Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012851.1 Kokia drynarioides strain JFW-HI SEQ_127865, 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: 213010
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:3242 original size:30 final size:30
Alignment explanation
Indices: 3086--3234 Score: 131
Period size: 30 Copynumber: 5.0 Consensus size: 30
3076 GTTGTAAATG
* **
3086 AATTTTTGGAAAGTTTAAGGG--ATAAATTT
1 AATTTTTAGAAAGTTTAAGGGTCA-AAACAT
* ** *
3115 GAATTTTTGGAAAGTTTGGGGGTCAAAATAT
1 -AATTTTTAGAAAGTTTAAGGGTCAAAACAT
* * * * *
3146 AATATTTGGAAAATTTAAAGTTCAAAACAT
1 AATTTTTAGAAAGTTTAAGGGTCAAAACAT
* * *
3176 AATTTTTAAAAAGTTCAGGGGTCAAAACAT
1 AATTTTTAGAAAGTTTAAGGGTCAAAACAT
3206 AATTTTTAGAAAGTTTAAGGGTCAAAACA
1 AATTTTTAGAAAGTTTAAGGGTCAAAACA
3235 CCATTTTTTA
Statistics
Matches: 96, Mismatches: 21, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
30 90 0.94
31 5 0.05
32 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (30 bp):
AATTTTTAGAAAGTTTAAGGGTCAAAACAT
Found at i:4559 original size:14 final size:14
Alignment explanation
Indices: 4540--4566 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4530 GTAATTGGAT
4540 ATTAAAATTAAAAA
1 ATTAAAATTAAAAA
4554 ATTAAAATTAAAA
1 ATTAAAATTAAAA
4567 TTTATTATTT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTAAAATTAAAAA
Found at i:5385 original size:18 final size:19
Alignment explanation
Indices: 5361--5414 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
5351 GTTATTAGGG
5361 TATTGGGTTTTAATTTGTA
1 TATTGGGTTTTAATTTGTA
* *
5380 -ATTGGGTTGTAATTTTTA
1 TATTGGGTTTTAATTTGTA
*
5398 TTATTGGGTTTTTATTT
1 -TATTGGGTTTTAATTT
5415 ATTTATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 16 0.55
20 13 0.45
ACGTcount: A:0.19, C:0.00, G:0.20, T:0.61
Consensus pattern (19 bp):
TATTGGGTTTTAATTTGTA
Found at i:13330 original size:32 final size:32
Alignment explanation
Indices: 13257--13354 Score: 100
Period size: 32 Copynumber: 3.2 Consensus size: 32
13247 AAGTTGACAC
* *
13257 TTTTTCTTAATTTGGTACCTAAACTT----TT
1 TTTTTCCTAATTTGGTACATAAACTTGACATT
*
13285 TTTTGGTCC-AATTTGGTAC-TCAAGCTTGACATT
1 TTTT--TCCTAATTTGGTACAT-AAACTTGACATT
13318 TTTTTCCTAATTTGGTACATAAACTTGACATT
1 TTTTTCCTAATTTGGTACATAAACTTGACATT
13350 TTTTT
1 TTTTT
13355 TTAAAGTTGG
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
28 5 0.09
29 15 0.26
30 2 0.03
31 3 0.05
32 26 0.45
33 7 0.12
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.51
Consensus pattern (32 bp):
TTTTTCCTAATTTGGTACATAAACTTGACATT
Found at i:13373 original size:32 final size:32
Alignment explanation
Indices: 13309--13375 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
13299 GGTACTCAAG
* *
13309 CTTGACATTTTTTTCCTAATTTGGTACATAAA
1 CTTGACATTTTTTTCCTAAGTTGGCACATAAA
* *
13341 CTTGACATTTTTTT-TTAAAGTTGGCACTTAAA
1 CTTGACATTTTTTTCCT-AAGTTGGCACATAAA
13373 CTT
1 CTT
13376 TTTGGAATCC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 1 0.03
32 29 0.97
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (32 bp):
CTTGACATTTTTTTCCTAAGTTGGCACATAAA
Found at i:13378 original size:92 final size:92
Alignment explanation
Indices: 13250--13428 Score: 204
Period size: 93 Copynumber: 1.9 Consensus size: 92
13240 GTATATGAAG
* * *
13250 TTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTTTGG-TCCAATTTGGTA-CTCAAGCTTG
1 TTGACACTTTTTCTTAAGTTGGCACCTAAAC--TTTTTTGGATCCAATTTGGTACCTCAA-CTTA
13313 AC-ATTTTTTTCCTAATTTGGTACATAAAC
63 ACTATTTTTTTCCTAATTTGGTACATAAAC
* * * * *
13342 TTGACATTTTTTTTTAAAGTTGGCACTTAAAC-TTTTTGGAATCCAATTTGGTACCTGAATTTAA
1 TTGACACTTTTTCTT-AAGTTGGCACCTAAACTTTTTTGG-ATCCAATTTGGTACCTCAACTTAA
*
13406 CTTTTTTTTTCCTAATTTGGTAC
64 CTATTTTTTTCCTAATTTGGTAC
13429 CTAATCATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
90 7 0.10
92 29 0.40
93 37 0.51
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (92 bp):
TTGACACTTTTTCTTAAGTTGGCACCTAAACTTTTTTGGATCCAATTTGGTACCTCAACTTAACT
ATTTTTTTCCTAATTTGGTACATAAAC
Found at i:15119 original size:59 final size:59
Alignment explanation
Indices: 15023--15153 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 59
15013 GCTTATGTGC
* * * * ** * **
15023 CAAATTAAGAAAAAATGTCAAGTTCAAGTACCAAATTGGATTCAAAAAAATTTAGGTAT
1 CAAATTAAAAAAAAATGTCAAATTCAAGTAACAAATTGAATGAAAAAAAAATTAAATAT
**
15082 CAAATTAAAAAAAAATGTCAAATTCAAGTAATTAATTGAATGAAAAAAAAATTAAATAT
1 CAAATTAAAAAAAAATGTCAAATTCAAGTAACAAATTGAATGAAAAAAAAATTAAATAT
15141 CAAATTAAAAAAA
1 CAAATTAAAAAAA
15154 TATCAAACTC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.26
Consensus pattern (59 bp):
CAAATTAAAAAAAAATGTCAAATTCAAGTAACAAATTGAATGAAAAAAAAATTAAATAT
Found at i:17765 original size:18 final size:18
Alignment explanation
Indices: 17742--17776 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
17732 TGAAAATTAA
17742 TAAATAATTTGATTACGG
1 TAAATAATTTGATTACGG
17760 TAAATAATTTGATTACG
1 TAAATAATTTGATTACG
17777 TTGGGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (18 bp):
TAAATAATTTGATTACGG
Found at i:18228 original size:6 final size:6
Alignment explanation
Indices: 18217--18247 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
18207 TTGTGAGTTA
18217 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG G
1 GGAGTG GGAGTG GGAGTG GGAGTG GGAGTG G
18248 ACTTGGAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GGAGTG
Found at i:19996 original size:34 final size:34
Alignment explanation
Indices: 19958--20025 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
19948 AAACATATAA
*
19958 ACAATCGATTCAAAAGAAGTGGTATTCCAACATG
1 ACAATCGATTCAAAAGAAGTAGTATTCCAACATG
*
19992 ACAATTGATTCAAAAGAAGTAGTATTCCAACATG
1 ACAATCGATTCAAAAGAAGTAGTATTCCAACATG
20026 GCAACTGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (34 bp):
ACAATCGATTCAAAAGAAGTAGTATTCCAACATG
Found at i:20035 original size:34 final size:34
Alignment explanation
Indices: 19964--20035 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
19954 ATAAACAATC
* *
19964 GATTCAAAAGAAGTGGTATTCCAACATGACAATT
1 GATTCAAAAGAAGTAGTATTCCAACATGACAACT
*
19998 GATTCAAAAGAAGTAGTATTCCAACATGGCAACT
1 GATTCAAAAGAAGTAGTATTCCAACATGACAACT
20032 GATT
1 GATT
20036 TAAACATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.26
Consensus pattern (34 bp):
GATTCAAAAGAAGTAGTATTCCAACATGACAACT
Found at i:27228 original size:16 final size:16
Alignment explanation
Indices: 27207--27251 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
27197 AATGGAATGA
27207 AAATAAATTTTTAATT
1 AAATAAATTTTTAATT
27223 AAATAAA--TTTAATT
1 AAATAAATTTTTAATT
*
27237 AATTAAAATTTTTAA
1 AAAT-AAATTTTTAA
27252 ACCCTAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 7 0.28
17 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAAATTTTTAATT
Found at i:28469 original size:23 final size:22
Alignment explanation
Indices: 28422--28465 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28412 ATACAATTAT
28422 TAAATATTAAAATAAAATAAAA
1 TAAATATTAAAATAAAATAAAA
*
28444 TAAATATTTAAAA-AAATTAAAA
1 TAAATA-TTAAAATAAAATAAAA
28466 ATAACATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAATATTAAAATAAAATAAAA
Found at i:28980 original size:65 final size:65
Alignment explanation
Indices: 28862--28984 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 65
28852 ATTTAAAAAA
* * * *
28862 TTTTATGGTTATATATAATTTGAATATCCTAAAAATTTTAGATAATGATATGTGATTTACTTATT
1 TTTTATGGTTATATATAATTTGAATACCCTAAAAATCTTAGATAATAACATGTGATTTACTTATT
**
28927 TTTTATGGTTATATATAATTTGAATACCCTAAAAATCTTAGATCCTAACATGTGATTT
1 TTTTATGGTTATATATAATTTGAATACCCTAAAAATCTTAGATAATAACATGTGATTT
28985 CTTCTTTCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (65 bp):
TTTTATGGTTATATATAATTTGAATACCCTAAAAATCTTAGATAATAACATGTGATTTACTTATT
Found at i:29790 original size:2 final size:2
Alignment explanation
Indices: 29785--29813 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29775 AACACATAAC
29785 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 T
29814 TGCTTGACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30580 original size:96 final size:96
Alignment explanation
Indices: 30411--30597 Score: 261
Period size: 96 Copynumber: 1.9 Consensus size: 96
30401 GGGAAAATGA
** **
30411 TATTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGTGCAATATTTCAAAATC
1 TATTCGATTATCTCGATTTGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAATATTTCAAAATC
*
30476 GAAGATAAAAAAACATTGCCTCGATTAAGGG
66 GAAGATAAAAAAACATTACCTCGATTAAGGG
* *
30507 TATTCGATTATTTCGATTTGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAA-ATTTTCGAAAC
1 TATTCGATTATCTCGATTTGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAATA-TTTC-AAAA
* *
30571 TCGAA-ATAAAAGAATATTACCTCGATT
64 TCGAAGATAAAAAAACATTACCTCGATT
30598 TTAAAGTCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
95 1 0.01
96 71 0.89
97 8 0.10
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (96 bp):
TATTCGATTATCTCGATTTGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAATATTTCAAAATC
GAAGATAAAAAAACATTACCTCGATTAAGGG
Found at i:31029 original size:30 final size:29
Alignment explanation
Indices: 30958--31273 Score: 299
Period size: 30 Copynumber: 10.8 Consensus size: 29
30948 TGAGGTCGAG
* *
30958 AATGGAATTTTTGG-A-TATCTGGGGT-AA
1 AATGGAATTTTTGGAAGTTTC-GAGGTAAA
30985 AATGGTAATTTTTGGAAGTTTCGAGGTCAAA
1 AATGG-AATTTTTGGAAGTTTCGAGGT-AAA
* * * * *
31016 AATGGATTTTTTGGAAATTTAGGGGTACA
1 AATGGAATTTTTGGAAGTTTCGAGGTAAA
*
31045 AATGGAATTTTTGGAAGTTTCAAGGTCAAA
1 AATGGAATTTTTGGAAGTTTCGAGGT-AAA
* *
31075 AATGGGATTTTTGGAAG-TTCGAGGGGTTAA
1 AATGGAATTTTTGGAAGTTTCGA--GGTAAA
31105 AATGGAATTTTTGGAAGTTTCGAGGTCAAA
1 AATGGAATTTTTGGAAGTTTCGAGGT-AAA
* *
31135 AATGGGATTTTTGGAAG-TTCGCGGGTAAA
1 AATGGAATTTTTGGAAGTTTCG-AGGTAAA
* * *
31164 AATGTAATTTTTGGAAGTTTTGGGGTTAAA
1 AATGGAATTTTTGGAAGTTTCGAGG-TAAA
*
31194 AATGGAATTTTTGGAAG-TTCGGGGGT-AA
1 AATGGAATTTTTGGAAGTTTC-GAGGTAAA
*
31222 AATGAAATTTTTGGAAGTTTCTGA-GTCAAA
1 AATGGAATTTTTGGAAGTTTC-GAGGT-AAA
31252 AATAGG-ATTTTTGGAAGTTTCG
1 AAT-GGAATTTTTGGAAGTTTCG
31274 GGACCTCTTG
Statistics
Matches: 242, Mismatches: 29, Indels: 34
0.79 0.10 0.11
Matches are distributed among these distances:
27 5 0.02
28 29 0.12
29 68 0.28
30 124 0.51
31 16 0.07
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (29 bp):
AATGGAATTTTTGGAAGTTTCGAGGTAAA
Found at i:31063 original size:59 final size:58
Alignment explanation
Indices: 30921--31267 Score: 364
Period size: 59 Copynumber: 5.9 Consensus size: 58
30911 TATACATTCG
* * * * * * *
30921 GGGGTAAAAGGGTAA-TTTT-GAGAGTTTTGAGGTCGAGAATGGAATTTTTGGATATCT-
1 GGGGTAAAATGG-AATTTTTGGA-AGTTTCGAGGTCAAAAATGGGATTTTTGGAAATTTA
30978 GGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAAT-GGATTTTTTGGAAATTTA
1 GGGGTAAAATGG-AATTTTTGGAAGTTTCGAGGTCAAAAATGGGA-TTTTTGGAAATTTA
* * *
31037 GGGGTACAAATGGAATTTTTGGAAGTTTCAAGGTCAAAAATGGGATTTTTGGAAGTTCGA
1 GGGGTA-AAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAATT-TA
* *
31097 GGGGTTAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGG-AAGTTC
1 GGGG-TAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAATTTA
* * * * * * **
31155 GCGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTCG
1 G-GGGT-AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAATTTA
* *
31215 GGGGTAAAATGAAATTTTTGGAAGTTTCTGA-GTCAAAAATAGGATTTTTGGAA
1 GGGGTAAAATGGAATTTTTGGAAGTTTC-GAGGTCAAAAATGGGATTTTTGGAA
31268 GTTTCGGGAC
Statistics
Matches: 248, Mismatches: 30, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
57 16 0.06
58 72 0.29
59 97 0.39
60 61 0.25
61 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (58 bp):
GGGGTAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAATTTA
Found at i:31133 original size:119 final size:118
Alignment explanation
Indices: 30958--31267 Score: 416
Period size: 119 Copynumber: 2.6 Consensus size: 118
30948 TGAGGTCGAG
*
30958 AATGGAATTTTTGG-A-TATCTGGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAAT-G
1 AATGGAATTTTTGGAAGT-TCGGGGGTAAAATGG-AATTTTTGGAAGTTTCGAGGTCAAAAATAG
* *
31020 GATTTTTTGGAAATTTAG-GGGTACAAATGGAATTTTTGGAAGTTTCAAGGTCAAA
64 GA-TTTTTGGAAAGTTAGCGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCAAA
* *
31075 AATGGGATTTTTGGAAGTTCGAGGGGTTAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATGGAATTTTTGGAAGTTCG-GGGG-TAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAG
* * *** *
31140 GATTTTTGG-AAGTTCGCGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTTAAA
64 GATTTTTGGAAAGTTAGCGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCAAA
*
31194 AATGGAATTTTTGGAAGTTCGGGGGTAAAATGAAATTTTTGGAAGTTTCTGA-GTCAAAAATAGG
1 AATGGAATTTTTGGAAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTTC-GAGGTCAAAAATAGG
31258 ATTTTTGGAA
65 ATTTTTGGAA
31268 GTTTCGGGAC
Statistics
Matches: 172, Mismatches: 13, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
117 55 0.32
118 15 0.09
119 91 0.53
120 11 0.06
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (118 bp):
AATGGAATTTTTGGAAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAGGA
TTTTTGGAAAGTTAGCGGGTAAAAATGGAATTTTTGGAAGTTTCAAGGTCAAA
Found at i:33158 original size:6 final size:6
Alignment explanation
Indices: 33141--33222 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
33131 ATTTAAATAG
* *
33141 ATTTAA ATTTTAA ATTTATA A--TAA AATTAA ATTT-A A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
33187 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
33223 CTTGTTGGGC
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
4 3 0.05
5 14 0.24
6 33 0.57
7 8 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:33170 original size:17 final size:17
Alignment explanation
Indices: 33144--33222 Score: 97
Period size: 17 Copynumber: 4.6 Consensus size: 17
33134 TAAATAGATT
*
33144 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
33162 TAAAATTAAATTT-AAG
1 TAAATTTAAATTTAAAA
*
33178 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
33195 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
33212 TAAATTTAAAT
1 TAAATTTAAAT
33223 CTTGTTGGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
16 12 0.24
17 35 0.69
18 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:33197 original size:33 final size:34
Alignment explanation
Indices: 33144--33221 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
33134 TAAATAGATT
* * *
33144 TAAATTTTAAATTTATAATAAAATTAAATTT-AAG
1 TAAA-TTTAAACTTAAAATAAAATTAAATTTAAAA
* *
33178 TAAATTTAAACTTAAAATAAATTTAATTTTAAAA
1 TAAATTTAAACTTAAAATAAAATTAAATTTAAAA
33212 TAAATTTAAA
1 TAAATTTAAA
33222 TCTTGTTGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATTTAAACTTAAAATAAAATTAAATTTAAAA
Found at i:44597 original size:29 final size:28
Alignment explanation
Indices: 44564--44629 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
44554 TACGATACGT
44564 TTAAATTAAAATATAATAA-AAAAATTGAA
1 TTAAATTAAAATATAA-AACAAAAATT-AA
* *
44593 TTAAATTAAATTATAAAACTCAAAATTAA
1 TTAAATTAAAATATAAAAC-AAAAATTAA
44622 TTAAATTA
1 TTAAATTA
44630 TTTTTTCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 2 0.06
29 25 0.76
30 6 0.18
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (28 bp):
TTAAATTAAAATATAAAACAAAAATTAA
Found at i:52553 original size:3 final size:3
Alignment explanation
Indices: 52545--52590 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
52535 CTATACAAGA
*
52545 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
52591 TGCCACTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:71614 original size:22 final size:22
Alignment explanation
Indices: 71584--71627 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
71574 AACTAAGTAT
*
71584 AAATAGGTTTGATTAAGG-TTAA
1 AAATAGG-TTAATTAAGGCTTAA
*
71606 AAATGGGTTAATTAAGGCTTAA
1 AAATAGGTTAATTAAGGCTTAA
71628 TGATGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (22 bp):
AAATAGGTTAATTAAGGCTTAA
Found at i:74586 original size:21 final size:22
Alignment explanation
Indices: 74543--74601 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
74533 TAGAGGTGAA
74543 ACTTGTATCGGTA-AAAGAGTC
1 ACTTGTATCGGTAGAAAGAGTC
**
74564 ACTTGTATCGGTAGAACTA-TC
1 ACTTGTATCGGTAGAAAGAGTC
*
74585 ACTTGTATTGGTAGAAA
1 ACTTGTATCGGTAGAAA
74602 TCTACACTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (22 bp):
ACTTGTATCGGTAGAAAGAGTC
Found at i:76280 original size:26 final size:26
Alignment explanation
Indices: 76269--76344 Score: 134
Period size: 26 Copynumber: 2.9 Consensus size: 26
76259 CTGGATATCG
76269 CTCTTACAAGCCAGTTCAGTATATAA
1 CTCTTACAAGCCAGTTCAGTATATAA
76295 CTCTTACAAGCCAGTTCAGTATATAA
1 CTCTTACAAGCCAGTTCAGTATATAA
* *
76321 CTCTTACAAGCCAATTCAATATAT
1 CTCTTACAAGCCAGTTCAGTATAT
76345 CTTCAGAGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.32
Consensus pattern (26 bp):
CTCTTACAAGCCAGTTCAGTATATAA
Found at i:85175 original size:15 final size:15
Alignment explanation
Indices: 85131--85176 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
85121 TCAGGTTACA
85131 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
* *
85146 TTTGAAAT-A-TTATG
1 TTT-TAGTCACTTATG
85160 TTTTAGTCACTTATG
1 TTTTAGTCACTTATG
85175 TT
1 TT
85177 AGCATTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (15 bp):
TTTTAGTCACTTATG
Found at i:86616 original size:2 final size:2
Alignment explanation
Indices: 86611--86645 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
86601 TCTCTCTCTC
86611 TA TA 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 TA TA T
86646 TTTATAAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:87617 original size:19 final size:21
Alignment explanation
Indices: 87577--87620 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
87567 ATTATTTTAA
87577 TATTTAATAATTTTATACTTTT
1 TATTTAATAATTTTATA-TTTT
87599 TATTTAATAATTTT-T-TTTT
1 TATTTAATAATTTTATATTTT
87618 TAT
1 TAT
87621 ATATGTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
21 1 0.05
22 14 0.64
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTAATAATTTTATATTTT
Found at i:88927 original size:10 final size:10
Alignment explanation
Indices: 88914--89034 Score: 83
Period size: 10 Copynumber: 12.6 Consensus size: 10
88904 CTTTATAAAA
88914 TTTTATAATT
1 TTTTATAATT
88924 TTTTAT-A-T
1 TTTTATAATT
* *
88932 TTCTAT-ATA
1 TTTTATAATT
88941 TTTTAT-ATT
1 TTTTATAATT
*
88950 TTTT-TACTAT
1 TTTTATAAT-T
**
88960 TTTTATAAAA
1 TTTTATAATT
*
88970 TTTTACAATT
1 TTTTATAATT
* *
88980 TTTTTTATTT
1 TTTTATAATT
*
88990 TTTTACAA-T
1 TTTTATAATT
*
88999 TTTTATATTT
1 TTTTATAATT
*
89009 TTTTCTAATT
1 TTTTATAATT
*
89019 TTTAATAATT
1 TTTTATAATT
89029 TTTTAT
1 TTTTAT
89035 TAAAATTTAA
Statistics
Matches: 82, Mismatches: 24, Indels: 10
0.71 0.21 0.09
Matches are distributed among these distances:
8 8 0.10
9 20 0.24
10 52 0.63
11 2 0.02
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:88928 original size:58 final size:56
Alignment explanation
Indices: 88866--89009 Score: 164
Period size: 56 Copynumber: 2.5 Consensus size: 56
88856 TTTTTACGAA
*
88866 TTTTATATTTCTTTATATTTTGTATAATTTTCTTACGA-CTTTATAAAATTTTATAATT
1 TTTTATATTTCTTTATA-TTT-TAT-ATTTTCTTACGATCTTTATAAAATTTTACAATT
* * * *
88924 TTTTATATTTCTATATATTTTATATTTTTTTACTATTTTTATAAAATTTTACAATT
1 TTTTATATTTCTTTATATTTTATATTTTCTTACGATCTTTATAAAATTTTACAATT
* * *
88980 TTTTTTATTTTTTTACAATTTTTATATTTT
1 TTTTATATTTCTTTA-TA-TTTTATATTTT
89010 TTTCTAATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
55 10 0.14
56 33 0.45
57 4 0.05
58 27 0.36
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (56 bp):
TTTTATATTTCTTTATATTTTATATTTTCTTACGATCTTTATAAAATTTTACAATT
Found at i:88954 original size:28 final size:26
Alignment explanation
Indices: 88912--89035 Score: 104
Period size: 28 Copynumber: 4.4 Consensus size: 26
88902 GACTTTATAA
* *
88912 AATTTTATAATTTTTTATATTTCTAT
1 AATTTTATATTTTTTTATATTTTTAT
88938 ATATTTTATATTTTTTTACTATTTTTAT
1 A-ATTTTATATTTTTTTA-TATTTTTAT
* * *
88966 AAAATTTTACAATTTTTTTTATTTTTTTAC
1 --AATTTTA-TA-TTTTTTTATATTTTTAT
*
88996 AATTTTTATATTTTTTTCTAATTTTTAAT
1 AA-TTTTATATTTTTTTAT-ATTTTT-AT
*
89025 AATTTTTTATT
1 AATTTTATATT
89036 AAAATTTAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.01
27 23 0.29
28 24 0.30
29 14 0.18
30 9 0.11
31 8 0.10
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (26 bp):
AATTTTATATTTTTTTATATTTTTAT
Found at i:88966 original size:56 final size:57
Alignment explanation
Indices: 88844--89030 Score: 188
Period size: 58 Copynumber: 3.3 Consensus size: 57
88834 TGGTACGATA
* * *
88844 ATTTTTATAAATTTTTTACGAA--TTTTATATTTCTTTATATTTTGTATAATTTTCTTACG
1 ATTTTTATAAA-ATTTTAC-AATTTTTTATATTTCTTTATATTTT-TAT-ATTTTTTTACT
* * *
88903 A-CTTTATAAAATTTTATAATTTTTTATATTTCTATATA-TTTTATATTTTTTTACT
1 ATTTTTATAAAATTTTACAATTTTTTATATTTCTTTATATTTTTATATTTTTTTACT
* * *
88958 ATTTTTATAAAATTTTACAATTTTTTTTATTTTTTTACAATTTTTATATTTTTTT-CT
1 ATTTTTATAAAATTTTACAATTTTTTATATTTCTTTA-TATTTTTATATTTTTTTACT
*
89015 AATTTTTA-ATAATTTT
1 -ATTTTTATAAAATTTT
89031 TTATTAAAAT
Statistics
Matches: 109, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
55 10 0.09
56 35 0.32
57 18 0.17
58 45 0.41
59 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (57 bp):
ATTTTTATAAAATTTTACAATTTTTTATATTTCTTTATATTTTTATATTTTTTTACT
Found at i:88993 original size:20 final size:20
Alignment explanation
Indices: 88941--89033 Score: 93
Period size: 19 Copynumber: 4.8 Consensus size: 20
88931 TTTCTATATA
*
88941 TTTTATATTTTTTTACTA-T
1 TTTTATATTTTTTTACAATT
***
88960 TTTTATAAAATTTTACAATT
1 TTTTATATTTTTTTACAATT
*
88980 TTTTTTATTTTTTTACAA-T
1 TTTTATATTTTTTTACAATT
88999 TTTTATATTTTTTT-CTAATT
1 TTTTATATTTTTTTAC-AATT
* *
89019 TTTAATAATTTTTTA
1 TTTTATATTTTTTTA
89034 TTAAAATTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
18 1 0.02
19 30 0.51
20 28 0.47
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATATTTTTTTACAATT
Found at i:89019 original size:39 final size:40
Alignment explanation
Indices: 88931--89033 Score: 111
Period size: 39 Copynumber: 2.6 Consensus size: 40
88921 ATTTTTTATA
* *
88931 TTTCTATATATTTTATATTTTTTTACTATTTTTATAAAATT
1 TTTCTA-ATTTTTTATATTTTTTTACAATTTTTATAAAATT
* * **
88972 TTAC-AATTTTTTTTATTTTTTTACAATTTTTAT-ATTTT
1 TTTCTAATTTTTTATATTTTTTTACAATTTTTATAAAATT
* *
89010 TTTCTAATTTTTAATAATTTTTTA
1 TTTCTAATTTTTTATATTTTTTTA
89034 TTAAAATTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
38 6 0.12
39 41 0.80
40 1 0.02
41 3 0.06
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (40 bp):
TTTCTAATTTTTTATATTTTTTTACAATTTTTATAAAATT
Found at i:92531 original size:145 final size:145
Alignment explanation
Indices: 92265--92558 Score: 448
Period size: 145 Copynumber: 2.0 Consensus size: 145
92255 TAAAATTTTA
*
92265 TCATTTTTAGGGGTCAAATTATAATTTTACCTTTACTAATTTAAAATTAAAAAAAAATTTAATAG
1 TCATTTTTAGGGGTCAAAGTATAATTTTACCTTTACTAATTTAAAATTAAAAAAAAATTTAATAG
* * * * *
92330 TCTACATAAAAAAAAATTTATTTTAAGGGGGTCAAGGCCCTTGCCAGCCCCTTGATTTTGCTCTT
66 TCTAAATAAAAAAAAATTTATTTTAAGGGCGTCAAGGCCCTTGCCAACCCCCTGATTTTGCTCCT
92395 GATATCATTTAAACT
131 GATATCATTTAAACT
* *
92410 TCATTTTTAGGGGTCAAAGTATAATTTTACCTTTACTAATTTAAAATTTAAAAAAATTTTAATAG
1 TCATTTTTAGGGGTCAAAGTATAATTTTACCTTTACTAATTTAAAATTAAAAAAAAATTTAATAG
* ** *
92475 TCTAAAT-GAAAAATTTTCTATTTTAAGGGCG-CCAGGACCCTTGCCAACCCCCTGATTTTGCTC
66 TCTAAATAAAAAAAAATT-TATTTTAAGGGCGTCAAGG-CCCTTGCCAACCCCCTGATTTTGCTC
92538 CTGATATCATTTAAACT
129 CTGATATCATTTAAACT
92555 TCAT
1 TCAT
92559 AACAAACAAT
Statistics
Matches: 135, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
144 11 0.08
145 124 0.92
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (145 bp):
TCATTTTTAGGGGTCAAAGTATAATTTTACCTTTACTAATTTAAAATTAAAAAAAAATTTAATAG
TCTAAATAAAAAAAAATTTATTTTAAGGGCGTCAAGGCCCTTGCCAACCCCCTGATTTTGCTCCT
GATATCATTTAAACT
Found at i:94332 original size:16 final size:16
Alignment explanation
Indices: 94311--94343 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
94301 ATAAAAATTA
94311 AAACTAAAATTTAACC
1 AAACTAAAATTTAACC
94327 AAACTAAAATTTAACC
1 AAACTAAAATTTAACC
94343 A
1 A
94344 TTATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (16 bp):
AAACTAAAATTTAACC
Found at i:97438 original size:3 final size:3
Alignment explanation
Indices: 97430--97467 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
97420 CACACACCTC
*
97430 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCA TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
97468 CCTTTTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:97561 original size:166 final size:165
Alignment explanation
Indices: 97279--97584 Score: 513
Period size: 166 Copynumber: 1.8 Consensus size: 165
97269 TCACACACCT
* *
97279 TTCTTCTTCATCTTCATCATCTTCCCTTTTGATTCTAATATCTTTAGTTACAATCTATCTCAAAG
1 TTCTTCTTCATCTTCATCATCTTCCCTTTTGATTCCAATATCTTTAGTTACAATCCATCTCAAAG
*
97344 CTTGAATCTTTGAAACCCATTAACCCAAAAAAACTTAACAAGAAGAAGATATTGGAATCAAAGAT
66 CTTGAATATTTGAAACCCATTAACCCAAAAAAACTTAACAAGAAGAAGATATTGGAATCAAAGAT
97409 AATGAATCTTCCACACACCTCTCTTCTTCTTCTTC
131 AATGAATCTTCCACACACCTCTCTTCTTCTTCTTC
* * * *
97444 TTCTTCTTCTTCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTTGTTACAAATCCGTCTCAAA
1 TTCTTCTTCATCTTCATCATCTTCCCTTTTGATTCCAATATCTTTAGTTAC-AATCCATCTCAAA
* *
97509 GCTTGAATATTTGAAACCCATTAACCCAAAAAAACTTAACAGGAATAAGATATTGGAATCAAAGA
65 GCTTGAATATTTGAAACCCATTAACCCAAAAAAACTTAACAAGAAGAAGATATTGGAATCAAAGA
*
97574 TATTGAATCTT
130 TAATGAATCTT
97585 TGGGTTAATG
Statistics
Matches: 130, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
165 47 0.36
166 83 0.64
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (165 bp):
TTCTTCTTCATCTTCATCATCTTCCCTTTTGATTCCAATATCTTTAGTTACAATCCATCTCAAAG
CTTGAATATTTGAAACCCATTAACCCAAAAAAACTTAACAAGAAGAAGATATTGGAATCAAAGAT
AATGAATCTTCCACACACCTCTCTTCTTCTTCTTC
Found at i:102158 original size:26 final size:27
Alignment explanation
Indices: 102101--102174 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 27
102091 TGAGGATTAA
* *
102101 TTGATTTTGGCTCGAAAGAGCGTTATT
1 TTGATTCTGGCTCGAAAGAGCGCTATT
* *
102128 CTGATTCTGGCTTGAAA-AGCGCTATT
1 TTGATTCTGGCTCGAAAGAGCGCTATT
*
102154 TTGATTCTGGCTCGAATGAGC
1 TTGATTCTGGCTCGAAAGAGC
102175 TAAAATCTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 22 0.56
27 17 0.44
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (27 bp):
TTGATTCTGGCTCGAAAGAGCGCTATT
Found at i:102192 original size:27 final size:27
Alignment explanation
Indices: 102162--102236 Score: 150
Period size: 27 Copynumber: 2.8 Consensus size: 27
102152 TTTTGATTCT
102162 GGCTCGAATGAGCTAAAATCTTTTTTG
1 GGCTCGAATGAGCTAAAATCTTTTTTG
102189 GGCTCGAATGAGCTAAAATCTTTTTTG
1 GGCTCGAATGAGCTAAAATCTTTTTTG
102216 GGCTCGAATGAGCTAAAATCT
1 GGCTCGAATGAGCTAAAATCT
102237 ATTACGGAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (27 bp):
GGCTCGAATGAGCTAAAATCTTTTTTG
Found at i:106833 original size:22 final size:20
Alignment explanation
Indices: 106808--106847 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
106798 GATGGTTAGA
106808 TATGAAACGTTAAATCTCTGAG
1 TATGAAAC--TAAATCTCTGAG
*
106830 TATGTAACTAAATCTCTG
1 TATGAAACTAAATCTCTG
106848 GTTTGTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
TATGAAACTAAATCTCTGAG
Found at i:116022 original size:28 final size:28
Alignment explanation
Indices: 115990--116043 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
115980 GAGAGCCTTG
*
115990 AGAAGCTTAATGACTTAGAGCACACTCT
1 AGAAGCTCAATGACTTAGAGCACACTCT
*
116018 AGAAGCTCAATGACTTAGATCACACT
1 AGAAGCTCAATGACTTAGAGCACACT
116044 ATAGGGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (28 bp):
AGAAGCTCAATGACTTAGAGCACACTCT
Found at i:116597 original size:19 final size:19
Alignment explanation
Indices: 116573--116610 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
116563 GAAATTACAA
* *
116573 TTTTTCTTTTTCTTTTTGT
1 TTTTTCTATTTCGTTTTGT
116592 TTTTTCTATTTCGTTTTGT
1 TTTTTCTATTTCGTTTTGT
116611 AGGTTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.79
Consensus pattern (19 bp):
TTTTTCTATTTCGTTTTGT
Found at i:117424 original size:50 final size:50
Alignment explanation
Indices: 117370--117464 Score: 111
Period size: 50 Copynumber: 1.9 Consensus size: 50
117360 GGCCTGCTAA
* *
117370 TGTAACTTTAATATGA-TCCACTGCAACTTCAGGGATATAAGATTTGATGT
1 TGTAA-TTTAATATGACTCCACTACAACTTCAGGGAAATAAGATTTGATGT
* * * * *
117420 TGTAATTTCATCTTACTCTACTACATCTTCAGGGAAATAAGATTT
1 TGTAATTTAATATGACTCCACTACAACTTCAGGGAAATAAGATTT
117465 TCTTCTGTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
49 7 0.19
50 30 0.81
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (50 bp):
TGTAATTTAATATGACTCCACTACAACTTCAGGGAAATAAGATTTGATGT
Found at i:117708 original size:101 final size:100
Alignment explanation
Indices: 117461--117780 Score: 339
Period size: 101 Copynumber: 3.2 Consensus size: 100
117451 GGGAAATAAG
* * * * *
117461 ATTTTCTTCTGTAGCTTCAATCCGACCTATTACAACTTCAAGGGTATAGGA-TTGTATGTTGTAG
1 ATTTTCTTTTGTAGCTTCAATCCAACCTACTACAACTTTAA-GGTATAGGATTTG-ATGTCGTAG
*
117525 CTTCATCTTGCTCTAC--T-ACTTCAGAGAGATAAAT
64 CTTCATCTTGCTCTACTGTAACTTTAGAGAGATAAAT
* * * * * * *
117559 ATTTGCTTTCGTAGATTCAATCTGATCC-ACTATAA-TTTCAAGGATATAGGATTTGATGTCATA
1 ATTTTCTTTTGTAGCTTCAATC-CAACCTACTACAACTTT-AAGG-TATAGGATTTGATGTCGTA
* * *
117622 GCTTCATCTTGCTCCACTGTAACTTTGGGGAGATAAAT
63 GCTTCATCTTGCTCTACTGTAACTTTAGAGAGATAAAT
* *
117660 ATTTTCTTTTGTAGCTTCAATCCAACCTACTACAACTTTAAGAGTATAGGATTTGGTTTCGTAGC
1 ATTTTCTTTTGTAGCTTCAATCCAACCTACTACAACTTTAAG-GTATAGGATTTGATGTCGTAGC
* *
117725 TTCATCTTGCTCTACTGCAACTTTAGAGAGATAAAG
65 TTCATCTTGCTCTACTGTAACTTTAGAGAGATAAAT
*
117761 ATTAGT-TTTTGTAGCTTCAA
1 ATT-TTCTTTTGTAGCTTCAA
117781 AATCTGATCC
Statistics
Matches: 180, Mismatches: 31, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
97 4 0.02
98 54 0.30
99 5 0.03
100 4 0.02
101 108 0.60
102 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (100 bp):
ATTTTCTTTTGTAGCTTCAATCCAACCTACTACAACTTTAAGGTATAGGATTTGATGTCGTAGCT
TCATCTTGCTCTACTGTAACTTTAGAGAGATAAAT
Found at i:121779 original size:79 final size:80
Alignment explanation
Indices: 121693--121847 Score: 249
Period size: 79 Copynumber: 1.9 Consensus size: 80
121683 TCTCTTTTCA
* * *
121693 TTTTCATCCCCTAAACTCAACACTTCCAATGATTCTTTGTCAAGTAAGATTT-TTTCTCATTTTG
1 TTTTCATCCCCCAAACTCAACACTTCCAATGATTCTTTGTCAAGTAAGATTTGTTTCTCATCTAG
121757 CTCAACCATTCTTCG
66 CTCAACCATTCTTCG
* * *
121772 TTTTCATCCCCCAAACTCAACACTTCCAATGATTCTTTGTGAGGTAAGATTTGTTTCTCGTCTAG
1 TTTTCATCCCCCAAACTCAACACTTCCAATGATTCTTTGTCAAGTAAGATTTGTTTCTCATCTAG
121837 CTCAACCATTC
66 CTCAACCATTC
121848 GTAGCAGATC
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 49 0.71
80 20 0.29
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (80 bp):
TTTTCATCCCCCAAACTCAACACTTCCAATGATTCTTTGTCAAGTAAGATTTGTTTCTCATCTAG
CTCAACCATTCTTCG
Found at i:130251 original size:27 final size:27
Alignment explanation
Indices: 130219--130293 Score: 88
Period size: 22 Copynumber: 3.0 Consensus size: 27
130209 GCACGACCCC
130219 AACCCGTTGACCCAAGTTGATCGACCT
1 AACCCGTTGACCCAAGTTGATCGACCT
*
130246 AACCCGTTGA-TCAAG-T--T-GACCT
1 AACCCGTTGACCCAAGTTGATCGACCT
* *
130268 AACCCATTGACCCGAGTTGATCGACC
1 AACCCGTTGACCCAAGTTGATCGACC
130294 CATTTACTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
22 14 0.36
23 4 0.10
24 1 0.03
25 1 0.03
26 5 0.13
27 14 0.36
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.23
Consensus pattern (27 bp):
AACCCGTTGACCCAAGTTGATCGACCT
Found at i:130323 original size:21 final size:21
Alignment explanation
Indices: 130293--130336 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
130283 GTTGATCGAC
*
130293 CCATTTACTTTGACCCATTGA
1 CCATTGACTTTGACCCATTGA
* *
130314 CCATTGACTTTGGCCTATTGA
1 CCATTGACTTTGACCCATTGA
130335 CC
1 CC
130337 CTACCCATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (21 bp):
CCATTGACTTTGACCCATTGA
Found at i:130395 original size:25 final size:26
Alignment explanation
Indices: 130344--130396 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
130334 ACCCTACCCA
130344 TTGACTTTGACCGTTGATCGTTGACT
1 TTGACTTTGACCGTTGATCGTTGACT
* *
130370 TTGACTTTGA-CTTTGATCGTTTACT
1 TTGACTTTGACCGTTGATCGTTGACT
130395 TT
1 TT
130397 TTTTAACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.15, C:0.17, G:0.19, T:0.49
Consensus pattern (26 bp):
TTGACTTTGACCGTTGATCGTTGACT
Found at i:149645 original size:15 final size:15
Alignment explanation
Indices: 149625--149662 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
149615 TTCAATTGAT
*
149625 CTTTTAATTGTTTTA
1 CTTTTAATTGTTTCA
*
149640 CTTTTACTTGTTTCA
1 CTTTTAATTGTTTCA
149655 -TTTTAATT
1 CTTTTAATT
149663 TCTTTGCAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (15 bp):
CTTTTAATTGTTTCA
Found at i:158507 original size:70 final size:70
Alignment explanation
Indices: 158433--158570 Score: 172
Period size: 70 Copynumber: 2.0 Consensus size: 70
158423 CATTTTATCA
* * * *
158433 TTCTTATCCAA-TTCGACAAACATTTCATTTATACTCA-ATCTACACAATTAATCATTCTTAAAT
1 TTCTTATCCAATTTC-ACAAACATTTCATTCATACTCATA-CCACACAATCAATAATTCTTAAAT
158496 TCATTCG
64 TCATTCG
* * * *
158503 TTCTTATTCAATTTCACAAACATTTTATTCATATTCATACCATACAATCAATAATTCTTAAATTC
1 TTCTTATCCAATTTCACAAACATTTCATTCATACTCATACCACACAATCAATAATTCTTAAATTC
158568 ATT
66 ATT
158571 TTGATCTTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
70 54 0.93
71 4 0.07
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.42
Consensus pattern (70 bp):
TTCTTATCCAATTTCACAAACATTTCATTCATACTCATACCACACAATCAATAATTCTTAAATTC
ATTCG
Found at i:161847 original size:233 final size:233
Alignment explanation
Indices: 161435--161900 Score: 914
Period size: 233 Copynumber: 2.0 Consensus size: 233
161425 TCATATCTAA
161435 CAATGTATTAAATTTGAATAAAAACATGATAGCGGAGGTTTTCAATCAATTCAAGATCAAACATC
1 CAATGTATTAAATTTGAATAAAAACATGATAGCGGAGGTTTTCAATCAATTCAAGATCAAACATC
161500 ACAATTCATCTCCCTATCACCCAAAAATGAGTGGGGCGATGGAGGCAGCTAATAAAAACATCAAG
66 ACAATTCATCTCCCTATCACCCAAAAATGAGTGGGGCGATGGAGGCAGCTAATAAAAACATCAAG
* *
161565 AAGATTGTTGCAAAGATGACAGAGACCTATGAAGATTGAAAATAGAAGTTATCATTTGCCTTTTT
131 AAGATTGTTGCAAAGATGACAGAGACCTATGAAGATTGAAAAAAGAAGTTATCATTTGCCCTTTT
161630 TGCTTATAGACCTTAGTCAAAACTTCTACTGGAGCTAC
196 TGCTTATAGACCTTAGTCAAAACTTCTACTGGAGCTAC
161668 CAATGTATTAAATTTGAATAAAAACATGATAGCGGAGGTTTTCAATCAATTCAAGATCAAACATC
1 CAATGTATTAAATTTGAATAAAAACATGATAGCGGAGGTTTTCAATCAATTCAAGATCAAACATC
161733 ACAATTCATCTCCCTATCACCCAAAAATGAGTGGGGCGATGGAGGCAGCTAATAAAAACATCAAG
66 ACAATTCATCTCCCTATCACCCAAAAATGAGTGGGGCGATGGAGGCAGCTAATAAAAACATCAAG
161798 AAGATTGTTGCAAAGATGACAGAGACCTATGAAGATTGAAAAAAGAAGTTATCATTTGCCCTTTT
131 AAGATTGTTGCAAAGATGACAGAGACCTATGAAGATTGAAAAAAGAAGTTATCATTTGCCCTTTT
161863 TGCTTATAGACCTTAGTCAAAACTTCTACTGGAGCTAC
196 TGCTTATAGACCTTAGTCAAAACTTCTACTGGAGCTAC
161901 ACCATTCTCG
Statistics
Matches: 231, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
233 231 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (233 bp):
CAATGTATTAAATTTGAATAAAAACATGATAGCGGAGGTTTTCAATCAATTCAAGATCAAACATC
ACAATTCATCTCCCTATCACCCAAAAATGAGTGGGGCGATGGAGGCAGCTAATAAAAACATCAAG
AAGATTGTTGCAAAGATGACAGAGACCTATGAAGATTGAAAAAAGAAGTTATCATTTGCCCTTTT
TGCTTATAGACCTTAGTCAAAACTTCTACTGGAGCTAC
Found at i:163310 original size:101 final size:102
Alignment explanation
Indices: 163185--163551 Score: 357
Period size: 101 Copynumber: 3.7 Consensus size: 102
163175 TGGAATGGAG
* ** *
163185 TGAAGCTACAACATCAAATATTATACCCCTGAAGTTTTAGTGGATCGAATTAAAATTACGA-AAG
1 TGAAGCTACAACATCAAATCTTATACCCCTGAAGTTGCAGTGGATCGAATTAAAACTACGAGAAG
* *
163249 CAAATCATTATCTCTCTAAAGTTGCAGCAGAGCAAAA
66 CAAATCTTTATCTCTCTAAAGTTGCAGCAGAGCAAGA
** * * * *
163286 TGAAGCTACAA-ATCCAAATCTTATACCTGTGAAGTTACAGTGGATCGAATTAAAGCCATGA-AA
1 TGAAGCTACAACAT-CAAATCTTATACCCCTGAAGTTGCAGTGGATCGAATTAAAACTACGAGAA
* * * **
163349 GCAAATCTTTATCTCACTAAAGTTACGGTGGAGCAAGA
65 GCAAATCTTTATCTCTCTAAAGTTGCAGCAGAGCAAGA
* * * *
163387 TGAAGCTACGACATCAAATC-TATACCTCTGAAGTTGCAATAGG-TCGGATT-----TAC-AGAA
1 TGAAGCTACAACATCAAATCTTATACCCCTGAAGTTGCAGT-GGATCGAATTAAAACTACGAGAA
* *
163444 GCAAAT-TTTATCTCTCTGAAGTTGCA-CTAGAGTAAGA
65 GCAAATCTTTATCTCTCTAAAGTTGCAGC-AGAGCAAGA
* * * * *
163481 TGAAGCTACAACACCAAATCTTATATCCTTGAAGTTGCAGTGGATCGAATTAGAACTACGATAA-
1 TGAAGCTACAACATCAAATCTTATACCCCTGAAGTTGCAGTGGATCGAATTAAAACTACGAGAAG
163545 CAAATCT
66 CAAATCT
163552 CAATCTTCTT
Statistics
Matches: 214, Mismatches: 38, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
94 44 0.21
95 31 0.14
100 33 0.15
101 104 0.49
102 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (102 bp):
TGAAGCTACAACATCAAATCTTATACCCCTGAAGTTGCAGTGGATCGAATTAAAACTACGAGAAG
CAAATCTTTATCTCTCTAAAGTTGCAGCAGAGCAAGA
Found at i:168052 original size:30 final size:28
Alignment explanation
Indices: 168018--168076 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
168008 ATCTTTCATC
168018 TCATTCTCAA-CTCAATTTCTCTAAACTAAT
1 TCATTCTCAATCTC-A-TTCTCTAAA-TAAT
* *
168048 TCATTTTTAATCTCATTCTCTAAATAAT
1 TCATTCTCAATCTCATTCTCTAAATAAT
168076 T
1 T
168077 TCCGAAGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 9 0.35
30 9 0.35
31 3 0.12
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (28 bp):
TCATTCTCAATCTCATTCTCTAAATAAT
Found at i:182402 original size:28 final size:28
Alignment explanation
Indices: 182371--182591 Score: 156
Period size: 28 Copynumber: 8.2 Consensus size: 28
182361 AATTTAAGAT
* *
182371 TGATTATGTTAAAGGAAGTCTTTGTGGC
1 TGATTTTGTTAAAGGAAGCCTTTGTGGC
* *
182399 TGATTTTGTTAAATGAAGTCTTTGTGGC
1 TGATTTTGTTAAAGGAAGCCTTTGTGGC
* * *
182427 TGATTTTGTTAAATGAAACCTTTGTGGA
1 TGATTTTGTTAAAGGAAGCCTTTGTGGC
* *
182455 TAATTTTGTTAAAGGAAGCCTTTGTAGC
1 TGATTTTGTTAAAGGAAGCCTTTGTGGC
* * * *
182483 TGA--TT-CT-ATGGAAGCCATTATGGC
1 TGATTTTGTTAAAGGAAGCCTTTGTGGC
* * * *
182507 TGATTCTGTTAAA-AAGAGCCTTTATGGT
1 TGATTTTGTTAAAGGA-AGCCTTTGTGGC
* *
182535 TGA--TT-CT-ATGGAAGCCTTTGTGGC
1 TGATTTTGTTAAAGGAAGCCTTTGTGGC
* * *
182559 TGATTCTGTTAAAAGGAA-TCTTTGTGGT
1 TGATTTTGTT-AAAGGAAGCCTTTGTGGC
182587 TGATT
1 TGATT
182592 CTATAAAGGG
Statistics
Matches: 149, Mismatches: 33, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
24 30 0.20
25 3 0.02
26 5 0.03
27 3 0.02
28 103 0.69
29 5 0.03
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (28 bp):
TGATTTTGTTAAAGGAAGCCTTTGTGGC
Found at i:182508 original size:24 final size:24
Alignment explanation
Indices: 182468--182565 Score: 88
Period size: 24 Copynumber: 3.9 Consensus size: 24
182458 TTTTGTTAAA
* *
182468 GGAAGCCTTTGTAGCTGATTCTAT
1 GGAAGCCTTTATGGCTGATTCTAT
* *
182492 GGAAGCCATTATGGCTGATTCTGTTAA
1 GGAAGCCTTTATGGCTGATTC---TAT
** *
182519 AAAGAGCCTTTATGGTTGATTCTAT
1 GGA-AGCCTTTATGGCTGATTCTAT
*
182544 GGAAGCCTTTGTGGCTGATTCT
1 GGAAGCCTTTATGGCTGATTCT
182566 GTTAAAAGGA
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
24 35 0.61
25 3 0.05
27 3 0.05
28 16 0.28
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (24 bp):
GGAAGCCTTTATGGCTGATTCTAT
Found at i:182528 original size:52 final size:52
Alignment explanation
Indices: 182471--182595 Score: 178
Period size: 52 Copynumber: 2.4 Consensus size: 52
182461 TGTTAAAGGA
* *
182471 AGCCTTTGTAGCTGATTCTATGGAAGCCATTATGGCTGATTCTGTTAAAAAG
1 AGCCTTTGTGGTTGATTCTATGGAAGCCATTATGGCTGATTCTGTTAAAAAG
* * * *
182523 AGCCTTTATGGTTGATTCTATGGAAGCCTTTGTGGCTGATTCTGTTAAAAGG
1 AGCCTTTGTGGTTGATTCTATGGAAGCCATTATGGCTGATTCTGTTAAAAAG
**
182575 AATCTTTGTGGTTGATTCTAT
1 AGCCTTTGTGGTTGATTCTAT
182596 AAAGGGCGCT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (52 bp):
AGCCTTTGTGGTTGATTCTATGGAAGCCATTATGGCTGATTCTGTTAAAAAG
Found at i:190159 original size:13 final size:13
Alignment explanation
Indices: 190141--190166 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
190131 CTAATTACAA
190141 ATATTTAATTATT
1 ATATTTAATTATT
190154 ATATTTAATTATT
1 ATATTTAATTATT
190167 TAAAATATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTAATTATT
Found at i:190249 original size:31 final size:29
Alignment explanation
Indices: 190206--190271 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
190196 TTTTATAAAT
190206 AATTAATATTTAT-TACTTAAAAATATTTAA
1 AATTAATATTTATATA-TT-AAAATATTTAA
* *
190236 AATTTATATTTTATATATTAAAATATTAATA
1 AATTAATA-TTTATATATTAAAATATTTA-A
190267 AATTA
1 AATTA
190272 TAATAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 16 0.53
31 12 0.40
32 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
AATTAATATTTATATATTAAAATATTTAA
Found at i:192975 original size:16 final size:17
Alignment explanation
Indices: 192954--192992 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
192944 ATTATTTTAC
*
192954 ATTTTTT-ATTTTATAT
1 ATTTTTTAATTGTATAT
192970 ATTTTTTAAATTGTATAT
1 ATTTTTT-AATTGTATAT
192988 ATTTT
1 ATTTT
192993 AAAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
18 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATTGTATAT
Found at i:196066 original size:34 final size:34
Alignment explanation
Indices: 196023--196138 Score: 155
Period size: 34 Copynumber: 3.4 Consensus size: 34
196013 TATAGTGTAT
* *
196023 TTGGTGTGTTGGTTGGATTAGCTCTTACGAGCAC
1 TTGGTGTGTTGGATGGACTAGCTCTTACGAGCAC
* *
196057 TTGGTGTGTTGGAGGGACTAGCTCTTACAAGCA-
1 TTGGTGTGTTGGATGGACTAGCTCTTACGAGCAC
*
196090 TATGGTGTGTTGGAT-GAGCTAGCTTTTACGAGCAC
1 T-TGGTGTGTTGGATGGA-CTAGCTCTTACGAGCAC
196125 TTGGTGTGTTGGAT
1 TTGGTGTGTTGGAT
196139 AGATTGGCTC
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
33 3 0.04
34 68 0.94
35 1 0.01
ACGTcount: A:0.17, C:0.13, G:0.34, T:0.36
Consensus pattern (34 bp):
TTGGTGTGTTGGATGGACTAGCTCTTACGAGCAC
Found at i:196166 original size:68 final size:68
Alignment explanation
Indices: 196041--196173 Score: 169
Period size: 68 Copynumber: 2.0 Consensus size: 68
196031 TTGGTTGGAT
* *
196041 TAGCTCTTACGAGCACTTGGTGTGTTGGAGGGACTAGCTCTTACAAGCATATGGTGTGTTGGATG
1 TAGCTCTTACGAGCACTTGGTGTGTTGGAGAGACTAGCTCTTACAAGCATATAGTGTGTTGGATG
196106 AGC
66 AGC
* * * * ** *
196109 TAGCTTTTACGAGCACTTGGTGTGTTGGATAGATTGGCTCATT-TGAGCATCTAGTGTGTTGGAT
1 TAGCTCTTACGAGCACTTGGTGTGTTGGAGAGACTAGCTC-TTACAAGCATATAGTGTGTTGGAT
196173 G
65 G
196174 GTTAACCGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 53 0.96
69 2 0.04
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.35
Consensus pattern (68 bp):
TAGCTCTTACGAGCACTTGGTGTGTTGGAGAGACTAGCTCTTACAAGCATATAGTGTGTTGGATG
AGC
Found at i:197610 original size:36 final size:36
Alignment explanation
Indices: 197536--197602 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
197526 AATTAACATC
* * *
197536 AAAATCCCAAAATAATTTAATAACGCATTAATCTGA
1 AAAATCCCAAAATAATTTAATAACGAAATAATATGA
197572 AAAATCCCAAAATAATTT-ATAA-GAAATAATA
1 AAAATCCCAAAATAATTTAATAACGAAATAATA
197603 AATGAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 6 0.21
35 4 0.14
36 18 0.64
ACGTcount: A:0.55, C:0.13, G:0.04, T:0.27
Consensus pattern (36 bp):
AAAATCCCAAAATAATTTAATAACGAAATAATATGA
Found at i:206805 original size:18 final size:18
Alignment explanation
Indices: 206782--206824 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
206772 GAATGGGTTT
206782 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
206800 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
206818 TTAATTA
1 TTAATTA
206825 CACTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:211937 original size:4 final size:4
Alignment explanation
Indices: 211928--211998 Score: 74
Period size: 4 Copynumber: 17.8 Consensus size: 4
211918 AATAAACGGA
* * *
211928 AAAG AAAG AAAGG AAAG AAAG AAAG AAAG AAAG -AAG GAAG AAGG AGAGG
1 AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A-AAG
*
211977 AAAG AAAG -AAG AAGG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAA
211999 AGTAATATGT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
3 6 0.10
4 44 0.76
5 8 0.14
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:211978 original size:36 final size:35
Alignment explanation
Indices: 211929--211997 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
211919 ATAAACGGAA
211929 AAGAAAGAAAGGAAAGAAAGAAAGAAAGAAAGAAGG
1 AAGAAAGAAAGGAAAGAAAG-AAGAAAGAAAGAAGG
* * *
211965 AAGAAGGAGAGGAAAGAAAGAAGAAGGAAAGAA
1 AAGAAAGAAAGGAAAGAAAGAAGAAAGAAAGAA
211998 AAGTAATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 12 0.40
36 18 0.60
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (35 bp):
AAGAAAGAAAGGAAAGAAAGAAGAAAGAAAGAAGG
Done.