Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011272.1 Kokia drynarioides strain JFW-HI SEQ_126251, 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: 181007
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:1167 original size:22 final size:22
Alignment explanation
Indices: 1142--1183 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1132 TATGTATGAT
1142 ATTA-AAATAAAAATTAAATTAA
1 ATTATAAATAAAAA-TAAATTAA
*
1164 ATTATAAGTAAAAATAAATT
1 ATTATAAATAAAAATAAATT
1184 TAAACACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTATAAATAAAAATAAATTAA
Found at i:1435 original size:22 final size:23
Alignment explanation
Indices: 1382--1432 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1372 CAAGTCCTAA
1382 TTTTTTATAAATTCAAAATAATT
1 TTTTTTATAAATTCAAAATAATT
* *
1405 TTTTTTATAATTTTTAAAAT-ATT
1 TTTTTTATAA-ATTCAAAATAATT
1428 TTTTT
1 TTTTT
1433 ATAGTTGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTTTATAAATTCAAAATAATT
Found at i:3699 original size:17 final size:18
Alignment explanation
Indices: 3665--3700 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3655 TGAATTTTTA
3665 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
3683 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
3700 T
1 T
3701 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:4165 original size:12 final size:13
Alignment explanation
Indices: 4132--4165 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4122 TGTTCTTCTA
4132 TTCCTTTTTTTGT
1 TTCCTTTTTTTGT
* *
4145 TTCTTTTTTTTTT
1 TTCCTTTTTTTGT
4158 TTCCTTTT
1 TTCCTTTT
4166 ATATCTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (13 bp):
TTCCTTTTTTTGT
Found at i:4247 original size:27 final size:31
Alignment explanation
Indices: 4199--4254 Score: 75
Period size: 28 Copynumber: 1.9 Consensus size: 31
4189 ATAATAACAT
*
4199 TAATAAATTAAAATTATCTATTTA-CTTAAA
1 TAATAAATTAAAATTATATATTTATCTTAAA
4229 TAATAAA-T-AAATTA-ATATTTATCTTA
1 TAATAAATTAAAATTATATATTTATCTTA
4255 CAAATGTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 10 0.42
29 1 0.04
30 7 0.29
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (31 bp):
TAATAAATTAAAATTATATATTTATCTTAAA
Found at i:4765 original size:25 final size:25
Alignment explanation
Indices: 4737--4784 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4727 AAAAATATAG
4737 AAAACCATGAAACCGTGGACAAAAT
1 AAAACCATGAAACCGTGGACAAAAT
* * *
4762 AAAACTATGAAACTGTGGGCAAA
1 AAAACCATGAAACCGTGGACAAA
4785 GCCACGATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.15
Consensus pattern (25 bp):
AAAACCATGAAACCGTGGACAAAAT
Found at i:5371 original size:15 final size:16
Alignment explanation
Indices: 5351--5381 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5341 ATTAATTTTC
5351 ATATTTTT-TATAAAT
1 ATATTTTTATATAAAT
5366 ATATTTTTATATAAAT
1 ATATTTTTATATAAAT
5382 TCGTCACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTTATATAAAT
Found at i:7077 original size:24 final size:24
Alignment explanation
Indices: 7046--7094 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
7036 TTTTTTAAAA
7046 AATTTAATTTATTA-ATAATTTTTT
1 AATTTAA-TTATTACATAATTTTTT
*
7070 AATTTAATTATTACATTATTTTTT
1 AATTTAATTATTACATAATTTTTT
7094 A
1 A
7095 GTGGATTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
AATTTAATTATTACATAATTTTTT
Found at i:7215 original size:2 final size:2
Alignment explanation
Indices: 7208--7241 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
7198 TATAAACAAA
7208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7242 AAAACTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9204 original size:20 final size:20
Alignment explanation
Indices: 9181--9263 Score: 87
Period size: 20 Copynumber: 4.1 Consensus size: 20
9171 ATTTACCTAT
*
9181 ATATCTAACGACTTATCAAA
1 ATATCTAACGATTTATCAAA
*
9201 ATATCTAATGATTTATCAAA
1 ATATCTAACGATTTATCAAA
* * * *
9221 ATTTCTATC-ATTTTACCAAT
1 ATATCTAACGA-TTTATCAAA
9241 ATAATCTAACGATTTATCAAA
1 AT-ATCTAACGATTTATCAAA
9262 AT
1 AT
9264 TTTTATCATT
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.02
20 33 0.67
21 14 0.29
22 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.39
Consensus pattern (20 bp):
ATATCTAACGATTTATCAAA
Found at i:9248 original size:41 final size:41
Alignment explanation
Indices: 9203--9283 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
9193 TTATCAAAAT
*
9203 ATCTAATGATTTATCAAAATTTCTATCATTTTACCAATATA
1 ATCTAACGATTTATCAAAATTTCTATCATTTTACCAATATA
* *
9244 ATCTAACGATTTATCAAAATTTTTATCATTTTATCAATAT
1 ATCTAACGATTTATCAAAATTTCTATCATTTTACCAATAT
9284 TTATAAAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (41 bp):
ATCTAACGATTTATCAAAATTTCTATCATTTTACCAATATA
Found at i:9277 original size:61 final size:60
Alignment explanation
Indices: 9172--9303 Score: 149
Period size: 61 Copynumber: 2.2 Consensus size: 60
9162 TATCTAAGAA
* * * ** *
9172 TTTACCTATATATCTAACGACTTATCAAAATATCTAATGATTTATCAAAATTTCTATCAT
1 TTTACCAATATATCTAACGACTTATCAAAATATCTAATCATTTATCAAAATTTATAAAAC
* * * *
9232 TTTACCAATATAATCTAACGATTTATCAAAAT-TTTTATCATTTTATCAATATTTATAAAAC
1 TTTACCAATAT-ATCTAACGACTTATCAAAATATCTAATCA-TTTATCAAAATTTATAAAAC
9293 TTTACCAATAT
1 TTTACCAATAT
9304 TTTCAAATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
60 15 0.25
61 45 0.75
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.43
Consensus pattern (60 bp):
TTTACCAATATATCTAACGACTTATCAAAATATCTAATCATTTATCAAAATTTATAAAAC
Found at i:9278 original size:20 final size:20
Alignment explanation
Indices: 9193--9285 Score: 73
Period size: 20 Copynumber: 4.6 Consensus size: 20
9183 ATCTAACGAC
* *
9193 TTATCAAAATATCTAATGA-T
1 TTATCAAAATTTCT-ATCATT
9213 TTATCAAAATTTCTATCATT
1 TTATCAAAATTTCTATCATT
* * * *
9233 TTACCAATATAATCTAACGA-T
1 TTATCAAAAT-TTCTATC-ATT
*
9254 TTATCAAAATTTTTATCATT
1 TTATCAAAATTTCTATCATT
*
9274 TTATCAATATTT
1 TTATCAAAATTT
9286 ATAAAACTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
19 4 0.07
20 38 0.67
21 14 0.25
22 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (20 bp):
TTATCAAAATTTCTATCATT
Found at i:9521 original size:20 final size:20
Alignment explanation
Indices: 9384--9535 Score: 67
Period size: 20 Copynumber: 7.5 Consensus size: 20
9374 TAAGGATTCC
*
9384 CAAAATATCTAATGATTTAT
1 CAAAATATCTAACGATTTAT
** * * *
9404 TGAAATTTTTAAAGATTTAT
1 CAAAATATCTAACGATTTAT
* * *
9424 CATAATATTTGACGATTT-T
1 CAAAATATCTAACGATTTAT
* * * *
9443 CCAAAATTTCCATC-ATTTTAC
1 -CAAAATATCTAACGA-TTTAT
* *
9464 CAATATATCTAACAATTTA-
1 CAAAATATCTAACGATTTAT
* * *
9483 CAAAAAAATTATAAGGATTTAT
1 C-AAAATA-TCTAACGATTTAT
*
9505 CAAAATATCTAACGATTTAC
1 CAAAATATCTAACGATTTAT
*
9525 CAAAATTTCTA
1 CAAAATATCTA
9536 TCATTTTATC
Statistics
Matches: 93, Mismatches: 32, Indels: 14
0.67 0.23 0.10
Matches are distributed among these distances:
19 3 0.03
20 74 0.80
21 15 0.16
22 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (20 bp):
CAAAATATCTAACGATTTAT
Found at i:9837 original size:20 final size:20
Alignment explanation
Indices: 9752--9838 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 20
9742 TATGACTTTG
*
9752 CCAAATTATCTAATAATTTA
1 CCAAAATATCTAATAATTTA
* * * * **
9772 TCAAATTTTTTAAGGATTTA
1 CCAAAATATCTAATAATTTA
* * **
9792 TCAATATATCTAGCAATTTA
1 CCAAAATATCTAATAATTTA
*
9812 CTAAAATATCTAATAATTTA
1 CCAAAATATCTAATAATTTA
9832 CCAAAAT
1 CCAAAAT
9839 TTTTATCGAT
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (20 bp):
CCAAAATATCTAATAATTTA
Found at i:9850 original size:20 final size:20
Alignment explanation
Indices: 9807--9900 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
9797 ATATCTAGCA
* * **
9807 ATTTACTAAAATATCTAATA
1 ATTTACCAAAATTTCTAACG
* *
9827 ATTTACCAAAATTTTTATCG
1 ATTTACCAAAATTTCTAACG
* * *
9847 ATTTACTAATATTTCTAAGG
1 ATTTACCAAAATTTCTAACG
* *
9867 ATTTATCAAAATATCTAACG
1 ATTTACCAAAATTTCTAACG
*
9887 ATTTACCAATATTT
1 ATTTACCAAAATTT
9901 ATGAAACTTT
Statistics
Matches: 55, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (20 bp):
ATTTACCAAAATTTCTAACG
Found at i:9851 original size:60 final size:60
Alignment explanation
Indices: 9753--9900 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 60
9743 ATGACTTTGC
* * * *
9753 CAAATTATCTAATAATTTATCAAATTTTTTAAGGATTTA-TCAATATATCT-AGCAATTTA-
1 CAAAATATCTAATAATTTACCAAAATTTTTAACGATTTACT-AATATATCTAAG-AATTTAT
* * *
9812 CTAAAATATCTAATAATTTACCAAAATTTTTATCGATTTACTAATATTTCTAAGGATTTAT
1 C-AAAATATCTAATAATTTACCAAAATTTTTAACGATTTACTAATATATCTAAGAATTTAT
** *
9873 CAAAATATCTAACGATTTACCAATATTT
1 CAAAATATCTAATAATTTACCAAAATTT
9901 ATGAAACTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
59 1 0.01
60 70 0.93
61 4 0.05
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.43
Consensus pattern (60 bp):
CAAAATATCTAATAATTTACCAAAATTTTTAACGATTTACTAATATATCTAAGAATTTAT
Found at i:9898 original size:40 final size:40
Alignment explanation
Indices: 9782--9900 Score: 130
Period size: 40 Copynumber: 3.0 Consensus size: 40
9772 TCAAATTTTT
* * * * *
9782 TAAGGATTTATCAATATATCTAGCAATTTACTAAAATATC
1 TAAGGATTTATCAAAATATCTAACGATTTACTAATATTTC
** * * * *
9822 TAATAATTTACCAAAATTTTTATCGATTTACTAATATTTC
1 TAAGGATTTATCAAAATATCTAACGATTTACTAATATTTC
*
9862 TAAGGATTTATCAAAATATCTAACGATTTACCAATATTT
1 TAAGGATTTATCAAAATATCTAACGATTTACTAATATTT
9901 ATGAAACTTT
Statistics
Matches: 62, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (40 bp):
TAAGGATTTATCAAAATATCTAACGATTTACTAATATTTC
Found at i:10031 original size:20 final size:20
Alignment explanation
Indices: 10006--10064 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
9996 TTTACAAAAA
* *
10006 ATCTAAGGATTTACCAATGT
1 ATCTAACGATTTACCAATAT
*
10026 ATCTAACGATTTACTAATAT
1 ATCTAACGATTTACCAATAT
*
10046 ATCTAACG-TTTTCCAATAT
1 ATCTAACGATTTACCAATAT
10065 TTGTAAGGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 9 0.26
20 25 0.74
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (20 bp):
ATCTAACGATTTACCAATAT
Found at i:10098 original size:20 final size:20
Alignment explanation
Indices: 10075--10144 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
10065 TTGTAAGGAC
10075 TTATCAAAATTTTTAAAGAT
1 TTATCAAAATTTTTAAAGAT
* * ** *
10095 TTATTAATACATTTAACGAT
1 TTATCAAAATTTTTAAAGAT
* * * *
10115 TCACCAAAATTTTTAAAAAA
1 TTATCAAAATTTTTAAAGAT
10135 TTATCAAAAT
1 TTATCAAAAT
10145 ATCTTACGAT
Statistics
Matches: 34, Mismatches: 16, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (20 bp):
TTATCAAAATTTTTAAAGAT
Found at i:10154 original size:40 final size:40
Alignment explanation
Indices: 10079--10166 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
10069 AAGGACTTAT
* * * *
10079 CAAAATTTTTAAAGATTTATTAATACATTTAACGATTCAC
1 CAAAATTTTTAAAAAATTATCAAAACATTTAACGATTCAC
* *
10119 CAAAATTTTTAAAAAATTATCAAAATATCTT-ACGATTTAC
1 CAAAATTTTTAAAAAATTATCAAAACAT-TTAACGATTCAC
*
10159 CAATATTT
1 CAAAATTT
10167 CCAAAATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 38 0.95
41 2 0.05
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.40
Consensus pattern (40 bp):
CAAAATTTTTAAAAAATTATCAAAACATTTAACGATTCAC
Found at i:17798 original size:2 final size:2
Alignment explanation
Indices: 17786--17820 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
17776 AAAATACAAA
17786 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17821 TAAAAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19710 original size:12 final size:12
Alignment explanation
Indices: 19695--19719 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19685 AGTTTATTGA
19695 AGAGTTTAAAAG
1 AGAGTTTAAAAG
19707 AGAGTTTAAAAG
1 AGAGTTTAAAAG
19719 A
1 A
19720 CATTTTGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (12 bp):
AGAGTTTAAAAG
Found at i:27109 original size:57 final size:59
Alignment explanation
Indices: 27019--27128 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 59
27009 ATTTGGTACT
* *
27019 TGAACTTGACACTTTTTCTAATTTGGTACCT-AAATTTTTTT-GACCTAATTTACTACA
1 TGAACTTGACAATTTTTCTAATTTGGTACCTAAAATTTTTTTGGACCAAATTTACTACA
*
27076 TGAACTTGA-AATTTTTCCTAATTTGGTATCTAAAATTTTTTTGGACCAAATTT
1 TGAACTTGACAATTTTT-CTAATTTGGTACCTAAAATTTTTTTGGACCAAATTT
27129 GATATCTGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
56 6 0.13
57 22 0.47
58 10 0.21
59 9 0.19
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (59 bp):
TGAACTTGACAATTTTTCTAATTTGGTACCTAAAATTTTTTTGGACCAAATTTACTACA
Found at i:28686 original size:9 final size:8
Alignment explanation
Indices: 28668--28705 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
28658 AAAGTGACGA
28668 TTTTTTAT
1 TTTTTTAT
28676 TTTTATTAT
1 TTTT-TTAT
28685 TTTTTT-T
1 TTTTTTAT
28692 TTTTTGTAT
1 TTTTT-TAT
28701 TTTTT
1 TTTTT
28706 ATCATGCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.22
8 7 0.26
9 14 0.52
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTTAT
Found at i:28688 original size:16 final size:17
Alignment explanation
Indices: 28667--28707 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
28657 CAAAGTGACG
28667 ATTTTTTATTTTTAT-T
1 ATTTTTTATTTTTATGT
*
28683 ATTTTTT-TTTTTTTGT
1 ATTTTTTATTTTTATGT
28699 ATTTTTTAT
1 ATTTTTTAT
28708 CATGCTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 15 0.68
17 1 0.05
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (17 bp):
ATTTTTTATTTTTATGT
Found at i:30583 original size:30 final size:32
Alignment explanation
Indices: 30549--30607 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
30539 AAATTAACTG
*
30549 TGAGTGACCAAAAT-GAAAA-TTTATTAAAAT
1 TGAGTGACCAAAATGGAAAAGGTTATTAAAAT
*
30579 TGAGTGACTAAAATGGAAAAGGTTATTAA
1 TGAGTGACCAAAATGGAAAAGGTTATTAA
30608 CAATAGTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.52
31 5 0.20
32 7 0.28
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.29
Consensus pattern (32 bp):
TGAGTGACCAAAATGGAAAAGGTTATTAAAAT
Found at i:32282 original size:16 final size:16
Alignment explanation
Indices: 32249--32282 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
32239 CAAAAATATC
* *
32249 TAAATTAATTAAATAA
1 TAAATTAATAAAAAAA
32265 TAAATTAATAAAAAAA
1 TAAATTAATAAAAAAA
32281 TA
1 TA
32283 TTCTAACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAATTAATAAAAAAA
Found at i:43538 original size:17 final size:16
Alignment explanation
Indices: 43512--43566 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
43502 CTTCTAAATT
43512 AATATTAAAATTTGAAA
1 AATA-TAAAATTTGAAA
*
43529 AATATAAAAATT-AAA
1 AATATAAAATTTGAAA
*
43544 AATGATGAAATTTGAGAA
1 AAT-ATAAAATTTGA-AA
43562 AATAT
1 AATAT
43567 TTAAATCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.19
16 14 0.44
17 7 0.22
18 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (16 bp):
AATATAAAATTTGAAA
Found at i:52788 original size:5 final size:5
Alignment explanation
Indices: 52778--52803 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52768 CAATTCTATG
52778 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
52804 GTAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:55091 original size:17 final size:18
Alignment explanation
Indices: 55055--55124 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
55045 AGATGTTATC
*
55055 ATTTAAAATATTATATAAA
1 ATTTAAAATA-TATAAAAA
55074 ATTTAAAA-ATATACAAAA
1 ATTTAAAATATATA-AAAA
*
55092 ATATTAAAAGTATA-AAGAA
1 AT-TTAAAA-TATATAAAAA
*
55111 ATTCAAAATATATA
1 ATTTAAAATATATA
55125 TTTAAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
17 8 0.19
18 12 0.28
19 19 0.44
20 1 0.02
21 3 0.07
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
ATTTAAAATATATAAAAA
Found at i:55098 original size:19 final size:18
Alignment explanation
Indices: 55066--55122 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
55056 TTTAAAATAT
*
55066 TATATAAAAT-TTAAAAA
1 TATAAAAAATATTAAAAA
*
55083 TATACAAAAATATTAAAAG
1 TATA-AAAAATATTAAAAA
* *
55102 TATAAAGAA-ATTCAAAA
1 TATAAAAAATATTAAAAA
55119 TATA
1 TATA
55123 TATTTAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 14 0.42
18 9 0.27
19 10 0.30
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
TATAAAAAATATTAAAAA
Found at i:56208 original size:31 final size:30
Alignment explanation
Indices: 56164--56241 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
56154 CGGATAAGTC
*
56164 TACAATTTAATCACTCAATTATTAATAAATT
1 TACAATTT-ATCACTCAACTATTAATAAATT
* *
56195 TATAATTTGATCACTCAACTATTAATAAGTT
1 TACAATTT-ATCACTCAACTATTAATAAATT
56226 TACAATTTAGTCACTC
1 TACAATTTA-TCACTC
56242 TCGACATGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.41
Consensus pattern (30 bp):
TACAATTTATCACTCAACTATTAATAAATT
Found at i:61592 original size:75 final size:75
Alignment explanation
Indices: 61469--61618 Score: 246
Period size: 75 Copynumber: 2.0 Consensus size: 75
61459 GGCCCTAAAC
* * **
61469 TCGAAGTTGCCTTTGAATAGGATAGGGTGTGAGCGTTGGCGATCGCCTGAGGCTCCATTCTGTAA
1 TCGAAGTTGCCTTTGAATAGGATAAGGTGTGAGCGCTAACGATCGCCTGAGGCTCCATTCTGTAA
61534 AATCAATTTT
66 AATCAATTTT
* *
61544 TCGAAGTTGCCTTTGAATAGGATAAGGTGTGAGTGCTAACGATCGCCTGAGGTTCCATTCTGTAA
1 TCGAAGTTGCCTTTGAATAGGATAAGGTGTGAGCGCTAACGATCGCCTGAGGCTCCATTCTGTAA
61609 AATCAATTTT
66 AATCAATTTT
61619 GATGCTGCTG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (75 bp):
TCGAAGTTGCCTTTGAATAGGATAAGGTGTGAGCGCTAACGATCGCCTGAGGCTCCATTCTGTAA
AATCAATTTT
Found at i:62857 original size:27 final size:27
Alignment explanation
Indices: 62827--62897 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
62817 AATTCAAAAC
*
62827 AAATTATAAAAACTTTTTAAAAATTA-A
1 AAATTATAAAAA-TTATTAAAAATTATA
* *
62854 AAATCATAAAAATTATTAAAATTTATA
1 AAATTATAAAAATTATTAAAAATTATA
* *
62881 AAAATATAAAAAATATT
1 AAATTATAAAAATTATT
62898 TTTTATATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
26 11 0.30
27 26 0.70
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATTATAAAAATTATTAAAAATTATA
Found at i:62865 original size:10 final size:9
Alignment explanation
Indices: 62807--62892 Score: 63
Period size: 9 Copynumber: 9.4 Consensus size: 9
62797 TTAATTTTTC
62807 AAAATT-TA
1 AAAATTATA
*
62815 AAAATTCAAA
1 AAAATT-ATA
62825 ACAAATTATA
1 A-AAATTATA
*
62835 AAAACTTTTTA
1 AAAA--TTATA
62846 AAAA-T-TA
1 AAAATTATA
*
62853 AAAATCATA
1 AAAATTATA
62862 AAAATTATTA
1 AAAATTA-TA
*
62872 AAATTTATA
1 AAAATTATA
62881 AAAA-TATA
1 AAAATTATA
62889 AAAA
1 AAAA
62893 ATATTTTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
7 6 0.10
8 15 0.24
9 16 0.25
10 13 0.21
11 13 0.21
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:62871 original size:19 final size:18
Alignment explanation
Indices: 62845--62894 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
62835 AAAACTTTTT
62845 AAAA-ATTAAAAATCATA
1 AAAATATTAAAAATCATA
* *
62862 AAAATTATTAAAATTTATA
1 AAAA-TATTAAAAATCATA
*
62881 AAAATATAAAAAAT
1 AAAATATTAAAAAT
62895 ATTTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 8 0.30
19 15 0.56
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATATTAAAAATCATA
Found at i:63775 original size:8 final size:8
Alignment explanation
Indices: 63750--63815 Score: 66
Period size: 8 Copynumber: 8.4 Consensus size: 8
63740 TAATTTTATT
63750 TAATTAAAA
1 TAATT-AAA
* *
63759 AAATAAAA
1 TAATTAAA
63767 TAATTAAA
1 TAATTAAA
63775 TAATTAAA
1 TAATTAAA
63783 TTAA--AAA
1 -TAATTAAA
*
63790 -AATAAAA
1 TAATTAAA
63797 TAATTAAA
1 TAATTAAA
63805 TAATTAAA
1 TAATTAAA
63813 TAA
1 TAA
63816 ATATTTTTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
5 2 0.04
7 6 0.12
8 34 0.71
9 6 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
TAATTAAA
Found at i:63777 original size:13 final size:13
Alignment explanation
Indices: 63759--63816 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
63749 TTAATTAAAA
63759 AAATAAAATAATT
1 AAATAAAATAATT
*
63772 AAAT-AATTAAATT
1 AAATAAAAT-AATT
*
63785 AAA-AAAATAA-A
1 AAATAAAATAATT
*
63796 ATAATTAAATAATT
1 A-AATAAAATAATT
63810 AAATAAA
1 AAATAAA
63817 TATTTTTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
11 1 0.03
12 7 0.21
13 25 0.74
14 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:63787 original size:30 final size:30
Alignment explanation
Indices: 63751--63813 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
63741 AATTTTATTT
63751 AATTAAAAAAATAAAATAATTAAATAATTA
1 AATTAAAAAAATAAAATAATTAAATAATTA
63781 AATTAAAAAAATAAAATAATTAAATAATTA
1 AATTAAAAAAATAAAATAATTAAATAATTA
63811 AAT
1 AAT
63814 AAATATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (30 bp):
AATTAAAAAAATAAAATAATTAAATAATTA
Found at i:63797 original size:22 final size:22
Alignment explanation
Indices: 63762--63805 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
63752 ATTAAAAAAA
* *
63762 TAAAATAATTAAATAATTAAAT
1 TAAAAAAATAAAATAATTAAAT
63784 TAAAAAAATAAAATAATTAAAT
1 TAAAAAAATAAAATAATTAAAT
63806 AATTAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAAAAATAAAATAATTAAAT
Found at i:63812 original size:17 final size:17
Alignment explanation
Indices: 63750--63812 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
63740 TAATTTTATT
* *
63750 TAATTAAAAAAATAAAA
1 TAATTAAATAATTAAAA
*
63767 TAATTAAATAATTAAAT
1 TAATTAAATAATTAAAA
63784 TAA--AAA-AA-TAAAA
1 TAATTAAATAATTAAAA
63797 TAATTAAATAATTAAA
1 TAATTAAATAATTAAA
63813 TAAATATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 7 0.18
14 2 0.05
15 6 0.16
16 2 0.05
17 21 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAATTAAATAATTAAAA
Found at i:63840 original size:18 final size:19
Alignment explanation
Indices: 63814--63849 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
63804 ATAATTAAAT
63814 AAATATTTTTGTTTAAGAC
1 AAATATTTTTGTTTAAGAC
63833 AAAT-TTTTTGTTTAAGA
1 AAATATTTTTGTTTAAGA
63850 GTCGAGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (19 bp):
AAATATTTTTGTTTAAGAC
Found at i:68857 original size:27 final size:30
Alignment explanation
Indices: 68787--68862 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
68777 TCGAAATTTT
*
68787 AAAAGTAC-AGAGACTAAAATTGACCAATTCA
1 AAAAGTACAAG-GACTAAAATTGACAAATT-A
68818 AAAAGTACAAGGACTAAAATTGA-AAATT-
1 AAAAGTACAAGGACTAAAATTGACAAATTA
*
68846 AAAA-TATAAGGACTAAA
1 AAAAGTACAAGGACTAAA
68863 TTCATAACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 12 0.29
28 4 0.10
30 4 0.10
31 20 0.48
32 2 0.05
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.20
Consensus pattern (30 bp):
AAAAGTACAAGGACTAAAATTGACAAATTA
Found at i:75805 original size:69 final size:67
Alignment explanation
Indices: 75693--75885 Score: 201
Period size: 69 Copynumber: 2.8 Consensus size: 67
75683 GAACAGTAGC
* * * * *
75693 GTGCTCTCTGTTTAGCACGTTTCGTGCCCTTTGATTAGCACTTTGTGTGCTCTCTAATTAGCACT
1 GTGCTCTCTG-TTAGCAC-TTTTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTAATTAGCACT
*
75758 TTGT
64 GTGT
* **
75762 GTGCTCTTTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACT
1 GTGCTCTCTG-TTAGCACTTT-TGTGCTCTCTGATTAGTACTTTGTGTACTCTCTAATTAGCACT
75827 GTGT
64 GTGT
* *
75831 GTACTCTCTGTTGCCCAGCACTTATGTGCTCTCTG-TTAGTACTTTG-GTACTCTCT
1 GTGCTCTCTGTT----AGCACTTTTGTGCTCTCTGATTAGTACTTTGTGTACTCTCT
75886 GTTTCTTTCG
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
68 5 0.05
69 72 0.68
70 11 0.10
71 11 0.10
72 7 0.07
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (67 bp):
GTGCTCTCTGTTAGCACTTTTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTAATTAGCACTGT
GT
Found at i:75838 original size:23 final size:23
Alignment explanation
Indices: 75693--75886 Score: 182
Period size: 23 Copynumber: 8.4 Consensus size: 23
75683 GAACAGTAGC
* *
75693 GTGCTCTCTGTTTAGCACGTTT-C
1 GTGCTCTCTGATTAGCAC-TTTGT
* *
75716 GTGCCCTTTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
75739 GTGCTCTCTAATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
75762 GTGCTCTTTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
75785 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * *
75808 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
75831 GTACTCTCTG-TTGCCCAGCAC-TTAT
1 GTGCTCTCTGATT----AGCACTTTGT
*
75856 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
75877 GTACTCTCTG
1 GTGCTCTCTG
75887 TTTCTTTCGT
Statistics
Matches: 144, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
21 13 0.09
22 7 0.05
23 106 0.74
25 13 0.09
26 5 0.03
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:82929 original size:19 final size:19
Alignment explanation
Indices: 82899--82949 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
82889 CAACAAGAAA
82899 TTTATTTTTTATT-AAATG
1 TTTATTTTTTATTGAAATG
*
82917 TTTATTATTTTATTGAAATT
1 TTTATT-TTTTATTGAAATG
*
82937 TTTGTATTTTTAT
1 TTTAT-TTTTTAT
82950 ATTTTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.21
19 7 0.25
20 14 0.50
21 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (19 bp):
TTTATTTTTTATTGAAATG
Found at i:82947 original size:20 final size:20
Alignment explanation
Indices: 82904--82949 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
82894 AGAAATTTAT
82904 TTTTTATTAAATGTTTATTA
1 TTTTTATTAAATGTTTATTA
82924 -TTTTATTGAAAT-TTT-TGTA
1 TTTTTATT-AAATGTTTAT-TA
82943 TTTTTAT
1 TTTTTAT
82950 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.04
19 12 0.52
20 10 0.43
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTTATTAAATGTTTATTA
Found at i:85164 original size:17 final size:17
Alignment explanation
Indices: 85144--85176 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
85134 TTAACCATGC
85144 TTTTATCTTAAAAAAAT
1 TTTTATCTTAAAAAAAT
85161 TTTTATCTTAAAAAAA
1 TTTTATCTTAAAAAAA
85177 CTCTATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTATCTTAAAAAAAT
Found at i:90735 original size:14 final size:14
Alignment explanation
Indices: 90716--90751 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
90706 GAAAAGTAAT
90716 TCATTTTCCAAAAA
1 TCATTTTCCAAAAA
*
90730 TCATTTTCCAGAAA
1 TCATTTTCCAAAAA
*
90744 CCATTTTC
1 TCATTTTC
90752 AGTAAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (14 bp):
TCATTTTCCAAAAA
Found at i:91318 original size:14 final size:14
Alignment explanation
Indices: 91299--91332 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
91289 ATTAAGATAT
91299 GTCACACTATGAAC
1 GTCACACTATGAAC
* *
91313 GTCACATTATGAAT
1 GTCACACTATGAAC
91327 GTCACA
1 GTCACA
91333 AGTAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (14 bp):
GTCACACTATGAAC
Found at i:96041 original size:12 final size:12
Alignment explanation
Indices: 96014--96064 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
96004 ACTATTTTCG
**
96014 TGTTATTTTTAC
1 TGTTATTTTTGT
96026 TGTTATTTTTGT
1 TGTTATTTTTGT
*
96038 TGTTGTTTTT-T
1 TGTTATTTTTGT
*
96049 TGCTATTTTTGT
1 TGTTATTTTTGT
96061 TGTT
1 TGTT
96065 TTTAATTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 9 0.28
12 23 0.72
ACGTcount: A:0.08, C:0.04, G:0.16, T:0.73
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:96046 original size:23 final size:23
Alignment explanation
Indices: 96020--96064 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
96010 TTCGTGTTAT
*
96020 TTTTACTGTTATTTTTGTTGTTG
1 TTTTACTGCTATTTTTGTTGTTG
**
96043 TTTTTTTGCTATTTTTGTTGTT
1 TTTTACTGCTATTTTTGTTGTT
96065 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.04, G:0.16, T:0.73
Consensus pattern (23 bp):
TTTTACTGCTATTTTTGTTGTTG
Found at i:102896 original size:23 final size:22
Alignment explanation
Indices: 102853--102896 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
102843 TTTCACTATT
**
102853 TTTATTTTAAAATTTTTAATTA
1 TTTATTTTAAAATTTGAAATTA
*
102875 TTTATTTGTATAATTTGAAATT
1 TTTATTT-TAAAATTTGAAATT
102897 TCAAATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTATTTTAAAATTTGAAATTA
Found at i:108212 original size:30 final size:30
Alignment explanation
Indices: 108173--108244 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
108163 ATTTAATGTG
* *
108173 AACTTTAATTTGGTATAATTATATACGTGA
1 AACTTTAATTTGGTATAAATATATACGTAA
* * * *
108203 AACTCTAATTGTGGTTTAAATGTATACTTAA
1 AACTTTAATT-TGGTATAAATATATACGTAA
108234 AACTTTAATTT
1 AACTTTAATTT
108245 TGATTTAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (30 bp):
AACTTTAATTTGGTATAAATATATACGTAA
Found at i:108229 original size:31 final size:31
Alignment explanation
Indices: 108194--108252 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
108184 GGTATAATTA
* *
108194 TATACGTGAAACTCTAATTGTGGTTTAAATG
1 TATACGTAAAACTCTAATTGTGATTTAAATG
* * *
108225 TATACTTAAAACTTTAATTTTGATTTAA
1 TATACGTAAAACTCTAATTGTGATTTAA
108253 TCATACACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (31 bp):
TATACGTAAAACTCTAATTGTGATTTAAATG
Found at i:119468 original size:29 final size:28
Alignment explanation
Indices: 119412--119469 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
119402 AAATATGAAC
* *
119412 AAAAAAAAATCTAAATATCAAATTACAA
1 AAAAAAAAATATAAATATCAAATGACAA
* *
119440 AAAAAAAAATATATAATTTCAAGTGACAA
1 AAAAAAAAATATA-AATATCAAATGACAA
119469 A
1 A
119470 TGTTATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.22
Consensus pattern (28 bp):
AAAAAAAAATATAAATATCAAATGACAA
Found at i:135502 original size:20 final size:21
Alignment explanation
Indices: 135474--135515 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
135464 AAATAAAGCC
135474 ACGAAATTATGAACA-AAATT
1 ACGAAATTATGAACAGAAATT
* *
135494 ACGATATTATGGACAGAAATT
1 ACGAAATTATGAACAGAAATT
135515 A
1 A
135516 AAAACAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (21 bp):
ACGAAATTATGAACAGAAATT
Found at i:137493 original size:18 final size:18
Alignment explanation
Indices: 137472--137509 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
137462 TAAATTTTCG
137472 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
137490 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
137508 AA
1 AA
137510 AACTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:147983 original size:22 final size:22
Alignment explanation
Indices: 147958--148020 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
147948 ATAATTATTT
147958 TTTTTTAAAAAATTAATAAAAA
1 TTTTTTAAAAAATTAATAAAAA
* ** *
147980 -TTTTCAAACAGCTTAAT-TAAA
1 TTTTTTAAA-AAATTAATAAAAA
148001 TTTTTTAAAAAATTAA-AAAA
1 TTTTTTAAAAAATTAATAAAA
148021 TATAATAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 7
0.67 0.18 0.16
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTTTTAAAAAATTAATAAAAA
Found at i:162091 original size:106 final size:106
Alignment explanation
Indices: 161901--162113 Score: 374
Period size: 106 Copynumber: 2.0 Consensus size: 106
161891 AGCATTTGAG
* *
161901 AGCAAAATGAGCGAAAATAAAAAATTCGAAACAAGTTTTAAGAGCCACACAAGCTTGGTCATTCT
1 AGCAAAATGAGAGAAAATAAAAAATTCGAAACAAGTTTTAAGAGCCACACAAGCTTGGTCATTCC
161966 ACACGAGCCAAAAACATGGTAATGTGAGCCCACAGGTTGCC
66 ACACGAGCCAAAAACATGGTAATGTGAGCCCACAGGTTGCC
*
162007 AGCAAAATGAGAGAAAATAAAAAATT-GAAAACAGGTTTTAAGAGCCACACAAGCTTGGTCATTC
1 AGCAAAATGAGAGAAAATAAAAAATTCG-AAACAAGTTTTAAGAGCCACACAAGCTTGGTCATTC
*
162071 CACACGAGCCAAAAATATGGTAATGTGAGCCCACAGGTTGCC
65 CACACGAGCCAAAAACATGGTAATGTGAGCCCACAGGTTGCC
162113 A
1 A
162114 CATGGCCATG
Statistics
Matches: 102, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
105 1 0.01
106 101 0.99
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (106 bp):
AGCAAAATGAGAGAAAATAAAAAATTCGAAACAAGTTTTAAGAGCCACACAAGCTTGGTCATTCC
ACACGAGCCAAAAACATGGTAATGTGAGCCCACAGGTTGCC
Found at i:164292 original size:15 final size:16
Alignment explanation
Indices: 164274--164312 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
164264 ACCGTTAGTG
164274 TATTTAATAAT-AATT
1 TATTTAATAATAAATT
*
164289 TATTTTATAATAAAATT
1 TATTTAATAAT-AAATT
164306 TATTTAA
1 TATTTAA
164313 AATTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 10 0.50
17 10 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTTAATAATAAATT
Found at i:174957 original size:6 final size:6
Alignment explanation
Indices: 174936--175026 Score: 57
Period size: 6 Copynumber: 15.5 Consensus size: 6
174926 TTTAAATTGG
** **
174936 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TGTTAAA TTTAAA TTTATCTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA--AA
** *
174985 TTTAAA TTTAAA TTT-GC CTTAAA TTTAAA TTT-AA -TTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
175027 GAATGGATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
4 4 0.06
5 8 0.13
6 45 0.71
7 2 0.03
8 4 0.06
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:174971 original size:17 final size:17
Alignment explanation
Indices: 174936--175026 Score: 94
Period size: 17 Copynumber: 5.2 Consensus size: 17
174926 TTTAAATTGG
174936 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
174954 TTTAAATTTATGTTAAA
1 TTTAAATTTATTTTAAA
174971 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA---TTTTAAA
***
174991 TTTAAATTTGCCTTAAA
1 TTTAAATTTATTTTAAA
*
175008 TTTAAATTTA-ATTAAA
1 TTTAAATTTATTTTAAA
175024 TTT
1 TTT
175027 GAATGGATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
16 8 0.13
17 30 0.48
18 10 0.16
20 15 0.24
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:174994 original size:37 final size:35
Alignment explanation
Indices: 174936--175017 Score: 119
Period size: 37 Copynumber: 2.3 Consensus size: 35
174926 TTTAAATTGG
**
174936 TTTAAATTTATTTTTAAATTTAAATTTATGTTAAA
1 TTTAAATTTATTTTTAAATTTAAATTTACCTTAAA
*
174971 TTTAAATTTATCTTTTTAAATTTAAATTTGCCTTAAA
1 TTTAAATTTA--TTTTTAAATTTAAATTTACCTTAAA
175008 TTTAAATTTA
1 TTTAAATTTA
175018 ATTAAATTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
35 10 0.24
37 32 0.76
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (35 bp):
TTTAAATTTATTTTTAAATTTAAATTTACCTTAAA
Found at i:175776 original size:15 final size:15
Alignment explanation
Indices: 175756--175796 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
175746 AATATCATTG
*
175756 ACAATATTAATGACA
1 ACAATAATAATGACA
175771 ACAATAATAATGACA
1 ACAATAATAATGACA
*
175786 TCAATAATAAT
1 ACAATAATAAT
175797 ATTAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (15 bp):
ACAATAATAATGACA
Found at i:176904 original size:29 final size:28
Alignment explanation
Indices: 176864--177180 Score: 182
Period size: 29 Copynumber: 10.9 Consensus size: 28
176854 GAAGGTCCCT
176864 AAACTATCCAAAAATTACCATTTTATCCCC
1 AAACT-TCCAAAAATTACCATTTTA-CCCC
* ** * *
176894 GAACTTCCAAAAATCCCCTTTTTTCCCCC
1 AAACTTCCAAAAATTACC-ATTTTACCCC
*
176923 AAACCTTCCAAAAATTACAATTTTACCCTC
1 AAA-CTTCCAAAAATTACCATTTTACCC-C
* *
176953 AAACTTCCAAAAA-TCCCATTTTGACCTCG
1 AAACTTCCAAAAATTACCATTTT-ACC-CC
* * * *
176982 AACCCTCTAAAAATTACCATTTCACCCCC
1 AAACTTCCAAAAATTACCATTTTA-CCCC
*
177011 AAACTCCCAAAAA-T-CTCATTTTAACCCC
1 AAACTTCCAAAAATTAC-CATTTT-ACCCC
** *
177039 AAAACTTTTAAAAATTACCATATTACCCTC
1 -AAACTTCCAAAAATTACCATTTTACCC-C
* * **
177069 GAGC-TCTCAAAAA-CCCCATTTTTGACCCC
1 AAACTTC-CAAAAATTACCA-TTTT-ACCCC
*
177098 TAAACTTCTAAAAATTACCA-TTTACCCC
1 -AAACTTCCAAAAATTACCATTTTACCCC
*
177126 TAAAC-TCCTAAAAA-TCCCATTTTGACCCC
1 -AAACTTCC-AAAAATTACCATTTT-ACCCC
* *
177155 GAAACATCCAAAAATTACTATTTTAC
1 -AAACTTCCAAAAATTACCATTTTAC
177181 TCTCGGATGT
Statistics
Matches: 217, Mismatches: 46, Indels: 49
0.70 0.15 0.16
Matches are distributed among these distances:
27 7 0.03
28 39 0.18
29 103 0.47
30 62 0.29
31 6 0.03
ACGTcount: A:0.37, C:0.32, G:0.03, T:0.29
Consensus pattern (28 bp):
AAACTTCCAAAAATTACCATTTTACCCC
Found at i:177021 original size:58 final size:57
Alignment explanation
Indices: 176864--177177 Score: 286
Period size: 58 Copynumber: 5.4 Consensus size: 57
176854 GAAGGTCCCT
* * * * * **
176864 AAACTATCCAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCCTTTTTTCCCCCA
1 AAACT-TCTAAAAATTACCA-TTTACCCCCAAACTCCCAAAAAT-CCCATTTTGACCCCA
* * * * * * *
176924 AACCTTCCAAAAATTACAATTTTACCCTCAAACTTCCAAAAATCCCATTTTGACCTCG
1 AAACTTCTAAAAATTACCA-TTTACCCCCAAACTCCCAAAAATCCCATTTTGACCCCA
* * * *
176982 AACCCTCTAAAAATTACCATTTCACCCCCAAACTCCCAAAAATCTCATTTTAACCCCA
1 AAACTTCTAAAAATTACCATTT-ACCCCCAAACTCCCAAAAATCCCATTTTGACCCCA
* * * * * * *
177040 AAACTTTTAAAAATTACCATATTACCCTCGAGCTCTCAAAAACCCCATTTTTGACCCCT
1 AAACTTCTAAAAATTACCAT-TTACCCCCAAACTCCCAAAAATCCCA-TTTTGACCCCA
* * *
177099 AAACTTCTAAAAATTACCATTTACCCCTAAACTCCTAAAAATCCCATTTTGACCCCG
1 AAACTTCTAAAAATTACCATTTACCCCCAAACTCCCAAAAATCCCATTTTGACCCCA
* * *
177156 AAACATCCAAAAATTACTATTT
1 AAACTTCTAAAAATTACCATTT
177178 TACTCTCGGA
Statistics
Matches: 209, Mismatches: 42, Indels: 9
0.80 0.16 0.03
Matches are distributed among these distances:
57 32 0.15
58 109 0.52
59 64 0.31
60 4 0.02
ACGTcount: A:0.37, C:0.32, G:0.03, T:0.29
Consensus pattern (57 bp):
AAACTTCTAAAAATTACCATTTACCCCCAAACTCCCAAAAATCCCATTTTGACCCCA
Found at i:177818 original size:16 final size:16
Alignment explanation
Indices: 177797--177830 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
177787 CTTCGATCAC
177797 TTTGAAATAGCGGGAT
1 TTTGAAATAGCGGGAT
177813 TTTGAAATAGCGGGAT
1 TTTGAAATAGCGGGAT
177829 TT
1 TT
177831 CCAAATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (16 bp):
TTTGAAATAGCGGGAT
Found at i:177836 original size:16 final size:16
Alignment explanation
Indices: 177801--177837 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
177791 GATCACTTTG
**
177801 AAATAGCGGGATTTTG
1 AAATAGCGGGATTTCC
177817 AAATAGCGGGATTTCC
1 AAATAGCGGGATTTCC
177833 AAATA
1 AAATA
177838 AACCCTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (16 bp):
AAATAGCGGGATTTCC
Done.