Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014932.1 Kokia drynarioides strain JFW-HI SEQ_129975, 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: 269992
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 549 characters in sequence are not A, C, G, or T
Found at i:2344 original size:47 final size:47
Alignment explanation
Indices: 2275--2365 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
2265 TAATGATAAA
*
2275 TAATAAAACACTCTTATTTTCTTGTTATTTTGAGAGAAATATTTCTT
1 TAATAAAACACTCTCATTTTCTTGTTATTTTGAGAGAAATATTTCTT
2322 TAATAAAACACTCTCATTTTCTTGTTATTTTGAGAGAAATATTT
1 TAATAAAACACTCTCATTTTCTTGTTATTTTGAGAGAAATATTT
2366 ATTACTTACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (47 bp):
TAATAAAACACTCTCATTTTCTTGTTATTTTGAGAGAAATATTTCTT
Found at i:2553 original size:62 final size:60
Alignment explanation
Indices: 2478--2768 Score: 237
Period size: 59 Copynumber: 4.9 Consensus size: 60
2468 TTACCAAATA
*
2478 AAAAGGGGGTGTCGGCCATTGCATAGCCAACACCAAAAAAATTTGAAATTTTTTTATCAGAG
1 AAAAGGGGGTGTCGGCCATTGCAT-GCCAACACAAAAAAAATTTG-AATTTTTTTATCAGAG
* * *
2540 AAAAGGGGATGTCGGCCATTGCATGGCCAACACAAAAAAAATTTGAATTTTTTTATCCGGG
1 AAAAGGGGGTGTCGGCCATTGCAT-GCCAACACAAAAAAAATTTGAATTTTTTTATCAGAG
* *
2601 AACAGGGGGTGTCGGCCATTGCATGACCAACAC-TAAAAAA--TGCAATTTTTTTATTCTA-A-
1 AAAAGGGGGTGTCGGCCATTGCATG-CCAACACAAAAAAAATTTG-AATTTTTTTA-TC-AGAG
* * * * ** *
2660 AAAAAGGGGTGTCAGCCA-TGTAATGACCAATAC-TTAAAAATGT-AATTTTTTT-T--GA-
1 AAAAGGGGGTGTCGGCCATTG-CATG-CCAACACAAAAAAAATTTGAATTTTTTTATCAGAG
* * *** *
2715 AAAAGAGAGTGTTAACCATTGCATAGTCAACACAAAAAAAATTTGAATTTTTTT
1 AAAAGGGGGTGTCGGCCATTGCAT-GCCAACACAAAAAAAATTTGAATTTTTTT
2769 TTCTCAAAAT
Statistics
Matches: 190, Mismatches: 27, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
55 21 0.11
56 10 0.05
57 10 0.05
58 4 0.02
59 50 0.26
60 9 0.05
61 44 0.23
62 42 0.22
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (60 bp):
AAAAGGGGGTGTCGGCCATTGCATGCCAACACAAAAAAAATTTGAATTTTTTTATCAGAG
Found at i:2608 original size:61 final size:62
Alignment explanation
Indices: 2478--2640 Score: 247
Period size: 61 Copynumber: 2.6 Consensus size: 62
2468 TTACCAAATA
* *
2478 AAAAGGGGGTGTCGGCCATTGCATAGCCAACACCAAAAAAATTTGAAATTTTTTTATCAGAG
1 AAAAGGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTGAAATTTTTTTATCAGAG
* * *
2540 AAAAGGGGATGTCGGCCATTGCATGGCCAACACAAAAAAAATTTG-AATTTTTTTATCCGGG
1 AAAAGGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTGAAATTTTTTTATCAGAG
* * *
2601 AACAGGGGGTGTCGGCCATTGCATGACCAACACTAAAAAA
1 AAAAGGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAA
2641 TGCAATTTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 50 0.54
62 42 0.46
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (62 bp):
AAAAGGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTGAAATTTTTTTATCAGAG
Found at i:2652 original size:61 final size:59
Alignment explanation
Indices: 2426--2654 Score: 232
Period size: 61 Copynumber: 3.8 Consensus size: 59
2416 AGGGGAAGTT
* * * * * * *
2426 GGTGTCGACCATTACATTACCAACACCAAAAAATAT-AA-TTTTTTACCAAATAAAAAGGG
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAAT-TGAATTTTTTTATCAGA-GAAAAGGG
2485 GGTGTCGGCCATTGCAT-AGCCAACACCAAAAAAATTTGAAATTTTTTTATCAGAGAAAAGGG
1 GGTGTCGGCCATTGCATGA-CCAACA-CAAAAAAA-TTG-AATTTTTTTATCAGAGAAAAGGG
* * * * *
2547 GATGTCGGCCATTGCATGGCCAACACAAAAAAAATTTGAATTTTTTTATCCGGGAACAGGG
1 GGTGTCGGCCATTGCATGACCAACAC-AAAAAAA-TTGAATTTTTTTATCAGAGAAAAGGG
*
2608 GGTGTCGGCCATTGCATGACCAACACTAAAAAA-TGCAATTTTTTTAT
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAATTG-AATTTTTTTAT
2655 TCTAAAAAAA
Statistics
Matches: 147, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
58 3 0.02
59 32 0.22
60 14 0.10
61 46 0.31
62 42 0.29
63 10 0.07
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (59 bp):
GGTGTCGGCCATTGCATGACCAACACAAAAAAATTGAATTTTTTTATCAGAGAAAAGGG
Found at i:2669 original size:59 final size:57
Alignment explanation
Indices: 2426--2711 Score: 209
Period size: 59 Copynumber: 4.8 Consensus size: 57
2416 AGGGGAAGTT
* * * * *
2426 GGTGTCGACCATTACATTACCAACACCAAAAAATATAA-TTTTTTACCAAATAAAAAGGG
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAATGTAATTTTTTTACC-AA-AAAAA-GG
* * *
2485 GGTGTCGGCCATTGCAT-AGCCAACACCAAAAAAATTTGAAATTTTTTTATCAGAGAAAAGG
1 GGTGTCGGCCATTGCATGA-CCAACA-CAAAAAAA--TGTAATTTTTTTACCA-AAAAAAGG
* * ** * *
2546 GGATGTCGGCCATTGCATGGCCAACACAAAAAAAATTTGAATTTTTTTATCCGGGAACAGGG
1 GG-TGTCGGCCATTGCATGACCAACAC-AAAAAAATGT-AATTTTTTTA-CC-AAAAAAAGG
* * *
2608 GGTGTCGGCCATTGCATGACCAACACTAAAAAATGCAATTTTTTTATTCTAAAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACACAAAAAAATGTAATTTTTTTA--CCAAAAAAAGG
* * * **
2667 GGTGTCAGCCA-TGTAATGACCAATACTTAAAAATGTAATTTTTTT
1 GGTGTCGGCCATTG-CATGACCAACACAAAAAAATGTAATTTTTTT
2712 TGAAAAAGAG
Statistics
Matches: 183, Mismatches: 30, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
58 3 0.02
59 73 0.40
60 17 0.09
61 38 0.21
62 43 0.23
63 9 0.05
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (57 bp):
GGTGTCGGCCATTGCATGACCAACACAAAAAAATGTAATTTTTTTACCAAAAAAAGG
Found at i:3851 original size:2 final size:2
Alignment explanation
Indices: 3844--3879 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3834 TCCATAGTAT
*
3844 TC TC TC TC T- TT TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3880 TTTACGCCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:8114 original size:14 final size:14
Alignment explanation
Indices: 8095--8121 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8085 GGGGGTGGTT
8095 GTCATGTTTGAAGA
1 GTCATGTTTGAAGA
8109 GTCATGTTTGAAG
1 GTCATGTTTGAAG
8122 TATTCTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (14 bp):
GTCATGTTTGAAGA
Found at i:16100 original size:21 final size:20
Alignment explanation
Indices: 16076--16114 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
16066 TGAATGATAA
16076 GAAAATAAAATTAGGAAATTT
1 GAAAATAAAATTA-GAAATTT
16097 GAAAATAAAATTAGAAAT
1 GAAAATAAAATTAGAAAT
16115 GGAGGAAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (20 bp):
GAAAATAAAATTAGAAATTT
Found at i:23366 original size:75 final size:75
Alignment explanation
Indices: 23287--23462 Score: 289
Period size: 75 Copynumber: 2.3 Consensus size: 75
23277 TTGTTCCAGT
*
23287 CTCCCCCTCCCCCACCACCACTCCCTCCATCCTCAGCTACATCTACATCTTCTTCTGTAAAGAAT
1 CTCCCCCTCCCCCACCACCACTCCCTCCATCCTCAGCTACATCTACATCTTCTACTGTAAAGAAT
*
23352 TCATTTTCAG
66 TCATCTTCAG
* * *
23362 CTCCCCCTCCCCCACCACCACTCCCTCCATTCTCAGCTATATCTCCATCTTCTACTGTAAAGAAT
1 CTCCCCCTCCCCCACCACCACTCCCTCCATCCTCAGCTACATCTACATCTTCTACTGTAAAGAAT
23427 TCATCTTCAG
66 TCATCTTCAG
* *
23437 CTCCCCCTCCTCCTCCACCACTCCCT
1 CTCCCCCTCCCCCACCACCACTCCCT
23463 AATGTGGCTT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.19, C:0.48, G:0.05, T:0.28
Consensus pattern (75 bp):
CTCCCCCTCCCCCACCACCACTCCCTCCATCCTCAGCTACATCTACATCTTCTACTGTAAAGAAT
TCATCTTCAG
Found at i:25651 original size:17 final size:18
Alignment explanation
Indices: 25629--25666 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25619 ACTACAAAGT
*
25629 TAATACCATGAA-CAAAA
1 TAATACCATAAATCAAAA
*
25646 TAATACCCTAAATCAAAA
1 TAATACCATAAATCAAAA
25664 TAA
1 TAA
25667 AAGAAAGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (18 bp):
TAATACCATAAATCAAAA
Found at i:33964 original size:63 final size:63
Alignment explanation
Indices: 33829--34019 Score: 312
Period size: 63 Copynumber: 3.0 Consensus size: 63
33819 TCCACTCTAC
** * * ** *
33829 TGATCTTTGAATCATTGTTTGAAACTCGTTAGTTGAACTTCAAT-AAAAGCTTATCAGCCCAA
1 TGATCTTTGAATTGTTGCTTGGAACTCACTAGCTGAACTTCAATAAAAAGCTTATCAGCCCAA
33891 TGATCTTTGAATTGTTGCTTGGAACTCACTAGCTGAACTTCAATAAAAAGCTTATCAGCCCAA
1 TGATCTTTGAATTGTTGCTTGGAACTCACTAGCTGAACTTCAATAAAAAGCTTATCAGCCCAA
33954 TGATCTTTGAATTGTTGCTTGGAACTCACTAGCTGAACTTCAATAAAAAGCTTATCAGCCCAA
1 TGATCTTTGAATTGTTGCTTGGAACTCACTAGCTGAACTTCAATAAAAAGCTTATCAGCCCAA
34017 TGA
1 TGA
34020 CCTAGATAAA
Statistics
Matches: 121, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
62 37 0.31
63 84 0.69
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (63 bp):
TGATCTTTGAATTGTTGCTTGGAACTCACTAGCTGAACTTCAATAAAAAGCTTATCAGCCCAA
Found at i:45739 original size:23 final size:24
Alignment explanation
Indices: 45712--45777 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 24
45702 TTTAATATTC
**
45712 ACGAACATGTTCATTTAAC-TTAA
1 ACGAACATGTTCATCGAACATTAA
* *
45735 TCGAACATATTCA-CGAACATTAA
1 ACGAACATGTTCATCGAACATTAA
45758 ACGAACATGTTCAT-GAACAT
1 ACGAACATGTTCATCGAACAT
45778 ATAATTGAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (24 bp):
ACGAACATGTTCATCGAACATTAA
Found at i:45798 original size:47 final size:46
Alignment explanation
Indices: 45712--45800 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 46
45702 TTTAATATTC
* *
45712 ACGAACATGTTCATTTAACTTAATCGAACATATTCACGAACATTAA
1 ACGAACATGTTCATTGAACTTAATCGAACACATTCACGAACATTAA
*
45758 ACGAACATGTTCA-TGAACATATAATTGAACACATTCACGAACA
1 ACGAACATGTTCATTGAAC-T-TAATCGAACACATTCACGAACA
45801 ATGTTAATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 4 0.11
46 14 0.37
47 20 0.53
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (46 bp):
ACGAACATGTTCATTGAACTTAATCGAACACATTCACGAACATTAA
Found at i:48128 original size:89 final size:86
Alignment explanation
Indices: 48024--48194 Score: 306
Period size: 86 Copynumber: 2.0 Consensus size: 86
48014 CCAATTAACA
48024 AAATTATAATTTGATATTTTATAAGTGACTAAATTTAAAAAAAAATAGACAATAATATAAGTCAC
1 AAATTATAATTTGATATTTTATAAGTGACTAAATTT--AAAAAAATA-ACAATAATATAAGTCAC
48089 TTCAAGATATTTAAAAAACTCGAG
63 TTCAAGATATTTAAAAAACTCGAG
*
48113 AAATTATAATTTGATATTTTATAAGTGACTAAATTTAAAAAAATAATAATAATATAAGTCACTTC
1 AAATTATAATTTGATATTTTATAAGTGACTAAATTTAAAAAAATAACAATAATATAAGTCACTTC
48178 AAGATATTTAAAAAACT
66 AAGATATTTAAAAAACT
48195 TAAGGGTCAA
Statistics
Matches: 81, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
86 36 0.44
87 9 0.11
89 36 0.44
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.35
Consensus pattern (86 bp):
AAATTATAATTTGATATTTTATAAGTGACTAAATTTAAAAAAATAACAATAATATAAGTCACTTC
AAGATATTTAAAAAACTCGAG
Found at i:56079 original size:18 final size:18
Alignment explanation
Indices: 56056--56090 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56046 AATTGGTTCT
*
56056 AAAGAATCAAAACATCTG
1 AAAGAAACAAAACATCTG
*
56074 AAAGAAACAAACCATCT
1 AAAGAAACAAAACATCT
56091 TTTAAGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAGAAACAAAACATCTG
Found at i:62579 original size:14 final size:16
Alignment explanation
Indices: 62556--62587 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
62546 GGCACGAGAG
62556 TTTTTATTATTAT-TA
1 TTTTTATTATTATATA
62571 TTTTT-TTATTATATA
1 TTTTTATTATTATATA
62586 TT
1 TT
62588 AATGTTGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTATTATTATATA
Found at i:63235 original size:2 final size:2
Alignment explanation
Indices: 63230--63283 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
63220 TCTTTTCTCT
*
63230 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CG
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
63272 CA CA CA CA CA CA
1 CA CA CA CA CA CA
63284 AAATTTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.50, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:65508 original size:73 final size:73
Alignment explanation
Indices: 65389--65534 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
65379 GGTAATCATG
65389 GCGATGCTGTAGTTGCTATGCCAGATTTCCAAGTGGAAAAAAGTAGCCACAAATCACTACCACCA
1 GCGATGCTGTAGTTGCTATGCCAGATTTCCAAGTGGAAAAAAGTAGCCACAAATCACTACCACCA
65454 TAACATTA
66 TAACATTA
65462 GCGATGCTGTAGTTGCTATGCCAGATTTCCAAGTGGAAAAAAGTAGCCACAAATCACTACCACCA
1 GCGATGCTGTAGTTGCTATGCCAGATTTCCAAGTGGAAAAAAGTAGCCACAAATCACTACCACCA
65527 TAACATTA
66 TAACATTA
65535 TACAATGAGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (73 bp):
GCGATGCTGTAGTTGCTATGCCAGATTTCCAAGTGGAAAAAAGTAGCCACAAATCACTACCACCA
TAACATTA
Found at i:67107 original size:12 final size:12
Alignment explanation
Indices: 67090--67115 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
67080 ACCACCATGA
67090 ACTGCATTAACT
1 ACTGCATTAACT
67102 ACTGCATTAACT
1 ACTGCATTAACT
67114 AC
1 AC
67116 GAATATTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (12 bp):
ACTGCATTAACT
Found at i:69281 original size:8 final size:8
Alignment explanation
Indices: 69268--69293 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
69258 CAGTATTCAA
69268 TTAATATT
1 TTAATATT
69276 TTAATATT
1 TTAATATT
69284 TTAATATT
1 TTAATATT
69292 TT
1 TT
69294 GCTCAACCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTAATATT
Found at i:71016 original size:17 final size:18
Alignment explanation
Indices: 70991--71027 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
70981 TCTTTTAAAA
70991 ATTATAAAT-ATATAAATT
1 ATTATAAATAATA-AAATT
71009 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
71026 AT
1 AT
71028 ATTTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:76638 original size:43 final size:43
Alignment explanation
Indices: 76554--76638 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 43
76544 ACATATTAAT
* * * * * *
76554 TTAAATTTTAAATCCTAAATATTAATATTCAGCCTTTAAAAAA
1 TTAAATTTTAAACCCTAAATACTAATACTAAACCTTAAAAAAA
* *
76597 TTAAATTTTAAACCCTAAATACTAATGCTAAATCTTAAAAAA
1 TTAAATTTTAAACCCTAAATACTAATACTAAACCTTAAAAAA
76639 GCATAATGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.36
Consensus pattern (43 bp):
TTAAATTTTAAACCCTAAATACTAATACTAAACCTTAAAAAAA
Found at i:99032 original size:113 final size:113
Alignment explanation
Indices: 98908--99122 Score: 360
Period size: 113 Copynumber: 1.9 Consensus size: 113
98898 TTGGCCCCTT
*
98908 AAAATATAAAAATTTGATTTAATTCTTTAAAAATTATAAAAATATAGGCTATTAAAATGATAAAA
1 AAAATATAAAAATTTGATTTAATCCTTTAAAAATTATAAAAATATAGGCTATTAAAATGATAAAA
* **
98973 TTGTATTTTTGTTA-TAGTAAAAATTACAATTTAATTTTGCCCCTCTTA
66 TTATATTTTTACTATTA-TAAAAATTACAATTTAATTTTGCCCCTCTTA
*
99021 AAAATATAAAAATTTGATTTAATCCTTTAAAAATTATAAAAATATATGCTATTAAAATGATAAAA
1 AAAATATAAAAATTTGATTTAATCCTTTAAAAATTATAAAAATATAGGCTATTAAAATGATAAAA
*
99086 TTATATTTTTACTATTATAAAAATTATAATTTAATTT
66 TTATATTTTTACTATTATAAAAATTACAATTTAATTT
99123 CGACCCTTAA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
113 93 0.98
114 2 0.02
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (113 bp):
AAAATATAAAAATTTGATTTAATCCTTTAAAAATTATAAAAATATAGGCTATTAAAATGATAAAA
TTATATTTTTACTATTATAAAAATTACAATTTAATTTTGCCCCTCTTA
Found at i:100387 original size:2 final size:2
Alignment explanation
Indices: 100380--100407 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
100370 GAGTTTAGAA
100380 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
100408 GATGTACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101458 original size:13 final size:13
Alignment explanation
Indices: 101440--101478 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
101430 AATTTAGCAT
101440 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
101453 TGC-TTTGAAAAAG
1 TGCTTTTG-AAAAG
*
101466 TGATTTTGAAAAG
1 TGCTTTTGAAAAG
101479 CTTGGTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 4 0.17
13 15 0.65
14 4 0.17
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:101978 original size:17 final size:16
Alignment explanation
Indices: 101952--101991 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
101942 ATTTAGTTAG
101952 ATAT-ATATAAAACAT
1 ATATAATATAAAACAT
*
101967 ATATCAATATAAAATAT
1 ATAT-AATATAAAACAT
101984 ATATAATA
1 ATATAATA
101992 ACAATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 4 0.18
17 14 0.64
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAATATAAAACAT
Found at i:104926 original size:97 final size:97
Alignment explanation
Indices: 104758--104944 Score: 243
Period size: 97 Copynumber: 1.9 Consensus size: 97
104748 GAAAAGGATG
* * *
104758 TTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGTACAAATTTCCAGAATCAG
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTCCAAAATCAG
* *
104823 AGAT-AAAGAAACATTGCCTCGATTTAAGGGTA
66 AAATAAAAG-AACATTACCTCGATTTAAGGGTA
* * * * *
104855 TTCGATTATTTCGATTTGAGGAAAAATTTCACCTAGTAAGTTAAGGCACAGATTTTCAAAATTCA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTCCAAAA-TCA
*
104920 -AAATAAAAGAATATTACCTCGATTT
65 GAAATAAAAGAACATTACCTCGATTT
104945 TAAAGTTTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
97 70 0.91
98 7 0.09
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (97 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTCCAAAATCAG
AAATAAAAGAACATTACCTCGATTTAAGGGTA
Found at i:105239 original size:30 final size:28
Alignment explanation
Indices: 105171--105276 Score: 99
Period size: 28 Copynumber: 3.7 Consensus size: 28
105161 TGGATGCCCG
* *
105171 GGGGT-AAAATGGTAATTTTGGACACTC
1 GGGGTAAAAATGGTATTTTTGGAAACTC
* *
105198 GGGGGAAAAATGGTATTTTTGGAAAGTTC
1 GGGGTAAAAATGGTATTTTTGGAAA-CTC
*
105227 GAGGGTAAAAAT-GTAATTTTTGGAAAATC
1 G-GGGTAAAAATGGT-ATTTTTGGAAACTC
* *
105256 GGGGTCAAAAATTGAATTTTT
1 GGGGT-AAAAATGGTATTTTT
105277 AATCACAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
27 4 0.06
28 21 0.32
29 20 0.30
30 21 0.32
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (28 bp):
GGGGTAAAAATGGTATTTTTGGAAACTC
Found at i:105266 original size:29 final size:29
Alignment explanation
Indices: 105171--105276 Score: 105
Period size: 29 Copynumber: 3.7 Consensus size: 29
105161 TGGATGCCCG
* *
105171 GGGGT-AAAATGGTAA-TTTTGGACACTC
1 GGGGTAAAAATGGTAATTTTTGGAAAATC
* *
105198 GGGGGAAAAATGGT-ATTTTTGGAAAGTTC
1 GGGGTAAAAATGGTAATTTTTGGAAA-ATC
105227 GAGGGTAAAAAT-GTAATTTTTGGAAAATC
1 G-GGGTAAAAATGGTAATTTTTGGAAAATC
*
105256 GGGGTCAAAAATTG-AATTTTT
1 GGGGT-AAAAATGGTAATTTTT
105277 AATCACAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
27 5 0.07
28 20 0.30
29 21 0.31
30 21 0.31
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (29 bp):
GGGGTAAAAATGGTAATTTTTGGAAAATC
Found at i:108004 original size:23 final size:23
Alignment explanation
Indices: 107956--108147 Score: 188
Period size: 23 Copynumber: 8.2 Consensus size: 23
107946 ACTAGCGCGT
* *
107956 TCTGTTTAGCAC-GTCTCGTGCTC
1 TCTGATTAGCACTGTGT-GTGCTC
107979 TCTGTTATTAGCACTGTGTGTGCTC
1 TCTG--ATTAGCACTGTGTGTGCTC
*
108004 TCTGATTAGCACTTTGTGTGCTC
1 TCTGATTAGCACTGTGTGTGCTC
* * * *
108027 TCTGATTAGTATTTTGTGTACTC
1 TCTGATTAGCACTGTGTGTGCTC
108050 TCTGTTATTAGCACTGTGTGTGCTC
1 TCTG--ATTAGCACTGTGTGTGCTC
* * *
108075 TCTGATTAGCACTTTATGTGTTC
1 TCTGATTAGCACTGTGTGTGCTC
* * * *
108098 TCTGATTTGTACTTTGTGTACTC
1 TCTGATTAGCACTGTGTGTGCTC
* *
108121 TCTGTTTAGGACTGTGTGTGCTC
1 TCTGATTAGCACTGTGTGTGCTC
108144 TCTG
1 TCTG
108148 TTGCCCAGCA
Statistics
Matches: 141, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
23 102 0.72
25 36 0.26
26 3 0.02
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (23 bp):
TCTGATTAGCACTGTGTGTGCTC
Found at i:108045 original size:48 final size:47
Alignment explanation
Indices: 107993--108181 Score: 167
Period size: 48 Copynumber: 4.0 Consensus size: 47
107983 TTATTAGCAC
107993 TGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTATT
1 TGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTATT
* * *
108040 T-TGTGTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTT
1 TGTGTGTGCTCTCTG--ATTAGCACTTTGTGTGCTCTCTGATTAGTA-TT
* * * * * * *
108089 TATGTGT--TCTCTGATTTGTACTTTGTGTACTCTCTGTTTAGGA-C
1 TGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTATT
*
108133 TGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTATT
1 TGTGTGTGCTCTCTGATT----AGCACTTTGTGTGCTCTCTGATTAGTATT
108181 T
1 T
108182 TGGTACTCTT
Statistics
Matches: 114, Mismatches: 17, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
44 6 0.05
45 2 0.02
46 42 0.37
47 6 0.05
48 47 0.41
49 6 0.05
50 5 0.04
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.47
Consensus pattern (47 bp):
TGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTATT
Found at i:108100 original size:71 final size:71
Alignment explanation
Indices: 107976--108195 Score: 308
Period size: 71 Copynumber: 3.1 Consensus size: 71
107966 ACGTCTCGTG
*
107976 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTATTT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTATTT
108041 TGTGTA
66 TGTGTA
* * *
108047 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGTTCTCTGATTTGTACTT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTATTT
108112 TGTGTA
66 TGTGTA
*
108118 CTCTCTG-T-TTAGGACTGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT----AGCACTTTATGTGCTCTCTGATTAGT
108178 ATTTTG-GTA
62 ATTTTGTGTA
*
108187 CTCTTTGTT
1 CTCTCTGTT
108196 TGTTCCGTAT
Statistics
Matches: 135, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
68 2 0.01
69 30 0.22
70 11 0.08
71 87 0.64
72 5 0.04
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.47
Consensus pattern (71 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTATTT
TGTGTA
Found at i:110428 original size:45 final size:45
Alignment explanation
Indices: 110345--110458 Score: 133
Period size: 45 Copynumber: 2.5 Consensus size: 45
110335 CGAAGTACTT
*
110345 AACAGTAAGCACACA-AGTGCTGGGAAACAGTAAGCACACAAAGTGC-A
1 AACAGTAAGCACACACAGTGC----AATCAGTAAGCACACAAAGTGCGA
* * *
110392 ATCCAGTATGCACACACAGTGCAATCAGTAAGCACACGAAGTGCGA
1 A-ACAGTAAGCACACACAGTGCAATCAGTAAGCACACAAAGTGCGA
110438 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACACAGTGC
110459 TGAACAGTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
45 38 0.66
46 2 0.03
47 1 0.02
48 12 0.21
49 5 0.09
ACGTcount: A:0.41, C:0.25, G:0.22, T:0.12
Consensus pattern (45 bp):
AACAGTAAGCACACACAGTGCAATCAGTAAGCACACAAAGTGCGA
Found at i:110464 original size:23 final size:21
Alignment explanation
Indices: 110345--110470 Score: 112
Period size: 23 Copynumber: 5.5 Consensus size: 21
110335 CGAAGTACTT
110345 AACAGTAAGCACACAAGTGCTGGG
1 AACAGTAAGCACACAAGTGC---G
110369 AAACAGTAAGCACACAAAGTGC-
1 -AACAGTAAGCACAC-AAGTGCG
*
110391 AATCCAGTATGCACACACAGTGC-
1 AA--CAGTAAGCACACA-AGTGCG
110414 AATCAGTAAGCACACGAAGTGCG
1 AA-CAGTAAGCACAC-AAGTGCG
110437 AAACAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACA-AGTGC-G
110461 AACAGTAAGC
1 AACAGTAAGC
110471 GCGCTAGCGT
Statistics
Matches: 89, Mismatches: 3, Indels: 20
0.79 0.03 0.18
Matches are distributed among these distances:
21 2 0.02
22 18 0.20
23 46 0.52
24 3 0.03
25 14 0.16
26 6 0.07
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (21 bp):
AACAGTAAGCACACAAGTGCG
Found at i:113105 original size:3 final size:3
Alignment explanation
Indices: 113097--113202 Score: 133
Period size: 3 Copynumber: 34.3 Consensus size: 3
113087 CTTTCTTTTC
* * **
113097 ATT ATT ATT AAT ATT AATT AAT ATT ATT ATT AATT ATT A-T ACCA ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT -ATT ATT ATT A-TT ATT
113144 ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
113190 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
113203 AAGCTATTTA
Statistics
Matches: 91, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
2 2 0.02
3 79 0.87
4 10 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:113894 original size:6 final size:6
Alignment explanation
Indices: 113883--113970 Score: 55
Period size: 6 Copynumber: 15.2 Consensus size: 6
113873 ATTATTTAAA
* *
113883 TAAATT TAAATT TAATATT TATAA-- TAAATT TAAATT CCAAA-- TGAATT
1 TAAATT TAAATT TAA-ATT TA-AATT TAAATT TAAATT -TAAATT TAAATT
* *
113930 TAAATT T-AATA T-AATCT TAAATT TAAA-A TAAATT TAAATT T
1 TAAATT TAAATT TAAAT-T TAAATT TAAATT TAAATT TAAATT T
113971 GTTGGGCCCG
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
4 4 0.06
5 13 0.20
6 34 0.53
7 12 0.19
8 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:113914 original size:34 final size:33
Alignment explanation
Indices: 113876--113970 Score: 82
Period size: 34 Copynumber: 2.6 Consensus size: 33
113866 AATGGATATT
*
113876 ATTTAAATAAATTTAAATTTAATATTTATAATAA
1 ATTTAAATAAATTTAAATTTAATA-TAATAATAA
**
113910 ATTTAAATTCCAAATGAATTTAAATTTAATATAATCTTAA
1 ATTTAAA-T----A--AATTTAAATTTAATATAATAATAA
113950 ATTTAAAATAAATTTAAATTT
1 ATTT-AAATAAATTTAAATTT
113971 GTTGGGCCCG
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
34 18 0.36
35 1 0.02
36 1 0.02
39 1 0.02
40 11 0.22
41 18 0.36
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (33 bp):
ATTTAAATAAATTTAAATTTAATATAATAATAA
Found at i:113949 original size:17 final size:17
Alignment explanation
Indices: 113889--113970 Score: 94
Period size: 17 Copynumber: 4.8 Consensus size: 17
113879 TAAATAAATT
*
113889 TAAATTTAATATTTATAA
1 TAAATTTAA-ATTTAAAA
**
113907 TAAATTTAAATTCCAAA
1 TAAATTTAAATTTAAAA
* *
113924 TGAATTTAAATTTAATA
1 TAAATTTAAATTTAAAA
113941 T-AATCTTAAATTTAAAA
1 TAAAT-TTAAATTTAAAA
113958 TAAATTTAAATTT
1 TAAATTTAAATTT
113971 GTTGGGCCCG
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
16 3 0.06
17 39 0.72
18 12 0.22
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:125980 original size:26 final size:29
Alignment explanation
Indices: 125951--126004 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 29
125941 TCGAAAGGTA
125951 AGCTTTTTCATTG-CGGTT-TCT-ATGAG
1 AGCTTTTTCATTGTCGGTTATCTGATGAG
125977 AGCTTTTTCATTGTCGGTTATCTGATGA
1 AGCTTTTTCATTGTCGGTTATCTGATGA
126005 TCTGGTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 13 0.52
27 5 0.20
28 3 0.12
29 4 0.16
ACGTcount: A:0.17, C:0.15, G:0.22, T:0.46
Consensus pattern (29 bp):
AGCTTTTTCATTGTCGGTTATCTGATGAG
Found at i:126826 original size:23 final size:21
Alignment explanation
Indices: 126775--126826 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
126765 TTTTGTGGAA
*
126775 TTGATTCACCATCTTATTCAG
1 TTGATTCACCATCTTATCCAG
* *
126796 TGGTATTCAATCATCTTATCCAG
1 TTG-ATTC-ACCATCTTATCCAG
126819 CTTGATTC
1 -TTGATTC
126827 TCTATCTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 4 0.17
23 16 0.67
24 2 0.08
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (21 bp):
TTGATTCACCATCTTATCCAG
Found at i:127705 original size:4 final size:4
Alignment explanation
Indices: 127698--127722 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
127688 TTTTAAAATT
127698 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
127723 CTAGGTGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:127865 original size:43 final size:43
Alignment explanation
Indices: 127804--127889 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
127794 CTTGATTGTT
127804 GAGTTAGTTATGACAATACACATCAATAAAAAAAAAATTCAAA
1 GAGTTAGTTATGACAATACACATCAATAAAAAAAAAATTCAAA
127847 GAGTTAGTTATGACAATACACATCAATAAAAAAAAAATTCAAA
1 GAGTTAGTTATGACAATACACATCAATAAAAAAAAAATTCAAA
127890 CTTTTAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (43 bp):
GAGTTAGTTATGACAATACACATCAATAAAAAAAAAATTCAAA
Found at i:128063 original size:25 final size:24
Alignment explanation
Indices: 128007--128073 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
127997 AAAACCCATC
*
128007 AAAATTATAAAAAAAAAAAAAAGT
1 AAAAATATAAAAAAAAAAAAAAGT
* * *
128031 AAAGAATATTAAAAATAAAAAAATT
1 AAA-AATATAAAAAAAAAAAAAAGT
*
128056 ATAAAATAGAAAAAAAAA
1 A-AAAATATAAAAAAAAA
128074 CCATTGAGGG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
24 3 0.09
25 29 0.85
26 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (24 bp):
AAAAATATAAAAAAAAAAAAAAGT
Found at i:128335 original size:27 final size:25
Alignment explanation
Indices: 128305--128367 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
128295 GTATGAGAGG
128305 ATTTTCTTATTTAATATTAATATAATT
1 ATTTT-TTATTTAATATTAA-ATAATT
*
128332 A-TTTTTATTTAATATTAAATTATT
1 ATTTTTTATTTAATATTAAATAATT
128356 ATTATTATTATT
1 ATT-TT-TTATT
128368 ATATTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 6 0.19
25 15 0.47
26 5 0.16
27 6 0.19
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTTTTATTTAATATTAAATAATT
Found at i:128341 original size:25 final size:24
Alignment explanation
Indices: 128311--128364 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
128301 GAGGATTTTC
*
128311 TTATTTAATATTAATATAATTATTT
1 TTATTTAATATTAA-ATAATTATTA
*
128336 TTATTTAATATTAAATTATTATTA
1 TTATTTAATATTAAATAATTATTA
128360 TTATT
1 TTATT
128365 ATTATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATTTAATATTAAATAATTATTA
Found at i:128352 original size:21 final size:19
Alignment explanation
Indices: 128321--128361 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
128311 TTATTTAATA
*
128321 TTAATATAATTATTTTTAT
1 TTAATATAATTATTATTAT
128340 TTAATATTAAATTATTATTAT
1 TTAATA-T-AATTATTATTAT
128361 T
1 T
128362 ATTATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAATATAATTATTATTAT
Found at i:149249 original size:2 final size:2
Alignment explanation
Indices: 149242--149268 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
149232 AGAGGGTGGA
149242 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
149269 GAAAGAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:157090 original size:31 final size:31
Alignment explanation
Indices: 156994--157090 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
156984 TATATTAACA
* * * *
156994 AATTTAAT-TCTCAATACTTATATATTCCATC
1 AATTTAATCTCTC-ATATTTAAAAATTTCATC
* *
157025 AATTTAATCT-T-A-ATTCTAAATAATTTAATA
1 AATTTAATCTCTCATATT-TAAA-AATTTCATC
*
157055 AATTTAATCTCTCATATTTACAAATTTCATC
1 AATTTAATCTCTCATATTTAAAAATTTCATC
157086 AATTT
1 AATTT
157091 GATCCTTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
28 2 0.04
29 4 0.08
30 15 0.29
31 22 0.43
32 5 0.10
33 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (31 bp):
AATTTAATCTCTCATATTTAAAAATTTCATC
Found at i:161229 original size:220 final size:220
Alignment explanation
Indices: 160994--161438 Score: 802
Period size: 220 Copynumber: 2.0 Consensus size: 220
160984 AAAAATGAAA
160994 AAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCAGAATTTGAGCCTATACTTGTCAATC
1 AAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCAGAATTTGAGCCTATACTTGTCAATC
* *
161059 CAATGACATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAATCCACAGTCAAAGG
66 CAATGACATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAAGCCACAATCAAAGG
161124 CCAGTTCTTTAAAAACAAAATCATCCCCAAACAATTAACAAGAAGTTCACTTTCTTCTAGATATA
131 CCAGTTCTTTAAAAACAAAATCATCCCCAAACAATTAACAAGAAGTTCACTTTCTTCTAGATATA
161189 TGCATTATCCCCATTAGCAAAA-AT
196 TGCATTATCCCCATTAGCAAAAGAT
* *
161213 GAAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCGGAATTTGAGCCTATTCTTGTCAAT
1 -AAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCAGAATTTGAGCCTATACTTGTCAAT
*
161278 CCAATGACATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAAGCCGCAATCAAAG
65 CCAATGACATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAAGCCACAATCAAAG
* * *
161343 GCCAGTTCTTTAAAAACAAAATCATCTCCAAACAATTAACAAGAAGTTCACTTTCTTTTAGGTAT
130 GCCAGTTCTTTAAAAACAAAATCATCCCCAAACAATTAACAAGAAGTTCACTTTCTTCTAGATAT
161408 ATGCATTATCCCCATTAGCAAAAGAT
195 ATGCATTATCCCCATTAGCAAAAGAT
161434 AAAAA
1 AAAAA
161439 GATTTTCAAC
Statistics
Matches: 216, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
220 214 0.99
221 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (220 bp):
AAAAAAAAATGTTTAGCTTATCTTTACTCCATCGATTTCAGAATTTGAGCCTATACTTGTCAATC
CAATGACATGGACATCAAGAAATTAAATATCAAGAACCTTTAAAGCATCAAGCCACAATCAAAGG
CCAGTTCTTTAAAAACAAAATCATCCCCAAACAATTAACAAGAAGTTCACTTTCTTCTAGATATA
TGCATTATCCCCATTAGCAAAAGAT
Found at i:163878 original size:18 final size:18
Alignment explanation
Indices: 163855--163899 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
163845 GCATGACTTT
*
163855 GCAAAGTACACTAATAGC
1 GCAAAGTACACTAAAAGC
163873 GCAAAGTACACTAAAAGC
1 GCAAAGTACACTAAAAGC
163891 GCAAAGTAC
1 GCAAAGTAC
163900 TGCAGAGGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (18 bp):
GCAAAGTACACTAAAAGC
Found at i:174902 original size:16 final size:18
Alignment explanation
Indices: 174869--174905 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
174859 TATTGTGATG
*
174869 TATATTATTTTATTTTTA
1 TATATTATTTTATATTTA
174887 TATATTA-TTTA-ATTTA
1 TATATTATTTTATATTTA
174903 TAT
1 TAT
174906 CATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 4 0.22
18 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATATTATTTTATATTTA
Found at i:181184 original size:19 final size:19
Alignment explanation
Indices: 181162--181203 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
181152 AGTAAATTTT
*
181162 AAAATAATTTTTAAAAA-TA
1 AAAAT-ATTTATAAAAATTA
181181 AAAATATTTATAAAAATTA
1 AAAATATTTATAAAAATTA
181200 AAAA
1 AAAA
181204 ATCTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATTTATAAAAATTA
Found at i:181210 original size:18 final size:18
Alignment explanation
Indices: 181173--181210 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
181163 AAATAATTTT
*
181173 TAAAAATAAAAATATTTA
1 TAAAAATAAAAATATCTA
181191 TAAAAATTAAAAA-ATCTA
1 TAAAAA-TAAAAATATCTA
181209 TA
1 TA
181211 TATTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAATAAAAATATCTA
Found at i:183599 original size:15 final size:16
Alignment explanation
Indices: 183579--183608 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
183569 GCCGTTGTTC
183579 GAAGAGAAA-AAGAGA
1 GAAGAGAAACAAGAGA
183594 GAAGAGAAACAAGAG
1 GAAGAGAAACAAGAG
183609 CTGAGATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (16 bp):
GAAGAGAAACAAGAGA
Found at i:184307 original size:17 final size:16
Alignment explanation
Indices: 184287--184356 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
184277 AAAATATTAG
184287 TAAAATTAATAATAATA
1 TAAAA-TAATAATAATA
*
184304 TAAAA-AATATATAACA
1 TAAAATAATA-ATAATA
** *
184320 TCCCAATAATAATAACAA
1 T-AAAATAATAATAA-TA
184338 TAAAATAATAATAATA
1 TAAAATAATAATAATA
184354 TAA
1 TAA
184357 CAGTGAAATG
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
15 4 0.10
16 10 0.24
17 22 0.52
18 6 0.14
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAATAATAATAATA
Found at i:194978 original size:25 final size:25
Alignment explanation
Indices: 194950--195022 Score: 112
Period size: 25 Copynumber: 2.9 Consensus size: 25
194940 TTTTAACAGA
194950 AAAAATTAATTTATTAATTTTTTTT
1 AAAAATTAATTTATTAATTTTTTTT
194975 AAAAATTAATTTATTAA-TTTTTTT
1 AAAAATTAATTTATTAATTTTTTTT
*
194999 AAAAATTAATATAATCTAATTTTT
1 AAAAATTAAT-TTAT-TAATTTTT
195023 AATATAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
24 17 0.39
25 20 0.45
26 3 0.07
27 4 0.09
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
AAAAATTAATTTATTAATTTTTTTT
Found at i:206320 original size:2 final size:2
Alignment explanation
Indices: 206313--206340 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
206303 CCAAATAATT
206313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
206341 GCTAAAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:209899 original size:21 final size:22
Alignment explanation
Indices: 209874--209918 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
209864 ATTTTTGTGA
*
209874 TATTTTTAT-TTATGATAATAT
1 TATTTTAATATTATGATAATAT
*
209895 TA-TTTAATATTATGATAATTT
1 TATTTTAATATTATGATAATAT
209916 TAT
1 TAT
209919 ATATCTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TATTTTAATATTATGATAATAT
Found at i:211271 original size:17 final size:17
Alignment explanation
Indices: 211241--211273 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
211231 TTTTTCTATC
211241 AAAATGAAAAAAAAAAT
1 AAAATGAAAAAAAAAAT
211258 AAAAT-AAAAGAAAAAA
1 AAAATGAAAA-AAAAAA
211274 GAAACAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAATGAAAAAAAAAAT
Found at i:211331 original size:18 final size:17
Alignment explanation
Indices: 211308--211357 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
211298 GTTCAAGGTA
211308 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAA-TTT
211326 TAATTAA-TTAATTAATTT
1 TAATTAATTTAA--AATTT
*
211344 TATTTAATTTAAAA
1 TAATTAATTTAAAA
211358 CATATTCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 6 0.21
18 16 0.57
19 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATTAATTTAAAATTT
Found at i:212279 original size:9 final size:9
Alignment explanation
Indices: 212259--212291 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
212249 AGTTTTCTTC
212259 CTTTTTT-T
1 CTTTTTTGT
212267 -TTTTTTGT
1 CTTTTTTGT
212275 CTTTTTTGT
1 CTTTTTTGT
212284 CTTTTTTG
1 CTTTTTTG
212292 GCGAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 6 0.26
8 1 0.04
9 16 0.70
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (9 bp):
CTTTTTTGT
Found at i:213227 original size:93 final size:93
Alignment explanation
Indices: 213040--213231 Score: 264
Period size: 93 Copynumber: 2.1 Consensus size: 93
213030 CATGAAACTG
* ** * *
213040 AAAGAAAATTTCTTTAGTGGTTCGGCTGAGAAATATGCTGGTGTGTTATATGGTCTTGGTGTTGA
1 AAAGAAAAGTTCTTTAGTGGTTCGAATGAGAAATATGCTGGTGTGTTATATGGCCTTGGTGTTCA
213105 GAATGGACAGAATACTCTCTAATAAATC
66 GAATGGACAGAATACTCTCTAATAAATC
*
213133 AAAGAAAAGTTCTTTAGTTGG-TCGAATGAGAAATATGCTGGTTTGTTATATGGCCTTGGTTGTT
1 AAAGAAAAGTTCTTTAG-TGGTTCGAATGAGAAATATGCTGGTGTGTTATATGGCCTTGG-TGTT
* *
213197 CAGAATTGACAGAATACT-TCTTAA-ATATC
64 CAGAATGGACAGAATACTCTC-TAATAAATC
213226 AAAGAA
1 AAAGAA
213232 TTATGAAATA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
93 62 0.70
94 26 0.30
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.34
Consensus pattern (93 bp):
AAAGAAAAGTTCTTTAGTGGTTCGAATGAGAAATATGCTGGTGTGTTATATGGCCTTGGTGTTCA
GAATGGACAGAATACTCTCTAATAAATC
Found at i:225578 original size:48 final size:48
Alignment explanation
Indices: 225519--225616 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
225509 GCCTGCTGAG
225519 AACCATCACCCTTTGTCTGACAATAAAACTGCTGGTGAGCCAGAGACA
1 AACCATCACCCTTTGTCTGACAATAAAACTGCTGGTGAGCCAGAGACA
225567 AACCATCACCCTTTGTCTGACAATAAAACTGCTGGTGAGCCAGAGACA
1 AACCATCACCCTTTGTCTGACAATAAAACTGCTGGTGAGCCAGAGACA
225615 AA
1 AA
225617 GGAGACTGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (48 bp):
AACCATCACCCTTTGTCTGACAATAAAACTGCTGGTGAGCCAGAGACA
Found at i:231174 original size:35 final size:35
Alignment explanation
Indices: 231135--231204 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
231125 AATCCAAACA
*
231135 AGAAA-AAAAAAAAAAAAAACATTTTCTTTCCCTTT
1 AGAAAGAAAAAAAAAAAAAACATTTT-TTTCACTTT
* * *
231170 AGAAAGATAAAGAAAAAAAAGATTTTTTTCACTTT
1 AGAAAGAAAAAAAAAAAAAACATTTTTTTCACTTT
231205 TTTTTTGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (35 bp):
AGAAAGAAAAAAAAAAAAAACATTTTTTTCACTTT
Found at i:234871 original size:4 final size:4
Alignment explanation
Indices: 234862--234889 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
234852 TACCCAAAAT
234862 ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG
234890 GGGAGATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:238984 original size:18 final size:18
Alignment explanation
Indices: 238956--238990 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
238946 AGTCAAATTA
238956 ATCTGCCATTTCCATTTCC
1 ATCTGCCATTT-CATTTCC
238975 ATCT-CCATTTCATTTC
1 ATCTGCCATTTCATTTC
238991 TTTTCATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.17, C:0.34, G:0.03, T:0.46
Consensus pattern (18 bp):
ATCTGCCATTTCATTTCC
Found at i:255059 original size:5 final size:5
Alignment explanation
Indices: 255049--255074 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
255039 ATGATACATC
255049 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
255075 GTCTAATGTT
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):
ATAAA
Found at i:263788 original size:24 final size:24
Alignment explanation
Indices: 263761--263814 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
263751 AAGATGACTG
*
263761 TATAAAAATTTTGAAATA-AAAATA
1 TATAAAAATATT-AAATATAAAATA
*
263785 TATAAAAATATTAAATATTAAATA
1 TATAAAAATATTAAATATAAAATA
263809 T-TAAAA
1 TATAAAA
263815 TAATATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
TATAAAAATATTAAATATAAAATA
Found at i:264674 original size:41 final size:43
Alignment explanation
Indices: 264606--264688 Score: 100
Period size: 40 Copynumber: 2.0 Consensus size: 43
264596 TTTCAAAAAA
*
264606 ATATATATTTAAAATAATTTTAAAAATTTTAACAATAAATTATAT
1 ATATATATTTAAAAT-ATTTTAAAAA-TTTAAAAATAAATTATAT
* *
264651 ATATATATTT-AAAT-TTTT-TAAATTTAAAAATTAATTAT
1 ATATATATTTAAAATATTTTAAAAATTTAAAAATAAATTAT
264689 TGATGTGGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 14 0.40
41 3 0.09
42 4 0.11
44 4 0.11
45 10 0.29
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (43 bp):
ATATATATTTAAAATATTTTAAAAATTTAAAAATAAATTATAT
Found at i:265090 original size:23 final size:24
Alignment explanation
Indices: 265064--265110 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
265054 AAAATAATGT
*
265064 AATTTAATAAAACA-TATATTAAA
1 AATTTAATAAAACAGTAAATTAAA
265087 AATTTAATAAAACAGTAAATTAAA
1 AATTTAATAAAACAGTAAATTAAA
265111 GAGGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
AATTTAATAAAACAGTAAATTAAA
Done.