Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020111.1 Corchorus olitorius cultivar O-4 contig20144, 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: 136029
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:5527 original size:10 final size:10
Alignment explanation
Indices: 5493--5518 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5483 CAGCCAACGG
5493 TTGTTAGAGT
1 TTGTTAGAGT
5503 TTGTTAGAGT
1 TTGTTAGAGT
5513 TTGTTA
1 TTGTTA
5519 AAGTCTGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (10 bp):
TTGTTAGAGT
Found at i:5891 original size:17 final size:18
Alignment explanation
Indices: 5857--5893 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5847 AACTAAAAAA
*
5857 TAATAAAATAATTGAAAT
1 TAATAAAAAAATTGAAAT
5875 TAATAAAAAAATT-AAAT
1 TAATAAAAAAATTGAAAT
5892 TA
1 TA
5894 TTATATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
TAATAAAAAAATTGAAAT
Found at i:7203 original size:30 final size:30
Alignment explanation
Indices: 7162--7227 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
7152 CATATACATC
*
7162 ATTTGTATATGTTTCCTTCTACTTCTTTGT
1 ATTTTTATATGTTTCCTTCTACTTCTTTGT
7192 ATTTTTATATGTTTCCTTCTACTTCTTTGT
1 ATTTTTATATGTTTCCTTCTACTTCTTTGT
7222 ATTTTT
1 ATTTTT
7228 TTACTTGACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.14, C:0.15, G:0.08, T:0.64
Consensus pattern (30 bp):
ATTTTTATATGTTTCCTTCTACTTCTTTGT
Found at i:8108 original size:26 final size:26
Alignment explanation
Indices: 8072--8122 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
8062 GGTACTGTAG
8072 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTGAATTTTTCTAAATAAAATAA
8098 AAATTGAATTTTTCTAAATAAAATA
1 AAATTGAATTTTTCTAAATAAAATA
8123 TTTTAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (26 bp):
AAATTGAATTTTTCTAAATAAAATAA
Found at i:9487 original size:350 final size:349
Alignment explanation
Indices: 8657--9701 Score: 1445
Period size: 350 Copynumber: 3.0 Consensus size: 349
8647 CAAATTGCCA
* * * * *
8657 AGCCAGATGTCTTGAAGGCTAAATCTAATATTCTTAAACCCAATTCGTTAATATGGAAACTCAAA
1 AGCCAGATGTCTTGAAGACTAAATCTGATATTCTTAGACTCAATTCGTTAATATGGAAACCCAAA
* *
8722 GAAGGAGTCCAAGTCCAATCAGTAATTATGATGCAGTAATGATTCAGTCCTGATGCAGCATTGTT
66 GAAGGAGTTCAAGTCCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGTT
*
8787 AAATCATATTCAAATG-AGAACTTCACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCT
131 AAATCATATTCAAAAGAAG-ACTTCACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCT
*
8851 AGAGCTCAGAAAAATGCAAATGAGGTACTGTTGGAAAGAGGATTCCAAAATCTACAACTTTTATG
195 AGAGCTCAGAAAAATGCAAATGAGGTACTGTTGGAAAGAGGATTCCAATATCTACAACTTTTATG
* * * * *
8916 TCATCTCGAGACCTAATTCTGTAGTTCCGATGGATGATTTTGCCCTTGAAATTTCTAGATAGAAT
260 TTACCTCGAGACCTAATTCTGCAGTTCCG-TGGACGATTTTGCCCTTGAAATTTCTAGACAGAAT
*
8981 TGATCTTCTCCTAAACCGACTTGGAG
324 TGATCTTCTTCTAAACCGACTTGGAG
* ** * *
9007 AGCCAGATGCCTTGAACCCTAAATCTGATATTCTTAG-GTCCAATTCGTTAACATGGAAACCCAA
1 AGCCAGATGTCTTGAAGACTAAATCTGATATTCTTAGACT-CAATTCGTTAATATGGAAACCCAA
* * * ** *
9071 AGAAGGAGTTCAAGTTCAATCAGTAATTATGATGCAATAATGATTCAACATTGATGCAACATTGT
65 AGAAGGAGTTCAAGTCCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGT
* * * *
9136 TAAATCATATTCAAAAGAAGACTTCACAAAAGCAGTTTTGGAAGAAAATTCATAACTTTTTAACT
130 TAAATCATATTCAAAAGAAGACTTCACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCT
* * * * *
9201 TGAGCTCAGAAAAATGCAAATAAGGTACTGTTAGAAAGAGGATTCTAATATCTATAACTTTTATG
195 AGAGCTCAGAAAAATGCAAATGAGGTACTGTTGGAAAGAGGATTCCAATATCTACAACTTTTATG
* * *
9266 TTTACCTCGAGACCTAATTCTGCAGTTCTTGTGGACGATTTTGCACTTGAAATTTCTAGACATAA
260 -TTACCTCGAGACCTAATTCTGCAGTTC-CGTGGACGATTTTGCCCTTGAAATTTCTAGACAGAA
9331 TTGATCTTCTTCTAAACCGACTTGGAG
323 TTGATCTTCTTCTAAACCGACTTGGAG
* * ** *
9358 AGCCAGATGTCTTGAAGAATAAATTTGATATTCTTAGACTCAATTTATTAATATGGAAGCCCAAA
1 AGCCAGATGTCTTGAAGACTAAATCTGATATTCTTAGACTCAATTCGTTAATATGGAAACCCAAA
* * * * *
9423 GAAGGAGTTCAAGTCCGACCAGTAATTATGAAGTAGTAATGATT-AGCCCTAATGCAGCATTGTT
66 GAAGGAGTTCAAGTCCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGTT
* *
9487 AAATCCTATTCAAAAGACGACTTCACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCTA
131 AAATCATATTCAAAAGAAGACTTCACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCTA
* * ** *
9552 GAGCTCA-AAAAAAGAAAATGAGGTACCATTGGAAAGAGGATTCCAATATCTACAATTTTTATG-
196 GAGCTCAGAAAAATGCAAATGAGGTACTGTTGGAAAGAGGATTCCAATATCTACAACTTTTATGT
* * * * *
9615 TACCTCGATACCTAATTCTGCAGTTCCGGTTGACAATTTTTCCCTTGAAATTTCTGGACAGAATT
261 TACCTCGAGACCTAATTCTGCAGTTCC-GTGGACGATTTTGCCCTTGAAATTTCTAGACAGAATT
9680 GATCTT-TTCCTAAACCGACTTG
325 GATCTTCTT-CTAAACCGACTTG
9702 AAGAATGTTT
Statistics
Matches: 606, Mismatches: 82, Indels: 17
0.86 0.12 0.02
Matches are distributed among these distances:
346 2 0.00
347 75 0.12
349 47 0.08
350 307 0.51
351 173 0.29
352 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (349 bp):
AGCCAGATGTCTTGAAGACTAAATCTGATATTCTTAGACTCAATTCGTTAATATGGAAACCCAAA
GAAGGAGTTCAAGTCCAATCAGTAATTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGTT
AAATCATATTCAAAAGAAGACTTCACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCTA
GAGCTCAGAAAAATGCAAATGAGGTACTGTTGGAAAGAGGATTCCAATATCTACAACTTTTATGT
TACCTCGAGACCTAATTCTGCAGTTCCGTGGACGATTTTGCCCTTGAAATTTCTAGACAGAATTG
ATCTTCTTCTAAACCGACTTGGAG
Found at i:10007 original size:15 final size:16
Alignment explanation
Indices: 9969--10014 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
9959 ATTTTAAATT
9969 TATATTTA-ATATAATTA
1 TATATTTATAT-TAA-TA
*
9986 TATATTTATGTTAATA
1 TATATTTATATTAATA
10002 TA-ATTTATATTAA
1 TATATTTATATTAA
10015 AAAATAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 10 0.38
16 4 0.15
17 11 0.42
18 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TATATTTATATTAATA
Found at i:15496 original size:16 final size:17
Alignment explanation
Indices: 15477--15516 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
15467 AGAAAAATGA
15477 TAATAAAATTA-AAAAT
1 TAATAAAATTATAAAAT
*
15493 TAATTAAA-TATAAAAT
1 TAATAAAATTATAAAAT
15509 T-ATAAAAT
1 TAATAAAAT
15517 AATTATCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAAAATTATAAAAT
Found at i:15578 original size:17 final size:19
Alignment explanation
Indices: 15558--15600 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
15548 AAATAAGTAT
15558 ATTATAT-AT-CATTGAAA
1 ATTATATCATACATTGAAA
* *
15575 ATTATATCATATATTTAAA
1 ATTATATCATACATTGAAA
15594 ATTATAT
1 ATTATAT
15601 TAATATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTATATCATACATTGAAA
Found at i:15608 original size:22 final size:21
Alignment explanation
Indices: 15555--15609 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
15545 TATAAATAAG
15555 TATATTATATATCATTGAAAAT
1 TATATTATATAT-ATTGAAAAT
*
15577 TATATCATATAT-TT-AAAAT
1 TATATTATATATATTGAAAAT
15596 TATATTAATATATA
1 TATATT-ATATATA
15610 ATATCATCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 10 0.34
20 8 0.28
22 11 0.38
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATTATATATATTGAAAAT
Found at i:18596 original size:57 final size:57
Alignment explanation
Indices: 18523--18637 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
18513 CTTCTTTATT
*
18523 TCCAGTGAGCACTTTTGAAACCAAATTTATATGGAGATATGCACATTTGGGTTCATA
1 TCCAGTGAGCACTTTTGAAACCAAATTTATATGGAGATATGCACATTTGAGTTCATA
*
18580 TCCAGTGAGCACTTTTGAAACCAAATTTATATGGATATATGCACATTTGAGTTCATA
1 TCCAGTGAGCACTTTTGAAACCAAATTTATATGGAGATATGCACATTTGAGTTCATA
18637 T
1 T
18638 GCAGATAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (57 bp):
TCCAGTGAGCACTTTTGAAACCAAATTTATATGGAGATATGCACATTTGAGTTCATA
Found at i:27483 original size:50 final size:50
Alignment explanation
Indices: 27426--28169 Score: 567
Period size: 51 Copynumber: 14.7 Consensus size: 50
27416 AATCTTTATG
* * * *
27426 TTAAAAGATGAAACTTTCAAGTAATTTGTAAATAAA-AAGGAGGTTTTTGA
1 TTAAAAGATGAAACTTTTAAGTAATTTGTAAATAAAGATGGA-ATTTTTAA
* *
27476 TTAAAAGATGAAAC-TTTAAGTAATTTGTAAATAAAAAT-GAGATTTTTGAG
1 TTAAAAGATGAAACTTTTAAGTAATTTGTAAATAAAGATGGA-ATTTTT-AA
* * * * * *
27526 TGAAAA-TTGAAGCTTTTAAGTAATTTATGAATAAAGATTGAATTTTTAA
1 TTAAAAGATGAAACTTTTAAGTAATTTGTAAATAAAGATGGAATTTTTAA
* * * * * *
27575 ATAAGAGGTTAAACCTTTTAAGCAATTTGTAAATAAAGATTGG-ATTTTTGA
1 TTAAAAGATGAAA-CTTTTAAGTAATTTGTAAATAAAGA-TGGAATTTTTAA
* * * *
27626 TTAAAAGATGCAACTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAA
1 TTAAAAGATGAAACTTTTAAGTAATTTGTAAATAAAGATGGAA-TTTTTAA
* * * *
27677 GTAAAAGATTAAACCTTTAAGTAATTTGTAAATAAAGATTGAATTTTTAA
1 TTAAAAGATGAAACTTTTAAGTAATTTGTAAATAAAGATGGAATTTTTAA
* * * * ** *
27727 TCAAAAGATTAAATCTTTTAAGTAGTTTGTAAATAGAA-ATGAAAGCTTTGA
1 TTAAAAGATGAAA-CTTTTAAGTAATTTGTAAATA-AAGATGGAATTTTTAA
* * * *
27778 GTAAAAGTTTG-AACTTTTAAGTAATTTGTAAATAAACATTGAATTTTTAA
1 TTAAAAG-ATGAAACTTTTAAGTAATTTGTAAATAAAGATGGAATTTTTAA
* * * * * * ** *
27828 TCAAAAGATTAAATTTTTTAAGTAGTTTGTAAATAAAAATGAAACCTTTGA
1 TTAAAAGATGAAA-CTTTTAAGTAATTTGTAAATAAAGATGGAATTTTTAA
* * * * * * *
27879 GTGAAAGATCAAGCTTTTAAGTAATTTTGTAAATAAAGGTTGAATTTCTAA
1 TTAAAAGATGAAACTTTTAAGTAA-TTTGTAAATAAAGATGGAATTTTTAA
* * **
27930 TTAAAAAGATTGAATCTTTTAAGTAATATGTAAATAAA-A-GTGAAGCCTTTAA
1 TT-AAAAGA-TGAAACTTTTAAGTAATTTGTAAATAAAGATG-GAA-TTTTTAA
* * * * * *
27982 GTAAAAGATCAAGCTTTTAGGTAATTTTTAAATAAAGATTGG-ATTTTTGA
1 TTAAAAGATGAAACTTTTAAGTAATTTGTAAATAAAGA-TGGAATTTTTAA
* * * *
28032 TTAAAAGATGAAACTTTTAAGTAATTTATGAATAAATATTGAATTTTTAA
1 TTAAAAGATGAAACTTTTAAGTAATTTGTAAATAAAGATGGAATTTTTAA
* *
28082 GTTAAAAAAATG-AAGTCTTTAAGTAATTTGTAAATAAAGATTGG-ATTTTTAA
1 -TT-AAAAGATGAAACT-TTTAAGTAATTTGTAAATAAAGA-TGGAATTTTTAA
* * *
28134 TGAAAAGATTAAACCTTTTAAGCAATTTGTAAATAA
1 TTAAAAGATGAAA-CTTTTAAGTAATTTGTAAATAA
28170 GAATGAAATC
Statistics
Matches: 540, Mismatches: 124, Indels: 59
0.75 0.17 0.08
Matches are distributed among these distances:
49 44 0.08
50 206 0.38
51 210 0.39
52 63 0.12
53 17 0.03
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.38
Consensus pattern (50 bp):
TTAAAAGATGAAACTTTTAAGTAATTTGTAAATAAAGATGGAATTTTTAA
Found at i:27611 original size:101 final size:101
Alignment explanation
Indices: 27428--28221 Score: 459
Period size: 101 Copynumber: 7.9 Consensus size: 101
27418 TCTTTATGTT
* * * * ** ** * * *
27428 AAAAGATGAAACTTTCAAGTAATTTGTAAATAAA-AAGGAGGTTTTTGATTAAAAGATGAAA-CT
1 AAAAGATGCAACTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAAATAAAAGATTAAACCT
27491 TTAAGTAATTTGTAAATAAA-AATGAGATTTTTGAGTG
66 TTAAGTAATTTGTAAATAAAGAATG-GATTTTTGA-TG
* * *
27528 AAAA-TTG-AAGCTTTTAAGTAATTTATGAATAAAGATTGAA-TTTTTAAATAAGAGGTTAAACC
1 AAAAGATGCAA-CTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAAATAAAAGATTAAACC
* * *
27590 TTTTAAGCAATTTGTAAATAAAGATTGGATTTTTGATT
65 -TTTAAGTAATTTGTAAATAAAGAATGGATTTTTGATG
*
27628 AAAAGATGCAACTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAAGTAAAAGATTAAACCT
1 AAAAGATGCAACTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAAATAAAAGATTAAACCT
* * * *
27693 TTAAGTAATTTGTAAATAAAGATTGAATTTTTAATC
66 TTAAGTAATTTGTAAATAAAGAATGGATTTTTGATG
** * * * *** * * * *
27729 AAAAGATTAAATCTTTTAAGTAGTTTGTAAATAGAA-A-TGAAAGCTTTGAGTAAAAGTTTGAAC
1 AAAAGATGCAA-CTTTTAAGTAATTTATGAATA-AAGATTGAATTTTTTAAATAAAAGATTAAAC
* * * * * *
27792 TTTTAAGTAATTTGTAAATAAACATTGAATTTTTAATC
64 CTTTAAGTAATTTGTAAATAAAGAATGGATTTTTGATG
** * * * * * *** * * * * * *
27830 AAAAGATTAAATTTTTTAAGTAGTTTGTAAATAAA-AATGAAACCTTTGAGTGAAAGATCAAGCT
1 AAAAGATGCAA-CTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAAATAAAAGATTAAACC
** * * * *
27894 TTTAAGTAATTTTGTAAATAAAGGTTGAATTTCTAATTA
65 TTTAAGTAA-TTTGTAAATAAAGAATGGATTTTTGA-TG
* * * * *** * * *
27933 AAAAGATTG-AATCTTTTAAGTAATATGTAAATAAA-AGTGAAGCCTTTAAGTAAAAGATCAAGC
1 AAAAGA-TGCAA-CTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAAATAAAAGATTAAAC
* * * * *
27996 TTTTAGGTAATTTTTAAATAAAGATTGGATTTTTGATT
64 CTTTAAGTAATTTGTAAATAAAGAATGGATTTTTGATG
* * * * * **
28034 AAAAGATGAAACTTTTAAGTAATTTATGAATAAATATTGAA-TTTTTAAGTTAAAAAAATGAAGT
1 AAAAGATGCAACTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAA-AT-AAAAGATTAAAC
* *
28098 CTTTAAGTAATTTGTAAATAAAGATTGGATTTTTAATG
64 CTTTAAGTAATTTGTAAATAAAGAATGGATTTTTGATG
** * * * * * * * *
28136 AAAAGATTAAACCTTTTAAGCAATTTGTAAAT-AAGAATGAAATCTTTAAAGCTAAAATATTGAA
1 AAAAGATGCAA-CTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAAA--TAAAAGATTAAA
*
28200 -C-TT-ATTAATTTGTAAATAAAGA
63 CCTTTAAGTAATTTGTAAATAAAGA
28222 TGAAATTTTT
Statistics
Matches: 582, Mismatches: 90, Indels: 44
0.81 0.13 0.06
Matches are distributed among these distances:
98 2 0.00
99 37 0.06
100 61 0.10
101 238 0.41
102 147 0.25
103 95 0.16
104 2 0.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (101 bp):
AAAAGATGCAACTTTTAAGTAATTTATGAATAAAGATTGAATTTTTTAAATAAAAGATTAAACCT
TTAAGTAATTTGTAAATAAAGAATGGATTTTTGATG
Found at i:27726 original size:152 final size:148
Alignment explanation
Indices: 27428--28169 Score: 658
Period size: 152 Copynumber: 4.9 Consensus size: 148
27418 TCTTTATGTT
* * ** *
27428 AAAAGATGAAACTTTCAAGTAATTTGTAAATAAAAAGGAGGTTTTTGATTAAAAGATGAAAC-TT
1 AAAAGATTAAACTTTTAAGTAATTTGTAAATAAAATTGA-ATTTTTGATTAAAAGATG-AACTTT
* * * * * *
27492 TAAGTAATTTGTAAATAAAAATGAGATTTTTGAGTGAAA-ATTGAAGCTTTTAAGTAATTTATGA
64 TAAGTAATTTGTAAATAAAATTGA-ATTTTTAAGTAAAAGATT-AAACTTTTAAGTAATTTGTAA
*
27556 ATAAAGATTGAATTTTTAAAT-
127 ATAAAGATTGAATTTTTGAATC
* * * *
27577 AAGAGGTTAAACCTTTTAAGCAATTTGTAAATAAAGATTGGATTTTTGATTAAAAGATGCAACTT
1 AAAAGATTAAA-CTTTTAAGTAATTTGTAAATAAA-ATTGAATTTTTGATTAAAAGATG-AACTT
* * *
27642 TTAAGTAATTTATGAATAAAGATTGAATTTTTTAAGTAAAAGATTAAACCTTTAAGTAATTTGTA
63 TTAAGTAATTTGTAAATAAA-ATTGAA-TTTTTAAGTAAAAGATTAAACTTTTAAGTAATTTGTA
27707 AATAAAGATTGAATTTTT-AATC
126 AATAAAGATTGAATTTTTGAATC
* ** * *
27729 AAAAGATTAAATCTTTTAAGTAGTTTGTAAATAGAAA-TGAAAGCTTTGAGTAAAAGTTTGAACT
1 AAAAGATTAAA-CTTTTAAGTAATTTGTAAATA-AAATTG-AATTTTTGATTAAAAG-ATGAACT
* *
27793 TTTAAGTAATTTGTAAATAAACATTGAATTTTTAA-TCAAAAGATTAAATTTTTTAAGTAGTTTG
62 TTTAAGTAATTTGTAAATAAA-ATTGAATTTTTAAGT-AAAAGATTAAA-CTTTTAAGTAATTTG
* ** *
27857 TAAATAAA-AATGAAACCTTTGAGT-
124 TAAATAAAGATTG-AATTTTTGAATC
* * * * * *
27881 GAAAGATCAAGCTTTTAAGTAATTTTGTAAATAAAGGTTGAATTTCTAATTAAAAAGATTGAATC
1 AAAAGATTAAACTTTTAAGTAA-TTTGTAAATAAA-ATTGAATTTTTGATT-AAAAGA-TGAA-C
* * ** * * * *
27946 TTTTAAGTAATATGTAAATAAAAGTGAAGCCTTTAAGTAAAAGATCAAGCTTTTAGGTAATTTTT
61 TTTTAAGTAATTTGTAAATAAAATTGAA-TTTTTAAGTAAAAGATTAAACTTTTAAGTAATTTGT
* *
28011 AAATAAAGATTGGATTTTTG-ATT
125 AAATAAAGATTGAATTTTTGAATC
* * * * * *
28034 AAAAGATGAAACTTTTAAGTAATTTATGAATAAATATTGAATTTTTAAGTTAAAAAAATGAAGTC
1 AAAAGATTAAACTTTTAAGTAATTTGTAAATAAA-ATTGAATTTTTGA-TT-AAAAGATGAACT-
* *
28099 TTTAAGTAATTTGTAAATAAAGATTGGATTTTTAA-TGAAAAGATTAAACCTTTTAAGCAATTTG
62 TTTAAGTAATTTGTAAATAAA-ATTGAATTTTTAAGT-AAAAGATTAAA-CTTTTAAGTAATTTG
28163 TAAATAA
124 TAAATAA
28170 GAATGAAATC
Statistics
Matches: 479, Mismatches: 85, Indels: 54
0.78 0.14 0.09
Matches are distributed among these distances:
149 8 0.02
150 42 0.09
151 62 0.13
152 228 0.48
153 99 0.21
154 39 0.08
155 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (148 bp):
AAAAGATTAAACTTTTAAGTAATTTGTAAATAAAATTGAATTTTTGATTAAAAGATGAACTTTTA
AGTAATTTGTAAATAAAATTGAATTTTTAAGTAAAAGATTAAACTTTTAAGTAATTTGTAAATAA
AGATTGAATTTTTGAATC
Found at i:28773 original size:19 final size:19
Alignment explanation
Indices: 28724--28765 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
28714 ACTTTGCAAA
28724 ATGACCAAAATGCCACTAG
1 ATGACCAAAATGCCACTAG
28743 ATGACCAAAATGCCACTAG
1 ATGACCAAAATGCCACTAG
28762 ATGA
1 ATGA
28766 GTAAAATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.17
Consensus pattern (19 bp):
ATGACCAAAATGCCACTAG
Found at i:28774 original size:28 final size:28
Alignment explanation
Indices: 28743--28824 Score: 119
Period size: 29 Copynumber: 2.9 Consensus size: 28
28733 ATGCCACTAG
28743 ATGACCAAAATGCCACTAGATGAGTAAA
1 ATGACCAAAATGCCACTAGATGAGTAAA
* *
28771 ATGACCAAAATGCCACTAGATGTGCAAAA
1 ATGACCAAAATGCCACTAGATGAG-TAAA
* *
28800 ATGACCAAAATGCCCCTGGATGAGT
1 ATGACCAAAATGCCACTAGATGAGT
28825 GACCCTAGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 23 0.49
29 24 0.51
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (28 bp):
ATGACCAAAATGCCACTAGATGAGTAAA
Found at i:29113 original size:35 final size:35
Alignment explanation
Indices: 29074--29344 Score: 382
Period size: 35 Copynumber: 7.7 Consensus size: 35
29064 TGAGTTCATA
* * *
29074 TTGAAAATGCTACATCGAGTCATCTGACTTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
*
29109 TTGAAGATGCTACACCGAGTCATCTGAATTCG-CT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
* * *
29143 TGTGAAGATGTTGCACCGAGTCATCTAAATTTGTCT
1 T-TGAAGATGCTACACCGAGTCATCTGAATTTGTCT
*
29179 TTGAAGATGCTACACCGAATCATCTGAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
* *
29214 TTGAAGATGCTGCACCGAATCATCTGAATTTGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
* *
29249 TTGAAGATGCTGCACCGAGTCATCTGAATTCGTCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
* *
29284 TTGAAGATGCTACACTGAGTCATCTGAATTTATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
* *
29319 ATGAAGACGCTACACCGAGTCATCTG
1 TTGAAGATGCTACACCGAGTCATCTG
29345 GATTCTTGAG
Statistics
Matches: 212, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
34 3 0.01
35 206 0.97
36 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT
Found at i:46061 original size:28 final size:29
Alignment explanation
Indices: 45992--46178 Score: 281
Period size: 29 Copynumber: 6.5 Consensus size: 29
45982 GAAGTGACTG
* *
45992 AAATACCCCTAGATGTGCAAAAATGACCA
1 AAATGCCCCTGGATGTGCAAAAATGACCA
46021 AAATGCCCC-GGATGTGC-AAAATGACCA
1 AAATGCCCCTGGATGTGCAAAAATGACCA
46048 AAATGCCCCTGGATGTGCAAAAATGACCA
1 AAATGCCCCTGGATGTGCAAAAATGACCA
* * *
46077 AAATGCCCCCGGATGAG-TAAAATGACCA
1 AAATGCCCCTGGATGTGCAAAAATGACCA
*
46105 AAATGCCCTTGGATGTGCAAAAAATGACCA
1 AAATGCCCCTGGATGTGC-AAAAATGACCA
*
46135 AAATGCCACTGGATGTGCAAAAATGACCA
1 AAATGCCCCTGGATGTGCAAAAATGACCA
46164 AAATGCCCCTGGATG
1 AAATGCCCCTGGATG
46179 AGTGACCCTA
Statistics
Matches: 142, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
27 19 0.13
28 39 0.27
29 58 0.41
30 26 0.18
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (29 bp):
AAATGCCCCTGGATGTGCAAAAATGACCA
Found at i:52308 original size:2 final size:2
Alignment explanation
Indices: 52303--52332 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52293 TTTTATTTTC
52303 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
52333 TGAGTGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52616 original size:18 final size:18
Alignment explanation
Indices: 52593--52629 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52583 AAAGGGTAGT
52593 TAAAAAAAAATGTTTTCA
1 TAAAAAAAAATGTTTTCA
* *
52611 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAATGTTTTCA
52629 T
1 T
52630 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (18 bp):
TAAAAAAAAATGTTTTCA
Found at i:57523 original size:50 final size:51
Alignment explanation
Indices: 57429--57589 Score: 130
Period size: 51 Copynumber: 3.2 Consensus size: 51
57419 AATATTTAGT
* ** * *
57429 AAAGATTAAAACTTTGGTAAGTTAATGATAAACATTCAATCTTT-AGTTCA
1 AAAGATTAAAATTTTGGTAAGTTAACCATAAACATTCAAACTTTAAGTTAA
**
57479 AAAGATTAAAATTTTGGTAAGTTAACCATAAAGGTGT-AAACTTTAAGTTAA
1 AAAGATTAAAATTTTGGTAAGTTAACCATAAACAT-TCAAACTTTAAGTTAA
* * * * **** * *
57530 AAAGATTGAATTTTTGATAAATTTTTAATAAA-AATAAAATCTTTAAGTTAA
1 AAAGATTAAAATTTTGGTAAGTTAACCATAAACATTCAAA-CTTTAAGTTAA
57581 AAAGATTAA
1 AAAGATTAA
57590 TTTTTGATAA
Statistics
Matches: 89, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
49 1 0.01
50 39 0.44
51 49 0.55
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.36
Consensus pattern (51 bp):
AAAGATTAAAATTTTGGTAAGTTAACCATAAACATTCAAACTTTAAGTTAA
Found at i:57561 original size:51 final size:51
Alignment explanation
Indices: 57506--57667 Score: 215
Period size: 50 Copynumber: 3.2 Consensus size: 51
57496 TAAGTTAACC
* *
57506 ATAAAGGTGTAAA-CTTTAAGTTAAAAAGATTGAATTTTTGATAAATTTTTA
1 ATAAAGATG-AAATCTTTAAGTTAAAAAGATTGAATTTTTGATAAATTTGTA
* * *
57557 ATAAAAATAAAATCTTTAAGTTAAAAAGATT-AATTTTTGATAAATTTGGA
1 ATAAAGATGAAATCTTTAAGTTAAAAAGATTGAATTTTTGATAAATTTGTA
*
57607 ATAAAGATGAAATCTTTAAATTAAAAAGATTGAA-TTTTGATAAACTTTGTA
1 ATAAAGATGAAATCTTTAAGTTAAAAAGATTGAATTTTTGATAAA-TTTGTA
57658 ATGAAA-ATGA
1 AT-AAAGATGA
57668 GAACCTTGGT
Statistics
Matches: 98, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
50 58 0.59
51 37 0.38
52 3 0.03
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (51 bp):
ATAAAGATGAAATCTTTAAGTTAAAAAGATTGAATTTTTGATAAATTTGTA
Found at i:57574 original size:101 final size:101
Alignment explanation
Indices: 57466--57665 Score: 244
Period size: 101 Copynumber: 2.0 Consensus size: 101
57456 ATAAACATTC
* * * * * *
57466 AATCTTT-AGTTCAAAAGATTAAAATTTTGGTAAGTTAACCATAAAGGTGTAAA-CTTTAAGTTA
1 AATCTTTAAGTTAAAAAGATT-AAATTTTGATAAATTAACAATAAAGATG-AAATCTTTAAATTA
*
57529 AAAAGATTGAATTTTTGATAAA-TTTTTAATAAAAATAA
64 AAAAGATTGAA-TTTTGATAAACTTTGTAATAAAAATAA
* ***
57567 AATCTTTAAGTTAAAAAGATTAATTTTTGATAAATTTGGAATAAAGATGAAATCTTTAAATTAAA
1 AATCTTTAAGTTAAAAAGATTAAATTTTGATAAATTAACAATAAAGATGAAATCTTTAAATTAAA
*
57632 AAGATTGAATTTTGATAAACTTTGTAATGAAAAT
66 AAGATTGAATTTTGATAAACTTTGTAATAAAAAT
57666 GAGAACCTTG
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
100 13 0.15
101 59 0.70
102 12 0.14
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (101 bp):
AATCTTTAAGTTAAAAAGATTAAATTTTGATAAATTAACAATAAAGATGAAATCTTTAAATTAAA
AAGATTGAATTTTGATAAACTTTGTAATAAAAATAA
Found at i:57684 original size:50 final size:51
Alignment explanation
Indices: 57519--57733 Score: 122
Period size: 51 Copynumber: 4.2 Consensus size: 51
57509 AAGGTGTAAA
* * ** * * *
57519 CTTTAAGTT-AAAAAGATTGAATTTTTGATAAA-TTTTTAATAAAAATAAAAT
1 CTTT-AGTTCAAAAGGATTGAA-TTTTGATAAACCTTGAAATAAAAAGAGAAC
* * * * *
57570 CTTTAAGTT-AAAAAGATT-AATTTTTGATAAA-TTTGGAATAAAGATGA-AAT
1 CTTT-AGTTCAAAAGGATTGAA-TTTTGATAAACCTTGAAATAAA-AAGAGAAC
* * * * *
57620 CTTTAAATT-AAAAAGATTGAATTTTGATAAACTTTGTAATGAAAATGAGAAC
1 CTTT-AGTTCAAAAGGATTGAATTTTGATAAACCTTGAAAT-AAAAAGAGAAC
* * * *
57672 C-TTGGTTCAAAAGGTTTGACTTTTGATAAACCTTGAAATAAAAAGATAAC
1 CTTTAGTTCAAAAGGATTGAATTTTGATAAACCTTGAAATAAAAAGAGAAC
57722 CTTTAGTTCAAA
1 CTTTAGTTCAAA
57734 GAGACGAGGT
Statistics
Matches: 140, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
50 64 0.46
51 70 0.50
52 6 0.04
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.37
Consensus pattern (51 bp):
CTTTAGTTCAAAAGGATTGAATTTTGATAAACCTTGAAATAAAAAGAGAAC
Found at i:57731 original size:51 final size:51
Alignment explanation
Indices: 57636--57733 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
57626 ATTAAAAAGA
* * * *
57636 TTGAATTTTGATAAACTTTGTAATGAAAATGAGAACCTTGGTTCAAAAGGT
1 TTGAATTTTGATAAACCTTGAAATGAAAAAGAGAACCTTAGTTCAAAAGGT
* *
57687 TTGACTTTTGATAAACCTTGAAAT-AAAAAGATAACCTTTAGTTCAAA
1 TTGAATTTTGATAAACCTTGAAATGAAAAAGAGAACC-TTAGTTCAAA
57734 GAGACGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
50 10 0.25
51 30 0.75
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (51 bp):
TTGAATTTTGATAAACCTTGAAATGAAAAAGAGAACCTTAGTTCAAAAGGT
Found at i:58258 original size:40 final size:40
Alignment explanation
Indices: 58202--58323 Score: 181
Period size: 40 Copynumber: 3.0 Consensus size: 40
58192 TGCTTCACTT
* * *
58202 TTCCCAAAATGCCCTTCCCAGTCGGAAGGAGTTATTTTTA
1 TTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTTTA
* * * *
58242 TTCCCAAATTGTCCTTCCCGGCCGGAAGGTGTTGTTCTTA
1 TTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTTTA
58282 TTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTTTA
1 TTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTTTA
58322 TT
1 TT
58324 ATTTTATTCC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (40 bp):
TTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTTTA
Found at i:58394 original size:47 final size:48
Alignment explanation
Indices: 58273--58407 Score: 209
Period size: 47 Copynumber: 2.8 Consensus size: 48
58263 CCGGAAGGTG
* * *
58273 TTGTTCTTATTCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTTTA
1 TTGTT-TTATTCCCAAAATGCCCTTCCCAATCGGAAGGTGTTGTTTTCA
* *
58322 TTATTTTATTCCCAAAATGCCCTTCCCAATAGGAAGGTGTTG-TTTCA
1 TTGTTTTATTCCCAAAATGCCCTTCCCAATCGGAAGGTGTTGTTTTCA
58369 TTGTTTTATTCCCAAAATGCCCTTCCCAATCGGAAGGTG
1 TTGTTTTATTCCCAAAATGCCCTTCCCAATCGGAAGGTG
58408 CCAGTTTTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
47 41 0.52
48 34 0.43
49 4 0.05
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (48 bp):
TTGTTTTATTCCCAAAATGCCCTTCCCAATCGGAAGGTGTTGTTTTCA
Found at i:61302 original size:13 final size:13
Alignment explanation
Indices: 61284--61333 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
61274 CAAGAGACAT
*
61284 TTTTCAAAAATTG
1 TTTTCAAAAATAG
61297 TTTTCAAGAAA-AGG
1 TTTTCAA-AAATA-G
61311 TTTTCAAAAATGAG
1 TTTTCAAAAAT-AG
61325 TTTTCAAAA
1 TTTTCAAAA
61334 GAGTTTTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.31
14 21 0.66
15 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAATAG
Found at i:61337 original size:12 final size:13
Alignment explanation
Indices: 61284--61340 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
61274 CAAGAGACAT
**
61284 TTTTCAAAAATTG
1 TTTTCAAAAAGAG
61297 TTTTCAAGAAA-AGG
1 TTTTCAA-AAAGA-G
61311 TTTTCAAAAATGAG
1 TTTTCAAAAA-GAG
61325 TTTTC-AAAAGAG
1 TTTTCAAAAAGAG
61337 TTTT
1 TTTT
61341 GAGTTTTCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
12 7 0.18
13 14 0.36
14 17 0.44
15 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAAGAG
Found at i:61984 original size:15 final size:16
Alignment explanation
Indices: 61964--62007 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
61954 GAAGCAATAA
*
61964 AAAAAGGAAAGAAA-G
1 AAAAAGGAAAGAAATC
61979 AAAAA-GAAAGAAATC
1 AAAAAGGAAAGAAATC
*
61994 AAAAAGAAAAGAAA
1 AAAAAGGAAAGAAA
62008 AAGATAAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.32
15 10 0.40
16 7 0.28
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAGGAAAGAAATC
Found at i:63186 original size:69 final size:69
Alignment explanation
Indices: 63097--63312 Score: 344
Period size: 69 Copynumber: 3.1 Consensus size: 69
63087 AATGCTTTGA
* * *
63097 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAGGCAGT-
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCA-TC
63161 AGGGG
65 AGGGG
*
63166 CTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCATCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCATCA
63231 GGGG
66 GGGG
* * *
63235 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTGCATCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCA-TC
63300 AGGGG
65 AGGGG
63305 CTTTTCCA
1 CTTTTCCA
63313 TAACCCAAGT
Statistics
Matches: 137, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
68 1 0.01
69 121 0.88
70 15 0.11
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCATCA
GGGG
Found at i:63485 original size:47 final size:47
Alignment explanation
Indices: 63434--63534 Score: 150
Period size: 47 Copynumber: 2.1 Consensus size: 47
63424 TCAGTTAATT
* * *
63434 TTTTCTCGCTTCTATGCGAATCTACAAG-TTGGTGACCACAGTTGGTC
1 TTTTCTCGCTTCCATGCGAATCTAC-AGTTTAGTAACCACAGTTGGTC
*
63481 TTTTCTCGCTTCCATGCGAGTCTACAGTTTAGTAACCACAGTTGGTC
1 TTTTCTCGCTTCCATGCGAATCTACAGTTTAGTAACCACAGTTGGTC
63528 TTTTCTC
1 TTTTCTC
63535 ACTTTGACGT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 2 0.04
47 47 0.96
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.39
Consensus pattern (47 bp):
TTTTCTCGCTTCCATGCGAATCTACAGTTTAGTAACCACAGTTGGTC
Found at i:67038 original size:50 final size:51
Alignment explanation
Indices: 66923--67043 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 51
66913 TGACCTTTAG
* * * **
66923 TTAAAATTTTGGTGAGTCAATAATAAAAATGTAATCTTTAGTTGGGAAAGA
1 TTAAAATTTTGGTAAGTTAATAATAAAAATGTAATCTATAGTTGCAAAAGA
* *
66974 TTAAAACTTTGGTAAGTTAATAATAAAGAT-TCAATCTATAGTT-CAAAAGA
1 TTAAAATTTTGGTAAGTTAATAATAAAAATGT-AATCTATAGTTGCAAAAGA
67024 TTAAAATTTTGGTAAGTTAA
1 TTAAAATTTTGGTAAGTTAA
67044 CCATAAAGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 25 0.41
51 36 0.59
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (51 bp):
TTAAAATTTTGGTAAGTTAATAATAAAAATGTAATCTATAGTTGCAAAAGA
Found at i:67150 original size:50 final size:50
Alignment explanation
Indices: 67055--67254 Score: 271
Period size: 50 Copynumber: 4.0 Consensus size: 50
67045 CATAAAGGTG
*
67055 AAAA-CTTTAAGTTAAAAAGATTGAATTTTTGATAAATTTGTAATAAAAAT
1 AAAATCTTTAAGTTAAAAAGATT-AATTTTTGATAAATTTGGAATAAAAAT
* *
67105 AAAATCTTTAAGTTAAAAATATTAGTTTTTGATAAATTTGGAATAAAAA-
1 AAAATCTTTAAGTTAAAAAGATTAATTTTTGATAAATTTGGAATAAAAAT
* *
67154 AAAATCTTTAAGTTAAAAAGATTGAA-TTTTGATAAATTGGGAATAAAGAT
1 AAAATCTTTAAGTTAAAAAGATT-AATTTTTGATAAATTTGGAATAAAAAT
* * *
67204 GAAATCTTTAAATTAAAAAGATTAACTTTTGATAAAATTTGGAATTAAAAA
1 AAAATCTTTAAGTTAAAAAGATTAATTTTTGAT-AAATTTGGAA-TAAAAA
67255 GAGAACCTTG
Statistics
Matches: 133, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
49 45 0.34
50 57 0.43
51 26 0.20
52 5 0.04
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (50 bp):
AAAATCTTTAAGTTAAAAAGATTAATTTTTGATAAATTTGGAATAAAAAT
Found at i:67211 original size:99 final size:100
Alignment explanation
Indices: 67055--67254 Score: 296
Period size: 99 Copynumber: 2.0 Consensus size: 100
67045 CATAAAGGTG
* * *
67055 AAAACTTTAAGTTAAAAAGATTGAATTTTTGATAAATTTGTAATAAAAATAAAATCTTTAAGTTA
1 AAAACTTTAAGTTAAAAAGATTGAATTTTTGATAAATTGGGAATAAAAATAAAATCTTTAAATTA
* **
67120 AAAATATTAGTTTTTGAT-AAATTTGGAATAAAAA
66 AAAAGATTAACTTTTGATAAAATTTGGAATAAAAA
* *
67154 AAAATCTTTAAGTTAAAAAGATTGAA-TTTTGATAAATTGGGAATAAAGATGAAATCTTTAAATT
1 AAAA-CTTTAAGTTAAAAAGATTGAATTTTTGATAAATTGGGAATAAAAATAAAATCTTTAAATT
*
67218 AAAAAGATTAACTTTTGATAAAATTTGGAATTAAAA
65 AAAAAGATTAACTTTTGATAAAATTTGGAATAAAAA
67254 A
1 A
67255 GAGAACCTTG
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
99 53 0.59
100 37 0.41
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.36
Consensus pattern (100 bp):
AAAACTTTAAGTTAAAAAGATTGAATTTTTGATAAATTGGGAATAAAAATAAAATCTTTAAATTA
AAAAGATTAACTTTTGATAAAATTTGGAATAAAAA
Found at i:67273 original size:50 final size:51
Alignment explanation
Indices: 67131--67323 Score: 134
Period size: 51 Copynumber: 3.8 Consensus size: 51
67121 AAATATTAGT
* * * *
67131 TTTTGAT-AAATTTGGAATAAAAA-AAAATCTTTAAGTT-AAAAAGATTGAA-
1 TTTTGATAAAACTTGGAATAAAAAGAGAACCTTT-AGTTCAAAAGGATT-AAC
* * * *
67180 TTTTGAT-AAA-TTGGGAATAAAGATGA-AATCTTTAAATT-AAAAAGATTAAC
1 TTTTGATAAAACTT-GGAATAAA-AAGAGAACCTTT-AGTTCAAAAGGATTAAC
* * * *
67230 TTTTGATAAAATTTGGAATTAAAAAGAGAACC-TTGGTTCAAAAGGTTTGAC
1 TTTTGATAAAACTTGGAA-TAAAAAGAGAACCTTTAGTTCAAAAGGATTAAC
* * *
67281 TTTTGATAAACCTTGGAATGAAAAGATAACCTTTAGTTCAAAA
1 TTTTGATAAAACTTGGAATAAAAAGAGAACCTTTAGTTCAAAA
67324 AGACGAGGTC
Statistics
Matches: 120, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
48 2 0.02
49 20 0.17
50 41 0.34
51 48 0.40
52 9 0.08
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (51 bp):
TTTTGATAAAACTTGGAATAAAAAGAGAACCTTTAGTTCAAAAGGATTAAC
Found at i:67911 original size:39 final size:40
Alignment explanation
Indices: 67792--67912 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 40
67782 GCTTCACTTC
* *
67792 TCCCAAAATGCCCTTTCCCAGTCGGAAGGTGTTATTTTTAT
1 TCCCAAATTGCCC-TTCCCAGTCGGAAGGTGTTGTTTTTAT
* * * *
67833 TCCTAAATTGCCCTTCCCGGCCGAAAGGTGTTGTTTTTAT
1 TCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTTTAT
*
67873 TCCCAAATTGCCC-TCCTAGTCGGAAGGTGTTGTTTTTAT
1 TCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTTTAT
67912 T
1 T
67913 ATTTTATTCC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
39 23 0.33
40 35 0.51
41 11 0.16
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (40 bp):
TCCCAAATTGCCCTTCCCAGTCGGAAGGTGTTGTTTTTAT
Found at i:67965 original size:47 final size:48
Alignment explanation
Indices: 67867--67996 Score: 192
Period size: 47 Copynumber: 2.8 Consensus size: 48
67857 AAGGTGTTGT
* * * *
67867 TTTTATTCCCAAATTGCCC-TCCTAGTCGGAAGGTGTTGTTTTTATTA
1 TTTTATTCCCAAAATGCCCTTCCCAATCGGAAGGTGTTGTTTTCATTA
* *
67914 TTTTATTCCCAAAATGCCCTTCCCAATAGGAAGGTGTTG-TTTCATTG
1 TTTTATTCCCAAAATGCCCTTCCCAATCGGAAGGTGTTGTTTTCATTA
67961 TTTTATTCCCAAAATGCCCTTCCCAATCGGAAGGTG
1 TTTTATTCCCAAAATGCCCTTCCCAATCGGAAGGTG
67997 CCAGTTTTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
47 59 0.79
48 16 0.21
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.38
Consensus pattern (48 bp):
TTTTATTCCCAAAATGCCCTTCCCAATCGGAAGGTGTTGTTTTCATTA
Found at i:69964 original size:30 final size:30
Alignment explanation
Indices: 69907--70006 Score: 125
Period size: 29 Copynumber: 3.4 Consensus size: 30
69897 TGTTTTCGTA
*
69907 TTTCCAATTTAAAGCCAAAT-TTGGCTTTG
1 TTTCCAAATTAAAGCCAAATATTGGCTTTG
*
69936 TTTCCAAATTAAAGCCAAATAGTGGCTTTG
1 TTTCCAAATTAAAGCCAAATATTGGCTTTG
* *
69966 TCT-CAATTTAAAGCCAAA-ATTGGCTTTTGG
1 TTTCCAAATTAAAGCCAAATATTGGC-TTT-G
69996 TTTCCAAATTA
1 TTTCCAAATTA
70007 TTCCCGACGG
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.08
29 36 0.60
30 13 0.22
31 6 0.10
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (30 bp):
TTTCCAAATTAAAGCCAAATATTGGCTTTG
Found at i:70225 original size:28 final size:28
Alignment explanation
Indices: 70171--70225 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
70161 AAGCCGACGG
*
70171 TATTAAGGCCAATTTGGCCTTAGTTTCA
1 TATTAAGGCCAAATTGGCCTTAGTTTCA
* *
70199 TATTAAAGGCTAAATTGGCTTTA-TTTC
1 TATT-AAGGCCAAATTGGCCTTAGTTTC
70226 TAGGTTGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (28 bp):
TATTAAGGCCAAATTGGCCTTAGTTTCA
Found at i:80366 original size:20 final size:20
Alignment explanation
Indices: 80337--80374 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
80327 TATTTTGGGA
80337 TTTTTATGGATGTTTATGTC
1 TTTTTATGGATGTTTATGTC
* *
80357 TTTTTTTGGATTTTTATG
1 TTTTTATGGATGTTTATG
80375 GAATATACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.18, T:0.66
Consensus pattern (20 bp):
TTTTTATGGATGTTTATGTC
Found at i:80370 original size:10 final size:10
Alignment explanation
Indices: 80334--80376 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
80324 TTATATTTTG
80334 GGATTTTTAT
1 GGATTTTTAT
*
80344 GGATGTTTAT
1 GGATTTTTAT
** *
80354 GTCTTTTTTT
1 GGATTTTTAT
80364 GGATTTTTAT
1 GGATTTTTAT
80374 GGA
1 GGA
80377 ATATACTTAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.58
Consensus pattern (10 bp):
GGATTTTTAT
Found at i:81648 original size:24 final size:24
Alignment explanation
Indices: 81616--81674 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
81606 TGACGATGAG
81616 CTACGGCCACGCCCAGTGGAGGTA
1 CTACGGCCACGCCCAGTGGAGGTA
81640 CTACGGCCACGCCCAGTGGAGGTA
1 CTACGGCCACGCCCAGTGGAGGTA
81664 CTACGGCCACG
1 CTACGGCCACG
81675 ACCCCTCTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.20, C:0.36, G:0.32, T:0.12
Consensus pattern (24 bp):
CTACGGCCACGCCCAGTGGAGGTA
Found at i:83924 original size:33 final size:33
Alignment explanation
Indices: 83863--83948 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
83853 TATTTACTGG
**
83863 TGCCGCCCTGCTAGGGCGGCGTGGCCATGGT-CA
1 TGCCGCCCTGCTAGGGCGGCGTAACCAT-GTCCA
83896 TGCCGCCCTAGC-AGGGCGGCGTAACCATGTCCA
1 TGCCGCCCT-GCTAGGGCGGCGTAACCATGTCCA
* * *
83929 TGGCGCCCTCCTTGGGCGGC
1 TGCCGCCCTGCTAGGGCGGC
83949 ATGACATTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
32 3 0.07
33 40 0.89
34 2 0.04
ACGTcount: A:0.10, C:0.36, G:0.36, T:0.17
Consensus pattern (33 bp):
TGCCGCCCTGCTAGGGCGGCGTAACCATGTCCA
Found at i:92916 original size:2 final size:2
Alignment explanation
Indices: 92909--92933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
92899 TTAGCAGTCC
92909 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
92934 TTTTAGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:105386 original size:15 final size:14
Alignment explanation
Indices: 105366--105400 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
105356 TTACTTTGTT
105366 TTGTTTCTAGTTTAA
1 TTGTTTCT-GTTTAA
*
105381 TTGTTTCTTTTTAA
1 TTGTTTCTGTTTAA
105395 TTGTTT
1 TTGTTT
105401 TCTTTGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (14 bp):
TTGTTTCTGTTTAA
Found at i:105402 original size:15 final size:14
Alignment explanation
Indices: 105366--105405 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
105356 TTACTTTGTT
*
105366 TTGTTTCTAGTTTAA
1 TTGTTTCT-TTTTAA
105381 TTGTTTCTTTTTAA
1 TTGTTTCTTTTTAA
105395 TTGTTTTCTTT
1 TTG-TTTCTTT
105406 GAACCTCTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.12, C:0.07, G:0.10, T:0.70
Consensus pattern (14 bp):
TTGTTTCTTTTTAA
Found at i:108748 original size:21 final size:21
Alignment explanation
Indices: 108715--108757 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
108705 CCGAGCTGCG
*
108715 CCGAGACACCTGCTCGGCCAC
1 CCGAGACACCTGCCCGGCCAC
* *
108736 CCGAGCCATCTGCCCGGCCAC
1 CCGAGACACCTGCCCGGCCAC
108757 C
1 C
108758 AGCGCTACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.51, G:0.23, T:0.09
Consensus pattern (21 bp):
CCGAGACACCTGCCCGGCCAC
Found at i:112373 original size:14 final size:15
Alignment explanation
Indices: 112354--112383 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
112344 TTGGATCTAG
112354 TTTAATTG-TTTCTT
1 TTTAATTGTTTTCTT
112368 TTTAATTGTTTTCTT
1 TTTAATTGTTTTCTT
112383 T
1 T
112384 CAACCTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (15 bp):
TTTAATTGTTTTCTT
Found at i:115873 original size:19 final size:19
Alignment explanation
Indices: 115848--115894 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
115838 CAAATTTTTC
115848 AGAGAGAGAGAGGCTTTGT
1 AGAGAGAGAGAGGCTTTGT
*
115867 TGAGAGAGAGAGGCTTTGT
1 AGAGAGAGAGAGGCTTTGT
115886 AGAGAGAGA
1 AGAGAGAGA
115895 CTTTTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.43, T:0.19
Consensus pattern (19 bp):
AGAGAGAGAGAGGCTTTGT
Found at i:115898 original size:15 final size:17
Alignment explanation
Indices: 115851--115898 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
115841 ATTTTTCAGA
*
115851 GAGAGAGAGGCTTTGTT
1 GAGAGAGAGACTTTGTT
115868 GAGAGAGAGAGGCTTTG-T
1 GAGAGAGAGA--CTTTGTT
115886 -AGAGAGAGACTTT
1 GAGAGAGAGACTTT
115899 TTTTCTTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
17 18 0.64
18 1 0.04
19 5 0.18
ACGTcount: A:0.29, C:0.06, G:0.40, T:0.25
Consensus pattern (17 bp):
GAGAGAGAGACTTTGTT
Found at i:117667 original size:27 final size:27
Alignment explanation
Indices: 117637--117695 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
117627 AATGCCCCTG
*
117637 AATGAAAAAAATGCCCTTGGACGTGCA
1 AATGAAAAAAATGCCCCTGGACGTGCA
**
117664 AATGACCAAAATGCCCCTGGACGTGCA
1 AATGAAAAAAATGCCCCTGGACGTGCA
117691 AATGA
1 AATGA
117696 CCCCAATGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (27 bp):
AATGAAAAAAATGCCCCTGGACGTGCA
Found at i:117704 original size:27 final size:27
Alignment explanation
Indices: 117644--117697 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
117634 CTGAATGAAA
*
117644 AAAATGCCCTTGGACGTGCAAATGACC
1 AAAATGCCCCTGGACGTGCAAATGACC
117671 AAAATGCCCCTGGACGTGCAAATGACC
1 AAAATGCCCCTGGACGTGCAAATGACC
117698 CCAATGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (27 bp):
AAAATGCCCCTGGACGTGCAAATGACC
Done.