Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014222.1 Kokia drynarioides strain JFW-HI SEQ_129255, 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: 68707
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:239 original size:29 final size:29
Alignment explanation
Indices: 147--501 Score: 246
Period size: 30 Copynumber: 12.0 Consensus size: 29
137 CCTTAAAGTT
* *
147 CCCTAAA-TTGTCCAAAAATTATATTTTAA
1 CCCTAAACTT-TCCAAAAATTACATTTTTA
* *
176 CCCCTAAACTTCTCCAAAAA-TATATTTTGA
1 -CCCTAAACTT-TCCAAAAATTACATTTTTA
*
206 CCCCTAAACTTTCAAAAAATTACATTTTTA
1 -CCCTAAACTTTCCAAAAATTACATTTTTA
*
236 CCCTCGAACTTTCC-AAAATT-CTATTTTTGA
1 CCCT-AAACTTTCCAAAAATTAC-ATTTTT-A
** * *
266 CCCTAATTTTTCCAAAAATAACAATTTTA
1 CCCTAAACTTTCCAAAAATTACATTTTTA
*
295 CCCCTAAA-TATTCC-AAAATTCCATTTTTGA
1 -CCCTAAACT-TTCCAAAAATTACATTTTT-A
** * *
325 CCC-CGA-TTTCACAAAAAAATGCATTTTTA
1 CCCTAAACTTTC-C-AAAAATTACATTTTTA
* *
354 CCGCCAAACTTTCC-AAAATTCCATTTTTAA
1 CC-CTAAACTTTCCAAAAATTACATTTTT-A
* *
384 CCCTAAAATTTCCAAAAATTACATTTTAA
1 CCCTAAACTTTCCAAAAATTACATTTTTA
* * *
413 CCCCCAAAC-TTCAAAAAATTCCATTTTTAA
1 -CCCTAAACTTTCCAAAAATTACATTTTT-A
* * *
443 CCTCAAAAATTTCAAAAAATTACATTTTTA
1 CC-CTAAACTTTCCAAAAATTACATTTTTA
473 CCCCTAAAC-TTCCAAAAATTACATTTTTA
1 -CCCTAAACTTTCCAAAAATTACATTTTTA
502 ATCCCGAAAC
Statistics
Matches: 263, Mismatches: 39, Indels: 47
0.75 0.11 0.13
Matches are distributed among these distances:
27 3 0.01
28 4 0.02
29 107 0.41
30 112 0.43
31 33 0.13
32 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATTACATTTTTA
Found at i:520 original size:60 final size:59
Alignment explanation
Indices: 151--510 Score: 295
Period size: 59 Copynumber: 6.0 Consensus size: 59
141 AAAGTTCCCT
* * * * ** * * *
151 AAATTGTCCAAAAATTATATTTTAACCCCTAAACTTCTCCAAAAATATATTTTGACCCCTA
1 AAATT-TCAAAAAATTACATTTTTACCCCTAAACTT-TCCAAAATTCCATTTTTAACCCGA
* * * * *
212 AACTTTCAAAAAATTACATTTTTA-CCCTCGAACTTTCCAAAATTCTATTTTTGACCCTA
1 AAATTTCAAAAAATTACATTTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCGA
** * * * *
271 ATTTTTCCAAAAATAACAATTTTACCCCTAAA-TATTCCAAAATTCCATTTTTGACCCCG-
1 AAATTTCAAAAAATTACATTTTTACCCCTAAACT-TTCCAAAATTCCATTTTT-AACCCGA
* * *
330 --ATTTCACAAAAAAATGCATTTTTACCGCC-AAACTTTCCAAAATTCCATTTTTAACCCTA
1 AAATTT--CAAAAAATTACATTTTTACC-CCTAAACTTTCCAAAATTCCATTTTTAACCCGA
* * * * *
389 AAATTTCCAAAAATTACATTTTAACCCCCAAAC-TTCAAAAAATTCCATTTTTAACCTCAA
1 AAATTTCAAAAAATTACATTTTTACCCCTAAACTTTC-CAAAATTCCATTTTTAACC-CGA
*
449 AAATTTCAAAAAATTACATTTTTACCCCTAAAC-TTCCAAAAATTACATTTTTAATCCCGA
1 AAATTTCAAAAAATTACATTTTTACCCCTAAACTTTCC-AAAATTCCATTTTTAA-CCCGA
509 AA
1 AA
511 CTTGTAAAAA
Statistics
Matches: 243, Mismatches: 40, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
57 3 0.01
58 10 0.04
59 135 0.56
60 85 0.35
61 10 0.04
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.35
Consensus pattern (59 bp):
AAATTTCAAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCGA
Found at i:3615 original size:19 final size:19
Alignment explanation
Indices: 3578--3620 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3568 TGAAAGAAAG
*
3578 AGATCGAAATTTGGTAAGA
1 AGATAGAAATTTGGTAAGA
*
3597 GGATAGAAATATTGG-AAGA
1 AGATAGAAAT-TTGGTAAGA
3616 AGATA
1 AGATA
3621 AGATGAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.47, C:0.02, G:0.28, T:0.23
Consensus pattern (19 bp):
AGATAGAAATTTGGTAAGA
Found at i:9842 original size:12 final size:12
Alignment explanation
Indices: 9825--9857 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
9815 TCTTTGCCTA
9825 CAGAACTTCAGT
1 CAGAACTTCAGT
9837 CAGAACTTCAGT
1 CAGAACTTCAGT
9849 CAGAACTTC
1 CAGAACTTC
9858 TACTGGGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (12 bp):
CAGAACTTCAGT
Found at i:11145 original size:115 final size:114
Alignment explanation
Indices: 10971--11177 Score: 310
Period size: 115 Copynumber: 1.8 Consensus size: 114
10961 GGTTTAAAGC
* * *
10971 GAGCAAATCTTCGAACCACAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGTAATAAAATGG
1 GAGCAAATCTTCGAACCACAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAA-AG
*
11036 TTAGCTTCCTGATGAGATACAT-AGAAGTATACCAACTCAGGGCTCGAAGT
65 CTAGCTTCCTGATGAGATAC-TGAGAAGTATACCAACTCAGGGCTCGAAGT
* * *
11086 GAGCAAATCTTCGAATCTCAGCTTCCTGATGAGATACTGAGAAGCAGGGT-GAAGAAATAAAAAG
1 GAGCAAATCTTCGAACCACAACTTCCTGATGAGATACTGAGAAGCA-GGTCGAAGAAATAAAAAG
11150 CTAGCTTCCTGATGAGATACTGAGAAGT
65 CTAGCTTCCTGATGAGATACTGAGAAGT
11178 GGACCAAATT
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
113 1 0.01
114 26 0.31
115 53 0.64
116 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (114 bp):
GAGCAAATCTTCGAACCACAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAAAGC
TAGCTTCCTGATGAGATACTGAGAAGTATACCAACTCAGGGCTCGAAGT
Found at i:11579 original size:206 final size:202
Alignment explanation
Indices: 11086--11883 Score: 940
Period size: 206 Copynumber: 3.9 Consensus size: 202
11076 GGCTCGAAGT
* * *
11086 GAGCAAATCTTCGAATCTCAGCTTCCTGATGAGATACTGAGAAGCAGGGT-GAAGAAATAAAAAG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA-GGTCGAAGCAATAAAAAG
* * * * *
11150 CTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGGTACAGAGAAGC
65 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGC
** * * * * *
11215 GGATTGAAACAAGTAAGGCGGTCATCTTCCTGATGAGATA-TAGAGAAGAATACCAACT--CGAG
130 GGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACT-GAGAAGAAGACCAAATAACCAC
*
11277 GCTCAATAC
194 GCTCAATGC
* * * * * *
11286 GGGTAAATTTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA-AG
* * * *
11351 TTAACCTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGA
65 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGC
* * * *
11416 GGATTGAAATAAGCGATGTGGTCACCTTCTTGATGAGATACTGAGAAGAAGACCAAATTGAACCC
130 GGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA-T-AA-CC
*
11481 ACGCTTAATGC
192 ACGCTCAATGC
11492 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGT-GAAGCAATAAAAAG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA-GGTCGAAGCAATAAAAA-
* * *
11556 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAAAG
64 GTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAG
* * * * *
11621 CGGATTGAAACAAACGATGCGATCATCTTCATGATGAGACACAGAGAAGAAGACCAAATCAAGTC
129 CGGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT-AA--C
* * *
11686 TACGCTCGATGT
191 CACGCTCAATGC
* * * *
11698 GAGCAAACCTTCGAACCCCAGCTTCCTAATTAGATACTGAGAAGCAGGTCGAAGTAATAAAATAG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA-AG
* * * * *
11763 TTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTAATGAAACACAGAGAAGT
65 TTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGC
** * * * *
11828 GGATCAAAACAAGTGATGCGGTCATCTTCCTGATAAGATACTAAGAAGAAGGCCAA
130 GGATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
11884 GTCAATGAAA
Statistics
Matches: 504, Mismatches: 81, Indels: 20
0.83 0.13 0.03
Matches are distributed among these distances:
199 3 0.01
200 50 0.10
201 103 0.20
202 2 0.00
205 6 0.01
206 336 0.67
207 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (202 bp):
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAAGT
TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCG
GATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATAACCACGC
TCAATGC
Found at i:11869 original size:412 final size:406
Alignment explanation
Indices: 11086--11883 Score: 1101
Period size: 412 Copynumber: 2.0 Consensus size: 406
11076 GGCTCGAAGT
* *
11086 GAGCAAATCTTCGAATCTCAGCTTCCTGATGAGATACTGAGAAGCAGGGTGAAGAAATAAAAAGC
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGTGAAGAAATAAAAAGC
* * *
11151 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGGTACAGAGAAGCG
66 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAAAGCG
** * * * * * *
11216 GATTGAAACAAGTAAGGCGGTCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCGAGGCTC
131 GATTGAAACAAACAAGGCGATCATCTTCATGATGAGACACAGAGAAGAAGACCAACTCGACGCTC
* * ** * *
11281 AATACGGGTAAATTTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAA
196 AATACGAGCAAACCTTCGAACCCCAGCTTCCTAATGAGACACTGAGAAGCAGGTCGAAGCAATAA
* * * * *
11346 AATGGTTAACCTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTAATGAGATACAGA
261 AATAGTTAACCTCCTGATGAGATACGGAGAAGTAAACCAAATCCGTCTTCCTAATGAAACACAGA
** * * * * *
11411 GAAGAGGATTGAAATAAGCGATGTGGTCACCTTCTTGATGAGATACTGAGAAGAAGACCAAATTG
326 GAAGAGGATCAAAACAAGCGATGCGGTCACCTTCCTGATAAGATACTAAGAAGAAGACCAAATTG
11476 AACCCACGCTTAATGC
391 AACCCACGCTTAATGC
*
11492 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGTGAAGCAATAAAAAGG
1 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGTGAAGAAATAAAAA-G
*
11557 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAAAGC
65 CTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAAAGC
* * *
11622 GGATTGAAACAAACGATGCGATCATCTTCATGATGAGACACAGAGAAGAAGACCAAATCAAGTCT
130 GGATTGAAACAAACAAGGCGATCATCTTCATGATGAGACACAGAGAAGAAGACC-AA-C---TCG
* ** * *
11687 ACGCTCGATGTGAGCAAACCTTCGAACCCCAGCTTCCTAATTAGATACTGAGAAGCAGGTCGAAG
190 ACGCTCAATACGAGCAAACCTTCGAACCCCAGCTTCCTAATGAGACACTGAGAAGCAGGTCGAAG
* * * *
11752 TAATAAAATAGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTAATGAAA
255 CAATAAAATAGTTAACCTCCTGATGAGATACGGAGAAGTAAACCAAATCCGTCTTCCTAATGAAA
* * * *
11817 CACAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATAAGATACTAAGAAGAAGGCC
320 CACAGAGAAGAGGATCAAAACAAGCGATGCGGTCACCTTCCTGATAAGATACTAAGAAGAAGACC
11882 AA
385 AA
11884 GTCAATGAAA
Statistics
Matches: 337, Mismatches: 49, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
406 60 0.18
407 107 0.32
408 2 0.01
409 1 0.00
412 167 0.50
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (406 bp):
GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGTGAAGAAATAAAAAGC
TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAAAGCG
GATTGAAACAAACAAGGCGATCATCTTCATGATGAGACACAGAGAAGAAGACCAACTCGACGCTC
AATACGAGCAAACCTTCGAACCCCAGCTTCCTAATGAGACACTGAGAAGCAGGTCGAAGCAATAA
AATAGTTAACCTCCTGATGAGATACGGAGAAGTAAACCAAATCCGTCTTCCTAATGAAACACAGA
GAAGAGGATCAAAACAAGCGATGCGGTCACCTTCCTGATAAGATACTAAGAAGAAGACCAAATTG
AACCCACGCTTAATGC
Found at i:12233 original size:6 final size:6
Alignment explanation
Indices: 12220--12275 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
12210 TTAGATTTAT
* *
12220 TTTAAA TTTGAA TTTAAA -TTAAT TTTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12266 TTTAAA TTTA
1 TTTAAA TTTA
12276 TTTTCAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
5 9 0.20
6 35 0.80
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:12244 original size:23 final size:23
Alignment explanation
Indices: 12209--12275 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
12199 CCGAGCCCCT
* * *
12209 TTTAGATTTATTTTAAATTTGAA
1 TTTAAATTAATTTTAAATTTAAA
12232 TTTAAATTAATTTTAAATTTAAA
1 TTTAAATTAATTTTAAATTTAAA
* *
12255 TTTAATTTAAATTTAAATTTA
1 TTTAAATTAATTTTAAATTTA
12276 TTTTCAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTAAATTAATTTTAAATTTAAA
Found at i:12274 original size:17 final size:17
Alignment explanation
Indices: 12224--12290 Score: 82
Period size: 17 Copynumber: 3.8 Consensus size: 17
12214 ATTTATTTTA
*
12224 AATTTGAATTTAAA-TT
1 AATTTAAATTTAAATTT
12240 AATTTTAAATTTAAATTT
1 AA-TTTAAATTTAAATTT
12258 AATTTAAATTTAAATTT
1 AATTTAAATTTAAATTT
*
12275 ATTTTCAAAATTTAAA
1 AATTT--AAATTTAAA
12291 AGATTATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
16 2 0.04
17 30 0.67
18 4 0.09
19 9 0.20
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTAAATTT
Found at i:14276 original size:39 final size:39
Alignment explanation
Indices: 14233--14312 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
14223 AACTAATACG
14233 AAGTAGCATTCTAAATGTTATTTTGGTAAAATAAAGTTT
1 AAGTAGCATTCTAAATGTTATTTTGGTAAAATAAAGTTT
14272 AAGTAGCATTCTAAATGTTATTTTGGTAAAATAAAGTTT
1 AAGTAGCATTCTAAATGTTATTTTGGTAAAATAAAGTTT
14311 AA
1 AA
14313 TAATTATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (39 bp):
AAGTAGCATTCTAAATGTTATTTTGGTAAAATAAAGTTT
Found at i:15485 original size:100 final size:100
Alignment explanation
Indices: 15312--15506 Score: 381
Period size: 100 Copynumber: 1.9 Consensus size: 100
15302 ATCTTGACCG
15312 TCTATTGTATTCACAAAGAAACAATACAAGCCTCCCCTCATTTGTAAAACACACTCCATACTCCA
1 TCTATTGTATTCACAAAGAAACAATACAAGCCTCCCCTCATTTGTAAAACACACTCCATACTCCA
15377 TTCTTTAGGGAGCCTCCCCTCATTTGTAAATGCTC
66 TTCTTTAGGGAGCCTCCCCTCATTTGTAAATGCTC
*
15412 TCTATTGTATTCACAAAGAAACAATACAAGCCTCCCCTCATTTGTAAAACACACTCCATACTTCA
1 TCTATTGTATTCACAAAGAAACAATACAAGCCTCCCCTCATTTGTAAAACACACTCCATACTCCA
15477 TTCTTTAGGGAGCCTCCCCTCATTTGTAAA
66 TTCTTTAGGGAGCCTCCCCTCATTTGTAAA
15507 ACACACTCCA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 94 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.30
Consensus pattern (100 bp):
TCTATTGTATTCACAAAGAAACAATACAAGCCTCCCCTCATTTGTAAAACACACTCCATACTCCA
TTCTTTAGGGAGCCTCCCCTCATTTGTAAATGCTC
Found at i:15509 original size:47 final size:47
Alignment explanation
Indices: 15340--15529 Score: 186
Period size: 47 Copynumber: 3.9 Consensus size: 47
15330 AAACAATACA
15340 AGCCTCCCCTCATTTGTAAAACACACTCCATACTCCATTCTTTAGGG
1 AGCCTCCCCTCATTTGTAAAACACACTCCATACTCCATTCTTTAGGG
** * * * ** ** **
15387 AGCCTCCCCTCATTTGT-AAATGCTCTCTATTGTATTCACAAAGAAACAATA-CA
1 AGCCTCCCCTCATTTGTAAAACACACTCCA---TACTC-C----ATTCTTTAGGG
*
15440 AGCCTCCCCTCATTTGTAAAACACACTCCATACTTCATTCTTTAGGG
1 AGCCTCCCCTCATTTGTAAAACACACTCCATACTCCATTCTTTAGGG
15487 AGCCTCCCCTCATTTGTAAAACACACTCCATACTCCATTCTTT
1 AGCCTCCCCTCATTTGTAAAACACACTCCATACTCCATTCTTT
15530 GTATTGTTTC
Statistics
Matches: 109, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
46 12 0.11
47 59 0.54
49 4 0.04
50 2 0.02
51 3 0.03
53 17 0.16
54 12 0.11
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.31
Consensus pattern (47 bp):
AGCCTCCCCTCATTTGTAAAACACACTCCATACTCCATTCTTTAGGG
Found at i:22124 original size:194 final size:194
Alignment explanation
Indices: 21628--22466 Score: 902
Period size: 194 Copynumber: 4.3 Consensus size: 194
21618 TGTCGTTGAT
* * ** *
21628 TTGGTTTACTTCT-TAGTATCTTATCAGGAAGATGACCGTATCGCTTGTTTCAATCCGCTTCTCT
1 TTGGTATACTTCTCT-GTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCT
* * * * * *
21692 GTACCTCATTAAGAAGACGAATTTGGTCTACTTCTCAGTATTTCATTAGGAAGCTAACCATTTTA
65 GTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTA
* * * * *
21757 TTGCTTCGACC-TGCTTCTCAATATCTTATTAGGAAGCTGGGATTTGAAGATTTGCTCACATCAA
130 TTGCTTCG-CCTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTG-T----TC--
** *
21821 GCCCTGAG
187 GCATTAAG
*
21829 TTGGTATACTTCTCTGTATCTCATCAGGAAGATAACCGCC-C-CGTTGGTTTCAATCCGCTTCTC
1 TTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCAC-TT-GTTTCAATCCGCTTCTC
* * * * *
21892 TGTACCTCATTAGGAAGATGAATTTGGTTCACTTCTCAGTGTCTCATTAGGAAGCTAACCTTTTT
64 TGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTT
* *
21957 ATTGCTTCGCCTTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTTTTCGCATTAA
129 ATTGCTTCGCCTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATTAA
22022 G
194 G
*
22023 TTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAAAT-CGCTTCTTT
1 TTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTC-AATCCGCTTCTCT
* * * * * *
22087 GTACTTCATCAGGAAGATGAATTTGGTCCATTTCTCAGTGTCTCATCAAGAAGCTAACTTTTTTA
65 GTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTA
* * * *
22152 TTGCTTCG-CTCTACTTCTC-GATATCTCATCAAGAAGCTGGGGTTCGAAGATTTGTTCACATTG
130 TTGCTTCGCCT-TGCTTCTCAG-TATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATTA
22215 AG
193 AG
* * * * * ** *
22217 TTGGTATACTTCTTTGTATCTCATCAGAAAGATTACCGCCTCACTTGTTTTAATTCATTTCTTTG
1 TTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTG
* * * * *
22282 TAACTCATCAGGAAGACAAATTTGGTCCGCATCTCAGTATCTCATCAGGAAGCTAACTTTTTTAT
66 TACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTAT
* * * *
22347 TGCTTTGCCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGTATTGAAC
131 TGCTTCGCCTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATT-AA-
*
22412 C
194 G
* * *
22413 TTGAGTTGTTACATTTCTCTGTATCTCATCAGGAAGACGACCACCTCAC-TGTTT
1 TTG-G-T-ATAC--TTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTT
22467 ATGGATAATT
Statistics
Matches: 552, Mismatches: 67, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
193 6 0.01
194 330 0.60
195 9 0.02
196 6 0.01
197 1 0.00
198 1 0.00
199 4 0.01
200 11 0.02
201 183 0.33
202 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (194 bp):
TTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTG
TACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTAT
TGCTTCGCCTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATTAAG
Found at i:34537 original size:58 final size:57
Alignment explanation
Indices: 34447--34729 Score: 177
Period size: 58 Copynumber: 4.9 Consensus size: 57
34437 GCAAAATGGT
* * * *
34447 AATTTTGGGAAAACCAGGGT-AAAAACGAGAATTTTAGACA-TAT-AAGGGTAAAATGATA
1 AATTTTGGG-AAATCAAGGTCAAAAATG-GAATTTTAGAAAGT-TCAAGGGT-AAATGATA
* **
34505 AATTTTGGTGAAATCAAGGTCAAAAATGGAATTTTTGAAAGTTCGGGGGTAAATGATA
1 AATTTTGG-GAAATCAAGGTCAAAAATGGAATTTTAGAAAGTTCAAGGGTAAATGATA
* * * * * *
34563 ATTTTTGGGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC-GGTGGAAAAATG-TA
1 AATTTTGGGAAATCAAGGTCAAAAATGGAATTTTAGAAAGTTCAAG-GG-TAAATGATA
* * * * * * * *
34620 ATTTTTGATGAAATCGAGG-CTAAAAATGGAAGTTTGGAAACTTCGAGGGTAAAATGGTA
1 AATTTTG-GGAAATCAAGGTC-AAAAATGGAATTTTAGAAAGTTCAAGGGT-AAATGATA
* * * * *
34679 ATTTTTGGTGAAATTAGGGT-TAAAATGGAATTTT-GAAAGTTCGAGGGTAAA
1 AATTTTGG-GAAATCAAGGTCAAAAATGGAATTTTAGAAAGTTCAAGGGTAAA
34730 AATGGTAATT
Statistics
Matches: 187, Mismatches: 25, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
56 5 0.03
57 56 0.30
58 97 0.52
59 29 0.16
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (57 bp):
AATTTTGGGAAATCAAGGTCAAAAATGGAATTTTAGAAAGTTCAAGGGTAAATGATA
Found at i:34592 original size:57 final size:58
Alignment explanation
Indices: 34491--34729 Score: 283
Period size: 58 Copynumber: 4.1 Consensus size: 58
34481 TAGACATATA
* * * *
34491 AGGGTAAAATGATAAATTTTGGTGAAATCAAGGTCAAAAATGGAATTTTTGAAAGTTCG
1 AGGGT-AAATGATAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCG
*
34550 GGGGTAAATGATAATTTTTGG-GAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCG
1 AGGGTAAATGATAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCG
* * * * *
34607 -GTGGAAAAATG-TAATTTTTGATGAAATCGAGGCTAAAAATGGAAGTTTGGAAACTTCG
1 AG-GG-TAAATGATAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCG
* *
34665 AGGGTAAAATGGTAATTTTTGGTGAAAT-TAGGGTT-AAAATGGAATTTT-GAAAGTTCG
1 AGGGT-AAATGATAATTTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTCG
34722 AGGGTAAA
1 AGGGTAAA
34730 AATGGTAATT
Statistics
Matches: 157, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
56 4 0.03
57 57 0.36
58 73 0.46
59 23 0.15
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (58 bp):
AGGGTAAATGATAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCG
Found at i:34634 original size:115 final size:116
Alignment explanation
Indices: 34491--34741 Score: 309
Period size: 115 Copynumber: 2.2 Consensus size: 116
34481 TAGACATATA
* * * * * *
34491 AGGGT-AAAATGATAAATTTTGGTGAAATCAAGG-TCAAAAATGGAATTTTTGAAAGTTCGGGGG
1 AGGGTAAAAATG-TAATTTTTGATGAAATCAAGGCT-AAAAATGGAAGTTTGGAAACTTCGAGGG
34554 T-AAATGATAATTTTTGG-GAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTCG
64 TAAAATGATAATTTTTGGTGAAAT-GAGGGTT-AAAATGGAATTTT-GAAAGTTCG
*
34607 -GTGG-AAAAATGTAATTTTTGATGAAATCGAGGCTAAAAATGGAAGTTTGGAAACTTCGAGGGT
1 AG-GGTAAAAATGTAATTTTTGATGAAATCAAGGCTAAAAATGGAAGTTTGGAAACTTCGAGGGT
* *
34670 AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAATGGAATTTTGAAAGTTCG
65 AAAATGATAATTTTTGGTGAAATGAGGGTTAAAATGGAATTTTGAAAGTTCG
34722 AGGGTAAAAATGGTAATTTT
1 AGGGTAAAAAT-GTAATTTT
34742 AGAAAGTTCG
Statistics
Matches: 117, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
115 55 0.47
116 45 0.38
117 17 0.15
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (116 bp):
AGGGTAAAAATGTAATTTTTGATGAAATCAAGGCTAAAAATGGAAGTTTGGAAACTTCGAGGGTA
AAATGATAATTTTTGGTGAAATGAGGGTTAAAATGGAATTTTGAAAGTTCG
Found at i:34760 original size:29 final size:30
Alignment explanation
Indices: 34526--34809 Score: 176
Period size: 30 Copynumber: 9.8 Consensus size: 30
34516 AATCAAGGTC
* *
34526 AAAAATGG-AATTTTTGAAAGTTCGGGGGT
1 AAAAATGGTAATTTTAGAAAGTTCGAGGGT
* * *
34555 --AAATGATAATTTTTGGGAAA--TCGAGGTT
1 AAAAATGGTAA-TTTT-AGAAAGTTCGAGGGT
*
34583 AAAAATGG-AATTTTGGAAAGTTCG-GTGG-
1 AAAAATGGTAATTTTAGAAAGTTCGAG-GGT
*
34611 AAAAAT-GTAATTTTTGATGAAA--TCGAGGCT
1 AAAAATGGTAA-TTTT-A-GAAAGTTCGAGGGT
* * *
34641 AAAAATGG-AAGTTTGGAAACTTCGAGGGT
1 AAAAATGGTAATTTTAGAAAGTTCGAGGGT
*
34670 -AAAATGGTAATTTTTGGTGAAA-TT--AGGGT
1 AAAAATGGTAA-TTTT--AGAAAGTTCGAGGGT
*
34699 TAAAATGG-AATTTT-GAAAGTTCGAGGGT
1 AAAAATGGTAATTTTAGAAAGTTCGAGGGT
*
34727 AAAAATGGTAATTTTAGAAAGTTCGGGGGT
1 AAAAATGGTAATTTTAGAAAGTTCGAGGGT
*
34757 AAAAAT-GTAATTTTCAAAAAGTTCGAGGGT
1 AAAAATGGTAATTTT-AGAAAGTTCGAGGGT
* * *
34787 CAAAAT-ATAATTTTTAGACAGTT
1 AAAAATGGTAA-TTTTAGAAAGTT
34810 TAAGGACCTC
Statistics
Matches: 205, Mismatches: 21, Indels: 57
0.72 0.07 0.20
Matches are distributed among these distances:
25 4 0.02
26 2 0.01
27 15 0.07
28 44 0.21
29 51 0.25
30 74 0.36
31 11 0.05
32 4 0.02
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (30 bp):
AAAAATGGTAATTTTAGAAAGTTCGAGGGT
Found at i:34762 original size:58 final size:58
Alignment explanation
Indices: 34491--34801 Score: 259
Period size: 58 Copynumber: 5.3 Consensus size: 58
34481 TAGACATATA
* * * *
34491 AGGGTAAAATGATAAATTTTGGTGAAA-TC-AAGGTCAAAAATGGAATTTTTGAAAGTTCG
1 AGGGTAAAATGGT-AATTTTTGAGAAATTCGAGGGT-AAAAATGGAA-TTTTGAAAGTTCG
* * * *
34550 GGGGT-AAATGATAATTTTTGGGAAA-TCGAGGTTAAAAATGGAATTTTGGAAAGTTCG
1 AGGGTAAAATGGTAATTTTTGAGAAATTCGAGGGTAAAAATGGAATTTT-GAAAGTTCG
* * * *
34607 -GTGGAAAAAT-GTAATTTTTGATGAAA-TCGAGGCTAAAAATGGAAGTTTGGAAACTTCG
1 AG-GGTAAAATGGTAATTTTTGA-GAAATTCGAGGGTAAAAATGGAA-TTTTGAAAGTTCG
* *
34665 AGGGTAAAATGGTAATTTTTGGTGAAATT--AGGGTTAAAATGGAATTTTGAAAGTTCG
1 AGGGTAAAATGGTAATTTTT-GAGAAATTCGAGGGTAAAAATGGAATTTTGAAAGTTCG
* * *
34722 AGGGTAAAAATGGTAA-TTTT-AGAAAGTTCGGGGGTAAAAATGTAATTTTCAAAAAGTTCG
1 AGGGT-AAAATGGTAATTTTTGAGAAA-TTCGAGGGTAAAAATGGAATTTT--GAAAGTTCG
*
34782 AGGGTCAAAAT-ATAATTTTT
1 AGGGT-AAAATGGTAATTTTT
34802 AGACAGTTTA
Statistics
Matches: 211, Mismatches: 24, Indels: 33
0.79 0.09 0.12
Matches are distributed among these distances:
55 4 0.02
56 7 0.03
57 63 0.30
58 89 0.42
59 24 0.11
60 24 0.11
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTTGAGAAATTCGAGGGTAAAAATGGAATTTTGAAAGTTCG
Found at i:36751 original size:16 final size:16
Alignment explanation
Indices: 36713--36752 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
36703 GTTTTCAATG
*
36713 TTGGGCCCGGTCAAAA
1 TTGGGCTCGGTCAAAA
36729 TTGGGCTCGGTCAAAA
1 TTGGGCTCGGTCAAAA
36745 TTGGGCTC
1 TTGGGCTC
36753 CACAATTGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (16 bp):
TTGGGCTCGGTCAAAA
Found at i:39325 original size:30 final size:30
Alignment explanation
Indices: 39289--39350 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
39279 TATTTTATTC
*
39289 TTAATTTTATTATTATTTTAGAGGCATTTG
1 TTAATTTTATTACTATTTTAGAGGCATTTG
*
39319 TTAATTTTATTACTATTTTTGAGGCATTTG
1 TTAATTTTATTACTATTTTAGAGGCATTTG
39349 TT
1 TT
39351 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTACTATTTTAGAGGCATTTG
Found at i:59897 original size:22 final size:22
Alignment explanation
Indices: 59869--59912 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
59859 AAATTTAAAA
* *
59869 GACTTGCATTTTATGTCCCATT
1 GACTTGCATTTTAAGGCCCATT
59891 GACTTGCATTTTAAGGCCCATT
1 GACTTGCATTTTAAGGCCCATT
59913 ACATTTGAGC
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:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (22 bp):
GACTTGCATTTTAAGGCCCATT
Found at i:63767 original size:15 final size:15
Alignment explanation
Indices: 63720--63770 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
63710 AATCAAGGCA
*
63720 ATCTTCTAATGGTGC
1 ATCTTCTAATAGTGC
*
63735 ATATTCTAATAGTGC
1 ATCTTCTAATAGTGC
63750 ATCTTCTAATAGTGC
1 ATCTTCTAATAGTGC
63765 ATCTTC
1 ATCTTC
63771 ATTTAGATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (15 bp):
ATCTTCTAATAGTGC
Found at i:68239 original size:14 final size:14
Alignment explanation
Indices: 68197--68239 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
68187 AAAATAAAAT
68197 AATTAAATTTCTAAA
1 AATTAAATTTC-AAA
*
68212 AA-TAAATATACAAA
1 AATTAAAT-TTCAAA
68226 AATTAAATTTCAAA
1 AATTAAATTTCAAA
68240 TACACAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTAAATTTCAAA
Done.