Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2062
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: 49320
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:84 original size:2 final size:2
Alignment explanation
Indices: 77--107 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
67 GAATTTTTAG
*
77 TA TA TA TA TA TA GA 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 T
108 CTAAAATGTA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1549 original size:19 final size:19
Alignment explanation
Indices: 1525--1561 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1515 TAAGTAGCTG
1525 AGCCTTCAAAGAGATCTAT
1 AGCCTTCAAAGAGATCTAT
*
1544 AGCCTTCAAAGTGATCTA
1 AGCCTTCAAAGAGATCTA
1562 GGTGTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (19 bp):
AGCCTTCAAAGAGATCTAT
Found at i:5580 original size:19 final size:18
Alignment explanation
Indices: 5535--5592 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 18
5525 ACTACCAGTT
5535 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
5554 TCCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
5573 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
5592 T
1 T
5593 ATCGATACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.54
20 16 0.43
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:5594 original size:13 final size:13
Alignment explanation
Indices: 5576--5601 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5566 TACAATGATC
5576 ATGTATCGATACA
1 ATGTATCGATACA
5589 ATGTATCGATACA
1 ATGTATCGATACA
5602 TCTGGGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7128 original size:13 final size:13
Alignment explanation
Indices: 7110--7135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7100 CATTATTCAA
7110 TGTATCGATACAT
1 TGTATCGATACAT
7123 TGTATCGATACAT
1 TGTATCGATACAT
7136 CTAGGAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9304 original size:51 final size:48
Alignment explanation
Indices: 9229--9357 Score: 177
Period size: 51 Copynumber: 2.6 Consensus size: 48
9219 AAATTTCTAG
*
9229 ATTTTTCATCTCGGGGATACTCCAATCCCGGTTCCATTTCCAAAACATCA
1 ATTTTTCA--TCGGGGATACTCCAACCCCGGTTCCATTTCCAAAACATCA
** *
9279 ATTTTTCTTAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCA
1 ATTTTTC---ATCGGGGATACTCCAACCCCGGTTCCATTTCCAAAACATCA
9330 ATTTTTCATCGGGGATACTCCAACCCCG
1 ATTTTTCATCGGGGATACTCCAACCCCG
9358 TTATTTTCGT
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
48 21 0.29
50 7 0.10
51 43 0.60
53 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (48 bp):
ATTTTTCATCGGGGATACTCCAACCCCGGTTCCATTTCCAAAACATCA
Found at i:9455 original size:79 final size:77
Alignment explanation
Indices: 9292--9486 Score: 232
Period size: 79 Copynumber: 2.5 Consensus size: 77
9282 TTTCTTAATC
* * *
9292 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATCAATTTTTAATCGGGAATACTCCAACCCC
* * *
9357 GTTATTTTCGTA
66 ATCATTTCCGTA
* * * * *
9369 -GGAATACTCTAACCCTGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGAATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATCAATTT-T--TAATCGGGAATACTCCAAC
9433 CCCATCATTTCCG-A
63 CCCATCATTTCCGTA
* *
9447 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAAT
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATCAAT
9487 CGGGGATACT
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
76 35 0.36
77 1 0.01
78 1 0.01
79 59 0.61
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (77 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATCAATTTTTAATCGGGAATACTCCAACCCC
ATCATTTCCGTA
Found at i:9597 original size:200 final size:196
Alignment explanation
Indices: 9288--9686 Score: 502
Period size: 200 Copynumber: 2.0 Consensus size: 196
9278 AATTTTTCTT
* * *
9288 AATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAA
1 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTACATCGGGGATACTCCAA
** * * * *
9353 CCCCGTTATTTTCGTAGGAATACTCTAACCCTGGCTTTATTTCTAAAAT-ATTAATTTCTCATAA
66 CCCCGTTATTTTCCAAGGAATACTCTAACCCTGACCTTATTTCT-AAATCATCAATTTCTCACAA
*
9417 TCG-GGAATACTCCAACCCCATCATTTCCGAGGGGATACTCCAACCCCGATTTTA-TTTCTAAAA
130 TCGAGG-ATACTCCAACCCCATCATTTCCGAGGGGATACTCCAACCCCGATTTCATTTTC-AAAA
9480 TACC
193 TACC
* *
9484 AATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTATCACAATTGGGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTT-T-AC-ATCGGGGATACT
* * * * *
9549 CCAACCTCGTTA-TTTCCAAGGGGATACTTTAAACCC-GACCTTATTTCTAAATCATCGATTTTT
62 CCAACCCCGTTATTTTCCAA-GGAATACTCT-AACCCTGACCTTATTTCTAAATCATCAATTTCT
* * *
9612 CACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTCATTTTCA
125 CACAATCGAGGATACTCCAACCCCATCATTTCCGAGGGGATACTCCAACCCCGATTTCATTTTCA
9677 AAATACC
190 AAATACC
9684 AAT
1 AAT
9687 TTTTATAATT
Statistics
Matches: 174, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
196 31 0.18
197 12 0.07
198 1 0.01
199 10 0.06
200 109 0.63
201 11 0.06
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (196 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTACATCGGGGATACTCCAA
CCCCGTTATTTTCCAAGGAATACTCTAACCCTGACCTTATTTCTAAATCATCAATTTCTCACAAT
CGAGGATACTCCAACCCCATCATTTCCGAGGGGATACTCCAACCCCGATTTCATTTTCAAAATAC
C
Found at i:9633 original size:79 final size:80
Alignment explanation
Indices: 9509--9733 Score: 217
Period size: 79 Copynumber: 2.9 Consensus size: 80
9499 AACTCCGATT
* * *
9509 TTATTTCTAAAAACACCAATTTATCACAATTGGGGATACTCCAACCTCGTTATTTCCAAGGGGAT
1 TTATTTCTAAAAACACCAATTTATCACAATCGAGGATACTCCAACCCCGTTATTTCCAAGGGGAT
9574 ACTTTAAACCCGACC
66 ACTTTAAACCCGACC
* * * * * *
9589 TTATTTCT-AAATCATCGATTTTTCACAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGAT
1 TTATTTCTAAAAACACCAATTTATCACAATCGAGGATACTCCAACCCCGTTATTTCCAAGGGGAT
** * *
9653 ACTCCAACCCCGA-T
66 ACTTTAAACCCGACC
* * * * * * *
9667 TTCATTT-TCAAAATACCAATTT-TTATAATTTG-GGATACTCCAACCCTGTTATTTCCTAGGGG
1 TT-ATTTCTAAAAACACCAATTTATCACAA-TCGAGGATACTCCAACCCCGTTATTTCCAAGGGG
9729 ATACT
64 ATACT
9734 CCAACCCCGG
Statistics
Matches: 119, Mismatches: 23, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
78 39 0.33
79 72 0.61
80 8 0.07
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (80 bp):
TTATTTCTAAAAACACCAATTTATCACAATCGAGGATACTCCAACCCCGTTATTTCCAAGGGGAT
ACTTTAAACCCGACC
Found at i:9728 original size:78 final size:78
Alignment explanation
Indices: 9488--9765 Score: 283
Period size: 78 Copynumber: 3.5 Consensus size: 78
9478 AATACCAATC
* * * * *
9488 GGGGATACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTATCACAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTT-TCAAAATACCAATTT-TTACAATTCGGGATACTCCAA
9553 -CCTCGTTATTTCCAA
64 CCCT-GTTATTTCCAA
** * ** * * *
9568 GGGGATACTTTAAACCCGACCTTA-TTTCTAAATCATCGATTTTTCACAA-TCGAGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAAT-ACCAATTTTT-ACAATTCG-GGATACTCCA
* * *
9631 ACCCCGTTATTTTCGA
63 ACCCTGTTATTTCCAA
* * *
9647 GGGGATACTCCAACCCCGATTTCATTTTCAAAATACCAATTTTTATAATTTGGGATACTCCAACC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTACAATTCGGGATACTCCAACC
*
9712 CTGTTATTTCCTA
66 CTGTTATTTCCAA
* *
9725 GGGGATACTCCAACCCCGGTTTTATTTCCAAAATACCAATT
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATT
9766 CTCCACAATC
Statistics
Matches: 159, Mismatches: 33, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
78 71 0.45
79 60 0.38
80 28 0.18
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTACAATTCGGGATACTCCAACC
CTGTTATTTCCAA
Found at i:9776 original size:157 final size:159
Alignment explanation
Indices: 9488--9789 Score: 369
Period size: 157 Copynumber: 1.9 Consensus size: 159
9478 AATACCAATC
* *
9488 GGGGATACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTATCACAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTCATTTCTAAAAACACCAATTTATCACAATTGGGGATACTCCAA
** * * * * *
9553 CCTCGTTATTTCCAAGGGGATACTTTAAACCCGACCTTATTTCTAAATCATCGATTTTTCACAAT
66 CCTCGTTATTTCCAAGGGGATACTCCAAACCCGACCTTATTTCAAAATCACCAATTCTCCACAAT
9618 CGAGGATACTCCAACCCCGTTATTTTCGA
131 CGAGGATACTCCAACCCCGTTATTTTCGA
* * * * *
9647 GGGGATACTCCAACCCCGATTTCATTT-TCAAAATACCAATTT-TTATAATTTGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTCATTTCTAAAAACACCAATTTATCACAATTGGGGATACTCCAA
* * ***
9710 CC-CTGTTATTTCCTAGGGGATACTCCAACCCCGGTTTTATTTCCAAAAT-ACCAATTCTCCACA
66 CCTC-GTTATTTCCAAGGGGATACTCCAAACCCGACCTTATTT-CAAAATCACCAATTCTCCACA
* *
9773 ATCGGGGATATTCCAAC
129 ATCGAGGATACTCCAAC
9790 TCTGATTTTA
Statistics
Matches: 120, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
156 1 0.01
157 76 0.63
158 18 0.15
159 25 0.21
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (159 bp):
GGGGATACTCCAACCCCGATTTCATTTCTAAAAACACCAATTTATCACAATTGGGGATACTCCAA
CCTCGTTATTTCCAAGGGGATACTCCAAACCCGACCTTATTTCAAAATCACCAATTCTCCACAAT
CGAGGATACTCCAACCCCGTTATTTTCGA
Found at i:9788 original size:51 final size:51
Alignment explanation
Indices: 9725--9844 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
9715 TTATTTCCTA
*
9725 GGGGATACTCCAACCCCGGTTTTATTTCCAAAATACCAATTCTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTCTCCACAATC
* * * * * *
9776 GGGGATATTCCAACTCTGATTTTATTTCCAAAATACTAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTCTCCACAATC
*
9827 GGGGATACTCCAAGCCCG
1 GGGGATACTCCAACCCCG
9845 TTATTTCATC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTCTCCACAATC
Found at i:9861 original size:28 final size:28
Alignment explanation
Indices: 9824--9900 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
9814 ATTTTTCACA
* *
9824 ATCGGGGATACTCCAAGCCCGTTATTTC
1 ATCGGAGATACTCCAACCCCGTTATTTC
* *
9852 ATCGGAGATATTCTAACCCCGTTATTT-
1 ATCGGAGATACTCCAACCCCGTTATTTC
*
9879 -TCGAGGGGATACTCCAACCCCG
1 ATC--GGAGATACTCCAACCCCG
9901 GCTTTATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.05
28 38 0.95
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (28 bp):
ATCGGAGATACTCCAACCCCGTTATTTC
Found at i:9963 original size:79 final size:80
Alignment explanation
Indices: 9852--10023 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 80
9842 CCGTTATTTC
* * * * * *
9852 ATCGGAGATATTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG-GCTTTATTTCCAAAA
1 ATCGGGGATACTCCAACCCCATTATCTTCGAGGGGATACACCAACCCCGAGCTTTATTTCCAAAA
*
9916 TATTGA-TTTCTCATA
66 CATTGATTTTC-CATA
* * ** *
9931 ATTGGGGATACTCCAACCCCATTATCTTCGAGGGGATACACCAATCCCGATTTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCATTATCTTCGAGGGGATACACCAACCCCGAGCTTTATTTCCAAAA
9996 CATTGATTTTCCATA
66 CATTGATTTTCCATA
10011 ATCGGGGATACTC
1 ATCGGGGATACTC
10024 TAGCCCCGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 41 0.53
80 33 0.42
81 4 0.05
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCATTATCTTCGAGGGGATACACCAACCCCGAGCTTTATTTCCAAAA
CATTGATTTTCCATA
Found at i:18575 original size:19 final size:18
Alignment explanation
Indices: 18551--18612 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
18541 ATTCATCATG
18551 TATCGATACAATGTGCAT
1 TATCGATACAATGTGCAT
*
18569 ATATCGATTC-AT-TG---
1 -TATCGATACAATGTGCAT
*
18583 TATCGATACAATGTCCAT
1 TATCGATACAATGTGCAT
18601 GTATCGATACAA
1 -TATCGATACAA
18613 ACAATGGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
13 8 0.24
14 2 0.06
15 1 0.03
17 2 0.06
18 2 0.06
19 19 0.56
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (18 bp):
TATCGATACAATGTGCAT
Found at i:18664 original size:20 final size:19
Alignment explanation
Indices: 18639--18713 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
18629 TACTGCCAGT
18639 TTCATGTATCGATACAATTG
1 TTCATGTATCGATACAA-TG
18659 TTCATGTATCGATACAATG
1 TTCATGTATCGATACAATG
* * *
18678 ATCATGTATTGATACAAAG
1 TTCATGTATCGATACAATG
*
18697 TATAATGTATCGATACA
1 T-TCATGTATCGATACA
18714 TCTGGGTGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
19 18 0.38
20 30 0.62
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (19 bp):
TTCATGTATCGATACAATG
Found at i:19611 original size:3 final size:3
Alignment explanation
Indices: 19605--19659 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
19595 AAGAAAAAAT
19605 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19653 ATA ATA A
1 ATA ATA A
19660 ATAACACAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21312 original size:2 final size:2
Alignment explanation
Indices: 21305--21334 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21295 AAAAATCAAA
21305 CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
21335 GTGGGTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21767 original size:116 final size:116
Alignment explanation
Indices: 21542--21757 Score: 303
Period size: 116 Copynumber: 1.9 Consensus size: 116
21532 CTTAGTGATT
* *
21542 ATGATGCATTTATATTTTTAAAATTCAATATTTTGCAAAAAAAATTAAGGTAATATTTCATGTCA
1 ATGATGCATTCATATTTTTAAAATTCAATATTTTGCAAAAAAAATTAAGGCAATATTTCATGTCA
* * ** *
21607 GTATTCCTCCTAGACTTGACATGGAAAATCTTTCCCAAACTAAATCTAGAA
66 ATATCCCTCCTAGACTTGACATCAAAAATCATTCCCAAACTAAATCTAGAA
* *
21658 ATGATGCATTCATAGTTTTT-AAATTCAATATTTTGCAAAGAAAATTGAGGCAATATTTCATGTC
1 ATGATGCATTCATA-TTTTTAAAATTCAATATTTTGCAAAAAAAATTAAGGCAATATTTCATGTC
21722 AATATCCCTCC-AGTACTTGACA-CAAAACATCATTCC
65 AATATCCCTCCTAG-ACTTGACATCAAAA-ATCATTCC
21758 GAAGTTAAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
115 5 0.06
116 78 0.89
117 5 0.06
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (116 bp):
ATGATGCATTCATATTTTTAAAATTCAATATTTTGCAAAAAAAATTAAGGCAATATTTCATGTCA
ATATCCCTCCTAGACTTGACATCAAAAATCATTCCCAAACTAAATCTAGAA
Found at i:22931 original size:78 final size:78
Alignment explanation
Indices: 22820--23010 Score: 210
Period size: 79 Copynumber: 2.4 Consensus size: 78
22810 TGGACATATA
* * *
22820 TCGATATGAAAATACAACATGATTCT-GGAGACTT-GATTTT-CTATGAAACTCACTAAAATGAC
1 TCGATATGAAAATACAACATGCTTCTAAG-GACTTGGATTTTAC-ATGAAACTCACTAAAAGGAC
22882 CTTAA-AGCACATGTC
64 CTTAATA-CACATGTC
* * *
22897 TCGATACGAAAATATCAACATGCTTCTAAGGACTTGGATTTTACATGAAACTTACTAAAAGGACT
1 TCGATATGAAAATA-CAACATGCTTCTAAGGACTTGGATTTTACATGAAACTCACTAAAAGGACC
22962 TTAATACACATGTC
65 TTAATACACATGTC
** * * *
22976 TTAATATGAAAATACCAATATGCTCCTAAAGACTT
1 TCGATATGAAAATA-CAACATGCTTCTAAGGACTT
23011 TTTTTTTTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
77 13 0.14
78 16 0.17
79 65 0.68
80 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (78 bp):
TCGATATGAAAATACAACATGCTTCTAAGGACTTGGATTTTACATGAAACTCACTAAAAGGACCT
TAATACACATGTC
Found at i:24949 original size:45 final size:46
Alignment explanation
Indices: 24900--24990 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
24890 GATACTTCTT
* *
24900 TTTGAC-TTTAAAATTCTGATTATT-AGAAGTCAAAG-ATTCAATATA
1 TTTGACTTTTAAAATTCTGATCATTGA-AAGCCAAAGTATT-AATATA
*
24945 TTTGACTTTTAAAATTTTGATCATTGAAAGCCAAAGTATTAATATA
1 TTTGACTTTTAAAATTCTGATCATTGAAAGCCAAAGTATTAATATA
24991 CTAAGGTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
45 6 0.15
46 30 0.75
47 4 0.10
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.41
Consensus pattern (46 bp):
TTTGACTTTTAAAATTCTGATCATTGAAAGCCAAAGTATTAATATA
Found at i:28221 original size:16 final size:16
Alignment explanation
Indices: 28200--28234 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28190 TCTTTTATTA
28200 TGTTTT-TTTTTAAATT
1 TGTTTTATTTTT-AATT
28216 TGTTTTATTTTTAATT
1 TGTTTTATTTTTAATT
28232 TGT
1 TGT
28235 ATTTGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (16 bp):
TGTTTTATTTTTAATT
Found at i:34142 original size:20 final size:21
Alignment explanation
Indices: 34105--34143 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
34095 AATATTATTC
* *
34105 AATTTTTGAATTTGATTAATT
1 AATTTTTGAAATTAATTAATT
34126 AATTTTT-AAATTAATTAA
1 AATTTTTGAAATTAATTAA
34144 CTTTACCGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
AATTTTTGAAATTAATTAATT
Found at i:35067 original size:21 final size:21
Alignment explanation
Indices: 35042--35086 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
35032 ATTGTCAAAT
35042 ATTTT-ATTAAAATAAATAAAA
1 ATTTTAATT-AAATAAATAAAA
* *
35063 ATTTTAATTATATTAATAAAA
1 ATTTTAATTAAATAAATAAAA
35084 ATT
1 ATT
35087 ATACTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTTAATTAAATAAATAAAA
Found at i:35097 original size:21 final size:21
Alignment explanation
Indices: 35056--35098 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35046 TATTAAAATA
*
35056 AATAAAAATTTTAATTATATT
1 AATAAAAATTATAATTATATT
* *
35077 AATAAAAATTATACTTTTATT
1 AATAAAAATTATAATTATATT
35098 A
1 A
35099 CACAAATTAA
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:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAAAAATTATAATTATATT
Found at i:35149 original size:23 final size:25
Alignment explanation
Indices: 35109--35155 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
35099 CACAAATTAA
35109 TTTTAAAATATTCGCATAA-AAATAT
1 TTTTAAAATATTC-CATAATAAATAT
*
35134 TTTTAATATATT-CATAATAAAT
1 TTTTAAAATATTCCATAATAAAT
35156 GAATAAACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 4 0.20
25 11 0.55
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTTAAAATATTCCATAATAAATAT
Found at i:38020 original size:35 final size:35
Alignment explanation
Indices: 37974--38178 Score: 340
Period size: 35 Copynumber: 5.9 Consensus size: 35
37964 TGAAAATCAA
*
37974 GGAATATAAAAATGAAGGCATGGAATGATGGGCAT
1 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
38009 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
1 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
38044 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
1 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
** *
38079 GGAATGTAAAAATGAAGGCATGGAATAATGGGCAT
1 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
* *
38114 GGAATAAAAAAATGAAGTCATAGAATGATGGGCAT
1 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
*
38149 GAAAT-AAAAAATGAAGGCATGGAATGATGG
1 GGAATAAAAAAATGAAGGCATGGAATGATGG
38179 ATAAAAAATG
Statistics
Matches: 158, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
34 23 0.15
35 135 0.85
ACGTcount: A:0.46, C:0.05, G:0.30, T:0.19
Consensus pattern (35 bp):
GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
Found at i:39499 original size:79 final size:79
Alignment explanation
Indices: 39395--40136 Score: 1173
Period size: 79 Copynumber: 9.4 Consensus size: 79
39385 AAGTTTCTTA
*
39395 AATTTTT-ACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
*
39459 ATTTCCAAAACATC
66 ATTTCTAAAACATC
* *
39473 AATTTTTCATAATCGGGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
* *
39538 ATTTATAAAACATT
66 ATTTCTAAAACATC
* * * *
39552 GATTTTTTACAATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTTCAACCCCGGTTTT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
* *
39617 ATCTCTAAAACACC
66 ATTTCTAAAACATC
* * *
39631 AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
39696 ATTTCTAAAACATC
66 ATTTCTAAAACATC
* *
39710 AATTTTTTACAATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
* *
39775 ATCTCTAAAACACC
66 ATTTCTAAAACATC
*
39789 AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
39854 ATTTCTAAAACATC
66 ATTTCTAAAACATC
* * *
39868 GATTTTTTACAATCGGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
39933 ATTTCTAAAACATC
66 ATTTCTAAAACATC
* * *
39947 GATTTTTTACAATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTT
1 AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
40012 ATTTCTAAAACA-C
66 ATTTCTAAAACATC
* ** *
40025 TAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTTCAACCCCGGTTT
1 -AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTT
40090 TATTTCTAAAACATC
65 TATTTCTAAAACATC
* *
40105 AATTTTTCATAATCGGGGATACTCTAACCCCG
1 AATTTTTCACAATCGGGGATACTCCAACCCCG
40137 ATTTTATTTT
Statistics
Matches: 610, Mismatches: 51, Indels: 5
0.92 0.08 0.01
Matches are distributed among these distances:
78 8 0.01
79 601 0.99
80 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTT
ATTTCTAAAACATC
Found at i:46552 original size:115 final size:115
Alignment explanation
Indices: 46341--46834 Score: 701
Period size: 115 Copynumber: 4.2 Consensus size: 115
46331 CTCTTTTAGC
* * *
46341 CCTTTAGTCCTCAAAGAGCAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTT-
1 CCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTC
* *
46405 TCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGTTGGCA
66 T-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
46456 CCTTCAGTCCTCAAAAAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTC
1 CCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTC
*
46521 TAGTCCTCAAAGAGTAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
66 TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
46571 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
1 C-CTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
*
46636 CCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
65 CTAGTCCTCAAAGAGCAGGACGCC---T--TTT-AAAGCCCACACAAGTTGGTGGCA
* * * *
46693 CCTTCAGTCCTCAAAGAGCAGGATG-C-TTTCTTTTTTCAAAACCCACACAAGTTGGTGGCACCT
1 CCTTCAGTCCTCAAAGAGCAGGACGCCTTTTC-CTTTT-AAAGCCCACACAAGTTGGTGGCA-TT
*
46756 TTC-AGTCCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCA
63 TTCTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
46808 -CTTCCTAGTCCTCAAAGAGCAGGACGC
1 CCTT-C-AGTCCTCAAAGAGCAGGACGC
46835 TCTCTCCTTT
Statistics
Matches: 345, Mismatches: 20, Indels: 26
0.88 0.05 0.07
Matches are distributed among these distances:
114 3 0.01
115 130 0.38
116 105 0.30
118 1 0.00
119 5 0.01
120 5 0.01
121 68 0.20
122 28 0.08
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (115 bp):
CCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTC
TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:46617 original size:61 final size:60
Alignment explanation
Indices: 46346--46844 Score: 626
Period size: 61 Copynumber: 8.5 Consensus size: 60
46336 TTAGCCCTTT
* *
46346 AGTCCTCAAAGAGCAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
46407 AGTCCTCAAAGAGCAGGACGCCTTT-C----AAAGCCCACACAAGTTGTTGGCAC-CTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
46461 AGTCCTCAAAAAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
*
46521 TAGTCCTCAAAGAGTAGGACG-----CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 -AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
46577 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-C
* *
46638 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC-CTTC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * *
46698 AGTCCTCAAAGAGCAGGATG-CTTTCTTTTTTCAAAACCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTC-CTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
*
46759 AGTCCTCAAAGAGCAGGA--CC---CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
*
46813 TAGTCCTCAAAGAGCAGGACGCTCTCTCCTTT
1 -AGTCCTCAAAGAGCAGGACGC-CTTTCCTTT
46845 CACCCTTTAG
Statistics
Matches: 388, Mismatches: 22, Indels: 56
0.83 0.05 0.12
Matches are distributed among these distances:
54 26 0.07
55 114 0.29
56 10 0.03
57 2 0.01
58 5 0.01
59 4 0.01
60 74 0.19
61 153 0.39
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (60 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:46767 original size:237 final size:231
Alignment explanation
Indices: 46345--46844 Score: 767
Period size: 237 Copynumber: 2.1 Consensus size: 231
46335 TTTAGCCCTT
* *
46345 TAGTCCTCAAAGAGCAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGT
1 TAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
*
46410 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGTTGGCACCTTCAGTCCTCAAAAAGC
66 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAAAGC
* * *
46475 AGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGTAGGA
131 AGGATGCCTTTTCCTTTTAAAACCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGA
* *
46540 CGCCTTTTAAAGCCCACACAAGTTGGTGGCACTT-T
196 CCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
*
46575 TCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAG
1 T-AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAG
46640 TCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC
65 TCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC
* *
46705 AAAGAGCAGGATG-C-TTTCTTTTTTCAAAACCCACACAAGTTGGTGGCACCTTTC-AGTCCTCA
124 AAAAAGCAGGATGCCTTTTC-CTTTT-AAAACCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCA
46767 AAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
186 AAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
46813 TAGTCCTCAAAGAGCAGGACG-CTCTCTCCTTT
1 TAGTCCTCAAAGAGCAGGACGCCT-TCTCCTTT
46845 CACCCTTTAG
Statistics
Matches: 246, Mismatches: 12, Indels: 17
0.89 0.04 0.06
Matches are distributed among these distances:
230 1 0.00
231 78 0.32
235 4 0.02
236 7 0.03
237 151 0.61
238 5 0.02
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (231 bp):
TAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAAAGC
AGGATGCCTTTTCCTTTTAAAACCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGA
CCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCC
Found at i:46944 original size:55 final size:55
Alignment explanation
Indices: 46877--46986 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
46867 AGGACGCCTT
* *
46877 CTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGA
1 CTCCTCTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGA
46932 CTCCTCTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGA
1 CTCCTCTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGA
46987 TACTCTCTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
54 4 0.08
55 48 0.92
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (55 bp):
CTCCTCTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGA
Found at i:46985 original size:155 final size:150
Alignment explanation
Indices: 46726--47297 Score: 785
Period size: 155 Copynumber: 3.7 Consensus size: 150
46716 TGCTTTCTTT
* * *
46726 TTTCAAAACCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-CCCTTTTAAAGC
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACTTCCTCTTAAAGC
46790 CCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTAG
66 CCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTAG
*
46855 TCTTCAAAGAGCAGGACGCC
131 TCCTCAAAGAGCAGGACGCC
46875 TTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-TCCTCT
1 TT-T-C----AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACTTCCTCT
** * *
46939 TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATACTCTCTTCTCTCACC
60 TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACC
47004 CTTTAGTCCTCAAAGAGCAGGACGCC
125 CTTTAGTCCTCAAAGAGCAGGACGCC
* * *
47030 TTTCAGAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAAGACGCCTTTTCCATTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC-AG--GAC--TTCC-TCT
* *
47094 TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGTTCTCTCCTTTCGCC
60 TAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACC
* *
47159 TTTTTGTCCTCAAAGAGCAGGACGCC
125 CTTTAGTCCTCAAAGAGCAGGACGCC
* * *
47185 TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGTCTTCTCATTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC-T-TCCTC--TTA
*
47250 GAGCCCACACAAGTTGGTGGCACCTT-C-AGTCCTCAAAGAGCAGGACGC
62 AAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACGC
47298 CTTTTCCTTT
Statistics
Matches: 377, Mismatches: 28, Indels: 32
0.86 0.06 0.07
Matches are distributed among these distances:
148 17 0.05
149 28 0.07
150 1 0.00
151 3 0.01
152 2 0.01
153 25 0.07
154 28 0.07
155 256 0.68
156 17 0.05
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (150 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACTTCCTCTTAAAGC
CCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCACCCTTTAG
TCCTCAAAGAGCAGGACGCC
Found at i:47072 original size:54 final size:57
Alignment explanation
Indices: 47003--47143 Score: 173
Period size: 54 Copynumber: 2.4 Consensus size: 57
46993 CTTCTCTCAC
* *
47003 CCTTTAGTCCTCAAAGAGCAGGACGCC-TTT-C-AGAGCCCACACAAGTTGGTGGCA
1 CCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTAAAGCCCACACAAGTTGGTGGCA
*
47057 CCTTCAGTCCTCAAAGAGCAAGACGCCTTTTCCATTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC----TAAAGCCCACACAAGTTGGTGGCA
47118 -CTTCCTAGTCCTCAAAGAGCAGGACG
1 CCTT-C-AGTCCTCAAAGAGCAGGACG
47144 TTCTCTCCTT
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
54 25 0.34
55 3 0.04
56 1 0.01
60 3 0.04
61 23 0.31
62 19 0.26
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (57 bp):
CCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTAAAGCCCACACAAGTTGGTGGCA
Found at i:47269 original size:60 final size:58
Alignment explanation
Indices: 47164--47359 Score: 265
Period size: 60 Copynumber: 3.3 Consensus size: 58
47154 TCGCCTTTTT
47164 GTCCTCAAAGAGCAGGACGCCTTTCA----AAGCCCACACAAGTTGGTGGCACTTTTCA
1 GTCCTCAAAGAGCAGGACGCCTTTCATTTTAAGCCCACACAAGTTGGTGGCAC-TTTCA
* * *
47219 GTCCTCAAAGAGCAGGACGTCTTCTCATTTTGAGCCCACACAAGTTGGTGGCACCTTCA
1 GTCCTCAAAGAGCAGGACGCCTT-TCATTTTAAGCCCACACAAGTTGGTGGCACTTTCA
* *
47278 GTCCTCAAAGAGCAGGACGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTA
1 GTCCTCAAAGAGCAGGACGCC-TTT-CATTTT-AAGCCCACACAAGTTGGTGGCACTTTC-A
47340 GTCCTCAAAGAGCAGGACGC
1 GTCCTCAAAGAGCAGGACGC
47360 TCTCTCCTTT
Statistics
Matches: 124, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
55 22 0.18
56 3 0.02
59 25 0.20
60 29 0.23
61 24 0.19
62 21 0.17
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (58 bp):
GTCCTCAAAGAGCAGGACGCCTTTCATTTTAAGCCCACACAAGTTGGTGGCACTTTCA
Found at i:47318 original size:215 final size:214
Alignment explanation
Indices: 47008--47570 Score: 867
Period size: 215 Copynumber: 2.6 Consensus size: 214
46998 CTCACCCTTT
47008 AGTCCTCAAAGAGCAGGACGCCTT-TCA----GAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
1 AGTCCTCAAAGAGCAGGACG-CTTCTCATTTTGAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
* *
47068 CAAAGAGCAAGACGCCTTTTCCATTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
65 CAAAGAGCAGGACGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
*
47133 AGAGCAGGACGTTCTCTCCTTTCGCCTTTTTGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
130 AGAGCAGGACGCTCTCTCCTTTCGCCTTTTTGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
47198 ACAAGTTGGTGGCACTTTTC
195 ACAAGTTGGTGGCACTTTTC
47218 AGTCCTCAAAGAGCAGGACGTCTTCTCATTTTGAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
1 AGTCCTCAAAGAGCAGGACG-CTTCTCATTTTGAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
47283 CAAAGAGCAGGACGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
65 CAAAGAGCAGGACGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAA
* *
47348 AGAGCAGGACGCTCTCTCCTTTCGCCTTTTTGTCCTCAAGGAGCAGGACGCCTTTTAAAGCCCAC
130 AGAGCAGGACGCTCTCTCCTTTCGCCTTTTTGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCAC
47413 ACAAGTTGGTGGCACTTTTC
195 ACAAGTTGGTGGCACTTTTC
* * * *
47433 AGTCCTCAAAGAGCAGGATGCTTC-CTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCC
1 AGTCCTCAAAGAGCAGGACGCTTCTCATTTT-GAGCCCACACAAGTTGGTGGCAC-CTTCAGTCC
* * * * *
47497 TCAAAGAGCAGGATG-C-TTT-CTTTTTGCAAATCTCACACTAGTTGGTGGCATCTTTC-AGTCC
64 TCAAAGAGCAGGACGCCTTTTCCTTTTT--AAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCC
47558 TCAAAGAGCAGGA
126 TCAAAGAGCAGGA
47571 TGCCTTTTCT
Statistics
Matches: 328, Mismatches: 15, Indels: 16
0.91 0.04 0.04
Matches are distributed among these distances:
210 23 0.07
211 3 0.01
212 6 0.02
213 8 0.02
214 65 0.20
215 223 0.68
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (214 bp):
AGTCCTCAAAGAGCAGGACGCTTCTCATTTTGAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC
AAAGAGCAGGACGCCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAA
GAGCAGGACGCTCTCTCCTTTCGCCTTTTTGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACA
CAAGTTGGTGGCACTTTTC
Found at i:47474 original size:59 final size:59
Alignment explanation
Indices: 47400--47632 Score: 351
Period size: 61 Copynumber: 3.9 Consensus size: 59
47390 GCAGGACGCC
*
47400 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTCCT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
47459 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
* * *
47518 TTTTGCAAATCTCACACTAGTTGGTGGCA-TCTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCT
1 TTTT--AAAGCCCACACAAGTTGGTGGCACT-TTTCAGTCCTCAAAGAGCAGGATG-C-TTTCT
* * *
47581 TTTCAAAGACCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAT
47633 ACACTTTTTT
Statistics
Matches: 159, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
59 62 0.39
60 1 0.01
61 86 0.54
62 2 0.01
63 8 0.05
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (59 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCT
Found at i:47731 original size:73 final size:74
Alignment explanation
Indices: 47649--47786 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 74
47639 TTTTCCCTTC
* *
47649 TTTTCTCTTTTGTCCTCAAAGAGCAGGACGCACTTT-ATTTTTCTTTTGTTCTCAAAGAGCAGGA
1 TTTTCTCTTTTGTCCTCAAAGAGCAGGACACACTTTCATTTTTCTTTTGTCCTCAAAGAGCAGGA
47713 CACACTTTA
66 CACACTTTA
* * * *
47722 TTTTTTCTTTTGTCCTCAAAGAGCAGGACACACTTTCCTTTTTCTTTTGTCCTTAGAGAGCAGGA
1 TTTTCTCTTTTGTCCTCAAAGAGCAGGACACACTTTCATTTTTCTTTTGTCCTCAAAGAGCAGGA
47787 TGTATTTCGT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
73 34 0.59
74 24 0.41
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (74 bp):
TTTTCTCTTTTGTCCTCAAAGAGCAGGACACACTTTCATTTTTCTTTTGTCCTCAAAGAGCAGGA
CACACTTTA
Found at i:47740 original size:37 final size:37
Alignment explanation
Indices: 47649--47786 Score: 206
Period size: 37 Copynumber: 3.8 Consensus size: 37
47639 TTTTCCCTTC
* *
47649 TTTTCTCTTTTGTCCTCAAAGAGCAGGACGCACTTTA
1 TTTTTTCTTTTGTCCTCAAAGAGCAGGACACACTTTA
*
47686 -TTTTTCTTTTGTTCTCAAAGAGCAGGACACACTTTA
1 TTTTTTCTTTTGTCCTCAAAGAGCAGGACACACTTTA
*
47722 TTTTTTCTTTTGTCCTCAAAGAGCAGGACACACTTTC
1 TTTTTTCTTTTGTCCTCAAAGAGCAGGACACACTTTA
* * *
47759 CTTTTTCTTTTGTCCTTAGAGAGCAGGA
1 TTTTTTCTTTTGTCCTCAAAGAGCAGGA
47787 TGTATTTCGT
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 33 0.36
37 59 0.64
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (37 bp):
TTTTTTCTTTTGTCCTCAAAGAGCAGGACACACTTTA
Found at i:48603 original size:35 final size:34
Alignment explanation
Indices: 48553--48756 Score: 320
Period size: 35 Copynumber: 5.9 Consensus size: 34
48543 TGAAAATCAA
48553 GGAATATAAAAATGAAGGCATGGAATGATGGGCAT
1 GGAATA-AAAAATGAAGGCATGGAATGATGGGCAT
48588 GGAATAAAAACATGAAGGCATGGAATGATGGGCAT
1 GGAATAAAAA-ATGAAGGCATGGAATGATGGGCAT
48623 GGAATAAAAAAATGAAGGCATGGAATGATGGGCAT
1 GGAAT-AAAAAATGAAGGCATGGAATGATGGGCAT
* *
48658 GGAATATAAAAATGAAGGCATGAAATAATGGGCAT
1 GGAATA-AAAAATGAAGGCATGGAATGATGGGCAT
* *
48693 GGAATAAAAAAATGAAGTCATAGAATGATGGGCAT
1 GGAAT-AAAAAATGAAGGCATGGAATGATGGGCAT
48728 GGAATAAAAAATGAAGGCATGG-ATGATGG
1 GGAATAAAAAATGAAGGCATGGAATGATGG
48757 ATAAAAAAAT
Statistics
Matches: 157, Mismatches: 8, Indels: 10
0.90 0.05 0.06
Matches are distributed among these distances:
33 7 0.04
34 20 0.13
35 124 0.79
36 6 0.04
ACGTcount: A:0.46, C:0.06, G:0.30, T:0.19
Consensus pattern (34 bp):
GGAATAAAAAATGAAGGCATGGAATGATGGGCAT
Found at i:48678 original size:21 final size:21
Alignment explanation
Indices: 48653--48718 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 21
48643 TGGAATGATG
48653 GGCATGGAATATAAAAATGAA
1 GGCATGGAATATAAAAATGAA
48674 GGCAT-GAA-AT---AATG--
1 GGCATGGAATATAAAAATGAA
*
48688 GGCATGGAATAAAAAAATGAA
1 GGCATGGAATATAAAAATGAA
* *
48709 GTCATAGAAT
1 GGCATGGAAT
48719 GATGGGCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 5 0.14
15 3 0.09
16 5 0.14
19 6 0.17
20 3 0.09
21 13 0.37
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.20
Consensus pattern (21 bp):
GGCATGGAATATAAAAATGAA
Done.