGCTTCCGCTGCTGCTTCCA
Found at i:43652 original size:15 final size:12
Alignment explanation
Indices: 43579--43654 Score: 63
Period size: 12 Copynumber: 6.6 Consensus size: 12
43569 TCTGCTGATA
*
43579 TGCTGCTTCTCTC
1 TGCTGCTTC-CGC
43592 T-CTGCTTCCGC
1 TGCTGCTTCCGC
*
43603 TGCTGC-TCTCAC
1 TGCTGCTTC-CGC
*
43615 TGCTTCTT---C
1 TGCTGCTTCCGC
43624 TGCTGCTTCCGC
1 TGCTGCTTCCGC
*
43636 TGCTGCTTCCAC
1 TGCTGCTTCCGC
43648 TGCTGCT
1 TGCTGCT
43655 CTCTATGCTT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
9 8 0.15
11 5 0.10
12 37 0.71
13 2 0.04
ACGTcount: A:0.03, C:0.39, G:0.18, T:0.39
Consensus pattern (12 bp):
TGCTGCTTCCGC
Found at i:51552 original size:77 final size:77
Alignment explanation
Indices: 51413--51555 Score: 234
Period size: 77 Copynumber: 1.9 Consensus size: 77
51403 TAATACAGGA
* *
51413 AAAAACAGAATAAGTTCATAATGTTTATAGATATAGAAAAACAAACGCAAACCTAACACACCCTA
1 AAAAACAGAATAACTTCATAATGTTGATAGATATAGAAAAACAAACGCAAACCTAACACACCCTA
51478 TTTCCAGACGAG
66 TTTCCAGACGAG
* *
51490 AAAAACAGAATAACTTCATAATGTTGATAGATATAGCAAAA-GAACGCAAACCTAACATCACCCT
1 AAAAACAGAATAACTTCATAATGTTGATAGATATAGAAAAACAAACGCAAACCTAACA-CACCCT
51554 AT
65 AT
51556 AACAAGATGT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
76 15 0.25
77 46 0.75
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (77 bp):
AAAAACAGAATAACTTCATAATGTTGATAGATATAGAAAAACAAACGCAAACCTAACACACCCTA
TTTCCAGACGAG
Found at i:55675 original size:50 final size:50
Alignment explanation
Indices: 55616--55741 Score: 171
Period size: 50 Copynumber: 2.5 Consensus size: 50
55606 GTAGCAGTAA
* *
55616 AGCGCGCCCCCCGAACCGCGTTATACGCTGATTTGGCACCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGATATACGCTGATTTGGCACCACGTGGGTAT
** * **
55666 AGCGCGCCCCCTGCCCCGCGATATACGGTGATTTGGCGTCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGATATACGCTGATTTGGCACCACGTGGGTAT
* *
55716 AGCGCGCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTGAACCGCGATATAC
55742 CTGGGTATCT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.16, C:0.36, G:0.29, T:0.20
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGATATACGCTGATTTGGCACCACGTGGGTAT
Found at i:55984 original size:17 final size:18
Alignment explanation
Indices: 55947--55987 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
55937 CTATTATGTA
*
55947 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
55965 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
55982 TTTACT
1 TTTACT
55988 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:56243 original size:111 final size:111
Alignment explanation
Indices: 56049--56381 Score: 603
Period size: 111 Copynumber: 3.0 Consensus size: 111
56039 TGAAAATCAT
* * *
56049 ATATCTCTACACTTTGCTGATATGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
56114 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
56160 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
56225 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* * *
56271 ATATCTCGACACTTTGTTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAATAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
56336 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
56382 TTTTTGTAAT
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:62604 original size:37 final size:36
Alignment explanation
Indices: 62552--62637 Score: 138
Period size: 37 Copynumber: 2.4 Consensus size: 36
62542 TCAAGTTTTT
*
62552 TAAAGAAAATCTAATATTAAACTTTTCTCATCTATTG
1 TAAAG-AAATTTAATATTAAACTTTTCTCATCTATTG
62589 TAAAGAATATTTAATATTAAACTTTTCTCATCTATTG
1 TAAAGAA-ATTTAATATTAAACTTTTCTCATCTATTG
62626 TAAA-AAATTTAA
1 TAAAGAAATTTAA
62638 CACTGATGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 6 0.13
36 4 0.09
37 37 0.79
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (36 bp):
TAAAGAAATTTAATATTAAACTTTTCTCATCTATTG
Found at i:63340 original size:24 final size:24
Alignment explanation
Indices: 63293--63343 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
63283 GTTCGTGAAC
*
63293 GTTCGATTATGTTCATTCGGTTAT
1 GTTCGATTATGTTCATTCAGTTAT
* *
63317 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGATTATGTTCATTCAGTTAT
63341 GTT
1 GTT
63344 TAACCCAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.55
Consensus pattern (24 bp):
GTTCGATTATGTTCATTCAGTTAT
Found at i:64277 original size:16 final size:16
Alignment explanation
Indices: 64258--64314 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
64248 CCAACGTTTA
*
64258 TGTTCATTTATGATCG
1 TGTTCATTTATGTTCG
64274 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
64290 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
64306 T-TT-ATTTAT
1 TGTTCATTTAT
64315 TAAATGAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 31 0.82
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:64397 original size:16 final size:16
Alignment explanation
Indices: 64376--64408 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
64366 AAAAAAAATT
64376 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
64392 TGTTCGTTTTTGTTCG
1 TGTTCGTTTATGTTCG
64408 T
1 T
64409 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.24, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Done.