Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003330.1 Kokia drynarioides strain JFW-HI SEQ_116031, 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: 85743
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:10278 original size:22 final size:22
Alignment explanation
Indices: 10250--10291 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10240 TAATATCATT
*
10250 AAAAATAAATTAAATAATTTCA
1 AAAAATAAAATAAATAATTTCA
*
10272 AAAAATAAAATAAATTATTT
1 AAAAATAAAATAAATAATTT
10292 TTATAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAATAAAATAAATAATTTCA
Found at i:10595 original size:21 final size:22
Alignment explanation
Indices: 10558--10600 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10548 CAGTAAATGA
*
10558 TTTTAAAATTATAAAAATTATT
1 TTTTAAAAATATAAAAATTATT
10580 TTTTAAAAATAT-AAAATTATT
1 TTTTAAAAATATAAAAATTATT
10601 AAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAAAAATATAAAAATTATT
Found at i:11319 original size:99 final size:99
Alignment explanation
Indices: 11199--11385 Score: 311
Period size: 99 Copynumber: 1.9 Consensus size: 99
11189 CTAAGAAATA
* * *
11199 AGATTGAAATAGAGAACCTTGAAAGGTTAAGAGAGTGATGGAAGAAGAAGAAGTCATGGTTTGAT
1 AGATTAAAATAGAGAACCTTGAAAGGTTAAGAGAGCGATGGAAGAAGAAGAAGCCATGGTTTGAT
11264 TCAAAATCCAAGTGGAGAAGTAGTCATGGTTATG
66 TCAAAATCCAAGTGGAGAAGTAGTCATGGTTATG
* ** *
11298 AGATTAAAATAGAGAACCTTGAAGGGTTGGGAGAGCGATGGAAGAAGAAGAAGCCATGGTTTGGT
1 AGATTAAAATAGAGAACCTTGAAAGGTTAAGAGAGCGATGGAAGAAGAAGAAGCCATGGTTTGAT
11363 TCAAAATCCAAGTGGAGAAGTAG
66 TCAAAATCCAAGTGGAGAAGTAG
11386 CCTTGGTTTG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 81 1.00
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.22
Consensus pattern (99 bp):
AGATTAAAATAGAGAACCTTGAAAGGTTAAGAGAGCGATGGAAGAAGAAGAAGCCATGGTTTGAT
TCAAAATCCAAGTGGAGAAGTAGTCATGGTTATG
Found at i:11563 original size:11 final size:11
Alignment explanation
Indices: 11549--11587 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
11539 AAAATTATTT
11549 AATAATTTTAA
1 AATAATTTTAA
11560 AATAATTTT--
1 AATAATTTTAA
11569 AATAATTTTAA
1 AATAATTTTAA
*
11580 AATCATTT
1 AATAATTT
11588 GCTGACGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 9 0.36
11 16 0.64
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
AATAATTTTAA
Found at i:11571 original size:20 final size:20
Alignment explanation
Indices: 11537--11587 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
11527 AAATTAAAAA
*
11537 TTAAAATTA-TTTAATAATT
1 TTAAAATAATTTTAATAATT
11556 TTAAAATAATTTTAATAATT
1 TTAAAATAATTTTAATAATT
*
11576 TTAAAATCATTT
1 TTAAAATAATTT
11588 GCTGACGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAAATAATTTTAATAATT
Found at i:11572 original size:9 final size:9
Alignment explanation
Indices: 11546--11579 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
11536 ATTAAAATTA
11546 TTTAATAAT
1 TTTAATAAT
11555 TTTAAAATAAT
1 TTT--AATAAT
11566 TTTAATAAT
1 TTTAATAAT
11575 TTTAA
1 TTTAA
11580 AATCATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 14 0.61
11 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTAATAAT
Found at i:13809 original size:28 final size:28
Alignment explanation
Indices: 13775--13829 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
13765 TAGGCATTTT
*
13775 ATATTATTTTAATATAAATAAGTTTTCG
1 ATATTATTTTAATATAAATAAATTTTCG
13803 ATATTATTTTAATATAAATAAATTTTC
1 ATATTATTTTAATATAAATAAATTTTC
13830 AAAAGGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (28 bp):
ATATTATTTTAATATAAATAAATTTTCG
Found at i:18935 original size:2 final size:2
Alignment explanation
Indices: 18928--18958 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18918 TTTATTGTAT
18928 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18959 TAAGGGGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19829 original size:20 final size:21
Alignment explanation
Indices: 19790--19831 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
19780 GATCAAGTAT
19790 CAAAATCTTATCTTTACTGAGG
1 CAAAATCTTATC-TTACTGAGG
19812 CAAAATCTTATC-TACTGAGG
1 CAAAATCTTATCTTACTGAGG
19832 TAGGAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (21 bp):
CAAAATCTTATCTTACTGAGG
Found at i:20474 original size:23 final size:23
Alignment explanation
Indices: 20435--20487 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
20425 TTATGGTATA
* *
20435 TAAAT-ATTAATTTTAAATATTTT
1 TAAATAATTAATTATAAAT-TATT
20458 TAAATAATTAA-TATAAATTATT
1 TAAATAATTAATTATAAATTATT
20480 TAAA-AATT
1 TAAATAATT
20488 TTAATTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 7 0.26
23 11 0.41
24 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAATAATTAATTATAAATTATT
Found at i:24605 original size:36 final size:36
Alignment explanation
Indices: 24565--24642 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
24555 TTACAATTCA
24565 CCTAAAAAAATCCTTAGTTTTAATCCTAAACAAAAG
1 CCTAAAAAAATCCTTAGTTTTAATCCTAAACAAAAG
*
24601 CCTAAAAAAATCCTTAGTTTTGATCCTAAACAAAAG
1 CCTAAAAAAATCCTTAGTTTTAATCCTAAACAAAAG
*
24637 CTTAAA
1 CCTAAA
24643 GAATATTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.28
Consensus pattern (36 bp):
CCTAAAAAAATCCTTAGTTTTAATCCTAAACAAAAG
Found at i:25700 original size:12 final size:11
Alignment explanation
Indices: 25659--25694 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
25649 AATAATTATT
25659 TTTTAAAA-TA
1 TTTTAAAATTA
25669 TTTTAAAATTA
1 TTTTAAAATTA
*
25680 ATTTAAAATTA
1 TTTTAAAATTA
25691 TTTT
1 TTTT
25695 TTAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:26527 original size:6 final size:6
Alignment explanation
Indices: 26516--26582 Score: 62
Period size: 6 Copynumber: 10.8 Consensus size: 6
26506 AAGGAAAATA
* * * *
26516 GAGAAG GAGAAG GGGAAG GGGAAG GGGAAG GAGAAAGG GGGAAG GAGAAG
1 GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAG-AA-G GAGAAG GAGAAG
* *
26566 GAGAAA GAGAAG AAGAA
1 GAGAAG GAGAAG GAGAA
26583 CAGAAAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
6 45 0.87
7 4 0.08
8 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GAGAAG
Found at i:26539 original size:12 final size:12
Alignment explanation
Indices: 26518--26577 Score: 75
Period size: 12 Copynumber: 4.8 Consensus size: 12
26508 GGAAAATAGA
26518 GAAGGAGAAGGG
1 GAAGGAGAAGGG
*
26530 GAAGGGGAAGGG
1 GAAGGAGAAGGG
26542 GAAGGAGAAAGGGG
1 GAAGGAG-AA-GGG
*
26556 GAAGGAGAAGGA
1 GAAGGAGAAGGG
*
26568 GAAAGAGAAG
1 GAAGGAGAAG
26578 AAGAACAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
12 28 0.67
13 4 0.10
14 10 0.24
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (12 bp):
GAAGGAGAAGGG
Found at i:26558 original size:20 final size:20
Alignment explanation
Indices: 26518--26572 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
26508 GGAAAATAGA
*
26518 GAAGGAGAAGG-GGAA-GGG
1 GAAGGAGAAGGAGAAAGGGG
*
26536 GAAGGGGAAGGAGAAAGGGG
1 GAAGGAGAAGGAGAAAGGGG
26556 GAAGGAGAAGGAGAAAG
1 GAAGGAGAAGGAGAAAG
26573 AGAAGAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 10 0.31
19 3 0.09
20 19 0.59
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (20 bp):
GAAGGAGAAGGAGAAAGGGG
Found at i:26565 original size:26 final size:25
Alignment explanation
Indices: 26516--26576 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
26506 AAGGAAAATA
*
26516 GAGAAGGAG-AAGGGGAAGGGGAAG
1 GAGAAGGAGAAAGGGGAAGGAGAAG
*
26540 GGGAAGGAGAAAGGGGGAAGGAGAAG
1 GAGAAGGAGAAA-GGGGAAGGAGAAG
*
26566 GAGAAAGAGAA
1 GAGAAGGAGAA
26577 GAAGAACAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 8 0.26
25 2 0.06
26 21 0.68
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (25 bp):
GAGAAGGAGAAAGGGGAAGGAGAAG
Found at i:27286 original size:147 final size:147
Alignment explanation
Indices: 27100--27449 Score: 428
Period size: 147 Copynumber: 2.4 Consensus size: 147
27090 TGATTAAAAT
* *
27100 AAAATCACTACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAACATCAAAACTT
1 AAAATCACTACTTTACTTAAAAATC-AAACATTTATTTCGAAATAGTTAAAAAA-ATCAAAACTT
* * *
27165 TGTTTAAAAATTTAA-GCTTTTTCTTTAAAATCACT-AAAAAACAGATTTTTATTTTCTAAAAAA
64 TATTTAAAAATTTAATGCTTTTTCTTCAAAATAACTAAAAAAACAGATTTTT-TTTT-T-AAAAA
27228 TCTAAAC-TT-T-TTTTTAATA-
126 TCTAAACTTTCTCTTTTTAA-AG
*
27247 AAAATCACTACTTTACTTAAAAATTCAAACATTTATTTCGAATTAGTT-AAAAAATCAAAACTTT
1 AAAATCACTACTTTACTTAAAAA-TCAAACATTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
** *
27311 ATTTAAAAATTTAATTTTTTTTCTTCAAAATAACTAAAAAAACAGATTTTTTTTTTTAAAATCTA
65 ATTTAAAAATTTAATGCTTTTTCTTCAAAATAACTAAAAAAACAGATTTTTTTTTTAAAAATCTA
27376 AACTTTCTCTTTTTAAAG
130 AACTTTCTCTTTTTAAAG
* * * * *
27394 AAAATCATTATTTTTCTTAAAAATCAAA-ACTTTAATTTTGAAATTGTTTAAAAAAA
1 AAAATCACTACTTTACTTAAAAATCAAACA-TTT-ATTTCGAAATAG-TTAAAAAAA
27450 AACCAAAACT
Statistics
Matches: 177, Mismatches: 15, Indels: 20
0.83 0.07 0.09
Matches are distributed among these distances:
144 11 0.06
145 28 0.16
146 35 0.20
147 93 0.53
148 4 0.02
149 6 0.03
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.41
Consensus pattern (147 bp):
AAAATCACTACTTTACTTAAAAATCAAACATTTATTTCGAAATAGTTAAAAAAATCAAAACTTTA
TTTAAAAATTTAATGCTTTTTCTTCAAAATAACTAAAAAAACAGATTTTTTTTTTAAAAATCTAA
ACTTTCTCTTTTTAAAG
Found at i:28151 original size:4 final size:4
Alignment explanation
Indices: 28142--28166 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28132 GCTTTCTGTG
28142 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
28167 TTAGGGTTTT
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):
TATT
Found at i:56435 original size:94 final size:94
Alignment explanation
Indices: 56274--56462 Score: 369
Period size: 94 Copynumber: 2.0 Consensus size: 94
56264 GGCCTATTGG
56274 AATAAGTAGTATTATGGATGTGATAATAGATTGTTTTGAGGTAAATCACAATTTAGAATGCAAGA
1 AATAAGTAGTATTATGGATGTGATAATAGATTGTTTTGAGGTAAATCACAATTTAGAATGCAAGA
56339 TATGGATACTTTCCTAGGCAAAAATTGTT
66 TATGGATACTTTCCTAGGCAAAAATTGTT
56368 AATAAGTAGTATTATGGATGTGATAATAGATTGTTTTGAGGTAAATCACAATTTAGAATGCAAGA
1 AATAAGTAGTATTATGGATGTGATAATAGATTGTTTTGAGGTAAATCACAATTTAGAATGCAAGA
*
56433 TATGGATATTTTCCTAGGCAAAAATTGTT
66 TATGGATACTTTCCTAGGCAAAAATTGTT
56462 A
1 A
56463 TTAGTTTCTT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (94 bp):
AATAAGTAGTATTATGGATGTGATAATAGATTGTTTTGAGGTAAATCACAATTTAGAATGCAAGA
TATGGATACTTTCCTAGGCAAAAATTGTT
Found at i:59348 original size:13 final size:14
Alignment explanation
Indices: 59316--59361 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
59306 TTATTTAGAT
*
59316 ATAATTAAATATTA
1 ATAAATAAATATTA
*
59330 AT-AATAACTATT-
1 ATAAATAAATATTA
59342 ATAAATAAATATTA
1 ATAAATAAATATTA
59356 ATAAAT
1 ATAAAT
59362 CTCATATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.07
13 17 0.63
14 8 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAATAAATATTA
Found at i:73306 original size:68 final size:68
Alignment explanation
Indices: 73197--73334 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
73187 AATATTTGGC
73197 CCTGTCGCGTGAGTCATGCTCATGGCTGTAAAGGCTGTGAAATGTTTAGTGCAAAAAAGGGGCTT
1 CCTGTCGCGTGAGTCATGCTCATGGCTGTAAAGGCTGTGAAATGTTTAGTGCAAAAAAGGGGCTT
73262 GTG
66 GTG
73265 CCTGTCGCGTGAGTCATGCTCATGGCTGTAAAGGCTGTGAAATGTTTAGTGCAAAAAAGGGGCTT
1 CCTGTCGCGTGAGTCATGCTCATGGCTGTAAAGGCTGTGAAATGTTTAGTGCAAAAAAGGGGCTT
73330 GTG
66 GTG
73333 CC
1 CC
73335 ATACACACGC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (68 bp):
CCTGTCGCGTGAGTCATGCTCATGGCTGTAAAGGCTGTGAAATGTTTAGTGCAAAAAAGGGGCTT
GTG
Found at i:74389 original size:5 final size:5
Alignment explanation
Indices: 74381--74405 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
74371 TGAGTTGAAT
74381 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
74406 ACACCATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:76558 original size:91 final size:91
Alignment explanation
Indices: 76403--76573 Score: 252
Period size: 91 Copynumber: 1.9 Consensus size: 91
76393 ATGATTAGCG
* * **
76403 AATTCACCAATATTGGTAAACCTTCTAAAATTGACGAGATACCACAAAGTGGTAAGCTCATTACT
1 AATTCACCAATATTGGCAAACCTTCTAAAATTGACAAGATACCACAAAGTGACAAGCTCATTACT
*
76468 TTGGCGAATTGGGATTGCAGGACAAA
66 TTGGCAAATTGGGATTGCAGGACAAA
* * * * *
76494 AATTCACCAATATTGGCAAACCTTCTAAGATTGGCAAGCTACCACAGAGTGACGAGCTCATTACT
1 AATTCACCAATATTGGCAAACCTTCTAAAATTGACAAGATACCACAAAGTGACAAGCTCATTACT
76559 TTGGCAAATTGGGAT
66 TTGGCAAATTGGGAT
76574 CGTACGACAA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 70 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (91 bp):
AATTCACCAATATTGGCAAACCTTCTAAAATTGACAAGATACCACAAAGTGACAAGCTCATTACT
TTGGCAAATTGGGATTGCAGGACAAA
Found at i:78390 original size:15 final size:15
Alignment explanation
Indices: 78353--78396 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
78343 TCTTGCAATT
*
78353 TATTGTATAAATCAA
1 TATTGTATAATTCAA
*
78368 -ATCAGTATAATTCAA
1 TAT-TGTATAATTCAA
78383 TATTGTATAATTCA
1 TATTGTATAATTCA
78397 TAATGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 2 0.08
15 20 0.83
16 2 0.08
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (15 bp):
TATTGTATAATTCAA
Found at i:79544 original size:115 final size:114
Alignment explanation
Indices: 79412--79639 Score: 341
Period size: 115 Copynumber: 2.0 Consensus size: 114
79402 ATTTCAAAAT
* * *
79412 AATTACATTTTTCTAAAAAAATAATAATAACA-ACTTTTAGATATTATAAAATTATTATTAAAAG
1 AATTACATTTTTATAAAAAAATAATAATAACACA-TTTAAGATATTATAAAATTACTATT-AAAG
* *
79476 TTGTTTAGATTTTAAAACTATTTAAAGATGAAAACTTTATATTATTCTAAC
64 TTGTTTAGATTTTAAAACTATTCAAAGATGAAAACTTTAGATTATTCTAAC
* * * *
79527 AATTATATTTTTATAAAAAATTAATAATAACACATTTAAGATATTATAAAATTCCTATTAAATTT
1 AATTACATTTTTATAAAAAAATAATAATAACACATTTAAGATATTATAAAATTACTATTAAAGTT
*
79592 GTTTCGATTTTAAAACTATTCAAAGATGAAAACTTTAGATTATTCTAA
66 GTTTAGATTTTAAAACTATTCAAAGATGAAAACTTTAGATTATTCTAA
79640 TTTTAACTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
114 50 0.49
115 51 0.50
116 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (114 bp):
AATTACATTTTTATAAAAAAATAATAATAACACATTTAAGATATTATAAAATTACTATTAAAGTT
GTTTAGATTTTAAAACTATTCAAAGATGAAAACTTTAGATTATTCTAAC
Found at i:79634 original size:114 final size:115
Alignment explanation
Indices: 79412--79639 Score: 343
Period size: 114 Copynumber: 2.0 Consensus size: 115
79402 ATTTCAAAAT
* * *
79412 AATTACATTTTTCTAAAAAAATAATAATAACAACTTTTAGATATTATAAAATTATTATTAAAAGT
1 AATTACATTTTTATAAAAAAATAATAATAACAACTTTAAGATATTATAAAATTACTATTAAAAGT
* *
79477 TGTTTAGATTTTAAAACTATTTAAAGATGAAAACTTTATATTATTCTAAC
66 TGTTTAGATTTTAAAACTATTCAAAGATGAAAACTTTAGATTATTCTAAC
* * * *
79527 AATTATATTTTTATAAAAAATTAATAATAAC-ACATTTAAGATATTATAAAATTCCTATT-AAAT
1 AATTACATTTTTATAAAAAAATAATAATAACAAC-TTTAAGATATTATAAAATTACTATTAAAAG
*
79590 TTGTTTCGATTTTAAAACTATTCAAAGATGAAAACTTTAGATTATTCTAA
65 TTGTTTAGATTTTAAAACTATTCAAAGATGAAAACTTTAGATTATTCTAA
79640 TTTTAACTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
114 52 0.51
115 50 0.49
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (115 bp):
AATTACATTTTTATAAAAAAATAATAATAACAACTTTAAGATATTATAAAATTACTATTAAAAGT
TGTTTAGATTTTAAAACTATTCAAAGATGAAAACTTTAGATTATTCTAAC
Found at i:80231 original size:17 final size:17
Alignment explanation
Indices: 80209--80241 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
80199 TTTAAAAGTC
*
80209 AATTTTTAATTAAAAAT
1 AATTTTTAATGAAAAAT
80226 AATTTTTAATGAAAAA
1 AATTTTTAATGAAAAA
80242 CACACAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AATTTTTAATGAAAAAT
Found at i:85613 original size:14 final size:15
Alignment explanation
Indices: 85570--85613 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
85560 CTTTTTTATT
85570 TTATTTATTTTAAAA
1 TTATTTATTTTAAAA
*
85585 TTATTTATTTCAAAA
1 TTATTTATTTTAAAA
85600 -TA-TTATTTTTAAAA
1 TTATTTA-TTTTAAAA
85614 AAAATAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 3 0.12
14 9 0.35
15 14 0.54
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTTATTTTAAAA
Found at i:85707 original size:2 final size:2
Alignment explanation
Indices: 85702--85743 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
85692 GATACGTGTG
85702 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.